Tag: BUSCO

Characteristics of Amorphophallus konjac as indicated by its genome

Genome assembly and annotation The DNA sequencing data (1119.58 Gb, average 110× coverage) of the A. konjac sample were obtained using the Illumina Hiseq 2500 sequencer. A summary of the sequence data used for the assembly is presented in Table S1. The estimated genome size is 4,512,012,462 bp using 19-mer frequency distribution based…

Continue Reading Characteristics of Amorphophallus konjac as indicated by its genome

A super-pangenome of the North American wild grape species | Genome Biology

Alston JM, Sambucci O. Grapes in the world economy. In: Cantu D, Walker MA, editors. The grape genome. Springer International Publishing; 2019. p. 1–24. Google Scholar  Rahemi A, Dodson Peterson JC, Lund KT. Grape rootstocks and related species. Cham: Springer International Publishing; 2022. Walker MA, Heinitz C, Riaz S, Uretsky…

Continue Reading A super-pangenome of the North American wild grape species | Genome Biology

Chromosome-level genome assembly of the Stoliczka’s Asian trident bat (Aselliscus stoliczkanus)

Dobson, G. E. On a new genus and species of Rhinolophidae, with description of a new species of Vesperus, and notes on some other species of insectivorous bats from Persia. J. Asiat. Soc. Bengal. 40, 455–461 (1871). Google Scholar  Bates, P., Bumrungsri, S., Francis, C., Csorba, G. & Furey, N….

Continue Reading Chromosome-level genome assembly of the Stoliczka’s Asian trident bat (Aselliscus stoliczkanus)

Maternal dominance contributes to subgenome differentiation in allopolyploid fishes

Otto, S. P. & Whitton, J. Polyploid incidence and evolution. Annu. Rev. Genet. 34, 401–437 (2000). Article  CAS  PubMed  Google Scholar  Van de Peer, Y., Maere, S. & Meyer, A. The evolutionary significance of ancient genome duplications. Nat. Rev. Genet. 10, 725–732 (2009). Article  PubMed  Google Scholar  Comai, L. The…

Continue Reading Maternal dominance contributes to subgenome differentiation in allopolyploid fishes

Chromosome-level genome assembly of the Asian spongy moths Lymantria dispar asiatica

Boukouvala, M. C. et al. Lymantria dispar (L.) (Lepidoptera: Erebidae): Current Status of Biology, Ecology, and Management in Europe with Notes from North America. Insects 13 (2022). Keena M. A., Richards, J. Y. Comparison of Survival and Development of Gypsy Moth Lymantria dispar L. (Lepidoptera: Erebidae) Populations from Different Geographic…

Continue Reading Chromosome-level genome assembly of the Asian spongy moths Lymantria dispar asiatica

Topological structures and syntenic conservation in sea anemone genomes

Putnam, N. H. et al. Sea anemone genome reveals ancestral eumetazoan gene repertoire and genomic organization. Science 317, 86–94 (2007). Article  ADS  CAS  PubMed  Google Scholar  Chapman, J. A. et al. The dynamic genome of Hydra. Nature 464, 592–596 (2010). Article  ADS  CAS  PubMed  PubMed Central  Google Scholar  Srivastava, M….

Continue Reading Topological structures and syntenic conservation in sea anemone genomes

Phyloecology of nitrate ammonifiers and their importance relative to denitrifiers in global terrestrial biomes

Steffen, W. et al. Planetary boundaries: guiding human development on a changing planet. Science 347, 1259855 (2015). Article  PubMed  Google Scholar  Kanter, D. R. et al. Nitrogen pollution policy beyond the farm. Nat. Food 1, 27–32 (2020). Article  ADS  Google Scholar  Tian, H. et al. A comprehensive quantification of global…

Continue Reading Phyloecology of nitrate ammonifiers and their importance relative to denitrifiers in global terrestrial biomes

Dispersal from the Qinghai-Tibet plateau by a high-altitude butterfly is associated with rapid expansion and reorganization of its genome

Zachos, J., Pagani, H., Sloan, L., Thomas, E. & Billups, K. Trends, rhythms, and aberrations in global climate 65 Ma to present. Science 292, 686–693 (2001). Article  ADS  CAS  PubMed  Google Scholar  Favre, A. et al. The role of the uplift of the Qinghai-Tibetan Plateau for the evolution of Tibetan…

Continue Reading Dispersal from the Qinghai-Tibet plateau by a high-altitude butterfly is associated with rapid expansion and reorganization of its genome

Origin and evolution of the triploid cultivated banana genome

Rouard, M. et al. Three new genome assemblies support a rapid radiation in Musa acuminata (wild banana). Genome Biol. Evol. 10, 3129–3140 (2018). CAS  PubMed  PubMed Central  Google Scholar  Langhe, E. D., Vrydaghs, L., Maret, P. D., Perrier, X. & Denham, T. Why bananas matter: an introduction to the history…

Continue Reading Origin and evolution of the triploid cultivated banana genome

Haplotype-resolved genome of heterozygous African cassava cultivar TMEB117 (Manihot esculenta)

Wang, P. et al. The genome evolution and domestication of tropical fruit mango. Genome Biol 21 (2020). Tang, C. et al. The rubber tree genome reveals new insights into rubber production and species adaptation. Nat Plants 2 (2016). Bredeson, J. V. et al. Sequencing wild and cultivated cassava and related…

Continue Reading Haplotype-resolved genome of heterozygous African cassava cultivar TMEB117 (Manihot esculenta)

Generating high-quality plant and fish reference genomes from field-collected specimens by optimizing preservation

Sample collection A total of nine species of marine fish were collected across three different sampling days (September 7th, 9th, and 12th 2022) under IACUC Animal Use Protocol S12219 (Supplementary Data 1). Six species were collected using a speargun donated by a local fisher. Fish were transported back to shore, euthanized,…

Continue Reading Generating high-quality plant and fish reference genomes from field-collected specimens by optimizing preservation

The MetaInvert soil invertebrate genome resource provides insights into below-ground biodiversity and evolution

FAO, ITPS, GSBI, CBD & EC. State of knowledge of soil biodiversity – Status, challenges and potentialities, Report 2020. (FAO). doi.org/10.4060/cb1928en. 2020. Potapov, A. M. et al. Feeding habits and multifunctional classification of soil-associated consumers from protists to vertebrates. Biol. Rev. 97, 1057–1117 (2022). Article  PubMed  Google Scholar  García-Palacios, P.,…

Continue Reading The MetaInvert soil invertebrate genome resource provides insights into below-ground biodiversity and evolution

A chromosome-level genome assembly for the Silkie chicken resolves complete sequences for key chicken metabolic, reproductive, and immunity genes

Friedman-Einat, M. & Seroussi, E. Avian leptin: bird’s-eye view of the evolution of vertebrate energy-balance control. Trends Endocrinol. Metab. 30, 819–832 (2019). Article  CAS  PubMed  Google Scholar  International Chicken Genome Sequencing C. Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. Nature 432, 695–716 (2004)….

