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Large-scale analysis reveals that the genome features of simple sequence repeats are generally conserved at the family level in insects

Overview of attention for article published in BMC Genomics, November 2017
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Title
Large-scale analysis reveals that the genome features of simple sequence repeats are generally conserved at the family level in insects
Published in
BMC Genomics, November 2017
DOI 10.1186/s12864-017-4234-0
Pubmed ID
Authors

Simin Ding, Shuping Wang, Kang He, Mingxing Jiang, Fei Li

Abstract

Simple sequence repeats (SSR), also called microsatellites, have been widely used as genetic markers, and have been extensively studied in some model insects. At present, the genomes of more than 100 insect species are available. However, the features of SSRs in most insect genomes remain largely unknown. We identified 15.01 million SSRs across 136 insect genomes. The number of identified SSRs was positively associated with genome size in insects, but the frequency and density per megabase of genomes were not. Most insect SSRs (56.2-93.1%) were perfect (no mismatch). Imperfect (at least one mismatch) SSRs (average length 22-73 bp) were longer than perfect SSRs (16-30 bp). The most abundant insect SSRs were the di- and trinucleotide types, which accounted for 27.2% and 22.0% of all SSRs, respectively. On average, 59.1%, 36.8%, and 3.7% of insect SSRs were located in intergenic, intronic, and exonic regions, respectively. The percentages of various types of SSRs were similar among insects from the same family. However, they were dissimilar among insects from different families within orders. We carried out a phylogenetic analysis using the SSR frequencies. Species from the same family were generally clustered together in the evolutionary tree. However, insects from the same order but not in the same family did not cluster together. These results indicated that although SSRs undergo rapid expansions and contractions in different populations of the same species, the general genomic features of insect SSRs remain conserved at the family level. Millions of insect SSRs were identified and their genome features were analyzed. Most insect SSRs were perfect and were located in intergenic regions. We presented evidence that the variance of insect SSRs accumulated after the differentiation of insect families.

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Mendeley readers

Mendeley readers

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Geographical breakdown

Country Count As %
Unknown 30 100%

Demographic breakdown

Readers by professional status Count As %
Student > Master 6 20%
Student > Ph. D. Student 4 13%
Student > Doctoral Student 3 10%
Student > Bachelor 3 10%
Professor 2 7%
Other 3 10%
Unknown 9 30%
Readers by discipline Count As %
Biochemistry, Genetics and Molecular Biology 9 30%
Agricultural and Biological Sciences 8 27%
Environmental Science 1 3%
Veterinary Science and Veterinary Medicine 1 3%
Arts and Humanities 1 3%
Other 1 3%
Unknown 9 30%
Attention Score in Context

Attention Score in Context

This research output has an Altmetric Attention Score of 1. This is our high-level measure of the quality and quantity of online attention that it has received. This Attention Score, as well as the ranking and number of research outputs shown below, was calculated when the research output was last mentioned on 12 June 2018.
All research outputs
#20,522,137
of 23,090,520 outputs
Outputs from BMC Genomics
#9,330
of 10,705 outputs
Outputs of similar age
#288,476
of 330,950 outputs
Outputs of similar age from BMC Genomics
#171
of 199 outputs
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