Chromosome-level genome assembly of Nibea coibor using PacBio HiFi reads and Hi-C technologies

被引:5
|
作者
Yekefenhazi, Dinaer [1 ]
He, Qiwei [1 ]
Wang, Xiaopeng [1 ]
Han, Wei [1 ]
Song, Chaowei [1 ]
Li, Wanbo [1 ]
机构
[1] Jimei Univ, Minist Agr & Rural Affairs, Key Lab Hlth Mariculture East China Sea, Xiamen, Peoples R China
基金
中国国家自然科学基金;
关键词
JUVENILE CHUS CROAKER; MITOCHONDRIAL GENOME; ANTIOXIDANT STATUS; PROVIDES INSIGHTS; BODY-COMPOSITION; FEED-UTILIZATION; GROWTH; ANNOTATION; ALIGNMENT; BLOCKS;
D O I
10.1038/s41597-022-01804-6
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
Nibea coibor belongs to Sciaenidae and is distributed in the South China Sea, East China Sea, India and the Philippines. In this study, we sequenced the DNA of a male Nibea coibor using PacBio long-read sequencing and generated chromatin interaction data. The genome size of Nibea coibor was estimated to be 611.85 similar to 633.88 Mb based on k-mer counts generated with Jellyfish. PacBio sequencing produced 29.26 Gb of HiFi reads, and Hifiasm was used to assemble a 627.60 Mb genome with a contig N50 of 10.66 Mb. We further found the canonical telomeric repeats "TTAGGG" to be present at the telomeres of all 24 chromosomes. The completeness of the assembly was estimated to be 98.9% and 97.8% using BUSCO and Merqury, respectively. Using the combination of ab initio prediction, protein homology and RNAseq annotation, we identified a total of 21,433 protein-coding genes. Phylogenetic analyses showed that Nibea coibor and Nibea albiflora are closely related. The results provide an important basis for research on the genetic breeding and genome evolution of Nibea coibor.
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页数:8
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