Genome-wide analysis of conservation and divergence of microsatellites in rice

Roorkiwal, Manish; Grover, Atul; Sharma, Prakash C.

doi:10.1007/s00438-009-0457-3

Cited by 12 publications

(11 citation statements)

References 63 publications

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“…In other plant species, the most frequent trinucleotide repeat motifs were AAC/TTG in wheat, AAG/TTC in soybean, and CCG/GGC in barley, rice, maize and sorghum [13, 8, 18]. The previous studies on Arabidopsis and soybean [15] also reported abundance of trinucleotide motif AAG, contrasting to the abundance of CCG motif in cereal species [6].…”

Section: Discussionmentioning

confidence: 99%

Mining functional microsatellites in legume unigenes

Roorkiwal¹,

Sharma²

2011

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Highly polymorphic and transferable microsatellites (SSRs) are important for comparative genomics, genome analysis and phylogenetic studies. Development of novel species-specific microsatellite markers remains a costly and labor-intensive project. Therefore, interest has been shifted from genomic to genic markers owing to their high inter-species transferability as they are developed from conserved coding regions of the genome. This study concentrates on comparative analysis of genic microsatellites in nine important legume (Arachis hypogaea, Cajanus cajan, Cicer arietinum, Glycine max, Lotus japonicus, Medicago truncatula, Phaseolus vulgaris, Pisum sativum and Vigna unguiculata) and two model plant species (Oryza sativa and Arabidopsis thaliana). Screening of a total of 228090 putative unique sequences spanning 219610522 bp using a microsatellite search tool, MISA, identified 12.18% of the unigenes containing 36248 microsatellite motifs excluding mononucleotide repeats. Frequency of legume unigene-derived SSRs was one SSR in every 6.0 kb of analyzed sequences. The trinucleotide repeats were predominant in all the unigenes with the exception of C. cajan, which showed prevalence of dinucleotide repeats over trinucleotide repeats. Dinucleotide repeats along with trinucleotides counted for more than 90% of the total microsatellites. Among dinucleotide and trinucleotide repeats, AG and AAG motifs, respectively, were the most frequent. Microsatellite positive chickpea unigenes were assigned Gene Ontology (GO) terms to identify the possible role of unigenes in various molecular and biological functions. These unigene based microsatellite markers will prove valuable for recording allelic variance across germplasm collections, gene tagging and searching for putative candidate genes.

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Section: Discussionmentioning

confidence: 99%

Mining functional microsatellites in legume unigenes

Roorkiwal¹,

Sharma²

2011

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“…Their biological significance to the host genomes has been a topic of debate in recent years. Moreover, little knowledge is available about their mutational dynamics [17, 18], primarily derived from the limited genomewide studies in model organisms [4, 5, 7]. Comprehensive surveys on microsatellite conservation across the species and within duplicated sequences of the same genome are, therefore, required to expand our understanding regarding their genomic significance.…”

Section: Resultsmentioning

confidence: 99%

“…Repeatmasker (http://www.repeatmasker.org/) with WU-blast [12] search engine was used with default sensitivity and rice as “DNA source” for mining of microsatellite repeats, which were subsequently aligned using glocal algorithm [13] in Vista Genome Browser (http://pipeline.lbl.gov/cgi-bin/gateway2) [14] following the method described earlier by Roorkiwal et al [7]. A simple sequence with repeat motif length of 1–6 bp spanning a minimal length of 20 bp was considered as a microsatellite.…”

Section: Methodsmentioning

confidence: 99%

“…Microsatellites are not expected to be conserved for long evolutionary periods either, as argued by Buschiazzo and Gemmell [3]. Nevertheless, models of microsatellite mutational dynamics have been developed based on comparison of orthologous microsatellite loci in related taxa [4–7]. However, whether these models also describe microsatellites at paralogous loci created by segmental changes within a genome remains to be investigated.…”

Section: Introductionmentioning

confidence: 99%

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Purifying Selection Bias against Microsatellites in Gene Rich Segmental Duplications in the Rice Genome

Sharma

Roorkiwal

Grover

2012

International Journal of Evolutionary Biology

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Little data is available on microsatellite dynamics in the duplicated regions of the rice genome, even though efforts have been made in the past to align genome sequences of its two sub-species. Based on the coordinates of duplicated sequences in the indica genome as available in the public domain, we identified microsatellites in these regions. CCG and GAAAA repeats occurred most frequently. In all, 259 microsatellites could be identified in the duplicated sequences using the criteria of minimum 90% alignability spread over a minimum of 1 Kb sequence. More than 25% of the repeats in duplicated regions occurred in the genic sequences. Only 45 (17%) of these 259 microsatellites were found conserved in the duplicated paralogues. Among these repeats, 40% maintained both sequence and length conservation. The effect of mutability of nearby regions could also be clearly seen in microsatellite regions. The overall purpose of this study was to investigate, whether microsatellites follow an independent course of evolutionary dynamics subsequent to events like genome reshuffling that simply drives these elements to different locations in the genome. To the best of our knowledge, this is the first comprehensive analysis of microsatellite conservation in the duplicated regions of any genome.

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“…Some data is available on the distribution of microsatellites in various genomes [6,17], but virtually no information is available till date on genomic distribution of minisatellites and satellites. Our experience of working with microsatellites, i.e., tandem repeats with shorter repeat motifs [7,18] suggests that the structure of tandem repeats may be regulated by their neighbouring components of the genome, as also reported for their mutability [19]. However, coding and non coding regions of a genome are regulated by differrent constraints and thus the fine genomic environment at these sites differs from one another.…”

Section: Discussionmentioning

confidence: 98%

Tandem repetitions in transcriptomes of some Solanaceae species

Grover¹,

Sharma²

2012

AJMB

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Characterization of occurrence, density and motif sequence of tandem repeats in the transcribed regions is helpful in understanding the functional significance of these repeats in the modern genomes. We analyzed tandem repeats present in expressed sequences of thirteen species belonging to genera Capsicum, Nicotiana, Petunia and Solanum of family Solanaceae and the genus Coffea of Rubiaceae to investigate the propagation and evolutionary sustenance of these repeats. Tandem repeat containing sequences constituted 1.58% to 7.46% of sequences analyzed. Tandem repetitions of size 2, 15, 18 and 21 bp motifs were more frequent. Repeats with unit sizes 21 and 22 bp were also abundant in genomic sequences of potato and tomato. While mutations occurring in these repeats may alter the repeat number, genomes adjust to these changes by keeping the translated products unaffected. Surprisingly, in majority of the species under study, tandem repeat motif length did not exceed 228 bp. Conserved tandem repeat motifs of sizes 180, 192 and 204 bp were also abundant in the genomic sequences. Our observations lead us to propose that these tandem repeats are actually remnants of ancestral megasatellite repeats, which have split into multiple repeats due to frequent insertions over the course of evolution.

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Genome-wide analysis of conservation and divergence of microsatellites in rice

Cited by 12 publications

References 63 publications

Mining functional microsatellites in legume unigenes

Mining functional microsatellites in legume unigenes

Purifying Selection Bias against Microsatellites in Gene Rich Segmental Duplications in the Rice Genome

Tandem repetitions in transcriptomes of some Solanaceae species

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