RT Journal
A1 Prasad, T.S. Keshava
A1 Mohanty, Ajeet Kumar
A1 Kumar, Manish
A1 Sreenivasamurthy, Sreelakshmi K.
A1 Dey, Gourav
A1 Nirujogi, Raja Sekhar
A1 Pinto, Sneha M.
A1 Madugundu, Anil K.
A1 Patil, Arun H.
A1 Advani, Jayshree
A1 Manda, Srikanth S.
A1 Gupta, Manoj Kumar
A1 Dwivedi, Sutopa B.
A1 Kelkar, Dhanashree S.
A1 Hall, Brantley
A1 Jiang, Xiaofang
A1 Peery, Ashley
A1 Rajagopalan, Pavithra
A1 Yelamanchi, Soujanya D.
A1 Solanki, Hitendra S.
A1 Raja, Remya
A1 Sathe, Gajanan J.
A1 Chavan, Sandip
A1 Verma, Renu
A1 Patel, Krishna M.
A1 Jain, Ankit P.
A1 Syed, Nazia
A1 Datta, Keshava K.
A1 Khan, Aafaque Ahmed
A1 Dammalli, Manjunath
A1 Jayaram, Savita
A1 Radhakrishnan, Aneesha
A1 Mitchell, Christopher J.
A1 Na, Chan-Hyun
A1 Kumar, Nirbhay
A1 Sinnis, Photini
A1 Sharakhov, Igor V.
A1 Wang, Charles
A1 Gowda, Harsha
A1 Tu, Zhijian
A1 Kumar, Ashwani
A1 Pandey, Akhilesh
T1 Integrating transcriptomic and proteomic data for accurate assembly and annotation of genomes
JF Genome Research 
JO Genome Research 
YR 2017 
FD January 01 
VO 27 
IS 1 
SP 133 
OP 144 
DO 10.1101/gr.201368.115 
UL http://genome.cshlp.org/content/27/1/133.abstract 
AB Complementing genome sequence with deep transcriptome and proteome data could enable more accurate assembly and annotation of newly sequenced genomes. Here, we provide a proof-of-concept of an integrated approach for analysis of the genome and proteome of Anopheles stephensi, which is one of the most important vectors of the malaria parasite. To achieve broad coverage of genes, we carried out transcriptome sequencing and deep proteome profiling of multiple anatomically distinct sites. Based on transcriptomic data alone, we identified and corrected 535 events of incomplete genome assembly involving 1196 scaffolds and 868 protein-coding gene models. This proteogenomic approach enabled us to add 365 genes that were missed during genome annotation and identify 917 gene correction events through discovery of 151 novel exons, 297 protein extensions, 231 exon extensions, 192 novel protein start sites, 19 novel translational frames, 28 events of joining of exons, and 76 events of joining of adjacent genes as a single gene. Incorporation of proteomic evidence allowed us to change the designation of more than 87 predicted “noncoding RNAs” to conventional mRNAs coded by protein-coding genes. Importantly, extension of the newly corrected genome assemblies and gene models to 15 other newly assembled Anopheline genomes led to the discovery of a large number of apparent discrepancies in assembly and annotation of these genomes. Our data provide a framework for how future genome sequencing efforts should incorporate transcriptomic and proteomic analysis in combination with simultaneous manual curation to achieve near complete assembly and accurate annotation of genomes.