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Illumina short-read sequencing data, de novo assembly and annotations of the Drosophila nasuta nasuta genome.

ABSTRACT: The Drosophila nasuta nasuta (D. n. nasuta) is a member of nasuta subgroup of immigrans species group of Drosophila widely distributed across South-East Asia and central to Southern Africa. It displays morphological similarities with other members of the nasuta subgroup with which it has a recent divergence history. The genomic DNA of D. n. nasuta Coorg strain was paired-end sequenced using Illumina HiSeq 2500 technology to obtain a draft genome assembly of 145.64 Mb. The generated assembly retrieved 93.6% of the conserved dipteran BUSCO orthologs. Approximately 85% of the ab initio predicted proteins exhibit sequence similarity to the proteins of D. albomicans which is the closest annotated species. This draft genome sequence is a valuable resource to Drosophila geneticists and evolutionary biologists to understand molecular organisation of the genome and its evolution during early stages of speciation.

SUBMITTER: DSouza S

PROVIDER: S-EPMC7773860 | biostudies-literature | 2021 Feb

REPOSITORIES: biostudies-literature

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Illumina short-read sequencing data, de novo assembly and annotations of the Drosophila nasuta nasuta genome.

DSouza Stafny S Ponnanna Koushik K Chokkanna Amruthavalli A Ramachandra Nallur N

Data in brief 20201219

The Drosophila nasuta nasuta (D. n. nasuta) is a member of nasuta subgroup of immigrans species group of Drosophila widely distributed across South-East Asia and central to Southern Africa. It displays morphological similarities with other members of the nasuta subgroup with which it has a recent divergence history. The genomic DNA of D. n. nasuta Coorg strain was paired-end sequenced using Illumina HiSeq 2500 technology to obtain a draft genome a ...[more]

PMID: 33409344

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Project description:BACKGROUND: RNA-seq has shown huge potential for phylogenomic inferences in non-model organisms. However, error, incompleteness, and redundant assembled transcripts for each gene in de novo assembly of short reads cause noise in analyses and a large amount of missing data in the aligned matrix. To address these problems, we compare de novo assemblies of paired end 90 bp RNA-seq reads using Oases, Trinity, Trans-ABySS and SOAPdenovo-Trans to transcripts from genome annotation of the model plant Ricinus communis. By doing so we evaluate strategies for optimizing total gene coverage and minimizing assembly chimeras and redundancy. RESULTS: We found that the frequency and structure of chimeras vary dramatically among different software packages. The differences were largely due to the number of trans-self chimeras that contain repeats in the opposite direction. More than half of the total chimeras in Oases and Trinity were trans-self chimeras. Within each package, we found a trade-off between maximizing reference coverage and minimizing redundancy and chimera rate. In order to reduce redundancy, we investigated three methods: 1) using cap3 and CD-HIT-EST to combine highly similar transcripts, 2) only retaining the transcript with the highest read coverage, or removing the transcript with the lowest read coverage for each subcomponent in Trinity, and 3) filtering Oases single k-mer assemblies by number of transcripts per locus and relative transcript length, and then finding the transcript with the highest read coverage. We then utilized results from blastx against model protein sequences to effectively remove trans chimeras. After optimization, seven assembly strategies among all four packages successfully assembled 42.9-47.1% of reference genes to more than 200 bp, with a chimera rate of 0.92-2.21%, and on average 1.8-3.1 transcripts per reference gene assembled. CONCLUSIONS: With rapidly improving sequencing and assembly tools, our study provides a framework to benchmark and optimize performance before choosing tools or parameter combinations for analyzing short-read RNA-seq data. Our study demonstrates that choice of assembly package, k-mer sizes, post-assembly redundancy-reduction and chimera cleanup, and strand-specific RNA-seq library preparation and assembly dramatically improves gene coverage by non-redundant and non-chimeric transcripts that are optimized for downstream phylogenomic analyses.

Dataset Information

Illumina short-read sequencing data, de novo assembly and annotations of the Drosophila nasuta nasuta genome.

Publications

Illumina short-read sequencing data, <i>de novo</i> assembly and annotations of the <i>Drosophila nasuta nasuta</i> genome.

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