NDLI: Near‐complete genome assembly and annotation of the yellow drum ( Nibea albiflora ) provide insights into population and evolutionary characteristics of this species

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Near‐complete genome assembly and annotation of the yellow drum ( Nibea albiflora ) provide insights into population and evolutionary characteristics of this species

Content Provider	Scilit
Author	Han, Zhaofang Li, Wan Bo Zhu, Wen Sun, Sha Ye, Kun Xie, Yangjie Wang, Zhiyong
Copyright Year	2018
Description	Journal: Ecology and Evolution Yellow drum (Nibea albiflora) is an important fish species in capture fishery and aquaculture in East Asia. We herein report the first and near‐complete genome assembly of an ultra‐homologous gynogenic female yellow drum using Illumina short sequencing reads. In summary, a total of 154.2 Gb of raw reads were generated via whole‐genome sequencing and were assembled to 565.3 Mb genome with a contig $N_{50}$ size of 50.3 kb and scaffold $N_{50}$ size of 2.2 Mb (BUSCO completeness of 97.7%), accounting for 97.3%–98.6% of the estimated genome size of this fish. We further identified 22,448 genes using combined methods of ab initio prediction, RNAseq annotation, and protein homology searching, of which 21,614 (96.3%) were functionally annotated in NCBI nr, trEMBL, SwissProt, and KOG databases. We also investigated the nucleotide diversity (around 1/390) of aquacultured individuals and found the genetic diversity of the aquacultured population decreased due to inbreeding. Evolutionary analyses illustrated significantly expanded and extracted gene families, such as myosin and sodium: neurotransmitter symporter (SNF), could help explain swimming motility of yellow drum. The presented genome will be an important resource for future studies on population genetics, conservation, understanding of evolutionary history and genetic breeding of the yellow drum and other Nibea species.
Related Links	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6342179/pdf
Ending Page	575
Page Count	8
Starting Page	568
ISSN	20457758
e-ISSN	20457758
DOI	10.1002/ece3.4778
Journal	Ecology and Evolution
Issue Number	1
Volume Number	9
Language	English
Publisher	Wiley-Blackwell
Publisher Date	2018-12-11
Access Restriction	Open
Subject Keyword	Journal: Ecology and Evolution Fisheries Sciences Genome Assembly Nucleotide Diversity Yellow Drum (nibea Albiflora)
Content Type	Text
Resource Type	Article
Subject	Ecology Ecology, Evolution, Behavior and Systematics Nature and Landscape Conservation

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