Literature DB >> 33409344

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

Stafny DSouza1, Koushik Ponnanna1, Amruthavalli Chokkanna1, Nallur Ramachandra1.   

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.
© 2020 The Authors. Published by Elsevier Inc.

Entities:  

Keywords:  Annotation; Genome assembly; Genome evolution; Illumina sequencing; Nasuta subgroup

Year:  2020        PMID: 33409344      PMCID: PMC7773860          DOI: 10.1016/j.dib.2020.106674

Source DB:  PubMed          Journal:  Data Brief        ISSN: 2352-3409


  14 in total

1.  BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs.

Authors:  Felipe A Simão; Robert M Waterhouse; Panagiotis Ioannidis; Evgenia V Kriventseva; Evgeny M Zdobnov
Journal:  Bioinformatics       Date:  2015-06-09       Impact factor: 6.937

2.  Minimap2: pairwise alignment for nucleotide sequences.

Authors:  Heng Li
Journal:  Bioinformatics       Date:  2018-09-15       Impact factor: 6.937

3.  The speciation history of the Drosophila nasuta complex.

Authors:  Doris Bachtrog
Journal:  Genet Res       Date:  2006-08       Impact factor: 1.588

4.  tRNAscan-SE: Searching for tRNA Genes in Genomic Sequences.

Authors:  Patricia P Chan; Todd M Lowe
Journal:  Methods Mol Biol       Date:  2019

5.  GeneMark-EP+: eukaryotic gene prediction with self-training in the space of genes and proteins.

Authors:  Tomáš Brůna; Alexandre Lomsadze; Mark Borodovsky
Journal:  NAR Genom Bioinform       Date:  2020-05-13

6.  Versatile and open software for comparing large genomes.

Authors:  Stefan Kurtz; Adam Phillippy; Arthur L Delcher; Michael Smoot; Martin Shumway; Corina Antonescu; Steven L Salzberg
Journal:  Genome Biol       Date:  2004-01-30       Impact factor: 13.583

7.  Toward almost closed genomes with GapFiller.

Authors:  Marten Boetzer; Walter Pirovano
Journal:  Genome Biol       Date:  2012-06-25       Impact factor: 13.583

8.  WebMGA: a customizable web server for fast metagenomic sequence analysis.

Authors:  Sitao Wu; Zhengwei Zhu; Liming Fu; Beifang Niu; Weizhong Li
Journal:  BMC Genomics       Date:  2011-09-07       Impact factor: 3.969

9.  Efficient de novo assembly of highly heterozygous genomes from whole-genome shotgun short reads.

Authors:  Rei Kajitani; Kouta Toshimoto; Hideki Noguchi; Atsushi Toyoda; Yoshitoshi Ogura; Miki Okuno; Mitsuru Yabana; Masayuki Harada; Eiji Nagayasu; Haruhiko Maruyama; Yuji Kohara; Asao Fujiyama; Tetsuya Hayashi; Takehiko Itoh
Journal:  Genome Res       Date:  2014-04-22       Impact factor: 9.043

10.  Redundans: an assembly pipeline for highly heterozygous genomes.

Authors:  Leszek P Pryszcz; Toni Gabaldón
Journal:  Nucleic Acids Res       Date:  2016-04-29       Impact factor: 16.971

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