Genome-wide characterization and analysis of microsatellite sequences in camelid species

Manee, Manee M.; Algarni, Abdulmalek T.; Alharbi, Sultan N.; Al-Shomrani, Badr M.; Ibrahim, Mohanad A.; Binghadir, Sarah A.; Al-Fageeh, Mohamed B.

doi:10.1007/s13364-019-00458-x

Cited by 8 publications

(15 citation statements)

References 67 publications

(105 reference statements)

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“…Tri-and tetranucleotide SSR types were found to have very similar frequencies in the five palm genomes. Hexanucleotide repeats were the least frequent SSR type in all five species, which is similar to what has been seen in previous studies (Subramanian et al 2002;Liu et al 2017;Manee et al 2019).…”

Section: Discussionsupporting

confidence: 91%

Genome-wide characterization of simple sequence repeats in Palmae genomes

2020

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Background Microsatellites or simple sequence repeats (SSRs) have become the most significant DNA marker technology used in genetic research. The availability of complete draft genomes for a number of Palmae species has made it possible to perform genome-wide analysis of SSRs in these species. Palm trees are tropical and subtropical plants with agricultural and economic importance due to the nutritional value of their fruit cultivars. Objective This is the first comprehensive study examining and comparing microsatellites in completely-sequenced draft genomes of Palmae species. Methods We identified and compared perfect SSRs with 1-6 bp nucleotide motifs to characterize microsatellites in Palmae species using PERF v0.2.5. We analyzed their relative abundance, relative density, and GC content in five palm species:

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Section: Discussionsupporting

confidence: 91%

Genome-wide characterization of simple sequence repeats in Palmae genomes

2020

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“…A possible mechanistic explanation for these taxon-specific signatures in primates and rodents is that SSRs could evolve differently among different lineages. There is a general consensus that the presence of SSRs in the genomes of organisms is biased toward certain specific repeat motifs in different clades (Alam et al, 2019;Manee et al, 2020;Qi et al, 2020). In this study, an enrichment trend of P-SSR density for certain motif types was observed among the five taxonomic orders (Figure 3), which was similar to the findings of a previous study (Srivastava et al, 2019).…”

Section: Taxon-specific Features Of P-ssrs In Euarchontoglires Genomessupporting

confidence: 89%

Comparison of the Microsatellite Distribution Patterns in the Genomes of Euarchontoglires at the Taxonomic Level

et al. 2021

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Microsatellite or simple sequence repeat (SSR) instability within genes can induce genetic variation. The SSR signatures remain largely unknown in different clades within Euarchontoglires, one of the most successful mammalian radiations. Here, we conducted a genome-wide characterization of microsatellite distribution patterns at different taxonomic levels in 153 Euarchontoglires genomes. Our results showed that the abundance and density of the SSRs were significantly positively correlated with primate genome size, but no significant relationship with the genome size of rodents was found. Furthermore, a higher level of complexity for perfect SSR (P-SSR) attributes was observed in rodents than in primates. The most frequent type of P-SSR was the mononucleotide P-SSR in the genomes of primates, tree shrews, and colugos, while mononucleotide or dinucleotide motif types were dominant in the genomes of rodents and lagomorphs. Furthermore, (A)n was the most abundant motif in primate genomes, but (A)n, (AC)n, or (AG)n was the most abundant motif in rodent genomes which even varied within the same genus. The GC content and the repeat copy numbers of P-SSRs varied in different species when compared at different taxonomic levels, reflecting underlying differences in SSR mutation processes. Notably, the CDSs containing P-SSRs were categorized by functions and pathways using Gene Ontology and Kyoto Encyclopedia of Genes and Genomes annotations, highlighting their roles in transcription regulation. Generally, this work will aid future studies of the functional roles of the taxonomic features of microsatellites during the evolution of mammals in Euarchontoglires.

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“…AC was the most abundant repeat categories in dinucleotides and CG was the least one, which are consistent with the cases in most vertebrates reported by Jiang et al 11 and in other eukaryotes. 40 AAT was the predominant trinucleotides type, which is similar to the situation in human, 41 camelid, 42 and many teleost fishes. 8,11 Interestingly, the higher proportions of penta-nucleotide than tri-and tetranucleotide motifs are consistent with the result characterized by using RAD sequencing, 25 but different from those reported by Li et al, 26 and the proportions of each repeat motifs of tri-, tetra-, penta-, and hexanucleotide repeats are different from those reported in two recent works about swamp eel.…”

Section: Discussionsupporting

confidence: 70%

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

Tian

Zhong

2021

Science Progress

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Objectives: Swamp eel is one model species for sexual reversion and an aquaculture fish in China. One local strain with deep yellow and big spots of Monopterus albus has been selected for consecutive selective breeding. The objectives of this study were characterizing the Simple Sequence Repeats (SSRs) of M. albus in the assembled genome obtained recently, and developing polymorphic SSRs for future breeding programs. Methods: The genome wide SSRs were mined by using MISA software, and their types and genomic distribution patterns were investigated. Based on the available flanking sequences, primer pairs were batched developed, and Polymorphic SSRs were identified by using Polymorphic SSR Retrieval tool. The obtained polymorphic SSRs were validated by using e-PCR and capillary electrophoresis, then they were used to investigate genetic diversity of one breeding population. Results: A total of 364,802 SSRs were identified in assembled M. albus genome. The total length, density and frequency of SSRs were 8,204,641 bp, 10,259 bp/Mb, and 456.16 loci/Mb, respectively. Mononucleotide repeats were predominant among SSRs (33.33%), and AC and AAT repeats were the most abundant di- and tri-nucleotide repeats motifs. A total of 287,189 primer pairs were designed, and a high-density physical map was constructed (359.11 markers per Mb). A total of 871 polymorphic SSRs were identified, and 38 SSRs of 101 randomly selected ones were validated by using e-PCR and capillary electrophoresis. Using these 38 polymorphic SSRs, 201 alleles were detected and genetic diversity level (Na, PIC, HO, and He) was evaluated. Conclusions: The genome-wide SSRs and newly developed SSR markers will provide a useful tool for genetic mapping, diversity analysis studies in swamp eel in the future. The high level of genetic diversity (Na = 5.29, PIC = 0.5068, HO = 0.4665, He = 0.5525) but excess of homozygotes ( FIS = 0.155) in one breeding population provide baseline information for future breeding program.

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Genome-wide characterization and analysis of microsatellite sequences in camelid species

Cited by 8 publications

References 67 publications

Genome-wide characterization of simple sequence repeats in Palmae genomes

Genome-wide characterization of simple sequence repeats in Palmae genomes

Comparison of the Microsatellite Distribution Patterns in the Genomes of Euarchontoglires at the Taxonomic Level

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

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