A chromosome-level genome assembly of the redfin culter (Chanodichthys erythropterus)

被引：7

作者：

Zhao, Shihu ^{[1
]}

Yang, Xiufeng ^{[1
]}

Pang, Bo ^{[2
]}

Zhang, Lei ^{[1
]}

Wang, Qi ^{[2
]}

He, Shangbin ^{[1
]}

Dou, Huashan ^{[2
]}

Zhang, Honghai ^{[1
]}

机构：

[1] Qufu Normal Univ, Coll Life Sci, Qufu 273165, Shandong, Peoples R China

[2] Hulunbuir Acad Inland Lakes Northern Cold & Arid, Hulunbuir 021000, Inner Mongolia, Peoples R China

来源：

SCIENTIFIC DATA | 2022年 / 9卷 / 01期

基金：

中国国家自然科学基金;

关键词：

LENGTH-WEIGHT; PREDICTION; SEQUENCE; GENES; CARP; TOOL; DIVERSITY; ALIGNMENT; PROGRAM; FISHES;

D O I：

10.1038/s41597-022-01648-0

中图分类号：

O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];

学科分类号：

07 ; 0710 ; 09 ;

摘要：

Chanodichthys erythropterus is a fierce carnivorous fish widely found in East Asian waters. It is not only a popular food fish in China, it is also a representative victim of overfishing. Genetic breeding programs launched to meet market demands urgently require high-quality genomes to facilitate genomic selection and genetic research. In this study, we constructed a chromosome-level reference genome of C. erythropterus by taking advantage of long-read single-molecule sequencing and de novo assembly by Oxford Nanopore Technology (ONT) and Hi-C. The 1.085 Gb C. erythropterus genome was assembled from 132 Gb of Nanopore sequence. The assembled genome represents 98.5% completeness (BUSCO) with a contig N50 length of 23.29 Mb. The contigs were clustered and ordered onto 24 chromosomes covering roughly 99.49% of the genome assembly with Hi-C data. Additionally, 33,041 (98.0%) genes were functionally annotated from a total of 33,706 predicted protein-coding sequences by combining transcriptome data from seven tissues. This high-quality assembled genome will be a precious resource for future molecular breeding and functional genomics research of C. erythropterus.

引用

页数：9

共 51 条

[21]

Kindong R., 2019, EGYPT J BAS APPL SCI, V4, P297, DOI [10.1016/j.ejbas.2017.10.001, DOI 10.1016/J.EJBAS.2017.10.001]

[22] Gene finding in novel genomes [J].

Korf, I .

BMC BIOINFORMATICS, 2004, 5 (1)

[23] A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data [J].

Li, Heng .

BIOINFORMATICS, 2011, 27 (21) :2987-2993

[24]

Li H, 2009, BIOINFORMATICS, V25, P1094, DOI [10.1093/bioinformatics/btp100, 10.1093/bioinformatics/btp324]

[25]

Li Hua Li Hua, 2009, Acta Nutrimenta Sinica, V31, P285

[26] Ontogenetic changes in isotopic signatures of an omnivorous fish Cultrichthys erythropterus in East Lake Taihu, China [J].

Li Yunkai ;

Zhang Miao .

CHINESE JOURNAL OF OCEANOLOGY AND LIMNOLOGY, 2015, 33 (03) :725-731

[27] tRNAscan-SE: A program for improved detection of transfer RNA genes in genomic sequence [J].

Lowe, TM ;

Eddy, SR .

NUCLEIC ACIDS RESEARCH, 1997, 25 (05) :955-964

[28] Length-weight relationships of five fishes from the middle Heilongjiang River, China [J].

Ma, B. ;

Li, L. ;

Wu, S. -F. .

JOURNAL OF APPLIED ICHTHYOLOGY, 2016, 32 (01) :156-157

[29] TigrScan and GlimmerHMM:: two open source ab initio eukaryotic gene-finders [J].

Majoros, WH ;

Pertea, M ;

Salzberg, SL .

BIOINFORMATICS, 2004, 20 (16) :2878-2879

[30] The structure of fish community and changes of fishery resources in Lake Hulun [J].

Mao Z. ;

Gu X. ;

Zeng Q. .

Hupo Kexue/Journal of Lake Sciences, 2016, 28 (02) :387-394

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