Discovery of Simple Sequence Repeat Markers through Transcriptome Analysis of Baccaurea motleyana

食品科学与工程:英文版(美国) Pub Date : 2020-06-28 DOI:10.17265/2159-5828/2020.02.001

K. Nasir, Muhammad Fairuz Mohd Yusof, M. S. F. A. Razak, Siti Norsaidah Ibrahim, Mira Farzana Mohamad Moktar, Khadijah Awang, M. Ali

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Abstract

Baccaurea motleyana (rambai) is underutilized fruits that are native to Malaysia, Indonesia and Thailand. In this study, a total of 54,779 unigenes identified from rambai transcriptome were used for simple sequence repeat (SSR) analysis by MIcroSAtellite (MISA). A total of 20,420 SSRs were found to be distributed within 37.27% of the total number of unigenes. Mononucleotide repeats represented the main type, accounting for 64.04%, followed by trinucleotide repeats (20.28%) and dinucleotide repeats (19.94%). Gene annotation to seven databases has a success ratio of 68.53% (National Center for Biotechnology Information (NCBI) protein sequences), 53.68% (NCBI nucleotide sequences), 27.43% (Kyoto Encyclopedia of Genes and Genome Ortholog), 56.0% (SwissProt), 52.44% (Protein family), 53.99% (Gene Ontology) and 26.44% (Kluster of Orthologous Group). Further rambai SSRs were randomly selected and validated to B. motleyana (rambai), B. macrocarpa (tampoi), B. polyneura (jentik-jentik), B. ramiflora (pupor) and B. scortechinii (setambun).

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通过对斑点芽孢杆菌转录组分析发现简单序列重复标记

蓝白是一种未被充分利用的水果，原产于马来西亚、印度尼西亚和泰国。本研究利用MIcroSAtellite (MISA)对从rambai转录组中鉴定出的54,779个单基因进行了SSR分析。共有20420个ssr分布在unigenes总数的37.27%以内。单核苷酸重复序列为主要类型，占64.04%，其次是三核苷酸重复序列(20.28%)和二核苷酸重复序列(19.94%)。对7个数据库的基因注释成功率分别为68.53% (NCBI蛋白质序列)、53.68% (NCBI核苷酸序列)、27.43%(京都基因与基因组同源百科全书)、56.0% (SwissProt)、52.44%(蛋白质家族)、53.99%(基因本体)和26.44% (Kluster of Orthologous Group)。进一步随机选择rambai SSRs，并对rambai、macrocarpa、polyneura (jentik-jentik)、ramiflora (pupor)和scortechinii (setambun)进行验证。

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食品科学与工程:英文版(美国)

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