Genome-wide identification of simple sequence repeats and development of polymorphic SSR markers in swamp eel (Monopterus albus)

Microsatellite Genome-Wide Database Development for the Commercial Blackhead Seabream (Acanthopagrus schlegelii)

Simple sequence repeats (SSRs), the markers with the highest polymorphism and co-dominance degrees, offer a crucial genetic research resource. Limited SSR markers in blackhead seabream have been reported. The availability of the blackhead seabream genome assembly provided the opportunity to carry out genome-wide identification for all microsatellite markers, and bioinformatic analyses open the way for developing a microsatellite genome-wide database in blackhead seabream. In this study, a total of 412,381 SSRs were identified in the 688.08 Mb genome by Krait software. Whole-genome sequences (10×) of 42 samples were aligned against the reference genome and genotyped using the HipSTR tools by comparing and counting repeat number variation across the SSR loci. A total of 156,086 SSRs with a 2–4 bp repeat were genotyped by HipSTR tools, which accounted for 55.78% of the 2–4 bp SSRs in the reference genome. High accuracy of genotyping was observed by comparing HipSTR tools and PCR amplification. A set of 109,131 loci with a number of alleles ≥ 3 and with a number of genotyped individuals ≥ 6 were reserved to constitute the polymorphic SSR database. Fifty-one polymorphic SSR loci were identified through PCR amplification. This strategy to develop polymorphic SSR markers not only obtained a large set of polymorphic SSRs but also eliminated the need for laborious experimental screening. SSR markers developed in this study may facilitate blackhead seabream research, which lays a certain foundation for further gene tagging and genetic linkage analysis, such as marker-assisted selection, genetic mapping, as well as comparative genomic analysis.

Identification of novel SSR markers for predicting the geographic origin of fungus Schizophyllum commune Fr

The fungus Schizophyllum commune is a cosmopolitan basidiomycete, which is popular as an edible, medical mushroom. It causes wood rot and often used as a model object in research. In this study, we analyzed thirty-two genomes of S. commune strains from the NCBI database and designed forty-seven unique SSR DNA markers. The detailed analysis revealed the enrichment of the S. commune genome for CG, GC, CTC, GAG, and TCG motifs. Principal components analysis confirmed the effectiveness of novel SSR DNA markers that preserve the initial heterogeneity of populations. The construction of a network between strains showed single one at a maximum similarity of 38%, and increasing the similarity to 55% breaks the linkage between large groups while separating two new groups containing strains of the population Ru and test cultures S. commune. The amplicons' presence was identified as a sufficient sign of relation of the culture to a specific population. Testing the novel SSR markers allowed to establish a clear delimitation of all groups by geographic location and to differentiate the H4-8 (GCA_000143185.1) strain from the USA population. This research is the basis for the further analysis of S. commune populations and improvement of approaches to determine its genetic diversity.

Microsatellite Characteristics of Silver Carp (Hypophthalmichthysmolitrix) Genome and Genetic Diversity Analysis in Four Cultured Populations

Hypophthalmichthys molitrix is one of the four most important fish in China and has high breeding potential. However, simple sequence repeat (SSR) markers developed on H. molitrix genome level for genetic diversity analysis are limited. In this study, the distribution characteristics of SSRs in the assembled H. molitrix genome were analyzed, and new markers were developed to preliminarily evaluate the genetic diversity of the four breeding populations. A total of 368,572 SSRs were identified from the H. molitrix genome. The total length of SSRs was 6,492,076 bp, accounting for 0.77% of the total length of the genome sequence. The total frequency and total density were 437.73 loci/Mb and 7713.16 bp/Mb, respectively. Among the 2–6 different nucleotide repeat types, SSRs were dominated by di-nucleotide repeats (204,873, 55.59%), and AC/GT was the most abundant motif. The number of SSRs on each chromosome was positively correlated with the length. The 13 pairs of markers developed were used to analyze the genetic diversity of four cultivated populations in Hubei Province. The results showed that the genetic diversity of the four populations was low, and the ranges of alleles (Na), effective alleles (Ne), observed heterozygosity (Ho), and Shannon’s index information (I) were 3.538–4.462, 2.045–2.461, 0.392–0.450, and 0.879–0.954, respectively. Genetic variation occurs mainly among individuals within populations (95.35%). UPGMA tree and Bayesian analysis showed that four populations could be divided into two different branches. Therefore, the genome-wide SSRs were effectively in genetic diversity analysis on H. molitrix.

The First Genome Survey and De Novo Assembly of the Short Mackerel (Rastrelliger brachysoma) and Indian Mackerel (Rastrelliger kanagurta)

Simple Summary

Mackerel species are commercially important marine species in Southeast Asia, especially short mackerel and Indian mackerel. However, genomic information about them is still limited. Genome survey of these two mackerel species was reported in this study. Next-generation sequencing and comprehensive bioinformatics were performed to obtain the genetic information. The estimated genome size of both species is around 680 Mbp. The heterozygosity of these species was very similar, while the repeat content for Indian mackerel was slightly higher than for short mackerel. Functional annotation also was reported in this study. This is the first reported genome survey and assembly of species in the genus Rastrelliger and could be useful for future comparative genomic studies.

Abstract

Rastrelliger brachysoma (short mackerel) and Rastrelliger kanagurta (Indian mackerel) are commercially important marine species in Southeast Asia. In recent years, numbers of these two species have been decreasing in the wild, and genomic information about them is still limited. We conducted a genome survey of these two mackerel species to acquire essential genomic information using next-generation sequencing data. To obtain this genetic information, comprehensive bioinformatics analyses were performed, including de novo assembly, gene prediction, functional annotation, and phylogenetic analysis. The estimated genome sizes were around 680.14 Mbp (R. brachysoma) and 688.82 Mbp (R. kanagurta). The heterozygosity of these species was very similar (≈0.81), while the repeat content for R. kanagurta (9.30%) was slightly higher than for R. brachysoma (8.30%). Functional annotation indicated that most of the genes predicted in these two species shared very close average amino acid identities (94.06%). The phylogenetic analysis revealed close phylogenetic relationships between these two species and other scombrids. This is the first reported genome survey and assembly of species in the genus Rastrelliger and could be useful for future comparative genomic studies.