Tag: BUSCO

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 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….

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…

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 …

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…

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…

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…

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…

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…

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…

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,…

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…

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 …

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 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…

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…

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…

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…

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…

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….

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….

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…

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,…

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….

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…

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…

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….

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 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…

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…

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 …

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…

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….

Course –Analysis of PROKARYOTIC PANGENOMES Dates: Online, 12-14 April 2023 COURSE OVERVIEW In this course, you will be introduced to the study of pangenomes and their implications in biological research. You will also be given the chance to put theory into practice. By the end of the first day, you…

Chromosomal-scale genome assembly and full spidroin gene set of T. clavata To explore dragline silk production in T. clavata, we sought to assemble a high-quality genome of this species. Thus, we first performed a cytogenetic analysis of T. clavata captured from the wild in Dali City, Yunnan Province, China, and…

Andersen LO, Bonde I, Nielsen HB, Stensvold CR. A retrospective metagenomics approach to studying Blastocystis. FEMS Microbiol Ecol. 2015. doi.org/10.1093/femsec/fiv072. Article  Google Scholar  Audebert C, Even G, Cian A, Loywick A, Merlin S, Viscogliosi E, et al. Colonization with the enteric protozoa Blastocystis is associated with increased diversity of human…

Genome assembly and chromosome identification A Plantago ovata genome reference was generated by utilizing a total of 5.98 M (7 cells, 40.21 Gb, N50 = 10.45 Kb, 50 bp–121.17 Kb) PacBio long reads and 636.5 million (47.74 Gb) Hi-C short-reads. PacBio reads were used to assemble contigs, while Hi-C reads were used to achieve chromosome-level assembly. The final…

Hall, B. K. & Wake, M. H. in The Origin and Evolution of Larval Forms (eds Hall, B. K. & Wake, M. H.) 1–19 (Academic Press, 1999). Nielsen, C. Animal phylogeny in the light of the trochaea theory. Biol. J. Linn. Soc. 25, 243–299 (2008). Article  Google Scholar  Garstang, W….

Materials Medakamo hakoo 311 was obtained from the personal aquarium of Prof. Kuroiwa (Kagurazaka, Tokyo, Japan)4. The M. hakoo strain was cultured in 0.05% HYPONeX (HYPONeX Japan Corp., Ltd., Osaka, Japan) liquid medium and on 0.05% HYPONeX gellan gum-based solid medium in plates. Cyanidioschyzon merolae 10D (Toda et al. 1995)…

Genomic features of two Anastatus wasps, A. japonicus and A. fulloi We employed PacBio high-fidelity (HiFi) long-read sequencing and Illumina short-read sequencing technologies to generate high-quality contigs for two Anastatus wasps, A. japonicus and A. fulloi (Supplementary Tables 1 and 2). These contigs were further scaffolded using Hi-C libraries to…

Low exonic mapping of RNASeq data to draft genome. Should I suspect poor annotation? 0 I am working on RNASeq data for DE from a non-traditional organism (Artemia franciscana, a eukaryotic arthropod) whose draft genome was published last year. I should note here that although the genome was assembled with…

Steen AD, Crits-Christoph A, Carini P, DeAngelis KM, Fierer N, Lloyd KG, Cameron TJ. High proportions of bacteria and archaea across most biomes remain uncultured. ISME J. 2019;13:3126–30. PubMed  PubMed Central  Google Scholar  Goh KM, Shahar S, Chan K-G, Chong CS, Amran SI, Sani MH, Zakaria II, Kahar UM. Current…

I’m trying to install busco, detonate, and transrate in conda but I keep getting this error: The environment is inconsistent, please check the package plan carefully The following packages are causing the inconsistency: – bioconda/linux-64::samtools==1.11=h6270b1f_0 – bioconda/linux-64::trinity==2.9.1=h8b12597_0 This is the command I enter conda install -c bioconda busco -y So…

Although the hypothesis of gene-regulatory network (GRN) cooption is a plausible model to explain the origin of morphological novelties (1), there has been limited empirical evidence to show that this mechanism led to the origin of any novel trait. Several hypotheses have been proposed for the origin of butterfly eyespots,…

1. Singh, A. et al. Phytochemical profile of sugarcane and its potential health aspects. Pharmacogn. Rev. 9, 45–54 (2015). CAS  PubMed  PubMed Central  Google Scholar  2. Eggleston, G. Positive aspects of cane sugar and sugar cane derived products in food and nutrition. J. Agric. Food Chem. 66, 4007–4012 (2018). CAS …

About Short intro Further reading How to cite Brief project history Authors Funding License and Terms of use Short intro QUAST evaluates genome assemblies by computing various metrics, including N50, length for which the collection of all contigs of that length or longer covers at least 50% of assembly length…

Significance Putatively ancient asexual species pose a challenge to theory because they appear to escape the predicted negative long-term consequences of asexuality. Although long-term asexuality is difficult to demonstrate, specific signatures of haplotype divergence, called the “Meselson effect,” are regarded as strong support for long-term asexuality. Here, we provide evidence…

Procambarus fallax collections and PCR genotyping Animals were collected from various wild populations (Table S1) in compliance with state and local regulations (Georgia department of natural resources scientific collection permit 115621108, state of Florida collection permits S-19-10 and S-20-04). DNA was isolated from abdominal muscle tissue using SDS-based extraction and precipitation…

Species invasions into novel habitats mark major transitions in the evolution of life on Earth. Some of these are relatively ancient, such as the vertebrate transition from the oceans to life on land (∼375 Mya) or the evolution of arboreal vertebrate species (∼160 Mya). When divergent lineages transition to the…

1. Edmonds, R. L. & Eglitis, A. The role of the Douglas-fir beetle and wood borers in the decomposition of and nutrient release from Douglas-fir logs. Can. J. Res. 19, 853–859 (1989). Article  Google Scholar  2. Hlásny, T. et al. Living with bark beetles: impacts, outlook and management options. In:…

Significance Some of the most spectacular adaptive radiations of plants and animals occur on remote oceanic islands, yet such radiations are preceded by founding events that severely limit genetic variation. How genetically depauperate founder populations give rise to the spectacular phenotypic and ecological diversity characteristic of island adaptive radiations is…

I don’t think there is a “best” approach in your situation, given 1) the taxonomy of the group is probably still flaky. 2) being draft genomes, they probably are spotty and have sizeable gaps, and maybe even contaminants. Repeat regions are often left out of such assemblies. Actually, a good…

BUSCO installation and run 2 That unil.ch link looks a bit too complicated, these are the commands I ran to get BUSCO via Singularity: Download the image: singularity pull Run the image with example genome.fasta, assuming it’s a genome and a plant: singularity run -B $(pwd):/busco_wd/ busco_v5.2.2_cv1.sif busco -l…