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

Near complete genome assembly of Yadong trout (Salmo trutta)

The Yadong trout (Salmo trutta), a species endemic to the Yatung River in Tibet, China, was classified as a second-class protected species in the 20th century. Now, it is considered one of the most important fishery resources in China. In this study, we assembled a near-complete genome of the S. trutta, integrating PacBio HiFi, Hi-C, and ONT sequencing technologies. The genome assembly spans 2.49 Gb, with 96.87% of the sequence anchored onto 40 chromosomes. In this assembly, a total of 12 chromosomes were assembled to a gap-free level, with 8 of them reaching the telomere-to-telomere level. The completeness of this assembly was assessed at 99.50% by BUSCO, containing approximately 63.24% repetitive sequences, and predicted to encode 41,782 protein-coding genes. This is the first near-complete genome assembly of the S. trutta, providing an essential resource for molecular breeding and germplasm conservation of this important species.

Genome-Wide Microsatellites in Acanthopagrus latus: Development, Distribution, Characterization, and Polymorphism

The yellowfin seabream (Acanthopagrus latus) is an economically important commercial mariculture fish in China and Southeast Asia. Only a few simple sequence repeats (SSRs) of A. latus have been isolated and reported, which has hindered breeding progress. A total of 318,862 SSRs were isolated and characterized from the A. latus genome in this study. All SSRs were 9,069,670 bp in length, accounting for 1.32% of the genome. The density and frequency of SSRs were 468.40 loci/Mb and 13,323.19 bp/Mb, respectively. The major SSRs were dinucleotides (accounting for 76.92%), followed by trinucleotides (15.75%). The most abundant SSR motif was (AC)n (168,390, accounting for 53%), with the highest frequency (245.78 loci/Mb) and density (7304.18 bp/Mb). Most SSRs were located in non-coding regions, such as intergenic regions (34.54%) and introns (56.91%). SSR-containing exons were distributed into 51 gene ontology (GO) terms and significantly enriched in immunity- and growth-related pathways. A total of 217,791 SSR markers were successfully designed. Nine SSR markers were amplified in 29 A. latus individuals, and eight of them possess high polymorphism. The cross-species transferability of 33 out of the 37 tested loci were successfully amplified in Acanthopagrus schlegelii. These results lay the foundation for the molecular marker-assisted breeding and genetic information assessment of A. latus.

Chromosome-Level Genome Assembly and Genetic Maker System of the Endangered Largemouth Bronze Gudgeon (Coreius guichenoti) with Focus on Conservation Applications

The largemouth bronze gudgeon (Coreius guichenoti), an endemic fish species, is distributed in the upper Yangtze River drainage. Due to anthropogenetic factors such as water pollution, overfishing, and dam construction, the wild populations of C. guichenoti have dramatically declined in recent decades. In this study, we generated a reference chromosomal-level genome assembly of C. guichenoti on the basis of PacBio HiFi sequencing and Hi-C scaffolding technologies. The final genome assembly was 1.10 Gb in length (contig N50: 28.64 Mb; scaffold N50: 42.39 Mb) with 25 chromosomes. The completeness score of the C. guichenoti genome was 96.4%, and high synteny was detected compared with Danio rerio and Ictalurus punctatus genomes. A total of 24 325 PCGs were annotated for the C. guichenoti genome. Comparative genomics analysis identified 986 expanded gene families in C. guichenoti, which were significantly enriched in GO items associated with the development and interaction of sperm and egg as well as immunity. Furthermore, positively selected genes (PSGs) detected in C. guichenoti were mainly associated with DNA repair, ATP binding, mitochondrion, and lipid homeostasis. Based on the reference genome and resequencing data, the polymorphic microsatellite (SSR) loci were comprehensively analyzed for C. guichenoti, and the top 15 tetra-nucleotide SSR loci were selected for the construction of the genetic maker system after validation through PCR and genotyping. All of these 15 tetra-nucleotide SSR loci without Hardy-Weinberg equilibrium (HWE) deviation showed high polymorphism, good amplification stability, and selective neutrality. The PID (sibs) curves revealed that the subset of four tetra-nucleotide SSR loci (cgui1, cgui5, cgui3, cgui13) was sufficient for accurate identification of C. guichenoti individuals (PIDsib < 0.01). These 15 tetra-nucleotide SSR loci could also serve as genetic markers in subsequent parentage identification and genetic diversity analysis. The chromosome-level genome assembly and findings laid solid foundations for molecular breeding, genomic research, and biological conservation of C. guichenoti.

Genome-wide identification of SSR markers from coding regions for endangered Argania spinosa L. skeels and construction of SSR database: AsSSRdb

Microsatellites [simple sequence repeats (SSRs)] are one of the most widely used sources of genetic markers, particularly prevalent in plants. Despite their importance in various applications, a comprehensive genome-wide identification of coding sequence (CDS)-associated SSR markers in the Argania spinosa L. genome has yet to be conducted. In this study, 66 280 CDSs containing 5351 SSRs within 4535 A. spinosa L. CDSs were identified. Among these, tri-nucleotide motifs (58.96%) were the most common, followed by hexa-nucleotide (15.71%) and di-nucleotide motifs (13.32%). The predominant SSR motif in the tri-nucleotide category was AAG (24.4%), while AG (94.1%) was the most abundant among di-nucleotide repeats. Furthermore, the extracted CDSs containing SSRs were subjected to functional annotation; 3396 CDSs (74.88%) exhibited homology with known proteins, 3341 CDSs (73.7%) were assigned Gene Ontology terms, 1004 CDSs were annotated with Enzyme Commission numbers, and 832 (18.3%) were annotated with KEGG pathways. A total of 3475 primer pairs were designed, out of which 3264 were successfully validated in silico against the A. spinosa L. genome, with 99.6% representing high-resolution markers yielding no more than three products. Additionally, the SSR markers demonstrated a low rate of transferability through in-silico verification in two species within the Sapotaceae family. Furthermore, we developed an online database, the "Argania spinosa L. SSR database: https://as-fmmdb.shinyapps.io/asssrdb/" (AsSSRdb) to provide access to the CDS-associated SSRs identified in this study. Overall, this research provides valuable marker resources for DNA fingerprinting, genetic studies, and molecular breeding in argan and related species. Database URL: https://as-fmmdb.shinyapps.io/asssrdb/.

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.