Categories
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…
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…
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….
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…
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…
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….
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…
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…
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…
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…
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,…
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.,…
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)….
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…
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…
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…
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…
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…
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…
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…
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…
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…
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…
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…
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…
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…
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….
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….
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…
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…
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…
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….
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…
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…
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 …
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…
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…
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…
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…
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…
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…
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…
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…
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 ”…
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…
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…
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…
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…
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…
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….
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…
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…
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…
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,…
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)…
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…
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…
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…
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,…
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. &…
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…
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….
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….
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…
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…
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.,…
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…
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…
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….
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…
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 …
Endogenous viral elements reveal associations between a non-retroviral RNA virus and symbiotic dinoflagellate genomes
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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…
Comparative genome features and secondary metabolite biosynthetic potential of Kutzneria chonburiensis and other species of the genus Kutzneria
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The draft genome sequence of the Japanese rhinoceros beetle Trypoxylus dichotomus septentrionalis towards an understanding of horn formation
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The first high-quality chromosome-level genome of the Sipuncula Sipunculus nudus using HiFi and Hi-C data
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Pangenomics of the death cap mushroom Amanita phalloides, and of Agaricales, reveals dynamic evolution of toxin genes in an invasive range
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Ancient gene linkages support ctenophores as sister to other animals
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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…
Immune gene variation associated with chromosome-scale differences among individual zebrafish genomes
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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…
[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…
Cuticle supplementation and nitrogen recycling by a dual bacterial symbiosis in a family of xylophagous beetles
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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…
Chromosome-level genome assembly and population genomic resource to accelerate orphan crop lablab breeding
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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…
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….
The little skate genome and the evolutionary emergence of wing-like fins
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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…
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,…
Super-pangenome analyses highlight genomic diversity and structural variation across wild and cultivated tomato species
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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…
Preadapted to adapt: underpinnings of adaptive plasticity revealed by the downy brome genome
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Identification and gene expression analysis of serine proteases and their homologs in the Asian corn borer Ostrinia furnacalis
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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,…
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…
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…
Hybrid de novo genome assembly and comparative genomics of three different isolates of Gnomoniopsis castaneae
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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…
Genome assembly and genetic dissection of a prominent drought-resistant maize germplasm
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