title: Integrating transcriptomic and proteomic data for accurate assembly and annotation of genomes.
abstract: 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.
authors.affiliation: Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka 560066, India.|YU-IOB Center for Systems Biology and Molecular Medicine, Yenepoya University, Mangalore 575018, India.|NIMHANS-IOB Proteomics and Bioinformatics Laboratory, Neurobiology Research Centre, National Institute of Mental Health and Neuro Sciences, Bangalore, Karnataka 560029, India.
authors.forename: T S Keshava
authors.initials: TS
authors.lastname: Prasad
authors.affiliation: National Institute of Malaria Research, Field Station, Goa 403001, India.|Department of Zoology, Goa University, Taleigao Plateau, Goa 403206, India.
authors.forename: Ajeet Kumar
authors.initials: AK
authors.lastname: Mohanty
authors.affiliation: Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka 560066, India.|Manipal University, Madhav Nagar, Manipal, Karnataka 576104, India.
authors.forename: Manish
authors.initials: M
authors.lastname: Kumar
authors.affiliation: Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka 560066, India.|Manipal University, Madhav Nagar, Manipal, Karnataka 576104, India.
authors.forename: Sreelakshmi K
authors.initials: SK
authors.lastname: Sreenivasamurthy
authors.affiliation: Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka 560066, India.|Manipal University, Madhav Nagar, Manipal, Karnataka 576104, India.
authors.forename: Gourav
authors.initials: G
authors.lastname: Dey
authors.affiliation: Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka 560066, India.|Centre for Bioinformatics, Pondicherry University, Puducherry 605014, India.
authors.forename: Raja Sekhar
authors.initials: RS
authors.lastname: Nirujogi
authors.affiliation: Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka 560066, India.|YU-IOB Center for Systems Biology and Molecular Medicine, Yenepoya University, Mangalore 575018, India.
authors.forename: Sneha M
authors.initials: SM
authors.lastname: Pinto
authors.affiliation: Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka 560066, India.|Centre for Bioinformatics, Pondicherry University, Puducherry 605014, India.
authors.forename: Anil K
authors.initials: AK
authors.lastname: Madugundu
authors.affiliation: Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka 560066, India.|School of Biotechnology, KIIT University, Bhubaneswar, Odisha 751024, India.
authors.forename: Arun H
authors.initials: AH
authors.lastname: Patil
authors.affiliation: Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka 560066, India.|Manipal University, Madhav Nagar, Manipal, Karnataka 576104, India.
authors.forename: Jayshree
authors.initials: J
authors.lastname: Advani
authors.affiliation: Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka 560066, India.|Centre for Bioinformatics, Pondicherry University, Puducherry 605014, India.
authors.forename: Srikanth S
authors.initials: SS
authors.lastname: Manda
authors.affiliation: Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka 560066, India.|Manipal University, Madhav Nagar, Manipal, Karnataka 576104, India.
authors.forename: Manoj Kumar
authors.initials: MK
authors.lastname: Gupta
authors.affiliation: Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka 560066, India.
authors.forename: Sutopa B
authors.initials: SB
authors.lastname: Dwivedi
authors.affiliation: Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka 560066, India.
authors.forename: Dhanashree S
authors.initials: DS
authors.lastname: Kelkar
authors.affiliation: Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, USA.
authors.forename: Brantley
authors.initials: B
authors.lastname: Hall
authors.affiliation: Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, USA.
authors.forename: Xiaofang
authors.initials: X
authors.lastname: Jiang
authors.affiliation: Department of Entomology, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, USA.
authors.forename: Ashley
authors.initials: A
authors.lastname: Peery
authors.affiliation: Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka 560066, India.|School of Biotechnology, KIIT University, Bhubaneswar, Odisha 751024, India.
authors.forename: Pavithra
authors.initials: P
authors.lastname: Rajagopalan
authors.affiliation: Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka 560066, India.|School of Biotechnology, KIIT University, Bhubaneswar, Odisha 751024, India.
authors.forename: Soujanya D
authors.initials: SD
authors.lastname: Yelamanchi
authors.affiliation: Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka 560066, India.|School of Biotechnology, KIIT University, Bhubaneswar, Odisha 751024, India.
authors.forename: Hitendra S
authors.initials: HS
authors.lastname: Solanki
authors.affiliation: Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka 560066, India.
authors.forename: Remya
authors.initials: R
authors.lastname: Raja
authors.affiliation: Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka 560066, India.|Manipal University, Madhav Nagar, Manipal, Karnataka 576104, India.