Continue Reading A chromosome-level genome assembly for the Silkie chicken resolves complete sequences for key chicken metabolic, reproductive, and immunity genes

A genome assembly for Orinus kokonorica provides insights into the origin, adaptive evolution and further diversification of two closely related grass genera

Jiao, Y. N. et al. Ancestral polyploidy in seed plants and angiosperms. Nature 473, 97–100 (2011). Article  PubMed  Google Scholar  Levin, D. A. Polyploidy and novelty in flowering plants. Am. Nat. 122, 1–25 (1983). Article  Google Scholar  Soltis, P. S. & Soltis, D. E. Ancient WGD events as drivers of…

Continue Reading A genome assembly for Orinus kokonorica provides insights into the origin, adaptive evolution and further diversification of two closely related grass genera

Dryad | Data — Progressive Cactus alignment of 298 drosophilid species

Long-read sequencing is driving rapid progress in genome assembly across all major groups of life, including species of the family Drosophilidae, a longtime model system for genetics, genomics, and evolution. Whole-genome sequence alignments link evolution at the nucleotide level across species and are a critical but computationally intensive step for…

Continue Reading Dryad | Data — Progressive Cactus alignment of 298 drosophilid species

Genomic analysis of Coccomyxa viridis, a common low-abundance alga associated with lichen symbioses

Honegger, R. The lichen symbiosis: What is so spectacular about it?. Lichenologist 30, 193–212 (1998). Article  Google Scholar  Grube, M. & Berg, G. Microbial consortia of bacteria and fungi with focus on the lichen symbiosis. Fung. Biol. Rev. 23, 72–85 (2009). Article  Google Scholar  Spribille, T. et al. Basidiomycete yeasts…

Continue Reading Genomic analysis of Coccomyxa viridis, a common low-abundance alga associated with lichen symbioses

Salpa genome and developmental transcriptome analyses reveal molecular flexibility enabling reproductive success in a rapidly changing environment

Loeb, V. et al. Effects of sea-ice extent and krill or salp dominance on the Antarctic food web. Nature 387, 897–900 (1997). Article  ADS  CAS  Google Scholar  Atkinson, A., Siegel, V., Pakhomov, E. & Rothery, P. Long-term decline in krill stock and increase in salps within the Southern Ocean. Nature…

Continue Reading Salpa genome and developmental transcriptome analyses reveal molecular flexibility enabling reproductive success in a rapidly changing environment

Chromosome-scale genome of the human blood fluke Schistosoma mekongi and its implications for public health | Infectious Diseases of Poverty

Barnett R. Schistosomiasis. (1474–547X (Electronic)). Steinmann P, Keiser J, Bos R, Tanner M, Utzinger J. Schistosomiasis and water resources development: systematic review, meta-analysis, and estimates of people at risk. Lancet Infect Dis. 2006;6(7):411–25. Article  PubMed  Google Scholar  Uthailak N, Adisakwattana P, Thiangtrongjit T, Limpanont Y, Chusongsang P, Chusongsang Y, et…

Continue Reading Chromosome-scale genome of the human blood fluke Schistosoma mekongi and its implications for public health | Infectious Diseases of Poverty

Ancient diversity in host-parasite interaction genes in a model parasitic nematode

Van Valen, L. A new evolutionary law. Evol. Theory 1, 1–30 (1973). Google Scholar  Woolhouse, M. E. J., Webster, J. P., Domingo, E., Charlesworth, B. & Levin, B. R. Biological and biomedical implications of the co-evolution of pathogens and their hosts. Nat. Genet. 32, 569–577 (2002). Article  CAS  PubMed  Google…

Continue Reading Ancient diversity in host-parasite interaction genes in a model parasitic nematode

The Rauvolfia tetraphylla genome suggests multiple distinct biosynthetic routes for yohimbane monoterpene indole alkaloids

Genome sequencing and assembly of R. tetraphylla After DNA extraction from young leaves and sequencing, the R. tetraphylla genome was first assembled into 1008 contigs with an N50 of 3.7 Mb. After haplotigs removal and a final pilon polishing, the 364,945,498 bp final assembly was distributed across 76 scaffolds with an N50…

Continue Reading The Rauvolfia tetraphylla genome suggests multiple distinct biosynthetic routes for yohimbane monoterpene indole alkaloids

Subgenome dominance shapes novel gene evolution in the decaploid pitcher plant Nepenthes gracilis

Soltis, D. E. et al. Polyploidy and angiosperm diversification. Am. J. Bot. 96, 336–348 (2009). Article  PubMed  Google Scholar  Van de Peer, Y., Mizrachi, E. & Marchal, K. The evolutionary significance of polyploidy. Nat. Rev. Genet. 18, 411–424 (2017). Article  PubMed  Google Scholar  Amborella Genome Project et al. The Amborella…

Continue Reading Subgenome dominance shapes novel gene evolution in the decaploid pitcher plant Nepenthes gracilis

De novo genome assembly of the invasive mosquito species Aedes japonicus and Aedes koreicus | Parasites & Vectors

Genome length and GC content Using a hybrid approach that combines Oxford Nanopore long reads and Illumina short reads data, we assembled a scaffold-level version of Ae. koreicus and Ae. japonicus genomes whose size was assessed as 1.24 and 1.39 gigabase (Gb) pairs, respectively. These dimensions resemble those of other…

Continue Reading De novo genome assembly of the invasive mosquito species Aedes japonicus and Aedes koreicus | Parasites & Vectors

Illumina versus Oxford Nanopore Technologies BUSCO Scores

Illumina versus Oxford Nanopore Technologies BUSCO Scores 1 Hello everyone, I was wondering if anyone has experience using Illumina and Oxford Nanopore Technologies to do a hybrid assembly of genomes? I have illumina and Oxford Nanopore reads and the BUSCO scores are vastly different to each other despite the sequencing…

Continue Reading Illumina versus Oxford Nanopore Technologies BUSCO Scores

Wheat Sequencing: The Pan-Genome and Opportunities for Accelerating Breeding

Abberton M, Batley J, Bentley A, Bryant J, Cai H, Cockram J, Costa de Oliveira A, Cseke LJ, Dempewolf H, De Pace C, Edwards D, Gepts P, Greenland A, Hall AE, Henry R, Hori K, Howe GT, Hughes S, Humphreys M, Lightfoot D, Marshall A, Mayes S, Nguyen HT, Ogbonnaya…

Continue Reading Wheat Sequencing: The Pan-Genome and Opportunities for Accelerating Breeding

Bacteria can maintain rRNA operons solely on plasmids for hundreds of millions of years

Egan, E. S., Fogel, M. A. & Waldor, M. K. Divided genomes: negotiating the cell cycle in prokaryotes with multiple chromosomes. Mol. Microbiol. 56, 1129–1138 (2005). Article  CAS  PubMed  Google Scholar  Harrison, P. W., Lower, R. P., Kim, N. K. & Young, J. P. Introducing the bacterial ‘chromid’: not a…

