Cargando…

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

BACKGROUND: Panulirus argus 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, includ...

Descripción completa

Detalles Bibliográficos
Autor principal: Baeza, J. Antonio
Formato: Online Artículo Texto
Lenguaje:English
Publicado: PeerJ Inc. 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7750000/
https://www.ncbi.nlm.nih.gov/pubmed/33362980
http://dx.doi.org/10.7717/peerj.10554
_version_ 1783625402432880640
author Baeza, J. Antonio
author_facet Baeza, J. Antonio
author_sort Baeza, J. Antonio
collection PubMed
description BACKGROUND: Panulirus argus 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 P. argus. RESULTS: Using a k-mer approach, the average haploid genome size estimated for P. argus 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 P. argus 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.
format Online
Article
Text
id pubmed-7750000
institution National Center for Biotechnology Information
language English
publishDate 2020
publisher PeerJ Inc.
record_format MEDLINE/PubMed
spelling pubmed-77500002020-12-24 Genome survey sequencing of the Caribbean spiny lobster Panulirus argus: Genome size, nuclear rRNA operon, repetitive elements, and microsatellite discovery Baeza, J. Antonio PeerJ Genetics BACKGROUND: Panulirus argus 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 P. argus. RESULTS: Using a k-mer approach, the average haploid genome size estimated for P. argus 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 P. argus 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. PeerJ Inc. 2020-12-17 /pmc/articles/PMC7750000/ /pubmed/33362980 http://dx.doi.org/10.7717/peerj.10554 Text en © 2020 Baeza https://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ) and either DOI or URL of the article must be cited.
spellingShingle Genetics
Baeza, J. Antonio
Genome survey sequencing of the Caribbean spiny lobster Panulirus argus: Genome size, nuclear rRNA operon, repetitive elements, and microsatellite discovery
title Genome survey sequencing of the Caribbean spiny lobster Panulirus argus: Genome size, nuclear rRNA operon, repetitive elements, and microsatellite discovery
title_full Genome survey sequencing of the Caribbean spiny lobster Panulirus argus: Genome size, nuclear rRNA operon, repetitive elements, and microsatellite discovery
title_fullStr Genome survey sequencing of the Caribbean spiny lobster Panulirus argus: Genome size, nuclear rRNA operon, repetitive elements, and microsatellite discovery
title_full_unstemmed Genome survey sequencing of the Caribbean spiny lobster Panulirus argus: Genome size, nuclear rRNA operon, repetitive elements, and microsatellite discovery
title_short Genome survey sequencing of the Caribbean spiny lobster Panulirus argus: Genome size, nuclear rRNA operon, repetitive elements, and microsatellite discovery
title_sort genome survey sequencing of the caribbean spiny lobster panulirus argus: genome size, nuclear rrna operon, repetitive elements, and microsatellite discovery
topic Genetics
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7750000/
https://www.ncbi.nlm.nih.gov/pubmed/33362980
http://dx.doi.org/10.7717/peerj.10554
work_keys_str_mv AT baezajantonio genomesurveysequencingofthecaribbeanspinylobsterpanulirusargusgenomesizenuclearrrnaoperonrepetitiveelementsandmicrosatellitediscovery