SSR marker development in Clerodendrum trichotomum using transcriptome sequencing

• Published in: PloS one Vol. 14; no. 11; p. e0225451
• Main Authors: Chen, Gongwei, Yue, Yuanzheng, Hua, Yajie, Hu, Die, Shi, Tingting, Chang, Zhaojing, Yang, Xiulian, Wang, Lianggui
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 20-11-2019; Public Library of Science (PLoS)
• Subjects: Alleles; Annotations; Biology and Life Sciences; Clerodendrum - genetics; Clerodendrum trichotomum; Conservation; Deoxyribonucleic acid; DNA; DNA, Plant - genetics; Ecology and Environmental Sciences; Forestry; Gene expression; Gene Expression Profiling - methods; Gene polymorphism; Gene sequencing; Genetic diversity; Genetic Markers; Genomes; Genomics; Germplasm; High-Throughput Nucleotide Sequencing - methods; Instrument industry (Equipment); Landscape architecture; Methods; Microsatellite Repeats; Molecular biology; Molecular Sequence Annotation; Ornamental plants; Physiology; Polymorphism; Research and analysis methods; Ribonucleic acid; RNA; RNA sequencing; Sequence Analysis, RNA - methods; Technology application; Trees; Whole Exome Sequencing - methods; United States; China; United States > US
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0225451

Clerodendrum trichotomum, a member of the Lamiaceae (Verbenaceae) family, is an ornamental plant widely distributed in South Asia. Previous studies have focused primarily on its growth characteristics, stress resistance, and pharmacological applications; however, molecular investigations remain limited. Considering germplasm conservation and the extensive applications of this plant, it is necessary to explore transcriptome resources and SSR makers for C. trichotomum. In the present study, RNA sequencing was used to determine the transcriptome of C. trichotomum. Subsequently, unigene annotations and classifications were obtained, and SSRs were mined with MIcroSAtellite. Finally, primer pairs designed with Oligo 6.0 were selected for polymorphism validation. In total, 127,325,666 high-quality reads were obtained, and 58,345 non-redundant unigenes were generated, of which 36,900 (63.24%) were annotated. Among the annotated unigenes, 35,980 (97.51%) had significant similarity to 607 species in Nr databases. In addition, a total of 6,444 SSRs were identified in 5,530 unigenes, and 200 random primer pairs were designed for polymorphism validation. Furthermore, after primary polymorphism identification, 30 polymorphic primer pairs were selected for the further polymorphism screening, and 200 alleles were identified, 197 of which showed polymorphism. In this work, a large number of unigenes were generated, and numerous SSRs were detected. These findings should be beneficial for further investigations into germplasm conservation and various applications of C. trichotomum. These results should also provide a solid foundation for future molecular biology studies in C. trichotomum.