Genome Survey Sequencing of an Iconic ‘Trophy’ Sportfish, the Roosterfish <i>Nematistius pectoralis</i>: Genome Size, Repetitive Elements, Nuclear RNA Gene Operon, and Microsatellite Discovery
The ‘Pez Gallo’ or the Roosterfish, <i>Nematistius pectoralis</i>, is an ecologically relevant species in the shallow water soft-bottom environments and a target of a most lucrative recreational sport fishery in the Central Eastern Pacific Ocean. According to the International Union for...
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oai:doaj.org-article:06bc048bc7a6467e9c8ffe66441c78162021-11-25T17:41:08ZGenome Survey Sequencing of an Iconic ‘Trophy’ Sportfish, the Roosterfish <i>Nematistius pectoralis</i>: Genome Size, Repetitive Elements, Nuclear RNA Gene Operon, and Microsatellite Discovery10.3390/genes121117102073-4425https://doaj.org/article/06bc048bc7a6467e9c8ffe66441c78162021-10-01T00:00:00Zhttps://www.mdpi.com/2073-4425/12/11/1710https://doaj.org/toc/2073-4425The ‘Pez Gallo’ or the Roosterfish, <i>Nematistius pectoralis</i>, is an ecologically relevant species in the shallow water soft-bottom environments and a target of a most lucrative recreational sport fishery in the Central Eastern Pacific Ocean. According to the International Union for Conservation of Nature, <i>N. pectoralis</i> is assessed globally as Data Deficient. Using low-coverage short Illumina 300 bp pair-end reads sequencing, this study reports, for the first time, the genome size, single/low-copy genome content, and nuclear repetitive elements, including the 45S rRNA DNA operon and microsatellites, in <i>N. pectoralis</i>. The haploid genome size estimated using a <i>k</i>-mer approach was 816.04 Mbp, which is within the range previously reported for other representatives of the Carangiformes order. Single/low-copy genome content (63%) was relatively high. A large portion of repetitive sequences could not be assigned to the known repeat element families. Considering only annotated repetitive elements, the most common were classified as Satellite DNA which were considerably more abundant than Class I-Long Interspersed Nuclear Elements and Class I-LTR Retroviral elements. The nuclear ribosomal operon in <i>N. pectoralis</i> consists of, in the following order: a 5′ ETS (length = 948 bp), ssrDNA (1835 bp), ITS1 (724 bp), a 5.8S rDNA (158 bp), ITS2 (508 bp), lsrDNA (3924 bp), and a 3′ ETS (32 bp). A total of 44 SSRs were identified. These newly developed genomic resources are most relevant for improving the understanding of biology, developing conservation plans, and managing the fishery of the iconic <i>N. pectoralis</i>.J. Antonio BaezaJosé Luis Molina-QuirósSebastián Hernández-MuñozMDPI AGarticlegenome skimminglow-pass genome sequencinggenomic resourcesGeneticsQH426-470ENGenes, Vol 12, Iss 1710, p 1710 (2021) |
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genome skimming low-pass genome sequencing genomic resources Genetics QH426-470 |
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genome skimming low-pass genome sequencing genomic resources Genetics QH426-470 J. Antonio Baeza José Luis Molina-Quirós Sebastián Hernández-Muñoz Genome Survey Sequencing of an Iconic ‘Trophy’ Sportfish, the Roosterfish <i>Nematistius pectoralis</i>: Genome Size, Repetitive Elements, Nuclear RNA Gene Operon, and Microsatellite Discovery |
| description |
The ‘Pez Gallo’ or the Roosterfish, <i>Nematistius pectoralis</i>, is an ecologically relevant species in the shallow water soft-bottom environments and a target of a most lucrative recreational sport fishery in the Central Eastern Pacific Ocean. According to the International Union for Conservation of Nature, <i>N. pectoralis</i> is assessed globally as Data Deficient. Using low-coverage short Illumina 300 bp pair-end reads sequencing, this study reports, for the first time, the genome size, single/low-copy genome content, and nuclear repetitive elements, including the 45S rRNA DNA operon and microsatellites, in <i>N. pectoralis</i>. The haploid genome size estimated using a <i>k</i>-mer approach was 816.04 Mbp, which is within the range previously reported for other representatives of the Carangiformes order. Single/low-copy genome content (63%) was relatively high. A large portion of repetitive sequences could not be assigned to the known repeat element families. Considering only annotated repetitive elements, the most common were classified as Satellite DNA which were considerably more abundant than Class I-Long Interspersed Nuclear Elements and Class I-LTR Retroviral elements. The nuclear ribosomal operon in <i>N. pectoralis</i> consists of, in the following order: a 5′ ETS (length = 948 bp), ssrDNA (1835 bp), ITS1 (724 bp), a 5.8S rDNA (158 bp), ITS2 (508 bp), lsrDNA (3924 bp), and a 3′ ETS (32 bp). A total of 44 SSRs were identified. These newly developed genomic resources are most relevant for improving the understanding of biology, developing conservation plans, and managing the fishery of the iconic <i>N. pectoralis</i>. |
| format |
article |
| author |
J. Antonio Baeza José Luis Molina-Quirós Sebastián Hernández-Muñoz |
| author_facet |
J. Antonio Baeza José Luis Molina-Quirós Sebastián Hernández-Muñoz |
| author_sort |
J. Antonio Baeza |
| title |
Genome Survey Sequencing of an Iconic ‘Trophy’ Sportfish, the Roosterfish <i>Nematistius pectoralis</i>: Genome Size, Repetitive Elements, Nuclear RNA Gene Operon, and Microsatellite Discovery |
| title_short |
Genome Survey Sequencing of an Iconic ‘Trophy’ Sportfish, the Roosterfish <i>Nematistius pectoralis</i>: Genome Size, Repetitive Elements, Nuclear RNA Gene Operon, and Microsatellite Discovery |
| title_full |
Genome Survey Sequencing of an Iconic ‘Trophy’ Sportfish, the Roosterfish <i>Nematistius pectoralis</i>: Genome Size, Repetitive Elements, Nuclear RNA Gene Operon, and Microsatellite Discovery |
| title_fullStr |
Genome Survey Sequencing of an Iconic ‘Trophy’ Sportfish, the Roosterfish <i>Nematistius pectoralis</i>: Genome Size, Repetitive Elements, Nuclear RNA Gene Operon, and Microsatellite Discovery |
| title_full_unstemmed |
Genome Survey Sequencing of an Iconic ‘Trophy’ Sportfish, the Roosterfish <i>Nematistius pectoralis</i>: Genome Size, Repetitive Elements, Nuclear RNA Gene Operon, and Microsatellite Discovery |
| title_sort |
genome survey sequencing of an iconic ‘trophy’ sportfish, the roosterfish <i>nematistius pectoralis</i>: genome size, repetitive elements, nuclear rna gene operon, and microsatellite discovery |
| publisher |
MDPI AG |
| publishDate |
2021 |
| url |
https://doaj.org/article/06bc048bc7a6467e9c8ffe66441c7816 |
| work_keys_str_mv |
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