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Genome annotation: From human genetics to biodiversity genomics

Guigó, Roderic·2023·Cell Genomics

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Crossref · 10.1016/j.xgen.2023.100375

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  • The number of protein-coding genes for each species is reasonably well-established for all species used in this analysis.

    “The number of protein-coding genes for each species is reasonably well-established for all the species used in this analysis (Tiessen et al. 2012, Guigó, 2023).”

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Research works printed but not linked: 96

  1. 2012, An integrated encyclopedia of DNA elements in the human genome, Nature, 489, 57, 10.1038/nature11247 · DOI · Paper page
  2. Frankish, 2023, GENCODE: reference annotation for the human and mouse genomes in 2023, Nucleic Acids Res., 51, D942, 10.1093/nar/gkac1071 · DOI
  3. Lewin, 2022, The Earth BioGenome Project 2020: Starting the clock, Proc. Natl. Acad. Sci. USA, 119, 10.1073/pnas.2115635118 · DOI
  4. Stein, 2001, Genome annotation: from sequence to biology, Nat. Rev. Genet., 2, 493, 10.1038/35080529 · DOI
  5. Gerstein, 2007, What is a gene, post-ENCODE? History and updated definition, Genome Res., 17, 669, 10.1101/gr.6339607 · DOI
  6. Djebali, 2012, Landscape of transcription in human cells, Nature, 489, 101, 10.1038/nature11233 · DOI · Paper page
  7. Fickett, 1982, Recognition of protein coding regions in DNA sequences, Nucleic Acids Res., 10, 5303, 10.1093/nar/10.17.5303 · DOI
  8. Mount, 1982, A catalogue of splice junction sequences, Nucleic Acids Res., 10, 459, 10.1093/nar/10.2.459 · DOI
  9. Gish, 1993, Identification of protein coding regions by database similarity search, Nat. Genet., 3, 266, 10.1038/ng0393-266 · DOI
  10. Crooks, 2004, WebLogo: a sequence logo generator, Genome Res., 14, 1188, 10.1101/gr.849004 · DOI
  11. Burset, 1996, Evaluation of gene structure prediction programs, Genomics, 34, 353, 10.1006/geno.1996.0298 · DOI
  12. Strausberg, 1999, The mammalian gene collection, Science, 286, 455, 10.1126/science.286.5439.455 · DOI
  13. Adams, 1991, Complementary DNA sequencing: expressed sequence tags and human genome project, Science, 252, 1651, 10.1126/science.2047873 · DOI
  14. Sakurai, 2002, On biased distribution of introns in various eukaryotes, Gene, 300, 89, 10.1016/S0378-1119(02)01035-1 · DOI
  15. Zhuo, 2001, Assembly, annotation, and integration of UNIGENE clusters into the human genome draft, Genome Res., 11, 904, 10.1101/gr.164501 · DOI
  16. Liang, 2000, Gene index analysis of the human genome estimates approximately 120,000 genes, Nat. Genet., 25, 239, 10.1038/76126 · DOI
  17. Roest Crollius, 2000, Estimate of human gene number provided by genome-wide analysis using Tetraodon nigroviridis DNA sequence, Nat. Genet., 25, 235, 10.1038/76118 · DOI
  18. Derrien, 2012, The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression, Genome Res., 22, 1775, 10.1101/gr.132159.111 · DOI
  19. Guttman, 2009, Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals, Nature, 458, 223, 10.1038/nature07672 · DOI · Paper page
  20. Wang, 2008, Alternative isoform regulation in human tissue transcriptomes, Nature, 456, 470, 10.1038/nature07509 · DOI · Paper page
  21. Hölzer, 2019, De novo transcriptome assembly: a comprehensive cross-species comparison of short-read RNA-Seq assemblers, GigaScience, 8, giz039, 10.1093/gigascience/giz039 · DOI
  22. Steijger, 2013, Assessment of transcript reconstruction methods for RNA-seq, Nat. Methods, 10, 1177, 10.1038/nmeth.2714 · DOI · Paper page
  23. Cook, 2019, Long-Read Annotation: Automated Eukaryotic Genome Annotation Based on Long-Read cDNA Sequencing, Plant Physiol., 179, 38, 10.1104/pp.18.00848 · DOI
