Characterization of Microsatellite Distribution in Siamese Fighting Fish Genome to Promote Conservation and Genetic Diversity

Abstract

The Siamese fighting fish (Betta splendens) is a well-known ornamental fish and emerging model species for studying animal morphology, physiology, and behavior. A key concern of betta inbreeding is the decline in genetic diversity resulting from commercial breeding programs. Therefore, it is essential to develop markers for understanding the genetic bases of the domestication and phenotypic diversification of this species. We utilized the previously assembled genome of Siamese fighting fish to identify and characterize microsatellites and compare their genomic organization across different species. We annotated 812,134 microsatellite loci spanning 30.70 Mb, accounting for 6.57% of the Siamese fighting fish genome. We performed in silico polymorphism screening of microsatellites in the Siamese fighting fish and related species and present these sequences as candidate markers for cross-species amplification. In addition, we successfully validated two microsatellite loci using PCR-based assays in different species, which can promote further genetic characterization of diverse betta lineages. The set of polymorphic markers identified in this study may facilitate the assessment of genetic diversity and population structure and marker-assisted selection, among other applications.

Genome-wide in silico characterization, validation, and cross-species transferability of microsatellite markers in Mallard and Muscovy ducks

“…Among the detected microsatellite loci in both Muscovy and Mallard genomes, the dinucleotide repeats were the most abundant (as shown in Tables 2 and 3); this is in agreement with that reported for most vertebrates [27][28][29]. The reductions in microsatellite abundance with increasing the length of repeats were previously documented [28,30,31].…”

In Silico Chromosome Mapping of the Male-Specific/Linked Loci in the Jade Perch (Scortum barcoo) Suggests Chromosome 19 as the Putative Y Sex Chromosome

“…Similar distribution of microsatellite repeats, identified by molecular cytogenetics, genome informatics, and chromosomics on sex chromosomes, has been reported in many vertebrates, suggesting the possible role of microsatellite repeats in sex chromosome differentiation and evolution [20,59,61,[64][65][66]. A high microsatellite distribution was identified around the SDR and its neighboring regions, which might expand the segment of differentiation on the sex chromosomes [51,67]. Eleven novel repetitive element types were observed in MLR2, of which one type was randomly distributed in other chromosomes with low copy numbers.…”

“…Microsatellites in the jade perch genome were identified using Krait version 1.3.3 [50] with default scanning parameters for perfect, imperfect, and compound microsatellites to examine the association between high density of microsatellite distribution and potential SDR [51,52]. The imperfect microsatellite selection criteria were as follows: (i) minimum sequence length and sequence repeat number were set to 8 bp and 3 times, (ii) maximum consecutive edits (including substitutions and indels) were specified as 3 bp, and (iii) the penalty cost was set to 1 for mismatch and 2 for indels (gaps), and the minimum required score to identify imperfect microsatellites was set to 10.…”

Should the Identification Guidelines for Siamese Crocodiles Be Revised? Differing Post-Occipital Scute Scale Numbers Show Phenotypic Variation Does Not Result from Hybridization with Saltwater Crocodiles

“…According to genetic diversity parameters and the STRUCTURE plot, great genetic diversity and large gene pools of both species likely remain in the population, while both species are very closely related lineages [ 15 ]. The two species may share some alleles of microsatellite repeats at the same genomic locus, which is often observed in many closely related species in vertebrates [ 61 , 62 ]. We, therefore, proposed criteria to screen hybrid crocodiles between Siamese and saltwater crocodiles as follows: ( i ) Consideration of genetic admixture at different K levels to examine the trend of clustering, separation of allelic signals and the majority of allelic pattern, although the best K level might be predicted from different algorithms; ( ii ) sharing a gene pool between the two species might be possible, but should not have more than a posterior probability of 0.05 at the K level, which shows the trend of separation between the two species; ( iii ) clustering by PCoA should be considered together with the STRUCTURE plot to test the group of crocodile specimens; ( iv ) determination of maternal lineage by mtDNA D-loop sequences may be added to confirm; and ( v ) external morphological observation with updated phenotypic variations in the P.O.…”