BUSCO Update: Novel and Streamlined Workflows along with Broader and Deeper Phylogenetic Coverage for Scoring of Eukaryotic, Prokaryotic, and Viral Genomes

Manni, Mosè; Berkeley, Matthew; Seppey, Mathieu; Simão, Felipe A.; Zdobnov, Evgeny M.

doi:10.1093/molbev/msab199

Cited by 3,230 publications

(2,028 citation statements)

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“…A total of 26,230 genes were functionally annotated. We evaluated the completeness of the predicted gene sets and extent of gene duplication with 4,896 BUSCOs from the Poales database (v10; Manni et al 2021 ), of which 3,930 (80.2%) were complete, indicating a relatively complete genome assembly and gene prediction ( table 1 ). An interesting observation among the complete BUSCO’s was the presence of 1,159 (30%) complete duplicated copies.…”

Section: Resultsmentioning

confidence: 99%

Chromosome Level Genome Assembly and Annotation of Highly Invasive Japanese Stiltgrass (Microstegium vimineum)

Ramachandran

Huebner

Daly

et al. 2021

Genome Biology and Evolution

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The invasive Japanese stiltgrass ( Microstegium vimineum ) affects a wide range of ecosystems and threatens biodiversity across the eastern USA. However, the mechanisms underlying rapid adaptation, plasticity, and epigenetics in the invasive range are largely unknown. We present a chromosome-level assembly for M. vimineum to investigate genome dynamics, evolution, adaptation, and the genomics of phenotypic plasticity. We generated a 1.12-Gb genome with scaffold N50 length of 53.44 Mb respectively, taking a de novo assembly approach that combined PacBio and Dovetail Genomics Omni-C sequencing. The assembly contains 23 pseudochromosomes, representing 99.96% of the genome. BUSCO assessment indicated that 80.3% of Poales gene groups are present in the assembly. The genome is predicted to contain 39,604 protein-coding genes, of which 26,288 are functionally annotated. Furthermore, 66.68% of the genome is repetitive, of which unclassified (35.63%) and long-terminal repeat (LTR) retrotransposons (26.90%) are predominant. Similar to other grasses, Gypsy (41.07%) and Copia (32%) are the most abundant LTR-retrotransposon families. The majority of LTR-retrotransposons are derived from a significant expansion in the past 1–2 Myr, suggesting the presence of relatively young LTR-retrotransposon lineages. We find corroborating evidence from Ks plots for a stiltgrass-specific duplication event, distinct from the more ancient grass-specific duplication event. The assembly and annotation of M. vimineum will serve as an essential genomic resource facilitating studies of the invasion process, the history and consequences of polyploidy in grasses, and provides a crucial tool for natural resource managers.

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Section: Resultsmentioning

confidence: 99%

Chromosome Level Genome Assembly and Annotation of Highly Invasive Japanese Stiltgrass (Microstegium vimineum)

Ramachandran

Huebner

Daly

et al. 2021

Genome Biology and Evolution

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“…While congruence is high especially for high-scoring assemblies, truly objective comparisons require reporting of the BUSCO versions, parameters, and lineage datasets used. Our data will enable future large-scale comparisons with results from the recently released BUSCO v5, which includes a new genome assessment strategy that improves efficiency and runtimes (Manni et al 2021). The automated analysis workflow to build and maintain NCBI genome assembly assessment catalogues for selected taxa allows users to build updatable community resources, here exemplified with the A 3 Cat that facilitates surveying of species coverage and data quality for available arthropod assemblies and serves to guide ongoing and future genome generation initiatives.…”

Section: Discussionmentioning

confidence: 99%

Assessing species coverage and assembly quality of rapidly accumulating sequenced genomes

