Chromosome-scale genome assembly of the freshwater cladoceran crustacean Chydorus sphaericus: A resource for discovery of genes responsive to ecological challenges.
Chromosome-scale genome assembly of the freshwater cladoceran crustacean Chydorus sphaericus: A resource for discovery of genes responsive to ecological challenges.
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DOI：
10.1016/j.aquatox.2023.106565
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发表时间：
2023-05
影响因子：
4.5
通讯作者：
Y. Pei;Zhixiong Deng;Xiuping Zhang;D. Blair;Wei Hu;Mingbo Yin
中科院分区：
文献类型：
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作者：
Y. Pei;Zhixiong Deng;Xiuping Zhang;D. Blair;Wei Hu;Mingbo Yin
The genusChydorusLeach 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 theC. sphaericusgenome 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 toC. sphaericus, mainly families enriched in functions related to immune response, visual senses and detoxification. Interestingly, we also found 53 significantly expanded gene families inC. sphaericus, mostly with functions related to detoxification. This high-quality assembly genome will act as a reference genome forC. sphaericusand benefit studies on functional and comparative genomics ofChydorusand other crustaceans.
