Dataset Information

Genome Survey Sequencing of an Iconic 'Trophy' Sportfish, the Roosterfish Nematistius pectoralis: Genome Size, Repetitive Elements, Nuclear RNA Gene Operon, and Microsatellite Discovery.

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.

SUBMITTER: Baeza JA

PROVIDER: S-EPMC8620147 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:BackgroundIdentification and mapping of repetitive elements is a key step for accurate gene prediction and overall structural annotation of genomes. During the assembly and annotation of three highly repetitive amoeba genomes, Entamoeba histolytica, Entamoeba dispar, and Entamoeba invadens, we performed comparative sequence analysis to identify and map all class I and class II transposable elements in their sequences.ResultsHere, we report the identification of two novel Entamoeba-specific repeats: ERE1 and ERE2; ERE1 is spread across the three genomes and associated with different repeats in a species-specific manner, while ERE2 is unique to E. histolytica. We also report the identification of two novel subfamilies of LINE and SINE retrotransposons in E. dispar and provide evidence for how the different LINE and SINE subfamilies evolved in these species. Additionally, we found a putative transposase-coding gene in E. histolytica and E. dispar related to the mariner transposon Hydargos from E. invadens. The distribution of transposable elements in these genomes is markedly skewed with a tendency of forming clusters. More than 70% of the three genomes have a repeat density below their corresponding average value indicating that transposable elements are not evenly distributed. We show that repeats and repeat-clusters are found at syntenic break points between E. histolytica and E. dispar and hence, could work as recombination hot spots promoting genome rearrangements.ConclusionThe mapping of all transposable elements found in these parasites shows that repeat coverage is up to three times higher than previously reported. LINE, ERE1 and mariner elements were present in the common ancestor to the three Entamoeba species while ERE2 was likely acquired by E. histolytica after its separation from E. dispar. We demonstrate that E. histolytica and E. dispar share their entire repertoire of LINE and SINE retrotransposons and that Eh_SINE3/Ed_SINE1 originated as a chimeric SINE from Eh/Ed_SINE2 and Eh_SINE1/Ed_SINE3. Our work shows that transposable elements are organized in clusters, frequently found at syntenic break points providing insights into their contribution to chromosome instability and therefore, to genomic variation and speciation in these parasites.

Project description:Although rarely considered predators, wildlife hunters can function as important ecological and evolutionary agents. In part, their influence relates to targeting of large reproductive adults within prey populations. Despite known impacts of size-selective harvests, however, we know little about what enables hunters to kill these older, rarer, and presumably more wary individuals. In other mammalian predators, predatory performance varies with knowledge and physical condition, which accumulates and declines, respectively, with age. Moreover, some species evolved camouflage as a physical trait to aid in predatory performance. In this work, we tested whether knowledge-based faculty (use of a hunting guide with accumulated experience in specific areas), physical traits (relative body mass [RBM] and camouflage clothing), and age can predict predatory performance. We measured performance as do many hunters: size of killed cervid prey, using the number of antler tines as a proxy. Examining ? 4300 online photographs of hunters posing with carcasses, we found that only the presence of guides increased the odds of killing larger prey. Accounting for this effect, modest evidence suggested that unguided hunters presumably handicapped with the highest RBM actually had greater odds of killing large prey. There was no association with hunter age, perhaps because of our coarse measure (presence of grey hair) and the performance trade-offs between knowledge accumulation and physical deterioration with age. Despite its prevalence among sampled hunters (80%), camouflage had no influence on size of killed prey. Should these patterns be representative of other areas and prey, and our interpretations correct, evolutionarily-enlightened harvest management might benefit from regulatory scrutiny on guided hunting. More broadly, we suggest that by being nutritionally and demographically de-coupled from prey and aided by efficient killing technology and road access, wildlife hunters in the developed world might have overcome many of the physical, but not knowledge-based, challenges of hunting.

Dataset Information

Genome Survey Sequencing of an Iconic 'Trophy' Sportfish, the Roosterfish Nematistius pectoralis: Genome Size, Repetitive Elements, Nuclear RNA Gene Operon, and Microsatellite Discovery.

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