Continue Reading Bacteria can maintain rRNA operons solely on plasmids for hundreds of millions of years

Comparative genomics and genome-wide SNPs of endangered Eld’s deer provide breeder selection for inbreeding avoidance

De novo genome assemblies and genome annotation We assembled a de novo genome of a seven-year-old male SED from Ubon Ratchathani Zoo using a combination of Illumina short-reads (92.94 × coverage) and PacBio long-reads (61.6 × coverage) (GenBank accession number: JACCHN000000000). Additionally, we used MGI short-reads (52.15 × coverage) to assemble a de novo genome of…

Continue Reading Comparative genomics and genome-wide SNPs of endangered Eld’s deer provide breeder selection for inbreeding avoidance

Unzipped chromosome-level genomes reveal allopolyploid nematode origin pattern as unreduced gamete hybridization

Nematode materials and species identification Mi, Mj, and Mg were collected from farmlands in Wuhan city of Hubei province, Longyan city of Fujian province, and Changsha city of Hunan Provinces, respectively. Two Ma samples were collected from farmlands in Shenyang city of Liaoning province and Shiping city of Yunnan province….

Continue Reading Unzipped chromosome-level genomes reveal allopolyploid nematode origin pattern as unreduced gamete hybridization

Chromosome-level genomes of three key Allium crops and their trait evolution

Chase, M. W. et al. An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants: APG IV. Bot. J. Linn. Soc. 181, 1–20 (2016). Article  Google Scholar  Jones, M. G. et al. Biosynthesis of the flavour precursors of onion and garlic. J. Exp. Bot….

Continue Reading Chromosome-level genomes of three key Allium crops and their trait evolution

Strain-level diversity of symbiont communities between individuals and populations of a bioluminescent fish

Sachs JL, Ehinger MO, Simms EL. Origins of cheating and loss of symbiosis in wild Bradyrhizobium. J Evol Biol. 2010;23:1075-89. Carrow HC, Batachari LE, Chu H. Strain diversity in the microbiome: Lessons from Bacteroides fragilis. PLoS Pathog. 2020;16:e1009056. Article  CAS  PubMed  PubMed Central  Google Scholar  Martinez J, Tolosana I, Ok…

Continue Reading Strain-level diversity of symbiont communities between individuals and populations of a bioluminescent fish

Invasive Californian death caps develop mushrooms unisexually and bisexually

Mushroom collecting Sporocarps were collected from various herbaria and during three expeditions to Point Reyes National Seashore (PRNS), California in 2004, 2014 and 2015, and in 2015 from three sites in Portugal. A total of 86 sporocarps were collected: 67 Californian sporocarps (one early herbarium sample dates to 1993), 11…

Continue Reading Invasive Californian death caps develop mushrooms unisexually and bisexually

How to make a proteome file

How to make a proteome file 0 I have the fasta files and genome annotation (gff) files for a number of species, and I am now trying to create proteome files for these species. I have tried extracting and translating only CDS sequences, and also only protein-coding gene sequences, however…

Continue Reading How to make a proteome file

Low mutation rate in epaulette sharks is consistent with a slow rate of evolution in sharks

Compagno, L. J. V. Alternative life-history styles of cartilaginous fishes in time and space. Environ. Biol. Fishes 28, 33–75 (1990). Article  Google Scholar  Kriwet, J., Witzmann, F., Klug, S. & Heidtke, U. H. J. First direct evidence of a vertebrate three-level trophic chain in the fossil record. Proc. Biol. Sci….

Continue Reading Low mutation rate in epaulette sharks is consistent with a slow rate of evolution in sharks

Range-wide and temporal genomic analyses reveal the consequences of near-extinction in Swedish moose

Ceballos, G., Ehrlich, P. R. & Raven, P. H. Vertebrates on the brink as indicators of biological annihilation and the sixth mass extinction. Proc. Natl Acad. Sci. USA 117, 13596–13602 (2020). Article  CAS  PubMed  PubMed Central  Google Scholar  Ceballos, G., Ehrlich, P. R. & Dirzo, R. Biological annihilation via the…

Continue Reading Range-wide and temporal genomic analyses reveal the consequences of near-extinction in Swedish moose

Missing BUSCOs are actually present in the transcriptome based on BLASTx?

Missing BUSCOs are actually present in the transcriptome based on BLASTx? 0 Hi, I was running BUSCO using euk and transcriptome mode and getting ~30% missing BUSCOs. I looked at the list of missing BUSCOs, and extracted their sequences from the fasta file inside the lineage directory. blastx of the…

Continue Reading Missing BUSCOs are actually present in the transcriptome based on BLASTx?

Pangenome analysis provides insight into the evolution of the orange subfamily and a key gene for citric acid accumulation in citrus fruits

Swingle, W. T. & Reece, P. C. In The Citrus Industry, History, World Distribution, Botany, and Varieties, Vol. 1 (eds Reuther, W. et al.) 190–143 (Univ. of California Press, 1967). Morton, C. M. & Telmer, C. New subfamily classification for the Rutaceae. Ann. Mo. Bot. Gard. 99, 620–641 (2014). Article …

Continue Reading Pangenome analysis provides insight into the evolution of the orange subfamily and a key gene for citric acid accumulation in citrus fruits

IJMS | Free Full-Text | Prioritizing Endangered Species in Genome Sequencing: Conservation Genomics in Action with the First Platinum-Standard Reference-Quality Genome of the Critically Endangered European Mink Mustela lutreola L., 1761

1. Introduction The alarming decline of biodiversity worldwide necessitates urgent conservation measures, particularly for wild, endangered, and understudied species. According to the International Union for Conservation of Nature’s (IUCN) Red List of Threatened Species, of the 5973 mammal species assessed, 1340 were classified as threatened with extinction, including 233 critically…

Continue Reading IJMS | Free Full-Text | Prioritizing Endangered Species in Genome Sequencing: Conservation Genomics in Action with the First Platinum-Standard Reference-Quality Genome of the Critically Endangered European Mink Mustela lutreola L., 1761

how to create a loop in R

I have a table of 18 columns and I want to test the linear correlation (regression) of one independent and one dependent variable each time. Before that, I have to scale my data but I also want to do that for each independent variable separately because the format of values…

Continue Reading how to create a loop in R

Mitochondrially mediated RNA interference, a retrograde signaling system affecting nuclear gene expression

Andersson DI, Jerlstrom-Hultqvist J, Nasvall J (2015) Evolution of new functions de novo and from preexisting genes. Cold Spring Harb Perspect Biol 7:a017996 Article  PubMed  PubMed Central  Google Scholar  Andrews S (2010) FastQC: a quality control tool for high throughput sequence data. www.bioinformatics.babraham.ac.uk/projects/fastqc/ Auyeung VC, Ulitsky I, McGeary SE, Bartel…

Continue Reading Mitochondrially mediated RNA interference, a retrograde signaling system affecting nuclear gene expression

High quality de novo genome assembly of the non-conventional yeast Kazachstania bulderi describes a potential low pH production host for biorefineries

