Identification of simple sequence repeat markers using restriction site-associated DNA sequencing (RADSeq) of Garcinia prainiana
2021
Siti Nadrah Abd Hisham | Muhammad Fairuz Mohd Yusof | Azuan Amron | Khairun Hisam Nasir | Siti Norsaidah Ibrahim
Garcinia prainiana (cerapu) is an underutilized fruit and native to Malaysia. A restriction site-associated DNA sequencing (RADSeq) of G. prainiana DNA using restriction enzyme EcoR1combined with Illumina paired-end sequencing generated a clean data of 910.3 Mbp reads. Data assemblies produced 245,721 scaffolds with 38.05% guanine-cytosine (GC-content). These sequences were mined for simple sequence repeats (SSRs) and a total of 5,086 SSRs were identified which consisted of mono- (33.21%), di- (19.94%), tri- (13.43%), tetra- (1.91%), penta- (0.59%) and hexanucleotide (0.11%) repeats. From the 100 SSRs selected for fragment analysis of cerapu accessions, 11 polymorphic SSRs were identified, and a phylogenetic tree was generated, which consisted of two main groups.
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