title: Annotation of the zebrafish genome through an integrated transcriptomic and proteomic analysis.
abstract: Accurate annotation of protein-coding genes is one of the primary tasks upon the completion of whole genome sequencing of any organism. In this study, we used an integrated transcriptomic and proteomic strategy to validate and improve the existing zebrafish genome annotation. We undertook high-resolution mass-spectrometry-based proteomic profiling of 10 adult organs, whole adult fish body, and two developmental stages of zebrafish (SAT line), in addition to transcriptomic profiling of six organs. More than 7,000 proteins were identified from proteomic analyses, and ∼ 69,000 high-confidence transcripts were assembled from the RNA sequencing data. Approximately 15% of the transcripts mapped to intergenic regions, the majority of which are likely long non-coding RNAs. These high-quality transcriptomic and proteomic data were used to manually reannotate the zebrafish genome. We report the identification of 157 novel protein-coding genes. In addition, our data led to modification of existing gene structures including novel exons, changes in exon coordinates, changes in frame of translation, translation in annotated UTRs, and joining of genes. Finally, we discovered four instances of genome assembly errors that were supported by both proteomic and transcriptomic data. Our study shows how an integrative analysis of the transcriptome and the proteome can extend our understanding of even well-annotated genomes.
authors: From the *Institute of Bioinformatics, International Technology Park, Bangalore 560 066, India; ‡Amrita School of Biotechnology, Amrita University, Kollam 690 525, India;
authors: Dhanashree S
authors: DS
authors: Kelkar
authors: §Department of Surgery, Johns Hopkins University, Baltimore, Maryland 21205;
authors: Elayne
authors: E
authors: Provost
authors: ¶McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, Maryland 21205;
authors: Raghothama
authors: R
authors: Chaerkady
authors: From the *Institute of Bioinformatics, International Technology Park, Bangalore 560 066, India; ‖Centre of Excellence in Bioinformatics, School of Life Sciences, Pondicherry University, Puducherry 605014, India;
authors: Babylakshmi
authors: B
authors: Muthusamy
authors: From the *Institute of Bioinformatics, International Technology Park, Bangalore 560 066, India; ‖Centre of Excellence in Bioinformatics, School of Life Sciences, Pondicherry University, Puducherry 605014, India; **Departments of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205;
authors: Srikanth S
authors: SS
authors: Manda
authors: From the *Institute of Bioinformatics, International Technology Park, Bangalore 560 066, India; ‡Amrita School of Biotechnology, Amrita University, Kollam 690 525, India;
authors: Tejaswini
authors: T
authors: Subbannayya
authors: From the *Institute of Bioinformatics, International Technology Park, Bangalore 560 066, India; ‡Amrita School of Biotechnology, Amrita University, Kollam 690 525, India;
authors: Lakshmi Dhevi N
authors: LD
authors: Selvan
authors: ¶McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, Maryland 21205;
authors: Chieh-Huei
authors: CH
authors: Wang
authors: From the *Institute of Bioinformatics, International Technology Park, Bangalore 560 066, India; ‡‡School of Biotechnology, KIIT University, Bhubaneswar, Odisha 751024, India;
authors: Keshava K
authors: KK
authors: Datta
authors: §§Department of Computer Science, University of California, San Diego, California 92093;
authors: Sunghee
authors: S
authors: Woo
authors: From the *Institute of Bioinformatics, International Technology Park, Bangalore 560 066, India; ‡Amrita School of Biotechnology, Amrita University, Kollam 690 525, India;
authors: Sutopa B
authors: SB
authors: Dwivedi
authors: From the *Institute of Bioinformatics, International Technology Park, Bangalore 560 066, India; ‡Amrita School of Biotechnology, Amrita University, Kollam 690 525, India;
authors: Santosh
authors: S
authors: Renuse
authors: ¶McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, Maryland 21205;
authors: Derese
authors: D
authors: Getnet
authors: ¶McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, Maryland 21205;
authors: Tai-Chung
authors: TC
authors: Huang
authors: ¶McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, Maryland 21205; **Departments of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205;
authors: Min-Sik
authors: MS
authors: Kim