Phenotypic characteristics of K. bulderi strains at low pH, organic acids, and antimicrobial drugs Since K. bulderi was isolated, only two studies have been conducted to investigate its physiological characteristics (7, 8). This species was shown to be able to grow efficiently at low pHs ranging from 5.0 to 2.5…

Continue Reading High quality de novo genome assembly of the non-conventional yeast Kazachstania bulderi describes a potential low pH production host for biorefineries

Short Read Data Genome Assembly

Short Read Data Genome Assembly 1 Hello, I have recently started working on genome assembly of a fungus genome.I have illumina short read sequencing paired-end (2x150bp) data taken from NCBI. Based on this data, I am trying to set up pipeline for genome assembly, which can later be used for…

Continue Reading Short Read Data Genome Assembly

Genome sequence and annotation of Periconia digitata a hopeful biocontrol agent of phytopathogenic oomycetes

Strain identification The strain Phoma sp. CNCM I-4278 was previously isolated from the rhizosphere of Nicotiana tabacum (cv Xanthi, Solanaceae) grown under controlled conditions17. The fungus was identified according to the closest similarity of its 18 S rRNA sequence (HM16174323) with those present in GenBank by that time and it was…

Continue Reading Genome sequence and annotation of Periconia digitata a hopeful biocontrol agent of phytopathogenic oomycetes

Genomic and transcriptomic analysis of camptothecin producing novel fungal endophyte: Alternaria burnsii NCIM 1409

Atanasov, A. G. et al. Discovery and resupply of pharmacologically active plant-derived natural products: A review. Biotechnol. Adv. 33, 1582–1614 (2015). Article  CAS  PubMed  PubMed Central  Google Scholar  Swamy, M. K. et al. Biotechnology of camptothecin production in Nothapodytes nimmoniana, Ophiorrhiza sp. and Camptotheca acuminata. Appl. Microbiol. Biotechnol. 105, 9089–9102…

Continue Reading Genomic and transcriptomic analysis of camptothecin producing novel fungal endophyte: Alternaria burnsii NCIM 1409

Multi-omics data provide insight into the adaptation of the glasshouse plant Rheum nobile to the alpine subnival zone

Yang, Y. et al. Advances in the studies of plant diversity and ecological adaptation in the subnival ecosystem of the Qinghai-Tibet plateau. Chin. Sci. Bull. 64, 2856–2864 (2019). Article  Google Scholar  Zhang, Y., Li, B. & Zheng, D. Datasets of the boundary and area of the Tibetan plateau. Acta Geographica…

Continue Reading Multi-omics data provide insight into the adaptation of the glasshouse plant Rheum nobile to the alpine subnival zone

How to set weight for merge legacy annotations

MAKER – How to set weight for merge legacy annotations 0 Good day. I am new to genome annotation.I am running maker to merge evidence from est, homolog, augustus and braker.The following is maker_opts.ctl: genome=genome.fasta est_gff=transcript.gff3 protein=homolog.gffs pred_gff=Augustus.gff3, Braker.gff3 I have executed the “mpiexec -n 30 maker > maker.out ”…

Continue Reading How to set weight for merge legacy annotations

Solanum americanum genome-assisted discovery of immune receptors that detect potato late blight pathogen effectors

Genome assembly and gene model prediction of S. americanum S. americanum is a globally distributed Solanaceae species that is resistant to many pathogens, including P. infestans and Ralstonia solanacearum25,29,33. Four S. americanum accessions SP1102, SP2271, SP2273 and SP2275 were selected for sequencing based on their variation in resistance to late…

Continue Reading Solanum americanum genome-assisted discovery of immune receptors that detect potato late blight pathogen effectors

investigate the inversions in comparison of assembled genome with reference genome

investigate the inversions in comparison of assembled genome with reference genome 0 Hi, I made scaffolds using ragtag with query assembled_genome.fasta and the reference genome which is already published. So now I made the dot plot for the comparison of two genomes. The reference genome has low BUSCO value than…

Continue Reading investigate the inversions in comparison of assembled genome with reference genome

Subtelomeric 5-enolpyruvylshikimate-3-phosphate synthase copy number variation confers glyphosate resistance in Eleusine indica

Genome assembly, annotation, and overview We assembled a chromosome-scale genome of a GS E. indica plant using PacBio Sequel II and long-range interaction (Hi-C) datasets. The assembly consists of nine chromosomes spanning 509,878,742 base pairs estimated to be ~97.8% complete by Benchmarking Universal Single-Copy Orthologs (BUSCO)28 analysis with an LTR…

Continue Reading Subtelomeric 5-enolpyruvylshikimate-3-phosphate synthase copy number variation confers glyphosate resistance in Eleusine indica

Evolutionary genomics of camouflage innovation in the orchid mantis

Sample collection Captive breeding individuals of H. coronatus (Mantodea, Hymenopodidae) hatched from the same ootheca that was collected from the Xishuangbanna rainforest, Yunnan Province, China in 2018. Individuals of D. lobata (Mantodea, Deroplatyidae) were collected from a captive breeding center in Beijing, China in 2018. All individuals were housed in semitransparent…

Continue Reading Evolutionary genomics of camouflage innovation in the orchid mantis

Comparative transcriptome profiling to unravel the key molecular signalling pathways and drought adaptive plasticity in shoot borne root system of sugarcane

Shrivastava, A. K. & Srivastava, S. Sugarcane: Physiological and molecular approaches for improving abiotic stress tolerance and sustaining crop productivity. (ed. Narendra Tuteja et al.) 885–992 (Wiley Blackell, Weinheim, 2012). Reyes, J. A. O., Casas, D. E., Gandia, J. L. & Delfin, E. F. Agricultural Research Updates Vol. 35 (ed…

Continue Reading Comparative transcriptome profiling to unravel the key molecular signalling pathways and drought adaptive plasticity in shoot borne root system of sugarcane

Multi-omic analyses reveal the unique properties of chia (Salvia hispanica) seed metabolism

Harley, R. M. et al. Labiatae. in Flowering Plants · Dicotyledons. The Families and Genera of Vascular Plants (ed. Kadereit, J. W.) vol. 7 167–275 (2004). Kokkini, S., Karousou, R. & Hanlidou, E. HERBS | Herbs of the Labiatae. Encyclopedia of Food Sciences and Nutrition 3082–3090 (2003) doi.org/10.1016/B0-12-227055-X/00593-9. Hao, D….

