A first nuclear and mitochondrial genomic portrait of Robinson Crusoe's (Juan Fernández Island) spiny lobster Jasus frontalis (Crustacea: Decapoda: Achelata).

IF 3.5 2区 生物学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY
J Antonio Baeza, Alyssa Baker, Sadia A Kamal, Vincent P Richards
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引用次数: 0

Abstract

Background: The Juan Fernández rock lobster Jasus frontalis (H. Milne-Edwards, 1837) is found along the Juan Fernández archipelago and Desventuradas Islands in the southeastern Pacific Ocean where it supports a profitable but likely unsustainable artisanal fishery. Only a few genomic resources are available for this species to support efficient managing practices. In this study, we took a first look at the genome of J. frontalis profiting from recently developed bioinformatics tools that mine for biological insight from low sequencing-depth datasets. Specifically, we have (i) estimated the nuclear genome size, (ii) assembled and described in detail the mitochondrial genome, (iii) discovered, quantified, and annotated nuclear transposable elements, and (iv) examined the phylogenetic position of the genus Jasus among spiny lobsters (family Palinuridae) using a maximum likelihood phylogenetic analysis based on translated mitochondrial protein coding genes (PCG's).

Results: Using an in-silico k-mer approach, the haploid nuclear genome size (GS) calculated for J. frontalis ranged between 1.42 Gbp (estimated using k-mer = 54 bp) and 1.65 Gbp (with k-mer = 18). Our GS estimates are well below the GS (= 4.56 Gbp) determined for the same species using flow cytometry. In J. frontalis, the circular mitochondrial genome is 15,514 bp in length and contains 22 transfer (tRNA) genes, 13 PCGs, and two ribosomal RNA genes (12 S and 16 S ribosomal RNA). In the nuclear genome of J. frontalis, repetitive elements content varied between 41% (with k-mer = 54) and 64% (using k-mer = 18 bp). Nearly a third (64.94%) of the transposable elements were not annotated. Among annotated transposable elements, Long Interspersed Nuclear Elements (LINEs, 12.64%), DNA transposons (7.35%), and Long Terminal Repeats (LTRs, 5.44%) were the most common. Less abundant transposable elements included Rolling Circles (1.3%), Short Interspersed Nuclear Elements (SINEs, 0.64%), Satellite DNA (0.43%), and simple repeats (0.42%), among others. A phylomitogenomic analysis based on PCGs indicated supported the monophyletic status of the infraorder Achelata and the superfamilies Paniluridae and Syllaridae. The genus Jasus together with Sagmariasus verreauxi were recovered as a monophyletic clade that also provided support for the monophyletic status of lobsters that do not produce sound ("Silentes").

Conclusion: The genomic resources developed in this study will support conservation strategies and efficient fisheries management in this spiny lobster that is likely overexploited.

鲁滨逊·克鲁索(Juan Fernández岛)的棘龙虾Jasus frontalis(甲壳纲:十足纲:棘足纲)的第一个核和线粒体基因组图谱。
背景:胡安Fernández岩龙虾Jasus frontalis (H. mile - edwards, 1837)发现于胡安Fernández群岛和太平洋东南部的Desventuradas群岛,在那里它支持着一种有利可图但可能不可持续的手工渔业。只有少数基因组资源可用于该物种,以支持有效的管理措施。在这项研究中,我们利用最近开发的生物信息学工具首次研究了J. frontalis的基因组,这些工具可以从低测序深度的数据集中挖掘生物学洞察力。具体来说,我们已经(i)估计了核基因组的大小,(ii)组装并详细描述了线粒体基因组,(iii)发现、量化和注释了核转座元件,以及(iv)使用基于翻译线粒体蛋白编码基因(PCG)的最大似然系统发育分析检查了Jasus属在刺龙虾(Palinuridae)中的系统发育位置。结果:利用k-mer方法计算得到的frontalis单倍体核基因组大小(GS)在1.42 Gbp (k-mer = 54 bp)和1.65 Gbp (k-mer = 18)之间。我们的GS估计值远低于流式细胞术对同一物种测定的GS值(= 4.56 Gbp)。在frontalis中,圆形线粒体基因组长度为15,514 bp,包含22个tRNA基因、13个PCGs基因和2个核糖体RNA基因(12s和16s核糖体RNA)。在frontalis的核基因组中,重复元素的含量在41% (k-mer = 54)和64% (k-mer = 18 bp)之间变化。近1 / 3(64.94%)的转座因子未被标注。在带注释的转座元件中,以长穿插核元件(LINEs, 12.64%)、DNA转座子(7.35%)和长末端重复序列(lts, 5.44%)最为常见。转座因子的丰度较低的有Rolling Circles(1.3%)、Short Interspersed Nuclear elements(0.64%)、Satellite DNA(0.43%)和simple repeats(0.42%)等。基于PCGs的动物基因组学分析支持了下目Achelata和超科Paniluridae和Syllaridae的单系地位。Jasus属与Sagmariasus verreauxi属被恢复为单系进化分支,这也为不发声的龙虾(“Silentes”)的单系地位提供了支持。结论:本研究开发的基因组资源将为这种可能被过度捕捞的龙虾的保护策略和有效的渔业管理提供支持。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
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来源期刊
BMC Genomics
BMC Genomics 生物-生物工程与应用微生物
CiteScore
7.40
自引率
4.50%
发文量
769
审稿时长
6.4 months
期刊介绍: BMC Genomics is an open access, peer-reviewed journal that considers articles on all aspects of genome-scale analysis, functional genomics, and proteomics. BMC Genomics is part of the BMC series which publishes subject-specific journals focused on the needs of individual research communities across all areas of biology and medicine. We offer an efficient, fair and friendly peer review service, and are committed to publishing all sound science, provided that there is some advance in knowledge presented by the work.
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