Genome Annotation: From Human Genetics to Biodiversity Genomics

Overview

Journal Cell Genom

Date 2023 Aug 21

PMID 37601977

Authors

Roderic Guigo

Affiliations

Soon will be listed here.

Abstract

Within the next decade, the genomes of 1.8 million eukaryotic species will be sequenced. Identifying genes in these sequences is essential to understand the biology of the species. This is challenging due to the transcriptional complexity of eukaryotic genomes, which encode hundreds of thousands of transcripts of multiple types. Among these, a small set of protein-coding mRNAs play a disproportionately large role in defining phenotypes. Due to their sequence conservation, orthology can be established, making it possible to define the universal catalog of eukaryotic protein-coding genes. This catalog should substantially contribute to uncovering the genomic events underlying the emergence of eukaryotic phenotypes. This piece briefly reviews the basics of protein-coding gene prediction, discusses challenges in finalizing annotation of the human genome, and proposes strategies for producing annotations across the eukaryotic Tree of Life. This lays the groundwork for obtaining the catalog of all genes-the Earth's code of life.

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References

Hosmani P, Shippy T, Miller S, Benoit J, Munoz-Torres M, Flores-Gonzalez M . A quick guide for student-driven community genome annotation. PLoS Comput Biol. 2019; 15(4):e1006682. PMC: 6447164. DOI: 10.1371/journal.pcbi.1006682. View

Sakurai A, Fujimori S, Kochiwa H, Washio T, Saito R, Carninci P . On biased distribution of introns in various eukaryotes. Gene. 2002; 300(1-2):89-95. DOI: 10.1016/s0378-1119(02)01035-1. View

Gramates L, Agapite J, Attrill H, Calvi B, Crosby M, Dos Santos G . FlyBase: a guided tour of highlighted features. Genetics. 2022; 220(4). PMC: 8982030. DOI: 10.1093/genetics/iyac035. View

Gingeras T . Implications of chimaeric non-co-linear transcripts. Nature. 2009; 461(7261):206-11. PMC: 4020519. DOI: 10.1038/nature08452. View

Forrest A, Kawaji H, Rehli M, Baillie J, de Hoon M, Haberle V . A promoter-level mammalian expression atlas. Nature. 2014; 507(7493):462-70. PMC: 4529748. DOI: 10.1038/nature13182. View

Gu W, Crawford E, ODonovan B, Wilson M, Chow E, Retallack H . Depletion of Abundant Sequences by Hybridization (DASH): using Cas9 to remove unwanted high-abundance species in sequencing libraries and molecular counting applications. Genome Biol. 2016; 17:41. PMC: 4778327. DOI: 10.1186/s13059-016-0904-5. View

Luu P, Ong P, Dinh T, Clark S . Benchmark study comparing liftover tools for genome conversion of epigenome sequencing data. NAR Genom Bioinform. 2021; 2(3):lqaa054. PMC: 7671393. DOI: 10.1093/nargab/lqaa054. View

Shefchek K, Harris N, Gargano M, Matentzoglu N, Unni D, Brush M . The Monarch Initiative in 2019: an integrative data and analytic platform connecting phenotypes to genotypes across species. Nucleic Acids Res. 2019; 48(D1):D704-D715. PMC: 7056945. DOI: 10.1093/nar/gkz997. View

Adhikari S, Nice E, Deutsch E, Lane L, Omenn G, Pennington S . A high-stringency blueprint of the human proteome. Nat Commun. 2020; 11(1):5301. PMC: 7568584. DOI: 10.1038/s41467-020-19045-9. View

10.

Liu Y, Harrison P, Kunin V, Gerstein M . Comprehensive analysis of pseudogenes in prokaryotes: widespread gene decay and failure of putative horizontally transferred genes. Genome Biol. 2004; 5(9):R64. PMC: 522871. DOI: 10.1186/gb-2004-5-9-r64. View

11.

Zhuo D, Zhao W, Wright F, Yang H, Wang J, Sears R . Assembly, annotation, and integration of UNIGENE clusters into the human genome draft. Genome Res. 2001; 11(5):904-18. PMC: 311045. DOI: 10.1101/gr.gr-1645r. View

12.

Sackton T, Clark N . Convergent evolution in the genomics era: new insights and directions. Philos Trans R Soc Lond B Biol Sci. 2019; 374(1777):20190102. PMC: 6560275. DOI: 10.1098/rstb.2019.0102. View

13.

An N, Zhang J, Mo F, Luan X, Tian L, Shen Q . De novo genes with an lncRNA origin encode unique human brain developmental functionality. Nat Ecol Evol. 2023; 7(2):264-278. PMC: 9911349. DOI: 10.1038/s41559-022-01925-6. View

14.

Tian L, Jabbari J, Thijssen R, Gouil Q, Amarasinghe S, Voogd O . Comprehensive characterization of single-cell full-length isoforms in human and mouse with long-read sequencing. Genome Biol. 2021; 22(1):310. PMC: 8582192. DOI: 10.1186/s13059-021-02525-6. View

15.

Ferreira P, Munoz-Aguirre M, Reverter F, Sa Godinho C, Sousa A, Amadoz A . The effects of death and post-mortem cold ischemia on human tissue transcriptomes. Nat Commun. 2018; 9(1):490. PMC: 5811508. DOI: 10.1038/s41467-017-02772-x. View

16.

Sievers F, Wilm A, Dineen D, Gibson T, Karplus K, Li W . Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega. Mol Syst Biol. 2011; 7:539. PMC: 3261699. DOI: 10.1038/msb.2011.75. View

17.

Holzer M, Marz M . De novo transcriptome assembly: A comprehensive cross-species comparison of short-read RNA-Seq assemblers. Gigascience. 2019; 8(5). PMC: 6511074. DOI: 10.1093/gigascience/giz039. View

18.

Pei B, Sisu C, Frankish A, Howald C, Habegger L, Mu X . The GENCODE pseudogene resource. Genome Biol. 2012; 13(9):R51. PMC: 3491395. DOI: 10.1186/gb-2012-13-9-r51. View

19.

Sun M, Wang Y, Zheng C, Wei Y, Hou J, Zhang P . Systematic functional interrogation of human pseudogenes using CRISPRi. Genome Biol. 2021; 22(1):240. PMC: 8381491. DOI: 10.1186/s13059-021-02464-2. View

20.

Chibucos M, Zweifel A, Herrera J, Meza W, Eslamfam S, Uetz P . An ontology for microbial phenotypes. BMC Microbiol. 2014; 14:294. PMC: 4287307. DOI: 10.1186/s12866-014-0294-3. View