Bicolor Angelfish () Provides the First Chromosome-level Genome of the Pomacanthidae Family

Overview

Journal GigaByte

Date 2023 Feb 24

PMID 36824335

Authors

Chunhua Li

Xianwei Yang

Libin Shao

Rui Zhang

Qun Liu

Mengqi Zhang

Shanshan Liu

Shanshan Pan

Weizhen Xue

Congyan Wang

Chunyan Mao

He Zhang

Guangyi Fan

Affiliations

Soon will be listed here.

Abstract

The Bicolor Angelfish, , is a tropical coral reef fish. It is named for its striking two-color body. However, a lack of high-quality genomic data means little is known about the genome of this species. Here, we present a chromosome-level genome constructed using Hi-C data. The assembled genome is 650 Mbp in size, with a scaffold N50 value of 4.4 Mbp, and a contig N50 value of 114 Kbp. Protein-coding genes numbering 21,774 were annotated. Our analysis will help others to choose the most appropriate genome sequencing strategy based on resources and target applications. To the best of our knowledge, this is the first chromosome-level genome for the Pomacanthidae family, which might contribute to further studies exploring coral reef fish evolution, diversity and conservation.

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References

Tillich M, Lehwark P, Pellizzer T, Ulbricht-Jones E, Fischer A, Bock R . GeSeq - versatile and accurate annotation of organelle genomes. Nucleic Acids Res. 2017; 45(W1):W6-W11. PMC: 5570176. DOI: 10.1093/nar/gkx391. View

Villaveces J, Jimenez R, Habermann B . KEGGViewer, a BioJS component to visualize KEGG Pathways. F1000Res. 2014; 3:43. PMC: 3954160. DOI: 10.12688/f1000research.3-43.v1. View

Wang Y, Tang H, DeBarry J, Tan X, Li J, Wang X . MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity. Nucleic Acids Res. 2012; 40(7):e49. PMC: 3326336. DOI: 10.1093/nar/gkr1293. View

Vurture G, Sedlazeck F, Nattestad M, Underwood C, Fang H, Gurtowski J . GenomeScope: fast reference-free genome profiling from short reads. Bioinformatics. 2017; 33(14):2202-2204. PMC: 5870704. DOI: 10.1093/bioinformatics/btx153. View

Jones P, Binns D, Chang H, Fraser M, Li W, McAnulla C . InterProScan 5: genome-scale protein function classification. Bioinformatics. 2014; 30(9):1236-40. PMC: 3998142. DOI: 10.1093/bioinformatics/btu031. View

Meng G, Li Y, Yang C, Liu S . MitoZ: a toolkit for animal mitochondrial genome assembly, annotation and visualization. Nucleic Acids Res. 2019; 47(11):e63. PMC: 6582343. DOI: 10.1093/nar/gkz173. View

Servant N, Varoquaux N, Lajoie B, Viara E, Chen C, Vert J . HiC-Pro: an optimized and flexible pipeline for Hi-C data processing. Genome Biol. 2015; 16:259. PMC: 4665391. DOI: 10.1186/s13059-015-0831-x. View

Bao W, Kojima K, Kohany O . Repbase Update, a database of repetitive elements in eukaryotic genomes. Mob DNA. 2015; 6:11. PMC: 4455052. DOI: 10.1186/s13100-015-0041-9. View

Stanke M, Keller O, Gunduz I, Hayes A, Waack S, Morgenstern B . AUGUSTUS: ab initio prediction of alternative transcripts. Nucleic Acids Res. 2006; 34(Web Server issue):W435-9. PMC: 1538822. DOI: 10.1093/nar/gkl200. View

10.

Dudchenko O, Batra S, Omer A, Nyquist S, Hoeger M, Durand N . De novo assembly of the genome using Hi-C yields chromosome-length scaffolds. Science. 2017; 356(6333):92-95. PMC: 5635820. DOI: 10.1126/science.aal3327. View

11.

Storer J, Hubley R, Rosen J, Wheeler T, Smit A . The Dfam community resource of transposable element families, sequence models, and genome annotations. Mob DNA. 2021; 12(1):2. PMC: 7805219. DOI: 10.1186/s13100-020-00230-y. View

12.

Durand N, Shamim M, Machol I, Rao S, Huntley M, Lander E . Juicer Provides a One-Click System for Analyzing Loop-Resolution Hi-C Experiments. Cell Syst. 2016; 3(1):95-8. PMC: 5846465. DOI: 10.1016/j.cels.2016.07.002. View

13.

Bairoch A, Apweiler R . The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000. Nucleic Acids Res. 1999; 28(1):45-8. PMC: 102476. DOI: 10.1093/nar/28.1.45. View

14.

Wang O, Chin R, Cheng X, Wu M, Mao Q, Tang J . Efficient and unique cobarcoding of second-generation sequencing reads from long DNA molecules enabling cost-effective and accurate sequencing, haplotyping, and de novo assembly. Genome Res. 2019; 29(5):798-808. PMC: 6499310. DOI: 10.1101/gr.245126.118. View

15.

Chen Y, Chen Y, Shi C, Huang Z, Zhang Y, Li S . SOAPnuke: a MapReduce acceleration-supported software for integrated quality control and preprocessing of high-throughput sequencing data. Gigascience. 2017; 7(1):1-6. PMC: 5788068. DOI: 10.1093/gigascience/gix120. View

16.

Wong K, Levy-Sakin M, Kwok P . De novo human genome assemblies reveal spectrum of alternative haplotypes in diverse populations. Nat Commun. 2018; 9(1):3040. PMC: 6072799. DOI: 10.1038/s41467-018-05513-w. View

17.

Stanke M, Schoffmann O, Morgenstern B, Waack S . Gene prediction in eukaryotes with a generalized hidden Markov model that uses hints from external sources. BMC Bioinformatics. 2006; 7:62. PMC: 1409804. DOI: 10.1186/1471-2105-7-62. View

18.

Ruan J, Li H, Chen Z, Coghlan A, Coin L, Guo Y . TreeFam: 2008 Update. Nucleic Acids Res. 2007; 36(Database issue):D735-40. PMC: 2238856. DOI: 10.1093/nar/gkm1005. View

19.

Tarailo-Graovac M, Chen N . Using RepeatMasker to identify repetitive elements in genomic sequences. Curr Protoc Bioinformatics. 2009; Chapter 4:4.10.1-4.10.14. DOI: 10.1002/0471250953.bi0410s25. View

20.

Doerks T, Copley R, Schultz J, Ponting C, Bork P . Systematic identification of novel protein domain families associated with nuclear functions. Genome Res. 2002; 12(1):47-56. PMC: 155265. DOI: 10.1101/gr.203201. View