Literature DB >> 28660309

Genome-wide comparative analysis of four Indian Drosophila species.

Sujata Mohanty1, Radhika Khanna2.   

Abstract

Comparative analysis of multiple genomes of closely or distantly related Drosophila species undoubtedly creates excitement among evolutionary biologists in exploring the genomic changes with an ecology and evolutionary perspective. We present herewith the de novo assembled whole genome sequences of four Drosophila species, D. bipectinata, D. takahashii, D. biarmipes and D. nasuta of Indian origin using Next Generation Sequencing technology on an Illumina platform along with their detailed assembly statistics. The comparative genomics analysis, e.g. gene predictions and annotations, functional and orthogroup analysis of coding sequences and genome wide SNP distribution were performed. The whole genome of Zaprionus indianus of Indian origin published earlier by us and the genome sequences of previously sequenced 12 Drosophila species available in the NCBI database were included in the analysis. The present work is a part of our ongoing genomics project of Indian Drosophila species.

Entities:  

Keywords:  Comparative genomics; De novo assembly; Drosophila; India; Next generation sequencing; WGS

Mesh:

Year:  2017        PMID: 28660309     DOI: 10.1007/s00438-017-1339-8

Source DB:  PubMed          Journal:  Mol Genet Genomics        ISSN: 1617-4623            Impact factor:   3.291


  60 in total

1.  Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures.

Authors:  Alexander Stark; Michael F Lin; Pouya Kheradpour; Jakob S Pedersen; Leopold Parts; Joseph W Carlson; Madeline A Crosby; Matthew D Rasmussen; Sushmita Roy; Ameya N Deoras; J Graham Ruby; Julius Brennecke; Emily Hodges; Angie S Hinrichs; Anat Caspi; Benedict Paten; Seung-Won Park; Mira V Han; Morgan L Maeder; Benjamin J Polansky; Bryanne E Robson; Stein Aerts; Jacques van Helden; Bassem Hassan; Donald G Gilbert; Deborah A Eastman; Michael Rice; Michael Weir; Matthew W Hahn; Yongkyu Park; Colin N Dewey; Lior Pachter; W James Kent; David Haussler; Eric C Lai; David P Bartel; Gregory J Hannon; Thomas C Kaufman; Michael B Eisen; Andrew G Clark; Douglas Smith; Susan E Celniker; William M Gelbart; Manolis Kellis
Journal:  Nature       Date:  2007-11-08       Impact factor: 49.962

Review 2.  Species and genetic diversity in the genus Drosophila inhabiting the Indian subcontinent.

Authors:  Bashisth N Singh
Journal:  J Genet       Date:  2015-06       Impact factor: 1.166

3.  Determining the evolutionary history of gene families.

Authors:  Ryan M Ames; Daniel Money; Vikramsinh P Ghatge; Simon Whelan; Simon C Lovell
Journal:  Bioinformatics       Date:  2011-10-28       Impact factor: 6.937

Review 4.  Human disease models in Drosophila melanogaster and the role of the fly in therapeutic drug discovery.

Authors:  Udai Bhan Pandey; Charles D Nichols
Journal:  Pharmacol Rev       Date:  2011-03-17       Impact factor: 25.468

Review 5.  Drosophila bipectinata species complex.

Authors:  S Singh; B N Singh
Journal:  Indian J Exp Biol       Date:  2001-09       Impact factor: 0.818

6.  DNA-Feulgen cytophotometric determination of genome size for the freshwater-invading copepod Eurytemora affinis.

Authors:  Ellen M Rasch; Carol Eunmi Lee; Grace A Wyngaard
Journal:  Genome       Date:  2004-06       Impact factor: 2.166

7.  Complete genome sequence of Nitrobacter hamburgensis X14 and comparative genomic analysis of species within the genus Nitrobacter.

Authors:  Shawn R Starkenburg; Frank W Larimer; Lisa Y Stein; Martin G Klotz; Patrick S G Chain; Luis A Sayavedra-Soto; Amisha T Poret-Peterson; Mira E Gentry; Daniel J Arp; Bess Ward; Peter J Bottomley
Journal:  Appl Environ Microbiol       Date:  2008-03-07       Impact factor: 4.792

8.  Extensive error in the number of genes inferred from draft genome assemblies.

Authors:  James F Denton; Jose Lugo-Martinez; Abraham E Tucker; Daniel R Schrider; Wesley C Warren; Matthew W Hahn
Journal:  PLoS Comput Biol       Date:  2014-12-04       Impact factor: 4.475

9.  Gene family evolution across 12 Drosophila genomes.

Authors:  Matthew W Hahn; Mira V Han; Sang-Gook Han
Journal:  PLoS Genet       Date:  2007-11       Impact factor: 5.917

10.  NCBI BLAST: a better web interface.

Authors:  Mark Johnson; Irena Zaretskaya; Yan Raytselis; Yuri Merezhuk; Scott McGinnis; Thomas L Madden
Journal:  Nucleic Acids Res       Date:  2008-04-24       Impact factor: 16.971

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  2 in total

1.  Rapid Divergence of Key Spermatogenesis Genes in nasuta-Subgroup of Drosophila.

Authors:  Rajanikanth Chowdanayaka; Ramachandra Nallur Basappa
Journal:  J Mol Evol       Date:  2021-11-22       Impact factor: 2.395

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

Authors:  Stafny DSouza; Koushik Ponnanna; Amruthavalli Chokkanna; Nallur Ramachandra
Journal:  Data Brief       Date:  2020-12-19
  2 in total

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