受过度捕捞严重影响的长寿命双壳类物种皮斯莫蛤的染色体长度基因组组装。

IF 3 2区 生物学 Q2 EVOLUTIONARY BIOLOGY
Kyle A Emery, Melissa B DeBiasse, Merly Escalona, Mohan P A Marimuthu, Oanh H Nguyen, Colin W Fairbairn, William Seligmann, Courtney Miller, Nicholas K Schooler, David M Hubbard, Jenifer E Dugan, Michael N Dawson
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引用次数: 0

摘要

皮斯莫蛤,学名Tivela stultorum,是一种重要的生态和经济物种,生活在美国加利福尼亚州中南部和墨西哥下加利福尼亚州北部的沙滩和潮下带。这种长寿命的venerid蛤蜊在加州具有重要的管理、文化和保护意义,几个世纪以来,当地居民一直在捕捞这种蛤蜊,但在20世纪中期,由于商业和娱乐性的过度捕捞,这种蛤蜊几乎灭绝。如今,加州的休闲渔业仍在继续,然而,T. stultorum面临着偷猎、过度捕捞以及海平面上升和海滩侵蚀导致的沙滩减少的压力。了解皮斯莫蛤对这些压力的敏感性和恢复力对它们的保护至关重要。我们使用Pacific Biosciences HiFi长测序reads和Dovetail Omni-C接近reads组装了一个高度连续的763 Mb的基因组。基因组的连续N50为13 Mb,支架N50为38 Mb, BUSCO完整性评分为95%。大部分基因组序列(96%)包含在19个至少10MB长的支架中,这与先前的证据一致,即蛤基因组由19个常染色体组成。该参考基因组将有助于通过种群基因组分析更全面地了解T. stultorum的生态和进化动态,这将有助于评估气候、渔业、环境变化和生活史敏感性带来的风险。我们的目标是更好地支持T. stultorum的持续恢复,明智的管理和保护,以及未来的持久性,T. stultorum是一个长寿和高价值的蛤蜊物种。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
A chromosome-length genome assembly for the Pismo clam, Tivela stultorum, a long-lived bivalve species severely impacted by overfishing.

The Pismo clam, Tivela stultorum, is an ecologically and economically important species that inhabiting sandy beaches and subtidal zones in central and southern California, USA, and northern Baja California, Mexico. This long lived venerid clam species is of great management, cultural and conservation interest in California where it was harvested for centuries by indigenous people and then nearly extirpated by intense commercial and recreational overfishing in the mid 1900's. A recreational fishery continues today in California, however T. stultorum faces pressure from poaching, overharvest, and the loss of sandy beaches from rising sea levels and beach erosion. Understanding the susceptibility and resilience of Pismo clams to these pressures is essential for their conservation. We used Pacific Biosciences HiFi long sequencing reads and Dovetail Omni-C proximity reads to assemble a highly contiguous genome of 763 Mb. The genome had a contig N50 of 13 Mb and a scaffold N50 of 38 Mb with a BUSCO completeness score of 95%. Most of the genome sequences (96%) were contained in 19 scaffolds at least 10MB long, consistent with prior evidence that venerid clam genomes are composed of 19 autosomes. This reference genome will enable a more complete understanding of the ecology and evolutionary dynamics of T. stultorum via population genomic analyses, which will help assess risks from climate, fishing, environmental change, and susceptibilities due to life history. Our goal is to better support the continued recovery, informed management and conservation, and future persistence of T. stultorum, a long lived and highly valued clam species.

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来源期刊
Journal of Heredity
Journal of Heredity 生物-遗传学
CiteScore
5.20
自引率
6.50%
发文量
63
审稿时长
6-12 weeks
期刊介绍: Over the last 100 years, the Journal of Heredity has established and maintained a tradition of scholarly excellence in the publication of genetics research. Virtually every major figure in the field has contributed to the journal. Established in 1903, Journal of Heredity covers organismal genetics across a wide range of disciplines and taxa. Articles include such rapidly advancing fields as conservation genetics of endangered species, population structure and phylogeography, molecular evolution and speciation, molecular genetics of disease resistance in plants and animals, genetic biodiversity and relevant computer programs.
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