authors: From the *Institute of Bioinformatics, International Technology Park, Bangalore 560 066, India; ¶McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, Maryland 21205; ¶¶Manipal University, Madhav Nagar, Manipal, Karnataka 576104, India;
authors: Sneha M
authors: SM
authors: Pinto
authors: ¶McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, Maryland 21205;
authors: Christopher J
authors: CJ
authors: Mitchell
authors: From the *Institute of Bioinformatics, International Technology Park, Bangalore 560 066, India;
authors: Anil K
authors: AK
authors: Madugundu
authors: From the *Institute of Bioinformatics, International Technology Park, Bangalore 560 066, India;
authors: Praveen
authors: P
authors: Kumar
authors: From the *Institute of Bioinformatics, International Technology Park, Bangalore 560 066, India; ¶¶Manipal University, Madhav Nagar, Manipal, Karnataka 576104, India;
authors: Jyoti
authors: J
authors: Sharma
authors: From the *Institute of Bioinformatics, International Technology Park, Bangalore 560 066, India;
authors: Jayshree
authors: J
authors: Advani
authors: From the *Institute of Bioinformatics, International Technology Park, Bangalore 560 066, India; ¶¶Manipal University, Madhav Nagar, Manipal, Karnataka 576104, India;
authors: Gourav
authors: G
authors: Dey
authors: From the *Institute of Bioinformatics, International Technology Park, Bangalore 560 066, India; ‖‖Department of Biotechnology, Kuvempu University, Shimoga 577 451, India;
authors: Lavanya
authors: L
authors: Balakrishnan
authors: From the *Institute of Bioinformatics, International Technology Park, Bangalore 560 066, India; Department of Biochemistry and Molecular Biology, School of Life Sciences, Pondicherry University, Puducherry 605 014, India;
authors: Nazia
authors: N
authors: Syed
authors: From the *Institute of Bioinformatics, International Technology Park, Bangalore 560 066, India; ‡Amrita School of Biotechnology, Amrita University, Kollam 690 525, India;
authors: Vishalakshi
authors: V
authors: Nanjappa
authors: From the *Institute of Bioinformatics, International Technology Park, Bangalore 560 066, India;
authors: Yashwanth
authors: Y
authors: Subbannayya
authors: From the *Institute of Bioinformatics, International Technology Park, Bangalore 560 066, India;
authors: Renu
authors: R
authors: Goel
authors: From the *Institute of Bioinformatics, International Technology Park, Bangalore 560 066, India; ‡Amrita School of Biotechnology, Amrita University, Kollam 690 525, India; ‖Centre of Excellence in Bioinformatics, School of Life Sciences, Pondicherry University, Puducherry 605014, India; ¶¶Manipal University, Madhav Nagar, Manipal, Karnataka 576104, India;
authors: T S Keshava
authors: TS
authors: Prasad
authors: §§Department of Computer Science, University of California, San Diego, California 92093;
authors: Vineet
authors: V
authors: Bafna
authors: From the *Institute of Bioinformatics, International Technology Park, Bangalore 560 066, India;
authors: Ravi
authors: R
authors: Sirdeshmukh
authors: From the *Institute of Bioinformatics, International Technology Park, Bangalore 560 066, India;
authors: Harsha
authors: H
authors: Gowda
authors: The Center for Genomics and Division of Microbiology & Molecular Genetics, School of Medicine, Loma Linda University, Loma Linda, California 92350; pandey@jhmi.edu sleach1@jhmi.edu chwang@llu.edu.
authors: Charles
authors: C
authors: Wang
authors: §Department of Surgery, Johns Hopkins University, Baltimore, Maryland 21205; ¶McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, Maryland 21205; pandey@jhmi.edu sleach1@jhmi.edu chwang@llu.edu.
authors: Steven D
authors: SD
authors: Leach
authors: From the *Institute of Bioinformatics, International Technology Park, Bangalore 560 066, India; ¶McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, Maryland 21205; **Departments of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205; Sol Goldman Pancreatic Cancer Research Center, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205; Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205 pandey@jhmi.edu sleach1@jhmi.edu chwang@llu.edu.
authors: Akhilesh
authors: A
authors: Pandey
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D001483:Base Sequence; D020869:Gene Expression Profiling; D016678:Genome / Q000235:genetics*; D059014:High-Throughput Nucleotide Sequencing; D013058:Mass Spectrometry; D058977:Molecular Sequence Annotation; D020543:Proteome / Q000032:analysis* / Q000235:genetics*; D040901:Proteomics; D017423:Sequence Analysis, RNA; D059467:Transcriptome / Q000235:genetics*; D015027:Zebrafish / Q000235:genetics*
chemical_list: D020543:Proteome