Integrating transcriptomic and proteomic data for accurate assembly and annotation of genomes

• DOI: 10.1101/gr.201368.115
• Publication Date: 2016-11-16T13:17:12Z
• Authors: T.S. Keshava Prasad; Ajeet Kumar Mohanty; Manish Kumar; Sreelakshmi K. Sr...; Gourav Dey; Raja Sekhar Nirujogi; Sneha M. Pinto; Anil K. Madugundu; Arun H. Patil; Jayshree Advani; Srikanth S. Manda; Manoj Kumar Gupta; Sutopa B. Dwivedi; Dhanashree S. Kelkar; Brantley Hall; Xiaofang Jiang; Ashley Peery; Pavithra Rajagopalan; Soujanya D. Yelam...; Hitendra S. Solanki; Remya Raja; Gajanan J. Sathe; Sandip Chavan; Renu Verma; Krishna M. Patel; Ankit P. Jain; Nazia Syed; Keshava K. Datta; Aafaque Ahmed Khan; Manjunath Dammalli; Savita Jayaram; Aneesha Radhakris...; Christopher J. Mi...; Chan-Hyun Na; Nirbhay Kumar; Photini Sinnis; Igor V. Sharakhov; Charles Wang; Harsha Gowda; Zhijian Tu; Ashwani Kumar; Akhilesh Pandey
• Keywords: Proteogenomics; Proteome; Gene prediction; Sequence assembly; Gene Annotation

Complementing genome sequence with deep transcriptome and proteome data could enable more accurate assembly annotation of newly sequenced genomes. Here, we provide a proof-of-concept an integrated approach for analysis the Anopheles stephensi, which is one most important vectors malaria parasite. To achieve broad coverage genes, carried out sequencing profiling multiple anatomically distinct sites. Based on transcriptomic alone, identified corrected 535 events incomplete involving 1196 scaffolds 868 protein-coding gene models. This proteogenomic enabled us to add 365 genes that were missed during identify 917 correction through discovery 151 novel exons, 297 protein extensions, 231 exon 192 start sites, 19 translational frames, 28 joining 76 adjacent as single gene. Incorporation proteomic evidence allowed change designation than 87 predicted "noncoding RNAs" conventional mRNAs coded by genes. Importantly, extension assemblies models 15 other assembled Anopheline genomes led large number apparent discrepancies in these Our framework how future efforts should incorporate combination simultaneous manual curation near complete