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Cloning and application of the complete nuclear ribosomal DNA (nrDNA) cistron sequence of Pyropia haitanensis (Bangiales, Rhodophyta)

He, Yuan, Shen, Songdong, Shen, Zonggen
Botanica marina 2017 v.60 no.3 pp. 327-337
Pyropia, cultivars, exons, genes, intergenic DNA, internal transcribed spacers, intraspecific variation, introns, ribosomal DNA, ribosomal RNA, species identification, transcription (genetics), China
Pyropia haitanensis (Bangiales, Rhodophyta)((T.J. Chang et B.F. Zheng) N. Kikuchi et M. Miyata) is a unique cultivar in China and the main problem with its cultivation lies in a lack of effective technology to distinguish intraspecific strains. In this study, we firstly obtained the complete sequence of rDNA of Pyropia haitanensis in China, which can help identify intraspecific variation within this species. The whole unit is composed of a small-subunit (SSU) rRNA gene with a full length of 2953 base pairs (bp) with two classes of introns and an exon sequence of 1837 bp; moreover, the complete sequence of the large-subunit (LSU) rRNA gene (length 4444 bp) also contains two introns; the length of the 5.8S rRNA gene is 158 bp; the length of internal transcribed spacers 1 (ITS1) is 334 bp and that of ITS2 is 678 bp; and the complete sequence of intergenic spacer (IGS) is 6969 bp. Some portions of the IGS sequences were used to analyze the similarities among five strains of Pyropia haitanensis; the sequence ranged from 4264 bp to 4273 bp and the G+C content was 53%. We also found 118 variable sites in the IGS which account for approximately 2.8% of the whole length. In conclusion, the nuclear ribosomal DNA sequence turned out to be an effective molecular marker for the taxonomic identification of Pyropia haitanensis.