Féron

Waterhouse

2021

Preprint

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Ambitious initiatives to coordinate genome sequencing of Earth's biodiversity mean that the accumulation of genomic data is growing rapidly. In addition to cataloguing biodiversity, these data provide the basis for understanding biological function and evolution. Accurate and complete genome assemblies offer a comprehensive and reliable foundation upon which to advance our understanding of organismal biology at genetic, species, and ecosystem levels. However, ever-changing sequencing technologies and analysis methods mean that available data are often heterogeneous in quality. In order to guide forthcoming genome generation efforts and promote efficient prioritisation of resources, it is thus essential to define and monitor taxonomic coverage and quality of the data. Here we present an automated analysis workflow that surveys genome assemblies from the United States National Center for Biotechnology Information (NCBI), assesses their completeness using the relevant Benchmarking Universal Single-Copy Orthologue (BUSCO) datasets, and collates the results into an interactively browsable resource. We apply our workflow to produce a community resource of available assemblies from the phylum Arthropoda, the Arthropoda Assembly Assessment Catalogue. Using this resource, we survey current taxonomic coverage and assembly quality at the NCBI, we examine how key assembly metrics relate to gene content completeness, and we compare results from using different BUSCO lineage datasets. These results demonstrate how the workflow can be used to build a community resource that enables large-scale assessments to survey species coverage and data quality of available genome assemblies, and to guide prioritisations for ongoing and future sampling, sequencing, and genome generation initiatives.

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“…Finally, SSPACE V2.0 (Boetzer and Pirovano, 2014) (-k 5 -T 25 -g 2) was used to further extend and fill up both contigs and scaffolds. Completeness assessment of the final genome assembly was performed by BUSCO v5.2.2 (Simão et al, 2015;Manni et al, 2021) (e-value ≤1e-3) with the popular actinopterygii_odb10 database.…”

Section: Genome Survey De Novo Assembly and Assessmentmentioning

confidence: 99%

“…This unpublished genome of S. anophthalmus was sequenced by us on both Illumina Hiseq2500 and PacBio Sequel platforms using muscle genomic DNAs, and the final assembly of 1.9 Gb (with a contig N50 of 229.8 kb, a scaffold N50 of 309.9 kb, and prediction of 49,865 protein-coding genes) was assembled by combining the corrected long PacBio reads and the primary assembly from short Illumina reads by DBG2OLC v1.1 (Ye et al, 2016). We also assessed the completeness of these proteincoding gene sets by BUSCO v5.2.2 (Manni et al, 2021).…”

Section: Gene Structure and Function Annotationsmentioning

confidence: 99%

Whole-Genome Sequencing of Sinocyclocheilus maitianheensis Reveals Phylogenetic Evolution and Immunological Variances in Various Sinocyclocheilus Fishes

Wang

Bian

et al. 2021

Front. Genet.

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An adult Sinocyclocheilus maitianheensis, a surface-dwelling golden-line barbel fish, was collected from Maitian river (Kunming City, Yunnan Province, China) for whole-genome sequencing, assembly, and annotation. We obtained a genome assembly of 1.7 Gb with a scaffold N50 of 1.4 Mb and a contig N50 of 24.7 kb. A total of 39,977 protein-coding genes were annotated. Based on a comparative phylogenetic analysis of five Sinocyclocheilus species and other five representative vertebrates with published genome sequences, we found that S. maitianheensis is close to Sinocyclocheilus anophthalmus (a cave-restricted species with similar locality). Moreover, the assembled genomes of S. maitianheensis and other four Sinocyclocheilus counterparts were used for a fourfold degenerative third-codon transversion (4dTv) analysis. The recent whole-genome duplication (WGD) event was therefore estimated to occur about 18.1 million years ago. Our results also revealed a decreased tendency of copy number in many important genes related to immunity and apoptosis in cave-restricted Sinocyclocheilus species. In summary, we report the first genome assembly of S. maitianheensis, which provides a valuable genetic resource for comparative studies on cavefish biology, species protection, and practical aquaculture of this potentially economical fish.

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BUSCO Update: Novel and Streamlined Workflows along with Broader and Deeper Phylogenetic Coverage for Scoring of Eukaryotic, Prokaryotic, and Viral Genomes

Cited by 3,230 publications

References 25 publications

Chromosome Level Genome Assembly and Annotation of Highly Invasive Japanese Stiltgrass (Microstegium vimineum)

Chromosome Level Genome Assembly and Annotation of Highly Invasive Japanese Stiltgrass (Microstegium vimineum)

Assessing species coverage and assembly quality of rapidly accumulating sequenced genomes

Whole-Genome Sequencing of Sinocyclocheilus maitianheensis Reveals Phylogenetic Evolution and Immunological Variances in Various Sinocyclocheilus Fishes

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