Continue Reading Multi-omic analyses reveal the unique properties of chia (Salvia hispanica) seed metabolism

Haplotype-resolved genomes of wild octoploid progenitors illuminate genomic diversifications from wild relatives to cultivated strawberry

Soltis, P. S. & Soltis, D. E. Polyploidy and Genome Evolution (Springer, 2012). Chen, J. Z. & Birchler, J. A. Polyploid and Hybrid Genomics (Wiley-Blackwell, 2013). Ye, C. Y. et al. The genomes of the allohexaploid Echinochloa crus-galli and its progenitors provide insights into polyploidization-driven adaptation. Mol. Plant 13, 1298–1310…

Continue Reading Haplotype-resolved genomes of wild octoploid progenitors illuminate genomic diversifications from wild relatives to cultivated strawberry

A chromosome-level genome assembly of Stenchaetothrips biformis and comparative genomic analysis highlights distinct host adaptations among thrips

Genome sequencing and assembly After filtering the adapters and low-quality reads, approximately 30.58 Gb of clean reads (~100×) were retained by Illumina paired-end short-reads sequencing, and about 63.24 Gb of subreads (~200×) were obtained by PacBio long-reads sequencing. The PacBio reads had an average length of 16.34 kb, with an N50 length of…

Continue Reading A chromosome-level genome assembly of Stenchaetothrips biformis and comparative genomic analysis highlights distinct host adaptations among thrips

Segmentation fault (core dumped) while running Augustus gene finder on Ubuntu

Segmentation fault (core dumped) while running Augustus gene finder on Ubuntu 1 Hi am Latha,am running Augustus using plant genome contigs. Though memory and space on my computer are sufficient for running this tool, am getting the below error:- kulaganathan@kulab:~/busco-master/augustus.2.5.5$ augustus –strand=both –species=rice –maxDNAPieceSize=20000000 sandalnew.fa >output1.gff replaced tx with 0…

Continue Reading Segmentation fault (core dumped) while running Augustus gene finder on Ubuntu

Genomic and phenotypic characterization of Acinetobacter colistiniresistens isolated from the feces of a healthy member of the community

Dwiyanto, J. et al. Pan-genome and resistome analysis of extended-spectrum ß-lactamase-producing Escherichia coli: A multi-setting epidemiological surveillance study from Malaysia. PLoS ONE 17, e0265142 (2022). Article  CAS  PubMed  PubMed Central  Google Scholar  Farrugia, D. N. et al. The complete genome and phenome of a community-acquired Acinetobacter baumannii. PLoS ONE 8,…

Continue Reading Genomic and phenotypic characterization of Acinetobacter colistiniresistens isolated from the feces of a healthy member of the community

Einkorn genomics sheds light on history of the oldest domesticated wheat

Plant materials The plant material used in this study was selected from a collection of 733 accessions of wild and domesticated einkorn held at the Wheat Genetics Resource Center (WGRC) at Kansas State University42. To generate reference assemblies, we selected one domesticated einkorn accession (T. monococcum L. subsp. monococcum; TA10622)…

Continue Reading Einkorn genomics sheds light on history of the oldest domesticated wheat

Rapid gene content turnover on the germline-restricted chromosome in songbirds

This work was carried out in accordance with ethical animal research requirements of Poland according to Polish law (the Act On the Protection of Animals used for Scientific or Educational Purposes, 15.01.2015, item 266, implementing Directive 2010/63/EU of the European Parliament and of the European Council of 22.09.2010). Experiments on…

Continue Reading Rapid gene content turnover on the germline-restricted chromosome in songbirds

Transcriptome assembler comparisons-Getting vastly different results

Transcriptome assembler comparisons-Getting vastly different results 0 Hi there I am comparing RNABLOOM2 (with and without Illumina shorts reads for polishing) and RATTLE for transcript assembly using reads from minion long read seq. The number of transcripts are extremely different. For RATTLE-50 000 transcripts; for RNABLOOM-about 160 000 transcripts (with…

Continue Reading Transcriptome assembler comparisons-Getting vastly different results

A high-quality genome assembly highlights the evolutionary history of the great bustard (Otis tarda, Otidiformes)

Formenti, G. et al. The era of reference genomes in conservation genomics. Trends Ecol. Evol. 37, 197–202 (2022). Article  CAS  PubMed  Google Scholar  Lee, H. et al. Third-generation sequencing and the future of genomics. bioRxiv, 048603 (2016). Irestedt, M. et al. A guide to avian museomics: Insights gained from resequencing…

Continue Reading A high-quality genome assembly highlights the evolutionary history of the great bustard (Otis tarda, Otidiformes)

Coevolution of the Tlx homeobox gene with medusa development (Cnidaria: Medusozoa)

Chang, E. S. et al. Genomic insights into the evolutionary origin of Myxozoa within Cnidaria. Proc. Natl Acad. Sci. USA 112, 14912–14917 (2015). Article  CAS  PubMed  PubMed Central  Google Scholar  Boero, F. et al. Inconsistent Evolution and Paedomorphosis among the Hydroids and Medusae of the Athecatae/Anthomedusae and the Thecatae/Leptomedusae (Cnidaria,…

Continue Reading Coevolution of the Tlx homeobox gene with medusa development (Cnidaria: Medusozoa)

The genome of the glasshouse plant noble rhubarb (Rheum nobile) provides a window into alpine adaptation

Billings, W. Adaptations and origins of alpine plants. Arct. Alp. Res. 6, 129–142 (1974). Article  Google Scholar  Agakhanjanz, O. & Breckle, W. Origin and evolution of the mountain flora in middle Asia and neighbouring mountain regions. in Arctic and Apine Biodiversity: Patterns, Causes and Ecosystem Consequences (eds. Chapin, F. &…

Continue Reading The genome of the glasshouse plant noble rhubarb (Rheum nobile) provides a window into alpine adaptation

Genome analysis of Parmales, the sister group of diatoms, reveals the evolutionary specialization of diatoms from phago-mixotrophs to photoautotrophs

Booth, B. C. & Marchant, H. J. Parmales, a new order of marine chrysophytes, with desriptions of three new genera and seven new species. J. Phycol. 23, 245–260 (1987). Article  Google Scholar  Ichinomiya, M. et al. Diversity and oceanic distribution of the Parmales (Bolidophyceae), a picoplanktonic group closely related to…

Continue Reading Genome analysis of Parmales, the sister group of diatoms, reveals the evolutionary specialization of diatoms from phago-mixotrophs to photoautotrophs

Influence of mobile genetic elements and insertion sequences in long- and short-term adaptive processes of Acidithiobacillus ferrooxidans strains

Moya-Beltrán, A. et al. Genomic evolution of the class Acidithiobacillia: Deep-branching Proteobacteria living in extreme acidic conditions. ISME J. 15, 3221–3238 (2021). Article  PubMed  PubMed Central  Google Scholar  Nuñez, H. et al. Molecular systematics of the genus Acidithiobacillus: Insights into the phylogenetic structure and diversification of the taxon. Front. Microbiol….

Continue Reading Influence of mobile genetic elements and insertion sequences in long- and short-term adaptive processes of Acidithiobacillus ferrooxidans strains

Parallel and convergent genomic changes underlie independent subterranean colonization across beetles

Conway Morris, S. The predictability of evolution: glimpses into a post-Darwinian world. Naturwissenschaften 96, 1313–1337 (2009). Article  ADS  CAS  PubMed  Google Scholar  Stern, D. L. The genetic causes of convergent evolution. Nat. Rev. Genet. 14, 751–764 (2013). Article  CAS  PubMed  Google Scholar  Christiansen, K. Convergence and parallelism in cave entomobryinae….