  24. Kovaka, 2019, Transcriptome assembly from long-read RNA-seq alignments with StringTie2, Genome Biol., 20, 278, 10.1186/s13059-019-1910-1 · DOI
  25. Shields, 2021, Genome annotation with long RNA reads reveals new patterns of gene expression and improves single-cell analyses in an ant brain, BMC Biol., 19, 254, 10.1186/s12915-021-01188-w · DOI
  26. C Yuen, 2017, Whole genome sequencing resource identifies 18 new candidate genes for autism spectrum disorder, Nat. Neurosci., 20, 602, 10.1038/nn.4524 · DOI · Paper page
  27. Lagarde, 2017, High-throughput annotation of full-length long noncoding RNAs with capture long-read sequencing, Nat. Genet., 49, 1731, 10.1038/ng.3988 · DOI
  28. Prjibelski, 2023, Accurate isoform discovery with IsoQuant using long reads, Nat. Biotechnol., 10.1038/s41587-022-01565-y · DOI
  29. Frankish, 2021, GENCODE 2021, Nucleic Acids Res., 49, D916, 10.1093/nar/gkaa1087 · DOI · Paper page
  30. Wilks, 2021, recount3: summaries and queries for large-scale RNA-seq expression and splicing, Genome Biol., 22, 323, 10.1186/s13059-021-02533-6 · DOI
  31. Amaral, 2023, The status of the human gene catalogue, arXiv
  32. O’Leary, 2016, Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation, Nucleic Acids Res., 44, D733, 10.1093/nar/gkv1189 · DOI · Paper page
  33. Wright, 2016, Improving GENCODE reference gene annotation using a high-stringency proteogenomics workflow, Nat. Commun., 7, 10.1038/ncomms11778 · DOI
  34. Mudge, 2022, Standardized annotation of translated open reading frames, Nat. Biotechnol., 40, 994, 10.1038/s41587-022-01369-0 · DOI
  35. Lin, 2011, PhyloCSF: a comparative genomics method to distinguish protein coding and non-coding regions, Bioinformatics, 27, i275, 10.1093/bioinformatics/btr209 · DOI
  36. Pujar, 2018, Consensus coding sequence (CCDS) database: a standardized set of human and mouse protein-coding regions supported by expert curation, Nucleic Acids Res., 46, D221, 10.1093/nar/gkx1031 · DOI · Paper page
  37. Prensner, 2021, Noncanonical open reading frames encode functional proteins essential for cancer cell survival, Nat. Biotechnol., 39, 697, 10.1038/s41587-020-00806-2 · DOI
  38. Guerra-Almeida, 2020, Small open reading frames: how important are they for molecular evolution?, Front. Genet., 11, 10.3389/fgene.2020.574737 · DOI
  39. Liu, 2005, NONCODE: an integrated knowledge database of non-coding RNAs, Nucleic Acids Res., 33, D112, 10.1093/nar/gki041 · DOI
  40. Tian, 2021, Comprehensive characterization of single-cell full-length isoforms in human and mouse with long-read sequencing, Genome Biol., 22, 310, 10.1186/s13059-021-02525-6 · DOI
  41. Boivin, 2020, Reducing the structure bias of RNA-Seq reveals a large number of non-annotated non-coding RNA, Nucleic Acids Res., 48, 2271, 10.1093/nar/gkaa028 · DOI
  42. Griffith, 2015, Informatics for RNA sequencing: A web resource for analysis on the cloud, PLoS Comput. Biol., 11, 10.1371/journal.pcbi.1004393 · DOI
  43. Farazi, 2008, The growing catalog of small RNAs and their association with distinct Argonaute/Piwi family members, Development, 135, 1201, 10.1242/dev.005629 · DOI
  44. Han, 2007, Promoter-associated RNA is required for RNA-directed transcriptional gene silencing in human cells, Proc. Natl. Acad. Sci. USA, 104, 12422, 10.1073/pnas.0701635104 · DOI
  45. He, 2019, In vivo study of gene expression with an enhanced dual-color fluorescent transcriptional timer, Elife, 8, 10.7554/eLife.46181 · DOI
  46. Ferreira, 2018, The effects of death and post-mortem cold ischemia on human tissue transcriptomes, Nat. Commun., 9, 490, 10.1038/s41467-017-02772-x · DOI
  47. Chen, 2022, Live-seq enables temporal transcriptomic recording of single cells, Nature, 608, 733, 10.1038/s41586-022-05046-9 · DOI
  48. Fatumo, 2022, A roadmap to increase diversity in genomic studies, Nat. Med., 28, 243, 10.1038/s41591-021-01672-4 · DOI · Paper page
