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加勒比刺龙虾的基因组调查测序：基因组大小、核 rRNA 操纵子、重复元件及微卫星发现

Genome survey sequencing of the Caribbean spiny lobster : Genome size, nuclear rRNA operon, repetitive elements, and microsatellite discovery.

作者信息

Baeza J Antonio

机构信息

Department of Biological Sciences, Clemson University, Clemson, SC, USA.

Departamento de Biologia Marina, Universidad Catolica del Norte, Coquimbo, IV Region, Chile.

出版信息

PeerJ. 2020 Dec 17;8:e10554. doi: 10.7717/peerj.10554. eCollection 2020.

DOI:10.7717/peerj.10554
PMID:33362980
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC7750000/
Abstract

BACKGROUND

is an ecologically relevant species in shallow water hard-bottom environments and coral reefs and target of the most lucrative fishery in the greater Caribbean region.

METHODS

This study reports, for the first time, the genome size and nuclear repetitive elements, including the 45S ribosomal DNA operon, 5S unit, and microsatellites, of .

RESULTS

Using a -mer approach, the average haploid genome size estimated for was 2.17 Gbp. Repetitive elements comprised 69.02% of the nuclear genome. In turn, 30.98% of the genome represented low- or single-copy sequences. A considerable proportion of repetitive sequences could not be assigned to known repeat element families. Taking into account only annotated repetitive elements, the most frequent belonged to Class I-LINE which were noticeably more abundant than Class I-LTR-Ty- 3/Gypsy, Class I-LTR-Penelope, and Class I-LTR-Ty-3/Bel-Pao elements. Satellite DNA was also abundant. The ribosomal operon in comprises, in the following order, a 5' ETS (length = 707 bp), ssrDNA (1,875 bp), ITS1 (736 bp), 5.8S rDNA (162 bp), ITS2 (1,314 bp), lsrDNA (5,387 bp), and 3' ETS (287 bp). A total of 1,281 SSRs were identified.

摘要

背景

是浅海硬底环境和珊瑚礁中的一种具有生态相关性的物种，也是大加勒比地区最有利可图的渔业的目标物种。

方法

本研究首次报告了的基因组大小和核重复元件，包括45S核糖体DNA操纵子、5S单元和微卫星。

结果

使用-mer方法，估计的平均单倍体基因组大小为2.17 Gbp。重复元件占核基因组的69.02%。相应地，基因组的30.98%代表低拷贝或单拷贝序列。相当一部分重复序列无法归类到已知的重复元件家族。仅考虑注释的重复元件，最常见的属于I类-LINE，其明显比I类-LTR-Ty-3/Gypsy、I类-LTR-Penelope和I类-LTR-Ty-3/Bel-Pao元件更丰富。卫星DNA也很丰富。的核糖体操纵子依次包括一个5' ETS（长度=707 bp）、ssrDNA（1,875 bp）、ITS1（736 bp）、5.8S rDNA（162 bp）、ITS2（1,314 bp）、lsrDNA（5,387 bp）和3' ETS（287 bp）。共鉴定出1,281个微卫星。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3eed/7750000/2cdb364fbeca/peerj-08-10554-g003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3eed/7750000/d74d5ac549b4/peerj-08-10554-g001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3eed/7750000/6ce7d962d7ea/peerj-08-10554-g002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3eed/7750000/2cdb364fbeca/peerj-08-10554-g003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3eed/7750000/d74d5ac549b4/peerj-08-10554-g001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3eed/7750000/6ce7d962d7ea/peerj-08-10554-g002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3eed/7750000/2cdb364fbeca/peerj-08-10554-g003.jpg

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