Distribution, Function and Polymorphism Characteristics of Microsatellites in Pyropia yezoensis Transcriptome

Abstract

The distribution, putative function and polymorphism characteristics of simple sequence repeats (SSRs) in P. yezoensis transcriptome were analyzed in this study. In total, 3076 SSRs were detected among 2681 unigenes. Trinucleotide types were dominant, constituting 91.87% of all the microsatellites. The most abundant SSR was CCG (71.03%) and the second abundant one was AGC (234, 7.61%). A total of 111 (3.61%) dinucleotide types were found and the most abundant one was AC (51, 1.66%) which was followed by CG (34, 1.11%). SSRs identified showed a GC bases preference; GC bases constituted 89.73% of all the SSR bases. SSRs occurrence number decreased as repetitions increased. Annotation results exhibited that the majority of SSRs-containing unigenes have the functions of ‘metabolic process’, ‘binding’ and ‘catalytic activity’ and existed as the forms of ‘cell’, ‘cell component’ and ‘organelle’. The dominant amino acids that SSRs coded were Ala (28.59%), Arg (26.02%), Gly (14.35%) and Pro (13.65%). Amplification results showed that 3 out 23 SSRs from transcriptome (13.04%) and 8 out 77 SSRs from genome (10.39%) were polymorphic.

Journal

Journal ID (publisher-id): JOUC

Title: Journal of Ocean University of China

Publisher: Science Press and Springer (China )

ISSN (Electronic): 1672-5182

Publication date (Electronic): 14 May 2019

Publication date (Print): 01 June 2019

Volume: 18

Issue: 3

Pages: 693-700

Affiliations

¹ Key Laboratory of Marine Genetics and Breeding (Ocean University of China), Ministry of Education, Qingdao 266003, China

² Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China

³ College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China

Author notes

*Corresponding author: MAO Yunxiang

Article

Publisher ID: s11802-019-3817-6

DOI: 10.1007/s11802-019-3817-6

Copyright statement: Copyright © Ocean University of China, Science Press and Springer-Verlag GmbH Germany 2019.

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Product

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