  49. Nozawa, 2007, Genomic drift and copy number variation of sensory receptor genes in humans, Proc. Natl. Acad. Sci. USA, 104, 20421, 10.1073/pnas.0709956104 · DOI
  50. Perry, 2007, Diet and the evolution of human amylase gene copy number variation, Nat. Genet., 39, 1256, 10.1038/ng2123 · DOI
  51. Gingeras, 2009, Implications of chimaeric non-co-linear transcripts, Nature, 461, 206, 10.1038/nature08452 · DOI
  52. Pei, 2012, The GENCODE pseudogene resource, Genome Biol., 13, R51, 10.1186/gb-2012-13-9-r51 · DOI
  53. Sun, 2021, Systematic functional interrogation of human pseudogenes using CRISPRi, Genome Biol., 22, 240, 10.1186/s13059-021-02464-2 · DOI
  54. Tress, 2007, The implications of alternative splicing in the ENCODE protein complement, Proc. Natl. Acad. Sci. USA, 104, 5495, 10.1073/pnas.0700800104 · DOI
  55. Ruiz-Orera, 2020, Evolution of new proteins from translated sORFs in long non-coding RNAs, Exp. Cell Res., 391, 10.1016/j.yexcr.2020.111940 · DOI
  56. An, 2023, De novo genes with an lncRNA origin encode unique human brain developmental functionality, Nat. Ecol. Evol., 7, 264, 10.1038/s41559-022-01925-6 · DOI
  57. Spencer, 2020, The LINC00961 transcript and its encoded micropeptide, small regulatory polypeptide of amino acid response, regulate endothelial cell function, Cardiovasc. Res., 116, 1981, 10.1093/cvr/cvaa008 · DOI
  58. Challis, 2023, Genomes on a Tree (GoaT): A versatile, scalable search engine for genomic and sequencing project metadata across the eukaryotic tree of life, Wellcome Open Res., 8, 24, 10.12688/wellcomeopenres.18658.1 · DOI
  59. 2022, Sequence locally, think globally: The Darwin Tree of Life Project, Proc. Natl. Acad. Sci. USA, 119
  60. Brůna, 2021, BRAKER2: automatic eukaryotic genome annotation with GeneMark-EP+ and AUGUSTUS supported by a protein database, NAR Genom. Bioinform., 3, lqaa108, 10.1093/nargab/lqaa108 · DOI
  61. Campbell, 2014, Genome Annotation and Curation Using MAKER and MAKER-P, Curr. Protoc. Bioinformatics, 48, 4.11.1, 10.1002/0471250953.bi0411s48 · DOI
  62. Haas, 2003, Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies, Nucleic Acids Res., 31, 5654, 10.1093/nar/gkg770 · DOI
  63. Levy, 2021, A stony coral cell atlas illuminates the molecular and cellular basis of coral symbiosis, calcification, and immunity, Cell, 184, 2973, 10.1016/j.cell.2021.04.005 · DOI
  64. Gu, 2016, Depletion of Abundant Sequences by Hybridization (DASH): using Cas9 to remove unwanted high-abundance species in sequencing libraries and molecular counting applications, Genome Biol., 17, 41, 10.1186/s13059-016-0904-5 · DOI
  65. Cartolano, 2016, cDNA Library Enrichment of Full Length Transcripts for SMRT Long Read Sequencing, PLoS One, 11, 10.1371/journal.pone.0157779 · DOI
  66. Carninci, 1996, High-efficiency full-length cDNA cloning by biotinylated CAP trapper, Genomics, 37, 327, 10.1006/geno.1996.0567 · DOI
  67. Morioka, 2020, Cap Analysis of Gene Expression (CAGE): A Quantitative and Genome-Wide Assay of Transcription Start Sites, Methods Mol. Biol., 2120, 277, 10.1007/978-1-0716-0327-7_20 · DOI
  68. Forrest, 2014, A promoter-level mammalian expression atlas, Nature, 507, 462, 10.1038/nature13182 · DOI · Paper page
  69. Luu, 2020, Benchmark study comparing liftover tools for genome conversion of epigenome sequencing data, NAR Genom. Bioinform., 2, lqaa054, 10.1093/nargab/lqaa054 · DOI
  70. Wang, 2022, The Human Pangenome Project: a global resource to map genomic diversity, Nature, 604, 437, 10.1038/s41586-022-04601-8 · DOI · Paper page
  71. Baranova, 2015, Extraordinary genetic diversity in a wood decay mushroom, Mol. Biol. Evol., 32, 2775, 10.1093/molbev/msv153 · DOI
  72. Kryukov, 2003, Characterization of mammalian selenoproteomes, Science, 300, 1439, 10.1126/science.1083516 · DOI
  73. Alioto, 2007, U12DB: a database of orthologous U12-type spliceosomal introns, Nucleic Acids Res., 35, D110, 10.1093/nar/gkl796 · DOI
