基因组
生物
顺序装配
康蒂格
基因
遗传学
比较基因组学
基因组计划
计算生物学
基因组学
进化生物学
转录组
基因表达
作者
Yifan Pei,Zhixiong Deng,Xiuping Zhang,David Blair,Wei Hu,Mingbo Yin
标识
DOI:10.1016/j.aquatox.2023.106565
摘要
The genus Chydorus Leach 1816 (family Chydoridae) is a diverse and ecologically important taxon within freshwater ecosystems. Despite having been widely used in ecological, evolutionary and eco-toxicological studies, no high-quality genomic resource is available for any member of the genus. Here, we present a high-quality chromosome-level assembly of the C. sphaericus genome by combining 7.40 Gb (∼ 50 × coverage) PacBio reads, 19.28 Gb (∼ 135 × coverage) Illumina paired-end reads, and 34.04 Gb Hi-C reads. Our genome assembly is approximately 151 Mb, with contig and scaffold N50 lengths of 1.09 Mb and 13.70 Mb, respectively. The assembly captured 94.9% of the complete eukaryotic BUSCO. Repetitive elements accounted for 17.6% of the genome, and 13,549 protein-coding genes were predicted (based on transcriptome sequencing data, ab-initio or homology-based prediction), of which 96.4% have been functionally annotated in the NCBI-NR database. We identified 303 gene families specific to C. sphaericus, mainly families enriched in functions related to immune response, visual senses and detoxification. Interestingly, we also found 53 significantly expanded gene families in C. sphaericus, mostly with functions related to detoxification. This high-quality assembly genome will act as a reference genome for C. sphaericus and benefit studies on functional and comparative genomics of Chydorus and other crustaceans.
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