Near-Chromosomal-Level Genome Assembly of the Sea Urchin Echinometra lucunter , a Model for Speciation in the Sea
Near-Chromosomal-Level Genome Assembly of the Sea Urchin Echinometra lucunter , a Model for Speciation in the Sea
复制标题
海胆 Echinometra lucunter 的近染色体水平基因组组装，海洋物种形成模型
DOI：
10.1093/gbe/evad093
复制
发表时间：
2023
影响因子：
3.3
通讯作者：
Prada, Carlos
中科院分区：
文献类型：
--
作者：
Davidson, Phillip L;Lessios, Harilaos A;Wray, Gregory A;McMillan, W Owen;Prada, Carlos
海胆（Echinometra lucunter）是一种广泛分布的海胆，也是繁殖、对气候变化的反应和物种形成的生态研究的模型。我们提出了一个近染色体水平的基因组组装E。lucunter，包括21个大于10 Mb的支架，预测代表该物种的每条染色体。760.4 Mb组装体包括30.0 Mb的支架N50和BUSCO（基准通用单拷贝直系同源物）单拷贝和重复评分分别为95.8%和1.4%。用转录组数据进行从头算基因模型预测和注释，构建了33，989个基因模型，占组装的50.4%，其中包括37，036个转录本。重复元件约占组装体的39.6%，未分辨的间隙序列估计为0.65%。与Echinometrasp. EZ的全基因组比对结果表明，两个物种之间具有高度的同线性和保守性，进一步支持Echinometra作为一个新兴的比较基因组学研究属。该基因组组装为该物种和更广泛的棘皮动物的未来进化和发育研究提供了高质量的基因组资源。
Echinometra lucunter, the rock-boring sea urchin, is a widely distributed echinoid and a model for ecological studies of reproduction, responses to climate change, and speciation. We present a near chromosome-level genome assembly ofE. lucunter, including 21 scaffolds larger than 10 Mb predicted to represent each of the chromosomes of the species. The 760.4 Mb assembly includes a scaffold N50 of 30.0 Mb and BUSCO (benchmarking universal single-copy orthologue) single copy and a duplicated score of 95.8% and 1.4%, respectively. Ab-initio gene model prediction and annotation with transcriptomic data constructed 33,989 gene models composing 50.4% of the assembly, including 37,036 transcripts. Repetitive elements make up approximately 39.6% of the assembly, and unresolved gap sequences are estimated to be 0.65%. Whole genome alignment withEchinometrasp.EZrevealed high synteny and conservation between the two species, further bolsteringEchinometraas an emerging genus for comparative genomics studies. This genome assembly represents a high-quality genomic resource for future evolutionary and developmental studies of this species and more broadly of echinoderms.