  74. Gramates, 2022, FlyBase: a guided tour of highlighted features, Genetics, 220, 10.1093/genetics/iyac035 · DOI
  75. Hosmani, 2019, A quick guide for student-driven community genome annotation, PLoS Comput. Biol., 15, 10.1371/journal.pcbi.1006682 · DOI
  76. Di Tommaso, 2015, The impact of Docker containers on the performance of genomic pipelines, PeerJ, 3, 10.7717/peerj.1273 · DOI
  77. Di Tommaso, 2017, Nextflow enables reproducible computational workflows, Nat. Biotechnol., 35, 316, 10.1038/nbt.3820 · DOI · Paper page
  78. Grealey, 2022, The carbon footprint of bioinformatics, Mol. Biol. Evol., 39, 10.1093/molbev/msac034 · DOI
  79. Tress, 2017, Alternative splicing may not be the key to proteome complexity, Trends Biochem. Sci., 42, 98, 10.1016/j.tibs.2016.08.008 · DOI
  80. Allmer, 2006, Mass spectrometric genomic data mining: Novel insights into bioenergetic pathways in Chlamydomonas reinhardtii, Proteomics, 6, 6207, 10.1002/pmic.200600208 · DOI
  81. Adhikari, 2020, A high-stringency blueprint of the human proteome, Nat. Commun., 11, 5301, 10.1038/s41467-020-19045-9 · DOI · Paper page
  82. Sackton, 2019, Convergent evolution in the genomics era: new insights and directions, Philos. Trans. R. Soc. Lond. B Biol. Sci., 374, 10.1098/rstb.2019.0102 · DOI · Paper page
  83. Christmas, 2023, Evolutionary constraint and innovation across hundreds of placental mammals, Science, 380, 10.1126/science.abn3943 · DOI · Paper page
  84. Kuderna, 2023, A global catalog of whole-genome diversity from 233 primate species, Science, 380, 906, 10.1126/science.abn7829 · DOI
  85. Tatusov, 2000, The COG database: a tool for genome-scale analysis of protein functions and evolution, Nucleic Acids Res., 28, 33, 10.1093/nar/28.1.33 · DOI
  86. Zhang, 2013, Comparative analysis of bat genomes provides insight into the evolution of flight and immunity, Science, 339, 456, 10.1126/science.1230835 · DOI
  87. Meyer, 2018, Ancient convergent losses of Paraoxonase 1 yield potential risks for modern marine mammals, Science, 361, 591, 10.1126/science.aap7714 · DOI
  88. MacDonald, 2010, Efficient learning of microbial genotype-phenotype association rules, Bioinformatics, 26, 1834, 10.1093/bioinformatics/btq305 · DOI
  89. Feldbauer, 2015, Prediction of microbial phenotypes based on comparative genomics, BMC Bioinf., 16, S1, 10.1186/1471-2105-16-S14-S1 · DOI
  90. Liu, 2004, Comprehensive analysis of pseudogenes in prokaryotes: widespread gene decay and failure of putative horizontally transferred genes, Genome Biol., 5, R64, 10.1186/gb-2004-5-9-r64 · DOI
  91. Chibucos, 2014, An ontology for microbial phenotypes, BMC Microbiol., 14, 294, 10.1186/s12866-014-0294-3 · DOI
  92. Brbić, 2016, The landscape of microbial phenotypic traits and associated genes, Nucleic Acids Res., 44, 10074
  93. Shefchek, 2020, The Monarch Initiative in 2019: an integrative data and analytic platform connecting phenotypes to genotypes across species, Nucleic Acids Res., 48, D704, 10.1093/nar/gkz997 · DOI
  94. Smith, 2020, Phylogenetics is the new genetics (for most of biodiversity), Trends Ecol. Evol., 35, 415, 10.1016/j.tree.2020.01.005 · DOI · Paper page
  95. Sievers, 2011, Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega, Mol. Syst. Biol., 7, 539, 10.1038/msb.2011.75 · DOI
  96. Garriga, 2019, Large multiple sequence alignments with a root-to-leaf regressive method, Nat. Biotechnol., 37, 1466, 10.1038/s41587-019-0333-6 · DOI

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Metadata

Authors
Guigó, R.
Venue
Cell Genomics
Publisher
Elsevier BV
Published
2023-08
Volume
3
Issue
8
Pages
100375
ISSN
2666-979X
Cited by
49
References
11
Language
en
Funders
  • Ministerio de Ciencia e Innovación
  • Institut d'Estudis Catalans
  • European Bioinformatics Institute
  • Generalitat de Catalunya

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