A reference genome for ecological restoration of the sunflower sea star, Pycnopodia helianthoides
A reference genome for ecological restoration of the sunflower sea star, Pycnopodia helianthoides
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DOI：
10.1093/jhered/esad054
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发表时间：
2023-10-27
影响因子：
3.1
通讯作者：
Dawson，Michael N.
中科院分区：
文献类型：
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作者：
Schiebelhut，Lauren M.;DeBiasse，Melissa B.;Dawson，Michael N.
野生动物疾病，例如 2010 年代中期爆发的海星消瘦症 (SSW) 流行病，似乎与急性和/或慢性非生物环境变化有关；区分不同驱动因素的影响可能很困难。向日葵海星Pycnopodia helianthoides是SSW爆发期间受影响最严重的物种，该爆发与异常大气和海洋条件时期重叠，目前尚未就其原因达成共识。基因组数据可能揭示涉及部分因素的潜在分子特征，从而澄清过去的事件，同时也为有效的恢复工作奠定基础。为了推进这一目标，我们使用 Pacific Biosciences HiFi 长测序读取和 Dovetail Omni-C 邻近读取来生成高度连续的基因组组装，然后使用 RNA-seq 通知的基因预测对其进行注释。基因组组装长 484 Mb，重叠群 N50 为 1.9 Mb，支架 N50 为 21.8 Mb，BUSCO 完整性评分为 96.1%，22 个主要支架与海星基因组包含 22 个常染色体的先前证据一致。这些统计数据通常介于远缘小行星 Pisaster 属中两个物种的其他最近组装的染色体规模组装的统计数据之间。这些新颖的基因组资源为 P。 helianthoides 将承担 SSW 和环境压力源的群体基因组、比较基因组和系统发育组分析及其跨尺度的整合。
Wildlife diseases, such as the sea star wasting (SSW) epizootic that outbroke in the mid-2010s, appear to be associated with acute and/or chronic abiotic environmental change; dissociating the effects of different drivers can be difficult. The sunflower sea star,Pycnopodia helianthoides, was the species most severely impacted during the SSW outbreak, which overlapped with periods of anomalous atmospheric and oceanographic conditions, and there is not yet a consensus on the cause(s). Genomic data may reveal underlying molecular signatures that implicate a subset of factors and, thus, clarify past events while also setting the scene for effective restoration efforts. To advance this goal, we used Pacific Biosciences HiFi long sequencing reads and Dovetail Omni-C proximity reads to generate a highly contiguous genome assembly that was then annotated using RNA-seq-informed gene prediction. The genome assembly is 484 Mb long, with contig N50 of 1.9 Mb, scaffold N50 of 21.8 Mb, BUSCO completeness score of 96.1%, and 22 major scaffolds consistent with prior evidence that sea star genomes comprise 22 autosomes. These statistics generally fall between those of other recently assembled chromosome-scale assemblies for two species in the distantly related asteroid genusPisaster. These novel genomic resources forP. helianthoideswill underwrite population genomic, comparative genomic, and phylogenomic analyses—as well as their integration across scales—of SSW and environmental stressors.