Abstract
The ‘Pez Gallo’ or the Roosterfish, Nematistius pectoralis, 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, N. pectoralis 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 N. pectoralis. The haploid genome size estimated using a k-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 N. pectoralis 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 N. pectoralis.
Highlights
IntroductionOne of the most speciose chordate clades, the marine and freshwater bony fishes (superclass Pisces; class Actinopterygii) [1], exhibit remarkable disparity in terms of morphology, physiology, behavior, and ecology [2]
Among vertebrates, one of the most speciose chordate clades, the marine and freshwater bony fishes [1], exhibit remarkable disparity in terms of morphology, physiology, behavior, and ecology [2]
Genome size varies moderately in fish belonging to the Carangiformes order sensu [8], from 0.39 Gbp in Pleuronectes platessus
Summary
One of the most speciose chordate clades, the marine and freshwater bony fishes (superclass Pisces; class Actinopterygii) [1], exhibit remarkable disparity in terms of morphology, physiology, behavior, and ecology [2]. The ‘Pez Gallo’ or the Roosterfish, Nematistius pectoralis Gill, 1862, is an ecologically relevant species in shallow (0–20 m) soft-bottom marine and estuarine environments [3,4,5,6] and a target of a lucrative sport fishery in the Central Eastern Pacific Ocean [3,7]. Sepmeecnifitcaanlldy, cuosninsgeravlaotwio-cno.verage short-read next-generation sequencing apprToahcihs,sthtuisdsytufdoyr,mfosr athpe afirrtstotfimaeb: reostaidmaetfefdorttheainmuceldeaartgdeneovmeleospizine,gesgteimnoatmedicsirnegsloeu- rces in Nco. ppyecatnordalloiswa-ncodpoytnhuemr bsperegceiense tgaerngoemteedcobnytetnhte, dsipscoorvtfeirsehdi,nagnninodtautesdtr, yanidn cthhaeraCcetenrtirzaedl Eastern PnauccifleicarOrecpeaetnit.ivSepeecleifmiceanltlsy,,aunsdinagssaemlobwle-dcoavnderaangneosthatoerdt-trheead45nSerxRtN-gAenDeNraAtioonpesreoqnu. Encing approach, this study, for the first time: estimated the nuclear genome size, estimated single-copy and low-copy number gene genome content, discovered, annotated, and characterized nuclear repetitive elements, and assembled and annotated the 45S rRNA DNA operon. A set of microsatellites or short sequence repeats (SSRs) was discovered.
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