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Palmae 基因组中简单重复序列的全基因组特征分析。

Genome-wide characterization of simple sequence repeats in Palmae genomes.

机构信息

National Center for Biotechnology, King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia.

Center of Excellence for Genomics, King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia.

出版信息

Genes Genomics. 2020 May;42(5):597-608. doi: 10.1007/s13258-020-00924-w. Epub 2020 Apr 3.

DOI:10.1007/s13258-020-00924-w
PMID:32246355
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC7181556/
Abstract

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: Phoenix dactylifera, Cocos nucifera, Calamus simplicifolius, Elaeis oleifera, and Elaeis guineensis.

RESULTS

A total of 118241, 328189, 450753, 176608, and 70694 SSRs were identified, respectively. The six repeat types were not evenly distributed across the five genomes. Mono- and dinucleotide SSRs were the most abundant, and GC content was highest in tri- and hexanucleotide SSRs.

CONCLUSION

We envisage that this analysis would further substantiate more in-depth computational, biochemical, and molecular studies on the roles SSRs may play in the genome organization of the palm species. The current study contributes a detailed characterization of simple sequence repeats in palm genomes.

摘要

背景

微卫星或简单重复序列 (SSR) 已成为遗传研究中使用最广泛的 DNA 标记技术。由于许多 Palmae 物种的完整草图基因组可用，因此可以对这些物种中的 SSR 进行全基因组分析。棕榈树是热带和亚热带植物，由于其果实品种的营养价值，具有农业和经济重要性。

目的

这是首次对 Palmae 物种完全测序的草图基因组中的微卫星进行综合研究和比较。

方法

我们使用 PERF v0.2.5 识别和比较具有 1-6 bp 核苷酸基序的完美 SSR，以表征 Palmae 物种中的微卫星。我们分析了它们在五个棕榈物种中的相对丰度、相对密度和 GC 含量：凤凰棕榈、椰子、剑叶龙血树、油棕和非洲油棕。

结果

总共鉴定出 118241、328189、450753、176608 和 70694 个 SSR。这六种重复类型在五个基因组中分布不均。单核苷酸和二核苷酸 SSR 最为丰富，三核苷酸和六核苷酸 SSR 的 GC 含量最高。

结论

我们设想，这项分析将进一步证实更深入的计算、生化和分子研究，以了解 SSR 在棕榈物种基因组组织中可能发挥的作用。本研究对棕榈基因组中的简单序列重复进行了详细的特征描述。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/16cb/7181556/80bbd782262c/13258_2020_924_Fig4_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/16cb/7181556/f25400edb1c7/13258_2020_924_Fig1_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/16cb/7181556/b97444635a22/13258_2020_924_Fig2_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/16cb/7181556/a627d22b9f81/13258_2020_924_Fig3_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/16cb/7181556/80bbd782262c/13258_2020_924_Fig4_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/16cb/7181556/f25400edb1c7/13258_2020_924_Fig1_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/16cb/7181556/b97444635a22/13258_2020_924_Fig2_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/16cb/7181556/a627d22b9f81/13258_2020_924_Fig3_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/16cb/7181556/80bbd782262c/13258_2020_924_Fig4_HTML.jpg

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