Continue Reading Parallel and convergent genomic changes underlie independent subterranean colonization across beetles

Whole-Genome Sequencing of Pseudomonas koreensis Isolated from Diseased Tor tambroides

Parte AC, Carbasse JS, Meier-Kolthoff JP et al (2020) List of prokaryotic names with standing in nomenclature (LPSN) moves to the DSMZ. Int J Syst Evol Microbiol 70(11):5607–5612. doi.org/10.1099/ijsem.0.004332 Article  PubMed  PubMed Central  Google Scholar  Duman M, Mulet M, Altun S et al (2021) The diversity of Pseudomonas species isolated…

Continue Reading Whole-Genome Sequencing of Pseudomonas koreensis Isolated from Diseased Tor tambroides

The genome of Acorus deciphers insights into early monocot evolution

Lughadha, E. N. et al. Counting counts: revised estimates of numbers of accepted species of flowering plants, seed plants, vascular plants and land plants with a review of other recent estimates. Phytotaxa 272, 82–88 (2016). Article  Google Scholar  Group, A. P. An update of the Angiosperm Phylogeny Group classification for…

Continue Reading The genome of Acorus deciphers insights into early monocot evolution

The chromosome-scale genome assembly of cluster bean provides molecular insight into edible gum (galactomannan) biosynthesis family genes

Purohit, J., Kumar, A., Hynniewta, M. & Satyawada, R. R. Karyomorphological studies in guar (Cyamopsis tetragonoloba (Linn.) Taub.)—An important gum yielding plant of Rajasthan, India. Cytologia 76(2), 163–169 (2011). Article  Google Scholar  Gillett, J. B. Indigofera (Microcharis) in tropical Africa with the related genera Cyamopsis and Rhynchotropis. H.M.S.O Kew Bull.,…

Continue Reading The chromosome-scale genome assembly of cluster bean provides molecular insight into edible gum (galactomannan) biosynthesis family genes

The Biostar Herald for Thursday, June 15, 2023

The Biostar Herald publishes user submitted links of bioinformatics relevance. It aims to provide a summary of interesting and relevant information you may have missed. You too can submit links here. This edition of the Herald was brought to you by contribution from Istvan Albert, and was edited by Istvan…

Continue Reading The Biostar Herald for Thursday, June 15, 2023

A graph-based genome and pan-genome variation of the model plant Setaria

Variation and evolution in Setaria We collected genome-wide resequencing data for 630 wild (S. viridis), 829 landrace and 385 modern cultivated accessions from the Setaria genus with an average sequencing depth of ~15×, of which 1,004 were newly generated and 840 were from previous studies16,21 (Supplementary Table 1). After aligning…

Continue Reading A graph-based genome and pan-genome variation of the model plant Setaria

busco id description

busco id description 0 Hi, I did a BUSCO analysis using lineage metazoa_odb10. Below is a snippet from my output, I am missing the column for gene ID description from my output. The metazoa_odb10 lineage dataset is missing the links_to_ODB10.txt file. So, I tried solutions from gitlab.com/ezlab/busco/-/issues/358 and thackl.github.io/BUSCO-gene-descriptions links….

Continue Reading busco id description

Characterization of metagenome-assembled genomes from the International Space Station | Microbiome

Metagenome-assembled bacterial genomes Out of the 42 ISS metagenomes submitted at NCBI, only PMA-treated metagenomes (n = 21) representing the viable/intact cells were used for generating bacterial MAGs. Characteristics of MAGs (n = 46) such as genome size (2.6 to 6.6 Mb), completeness, contamination percentage, the average mean coverage, number…

Continue Reading Characterization of metagenome-assembled genomes from the International Space Station | Microbiome

Backcrossing to different parents produced two distinct hybrid species

Alexander DH, Lange K (2011) Enhancements to the ADMIXTURE algorithm for individual ancestry estimation. BMC Bioinforma 12:246. doi.org/10.1186/1471-2105-12-246 Article  Google Scholar  Anderegg WRL, Flint A, Huang C-Y, Flint L, Berry JA, Davis FW et al. (2015) Tree mortality predicted from drought-induced vascular damage. Nat Geosci 8:367–371 Article  CAS  Google Scholar …

Continue Reading Backcrossing to different parents produced two distinct hybrid species

Endogenous viral elements reveal associations between a non-retroviral RNA virus and symbiotic dinoflagellate genomes

Johnson, W. E. Endogenous retroviruses in the genomics era. Annu. Rev. Virol. 2, 135–159 (2015). Article  CAS  PubMed  Google Scholar  Johnson, W. E. Origins and evolutionary consequences of ancient endogenous retroviruses. Nat. Rev. Microbiol. 17, 355–370 (2019). Article  CAS  PubMed  Google Scholar  Johnson, W. E. Endless forms most viral. PLoS…

Continue Reading Endogenous viral elements reveal associations between a non-retroviral RNA virus and symbiotic dinoflagellate genomes

Chromosome-level genome assemblies from two sandalwood species provide insights into the evolution of the Santalales

Genome sequencing and assembly We sequenced and assembled genomes for the sandalwood species S. album and S. yasi (Fig. 1). In total, ~23 Gb and ~25 Gb of clean short reads of S. album and S. yasi were obtained for the genomic survey, respectively (Supplementary Tables 1 and 2). According to k-mer analysis, the…

Continue Reading Chromosome-level genome assemblies from two sandalwood species provide insights into the evolution of the Santalales

Comparative genome features and secondary metabolite biosynthetic potential of Kutzneria chonburiensis and other species of the genus Kutzneria

Adamek, M., Spohn, M., Stegmann, E. & Ziemert, N. Mining bacterial genomes for secondary metabolite gene clusters. Methods Mol. Biol. 1520, 23–47 (2017). CAS  PubMed  Google Scholar  Belknap, K. C., Park, C. J., Barth, B. M. & Andam, C. P. Genome mining of biosynthetic and chemotherapeutic gene clusters in Streptomyces…

Continue Reading Comparative genome features and secondary metabolite biosynthetic potential of Kutzneria chonburiensis and other species of the genus Kutzneria

The draft genome sequence of the Japanese rhinoceros beetle Trypoxylus dichotomus septentrionalis towards an understanding of horn formation

Hunt, T. et al. A comprehensive phylogeny of beetles reveals the evolutionary origins of a superradiation. Science 318, 1913–1916 (2007). Article  ADS  CAS  PubMed  Google Scholar  Crowson, R. A. The phylogeny of coleoptera. Annu. Rev. Entomol. 5, 111–134 (1960). Article  Google Scholar  Darwin, C. The Descent of Man, and Selection…

Continue Reading The draft genome sequence of the Japanese rhinoceros beetle Trypoxylus dichotomus septentrionalis towards an understanding of horn formation

The first high-quality chromosome-level genome of the Sipuncula Sipunculus nudus using HiFi and Hi-C data

