MSDB: A Comprehensive Database of Simple Sequence Repeats

Avvaru, Akshay Kumar; Saxena, Saketh; Sowpati, Divya Tej; Mishra, Rakesh

doi:10.1093/gbe/evx132

Cited by 24 publications

(17 citation statements)

References 16 publications

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“…Based on the SSR-enriched library, we obtained an average of 1,225,072 SSRs in the four pig breeds, which is less than the number of SSRs in the MicroSatellite DataBase (MSDB) [ 54 ]. In addition, Hexa- and Tetra-SSR were the most abundant types in the MSDB (56%) and another previous study (31.3%) [ 18 ], respectively.…”

Section: Discussionmentioning

confidence: 99%

Genome-Wide Characterization and Comparative Analyses of Simple Sequence Repeats among Four Miniature Pig Breeds

Wang

et al. 2020

Animals

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Simple sequence repeats (SSRs) are commonly used as molecular markers in research on genetic diversity and discrimination among taxa or breeds because polymorphisms in these regions contribute to gene function and phenotypically important traits. In this study, we investigated genome-wide characteristics, repeat units, and polymorphisms of SSRs using sequencing data from SSR-enriched libraries created from Wuzhishan (WZS), Bama (BM), inbred Luchuan (LC) and Zangxiang (ZX) miniature pig breeds. The numbers and types of SSRs, distributions of repeat units and polymorphic SSRs varied among the four breeds. Compared to the Duroc pig reference genome, 2518 polymorphic SSRs were unique and common to all four breeds and functional annotation revealed that they may affect the coding and regulatory regions of genes. Several examples, such as FGF23, MYF6, IGF1R, and LEPROT, are associated with growth and development in pigs. Three of the polymorphic SSRs were selected to confirm the polymorphism and the corresponding alleles through fluorescence polymerase chain reaction (PCR) and capillary electrophoresis. Together, this study provides useful insights into the discovery, characteristics and distribution of SSRs in four pig breeds. The polymorphic SSRs, especially those common and unique to all four pig breeds, might affect associated genes and play important roles in growth and development.

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Section: Discussionmentioning

confidence: 99%

Genome-Wide Characterization and Comparative Analyses of Simple Sequence Repeats among Four Miniature Pig Breeds

Wang

et al. 2020

Animals

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“…: “FBIS: A regional DNA barcode archival and analysis system for Indian fishes” introduced by [ 109 ], “FMiR: A Curated Resource of Mitochondrial DNA Information for Fish” introduced by [ 110 ], “FishMicrosat: a microsatellite database of commercially important fishes and shellfishes of the Indian subcontinent” by [ 111 ]. Microsatellites of 31 fish species not confined to India are available in the microsatellite database MSDB [ 112 ]. The particularly important tool “Fish Karyome” is now available in its upgraded version [ 113 ].…”

Section: Fish Cytogenetics and Cytogenomics In The Era Of Digitalimentioning

confidence: 99%

Vertebrate Genome Evolution in the Light of Fish Cytogenomics and rDNAomics

Symonová

Howell

2018

Genes

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To understand the cytogenomic evolution of vertebrates, we must first unravel the complex genomes of fishes, which were the first vertebrates to evolve and were ancestors to all other vertebrates. We must not forget the immense time span during which the fish genomes had to evolve. Fish cytogenomics is endowed with unique features which offer irreplaceable insights into the evolution of the vertebrate genome. Due to the general DNA base compositional homogeneity of fish genomes, fish cytogenomics is largely based on mapping DNA repeats that still represent serious obstacles in genome sequencing and assembling, even in model species. Localization of repeats on chromosomes of hundreds of fish species and populations originating from diversified environments have revealed the biological importance of this genomic fraction. Ribosomal genes (rDNA) belong to the most informative repeats and in fish, they are subject to a more relaxed regulation than in higher vertebrates. This can result in formation of a literal ‘rDNAome’ consisting of more than 20,000 copies with their high proportion employed in extra-coding functions. Because rDNA has high rates of transcription and recombination, it contributes to genome diversification and can form reproductive barrier. Our overall knowledge of fish cytogenomics grows rapidly by a continuously increasing number of fish genomes sequenced and by use of novel sequencing methods improving genome assembly. The recently revealed exceptional compositional heterogeneity in an ancient fish lineage (gars) sheds new light on the compositional genome evolution in vertebrates generally. We highlight the power of synergy of cytogenetics and genomics in fish cytogenomics, its potential to understand the complexity of genome evolution in vertebrates, which is also linked to clinical applications and the chromosomal backgrounds of speciation. We also summarize the current knowledge on fish cytogenomics and outline its main future avenues.

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“…Perfect SSRs >= 12nt in length were identified from sequences of all downloaded genomes using a Python-based exhaustive algorithm, PERF . The 5356 possible permutations of 1-6nt long DNA motifs were grouped into 501 unique classes of SSRs based on the cyclical variations and strand of the motif sequence, as described previously (Avvaru, Saxena, et al 2017). A repeat class motif represents all the motifs which are cyclical variations of itself and of its reverse complement (Additional File 4).…”

Section: Identification Of Ssrsmentioning

confidence: 99%

Patterns of microsatellite distribution reflect the evolution of biological complexity

Surabhi

Avvaru

Sowpati

et al. 2018

Preprint

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Microsatellites, also known as Simple Sequence Repeats (SSRs), are evolutionarily conserved repeat elements distributed non-randomly in all genomes. Many studies have investigated their pattern of occurrence in order to understand their role, but their identification has largely been nonexhaustive and limited to a few related species or model organisms. Here, we identify ~685 million microsatellites from 719 eukaryotes and analyze their evolutionary trends from protists to mammals. We document novel patterns uniquely demarcating closely related species, including in pathogens like Leishmania as well as in higher organisms such as Drosophila, birds, primates, and cereal crops. The distribution of SSRs in coding and non-coding regions reveals taxon-specific variations in their exonic, intronic and intergenic densities. We also show that specific SSRs accumulate at longer lengths in higher organisms indicating an evolutionary selection pressure. In general, we observe greater constraints in the SSR composition of multicellular organisms with complex cell types, while simpler organisms show more diversity. The conserved microsatellite trends and species-specific signatures identified in this study closely mirror phylogenetic relationships and we hypothesize that SSRs are integral components in speciation and the evolution of organismal complexity. The microsatellite dataset generated in this work provides a large number of candidates for functional analysis and unparalleled scope for understanding their roles across the evolutionary landscape.peer-reviewed)

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MSDB: A Comprehensive Database of Simple Sequence Repeats

Cited by 24 publications

References 16 publications

Genome-Wide Characterization and Comparative Analyses of Simple Sequence Repeats among Four Miniature Pig Breeds

Genome-Wide Characterization and Comparative Analyses of Simple Sequence Repeats among Four Miniature Pig Breeds

Vertebrate Genome Evolution in the Light of Fish Cytogenomics and rDNAomics

Patterns of microsatellite distribution reflect the evolution of biological complexity

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