Distinct patterns of SSR distribution in the Arabidopsis thaliana and rice genomes
Mark J. Lawson,Liqing Zhang +1 more
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TLDR
Insight is provided into the evolution and distribution of SSRs in the two sequenced model plant genomes of monocots and dicots and reveals that the distributions appear highly non-random and vary a great deal in different regions of the genes in the genomes.Abstract:
Simple sequence repeats (SSRs) in DNA have been traditionally thought of as functionally unimportant and have been studied mainly as genetic markers. A recent handful of studies have shown, however, that SSRs in different positions of a gene can play important roles in determining protein function, genetic development, and regulation of gene expression. We have performed a detailed comparative study of the distribution of SSRs in the sequenced genomes of Arabidopsis thaliana and rice. SSRs in different genic regions - 5'untranslated region (UTR), 3'UTR, exon, and intron - show distinct patterns of distribution both within and between the two genomes. Especially notable is the much higher density of SSRs in 5'UTRs compared to the other regions and a strong affinity towards trinucleotide repeats in these regions for both rice and Arabidopsis. On a genomic level, mononucleotide repeats are the most prevalent type of SSRs in Arabidopsis and trinucleotide repeats are the most prevalent type in rice. Both plants have the same most common mononucleotide (A/T) and dinucleotide (AT and AG) repeats, but have little in common for the other types of repeats. Our work provides insight into the evolution and distribution of SSRs in the two sequenced model plant genomes of monocots and dicots. Our analyses reveal that the distributions of SSRs appear highly non-random and vary a great deal in different regions of the genes in the genomes.read more
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Microsatellite markers: an overview of the recent progress in plants
TL;DR: The recent developments in plant genetics using SSR markers are discussed and a quantum of literature has accumulated regarding the applicability of SSR based techniques.
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Microsatellite markers: what they mean and why they are so useful.
TL;DR: This review aims to address some theoretical aspects of SSRs, including definition, characterization and biological function, and confirms the current relevance ofSSRs and indicates their continuous utilization in plant science.
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The genetic map of finger millet, Eleusine coracana.
Mathews M. Dida,Mathews M. Dida,Mathews M. Dida,Srinivasachary,Srinivasachary,Sujatha Ramakrishnan,Jeffrey L. Bennetzen,Jeffrey L. Bennetzen,Michael D. Gale,Katrien M. Devos,Katrien M. Devos +10 more
TL;DR: A genetic map of the tetraploid finger millet genome was generated and a first set of 82 SSR markers was developed to facilitate the use of marker-assisted selection in finger Millet.
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Development and genetic mapping of microsatellite markers from genome survey sequences in Brassica napus.
Xiaomao Cheng,Jinsong Xu,Shu Xia,Jianxun Gu,Yuan Yang,Jie Fu,Xiaoju Qian,Shunchang Zhang,Jiangsheng Wu,Kede Liu +9 more
TL;DR: A total of 627 new SSR markers were developed based on publicly available genome survey sequences and used to survey polymorphisms among six B. napus cultivars that serve as parents for established populations, finding no correlation was observed between SSR motifs, repeat number or repeat length with polymorphism levels.
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Transcriptome Sequencing and De Novo Analysis for Ma Bamboo (Dendrocalamus latiflorus Munro) Using the Illumina Platform
TL;DR: In this paper, the authors performed de novo transcriptome sequencing for the first time to produce a comprehensive dataset for the Ma bamboo (Dendrocalamus latiflorus Munro).
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