Cutler, E. B. The Sipuncula: Their Systematics, Biology, And Evolution (New York: Cornell University Press, doi.org/10.7591/9781501723643, 1994) Nielsen, C. Some aspects of spiralian development. Acta Zool. 91, 20–28, doi.org/10.1111/j.1463-6395.2009.00421.x (2010). Article  Google Scholar  Huang, D. Y., Chen, J. Y., Vannier, J. & Saiz Salinas, J. I. Early Cambrian sipunculan worms…

Continue Reading The first high-quality chromosome-level genome of the Sipuncula Sipunculus nudus using HiFi and Hi-C data

Pangenomics of the death cap mushroom Amanita phalloides, and of Agaricales, reveals dynamic evolution of toxin genes in an invasive range

Sakai AK, Allendorf FW, Holt JS, Lodge DM, Molofsky J, With KA, et al. The population biology of invasive species. Annu Rev Ecol Syst. 2001;32:305–32. Article  Google Scholar  Allendorf FW, Lundquist LL. Introduction: population biology, evolution, and control of invasive species. Conserv Biol. 2003;17:24–30. Article  Google Scholar  Erickson AB. The…

Continue Reading Pangenomics of the death cap mushroom Amanita phalloides, and of Agaricales, reveals dynamic evolution of toxin genes in an invasive range

Ancient gene linkages support ctenophores as sister to other animals

Ryan, J. F. et al. The genome of the ctenophore Mnemiopsis leidyi and its implications for cell type evolution. Science 342, 1242592 (2013). Article  PubMed  PubMed Central  Google Scholar  Halanych, K. M. The ctenophore lineage is older than sponges? That cannot be right! Or can it? J. Exp. Biol. 218,…

Continue Reading Ancient gene linkages support ctenophores as sister to other animals

Chromosome-level assembly of Dictyophora rubrovolvata genome using third-generation DNA sequencing and Hi-C analysis

Dictyophora rubrovolvata, a rare edible mushroom with both nutritional and medicinal values, was regarded as the “queen of the mushroom” for its attractive appearance. D. rubrovolvata has been widely cultivated in China in recent years, and many researchers were focusing on its nutrition, culture condition and artificial cultivation. Due to…

Continue Reading Chromosome-level assembly of Dictyophora rubrovolvata genome using third-generation DNA sequencing and Hi-C analysis

Immune gene variation associated with chromosome-scale differences among individual zebrafish genomes

Litman, G. W., Cannon, J. P. & Dishaw, L. J. Reconstructing immune phylogeny: New perspectives. Nat. Rev. Immunol. 5, 866–879 (2005). Article  CAS  PubMed  PubMed Central  Google Scholar  Criscitiello, M. F. & de Figueiredo, P. Fifty shades of immune defense. Heitman J, editor. PLoS Pathog. 9, e1003110 (2013). Article  CAS …

Continue Reading Immune gene variation associated with chromosome-scale differences among individual zebrafish genomes

A high-quality chromosomal-level genome assembly of Greater Scaup (Aythya marila)

Ethics statement All animal experimental procedures were approved by the Biomedical Ethics Committee of Qufu Normal University (approval number: 2022001). Sampling and sequening The experimental sample is a wounded male duck found during the wild bird survey in Jiangsu, China, which died unexpectedly during rescue. We dissected the sample and…

Continue Reading A high-quality chromosomal-level genome assembly of Greater Scaup (Aythya marila)

[Metagenome assembly] Reassembling bacterial genome using Nanopore contig/reads

[Metagenome assembly] Reassembling bacterial genome using Nanopore contig/reads 0 Hello everyone, We did a metagenome sequencing on ONT and ran metaFlye to obtain contigs and polished with medaka. Out of the 318 contigs, around 21 contigs were prokaryotic contigs, and two of the contigs had 16S rRNA sequences annotated which…

Continue Reading [Metagenome assembly] Reassembling bacterial genome using Nanopore contig/reads

Cuticle supplementation and nitrogen recycling by a dual bacterial symbiosis in a family of xylophagous beetles

Feldhaar H. Bacterial symbionts as mediators of ecologically important traits of insect hosts. Ecol Entomol. 2011;36:533–43. Article  Google Scholar  Douglas AE. Symbiosis as a general principle in eukaryotic evolution. Cold Spring Harb Perspect Biol. 2014;6:a016113–a016113. Article  PubMed  PubMed Central  Google Scholar  Flórez LV, Biedermann PHW, Engl T, Kaltenpoth M. Defensive…

Continue Reading Cuticle supplementation and nitrogen recycling by a dual bacterial symbiosis in a family of xylophagous beetles

Inference of phylogenetic trees directly from raw sequencing reads using Read2Tree

State-of-the-art phylogenomic pipelines require many steps, which can be both time consuming and error prone (Fig. 1a). With Read2Tree, we directly process raw sequencing reads and reconstruct sequence alignments for conventional tree inference methods (Fig. 1b and Supplementary Fig. 1). We start by aligning raw reads to nucleotide sequences derived…

Continue Reading Inference of phylogenetic trees directly from raw sequencing reads using Read2Tree

Chromosome-level genome assembly and population genomic resource to accelerate orphan crop lablab breeding

FAO. Faostat: FAO Statistical Databases. (Food & Agriculture Organization of the United Nations (FAO), 2000). The war in Ukraine is exposing gaps in the world’s food-systems research. Nature 604, 217–218 (2022). Chapman, M. A., He, Y. & Zhou, M. Beyond a reference genome: pangenomes and population genomics of underutilized and…

Continue Reading Chromosome-level genome assembly and population genomic resource to accelerate orphan crop lablab breeding

Integrated transcriptome catalog of Tenualosa ilisha as a resource for gene discovery and expression profiling

Ahsan, D. A., Naser, M. N., Bhaumik, U., Hazra, S. & Bhattacharya, S. B. Migration, Spawning Patterns and Conservation of Hilsa Shad (Tenualosa ilisha) in Bangladesh and India. Publ. by Acad. Found. India, New Delhi Int. Union Conserv. Nat. Nat. Resour. 95 (2014). De, D. et al. Nutritional profiling of…

Continue Reading Integrated transcriptome catalog of Tenualosa ilisha as a resource for gene discovery and expression profiling

Supported Tools – MultiQC

Tool Tool Name Description Removes adapter sequences and trims low quality bases from the 3′ end of reads. Overlapping paired-ended reads can be merged into consensus sequences and adapter sequence can be found for paired-ended data if not known. Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data….

Continue Reading Supported Tools – MultiQC

The little skate genome and the evolutionary emergence of wing-like fins

Nakamura, T. et al. Molecular mechanisms underlying the exceptional adaptations of batoid fins. Proc. Natl Acad. Sci. USA 112, 15940–15945 (2015). Article  ADS  CAS  PubMed  PubMed Central  Google Scholar  Turner, N. et al. The evolutionary origins and diversity of the neuromuscular system of paired appendages in batoids. Proc. Biol. Sci….