authors.forename: Gajanan J
authors.initials: GJ
authors.lastname: Sathe
authors.affiliation: Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka 560066, India.|Manipal University, Madhav Nagar, Manipal, Karnataka 576104, India.
authors.forename: Sandip
authors.initials: S
authors.lastname: Chavan
authors.affiliation: Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka 560066, India.|School of Biotechnology, KIIT University, Bhubaneswar, Odisha 751024, India.
authors.forename: Renu
authors.initials: R
authors.lastname: Verma
authors.affiliation: Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka 560066, India.
authors.forename: Krishna M
authors.initials: KM
authors.lastname: Patel
authors.affiliation: Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka 560066, India.|School of Biotechnology, KIIT University, Bhubaneswar, Odisha 751024, India.
authors.forename: Ankit P
authors.initials: AP
authors.lastname: Jain
authors.affiliation: Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka 560066, India.|Department of Biochemistry and Molecular Biology, Pondicherry University, Puducherry 605014, India.
authors.forename: Nazia
authors.initials: N
authors.lastname: Syed
authors.affiliation: Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka 560066, India.|School of Biotechnology, KIIT University, Bhubaneswar, Odisha 751024, India.
authors.forename: Keshava K
authors.initials: KK
authors.lastname: Datta
authors.affiliation: Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka 560066, India.|School of Biotechnology, KIIT University, Bhubaneswar, Odisha 751024, India.
authors.forename: Aafaque Ahmed
authors.initials: AA
authors.lastname: Khan
authors.affiliation: Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka 560066, India.|Department of Biotechnology, Siddaganga Institute of Technology, Tumkur, Karnataka 572103, India.
authors.forename: Manjunath
authors.initials: M
authors.lastname: Dammalli
authors.affiliation: Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka 560066, India.|Manipal University, Madhav Nagar, Manipal, Karnataka 576104, India.
authors.forename: Savita
authors.initials: S
authors.lastname: Jayaram
authors.affiliation: Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka 560066, India.|Department of Biochemistry and Molecular Biology, Pondicherry University, Puducherry 605014, India.
authors.forename: Aneesha
authors.initials: A
authors.lastname: Radhakrishnan
authors.affiliation: McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA.
authors.forename: Christopher J
authors.initials: CJ
authors.lastname: Mitchell
authors.affiliation: Department of Neurology, Johns Hopkins University, Baltimore, Maryland 21205, USA.
authors.forename: Chan-Hyun
authors.initials: CH
authors.lastname: Na
authors.affiliation: Department of Tropical Medicine, Tulane University School of Public Health and Tropical Medicine, New Orleans, Louisiana 70112, USA.
authors.forename: Nirbhay
authors.initials: N
authors.lastname: Kumar
authors.affiliation: Malaria Research Institute, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland 21205, USA.
authors.forename: Photini
authors.initials: P
authors.lastname: Sinnis
authors.affiliation: Department of Entomology, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, USA.
authors.forename: Igor V
authors.initials: IV
authors.lastname: Sharakhov
authors.affiliation: Center for Genomics and Department of Basic Sciences, School of Medicine, Loma Linda University, Loma Linda, California 92350, USA.
authors.forename: Charles
authors.initials: C
authors.lastname: Wang
authors.affiliation: Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka 560066, India.|YU-IOB Center for Systems Biology and Molecular Medicine, Yenepoya University, Mangalore 575018, India.
authors.forename: Harsha
authors.initials: H
authors.lastname: Gowda
authors.affiliation: Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, USA.
authors.forename: Zhijian
authors.initials: Z
authors.lastname: Tu
authors.affiliation: National Institute of Malaria Research, Field Station, Goa 403001, India.
authors.forename: Ashwani
authors.initials: A
authors.lastname: Kumar
authors.affiliation: Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka 560066, India.|McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA.|Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA.|Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA.|Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA.
authors.forename: Akhilesh
authors.initials: A
authors.lastname: Pandey
mesh_terms: D000818:Animals; D000852:Anopheles / Q000235:genetics; D005091:Exons / Q000235:genetics; D020869:Gene Expression Profiling; D016678:Genome / Q000235:genetics*; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D058977:Molecular Sequence Annotation; D020543:Proteome / Q000235:genetics; D040901:Proteomics; D059467:Transcriptome / Q000235:genetics*
chemical_list: D020543:Proteome