Continue Reading The little skate genome and the evolutionary emergence of wing-like fins

Whole-genome sequencing and analysis of Apocynum cannabinum

Sequencing data statistics The PacBio platform were used for whole genome sequencing the A. cannabinum genome. Table 1 represents total sequencing volume was 117.13 G, and the coverage was 490.04 X based on calculations of the genome size (239.02 M) estimated from a survey [41]. In addition, the Illumina platform…

Continue Reading Whole-genome sequencing and analysis of Apocynum cannabinum

Genomic insights into the coupling of a Chlorella-like microeukaryote and sulfur bacteria in the chemocline of permanently stratified Lake Cadagno

Philippi M, Kitzinger K, Berg JS, Tschitschko B, Kidane AT, Littmann S, et al. Purple sulfur bacteria fix N2 via molybdenum-nitrogenase in a low molybdenum Proterozoic ocean analogue. Nat Commun. 2021;12:4774. Article  CAS  PubMed  PubMed Central  Google Scholar  Xiong Y, Guilbaud R, Peacock CL, Cox RP, Canfield DE, Krom MD,…

Continue Reading Genomic insights into the coupling of a Chlorella-like microeukaryote and sulfur bacteria in the chemocline of permanently stratified Lake Cadagno

Super-pangenome analyses highlight genomic diversity and structural variation across wild and cultivated tomato species

Giovannoni, J. J. Genetic regulation of fruit development and ripening. Plant Cell 16, S170–S180 (2004). CAS  PubMed  PubMed Central  Google Scholar  Tieman, D. et al. A chemical genetic roadmap to improved tomato flavor. Science 355, 391–394 (2017). CAS  PubMed  Google Scholar  Peralta, I. E., Spooner, D. M. & Knapp, S….

Continue Reading Super-pangenome analyses highlight genomic diversity and structural variation across wild and cultivated tomato species

Chromosome-level genome assembly of the critically endangered Baer’s pochard (Aythya baeri)

Ethics statement All animal handling and experimental procedures were approved by the Qufu Normal University Biomedical Ethics Committee (approval number: 2022001). Sample and sequencing Baer’s pochard tissue for whole-genome sequencing was obtained from a dead individual that had strayed into a fishing net in Shandong (China). The muscle tissue that…

Continue Reading Chromosome-level genome assembly of the critically endangered Baer’s pochard (Aythya baeri)

Preadapted to adapt: underpinnings of adaptive plasticity revealed by the downy brome genome

Bradley, B. A. et al. Cheatgrass (Bromus tectorum) distribution in the intermountain western United States and its relationship to fire frequency, seasonality, and ignitions. Biol. Invasions 20, 1493–1506 (2018). Article  Google Scholar  Balch, J. K., Bradley, B. A., D’Antonio, C. M. & Gomez-Dans, J. Introduced annual grass increases regional fire…

Continue Reading Preadapted to adapt: underpinnings of adaptive plasticity revealed by the downy brome genome

Identification and gene expression analysis of serine proteases and their homologs in the Asian corn borer Ostrinia furnacalis

Ross, J., Jiang, H., Kanost, M. R. & Wang, Y. Serine proteases and their homologs in the Drosophila melanogaster genome: An initial analysis of sequence conservation and phylogenetic relationships. Gene 304, 117–131 (2003). Article  CAS  PubMed  Google Scholar  Rawlings, N. D. & Barrett, A. J. Evolutionary families of peptidases. Biochem….

Continue Reading Identification and gene expression analysis of serine proteases and their homologs in the Asian corn borer Ostrinia furnacalis

Salamandra salamandra homology annotation blastp-swissprot

Dispersal is a key process in ecology and evolutionary biology, as it shapes biodiversity patterns over space and time. Mounting evidence is showing that attitude to disperse is unevenly distributed among individuals within animal populations, and that individual personality can have pivotal roles in the shaping of this attitude. Here,…

Continue Reading Salamandra salamandra homology annotation blastp-swissprot

Snakemake error to build synteny from BUSCO .tsv

Snakemake error to build synteny from BUSCO .tsv 0 Hi, I am trying to run (on CAMP) protocol 2 (currentprotocols.onlinelibrary.wiley.com/doi/full/10.1002/cpz1.323) of BUSCO with test data, but I am getting this error: [diego@login001 plot_syntenies]$ snakemake -core 2 –use-conda –jobs 1 Building DAG of jobs… MissingRuleException: No rule to produce 2 (if…

Continue Reading Snakemake error to build synteny from BUSCO .tsv

A hydrogenotrophic Sulfurimonas is globally abundant in deep-sea oxygen-saturated hydrothermal plumes

Inagaki, F., Takai, K., Kobayashi, H., Nealson, K. H. & Horikoshi, K. Sulfurimonas autotrophica gen. nov., sp. nov., a novel sulfur-oxidizing e-proteobacterium isolated from hydrothermal sediments in the Mid-Okinawa Trough. Int. J. Syst. Evol. Microbiol. 53, 1801–1805 (2003). Article  CAS  PubMed  Google Scholar  Timmer-Ten Hoor, A. A new type of…

Continue Reading A hydrogenotrophic Sulfurimonas is globally abundant in deep-sea oxygen-saturated hydrothermal plumes

Hybrid de novo genome assembly and comparative genomics of three different isolates of Gnomoniopsis castaneae

Crous, P. et al. Fungal planet description sheets: 107–127. Pers. Mol. Phylogeny Evol. Fungi 28, 138–182. doi.org/10.3767/003158512X652633 (2012). Article  CAS  Google Scholar  Visentin, I. et al. Gnomoniopsis castanea sp. nov. (Gnomoniaceae, Diaporthales) as the causal agent of nut rot in sweet chestnut. J. Plant Pathol. 94, 411–419. doi.org/10.4454/JPP.FA.2012.045 (2012). Article …

Continue Reading Hybrid de novo genome assembly and comparative genomics of three different isolates of Gnomoniopsis castaneae

Adaptations of Pseudoxylaria towards a comb-associated lifestyle in fungus-farming termite colonies

Genome reduction is associated with a termite comb-associated lifestyle For our studies, we collected fungus comb samples originating from mounds of Macrotermes natalensis, Odontotermes spp., and Microtermes spp. termites and were able to obtain seven viable Pseudoxylaria cultures (X802 [Microtermes sp.], Mn132, Mn153, X187, X3-2 [Macrotermes natalensis], and X167, X170LB [Odontotermes…

Continue Reading Adaptations of Pseudoxylaria towards a comb-associated lifestyle in fungus-farming termite colonies

Genome assembly and genetic dissection of a prominent drought-resistant maize germplasm

Gupta, A., Rico-Medina, A. & Cano-Delgado, A. I. The physiology of plant responses to drought. Science 368, 266–269 (2020). Article  CAS  PubMed  Google Scholar  Hu, H. & Xiong, L. Genetic engineering and breeding of drought-resistant crops. Annu Rev. Plant Biol. 65, 715–741 (2014). Article  CAS  PubMed  Google Scholar  Ashraf, M….

Continue Reading Genome assembly and genetic dissection of a prominent drought-resistant maize germplasm