SSR marker development in Clerodendrum trichotomum using transcriptome sequencing


Autoři: Gongwei Chen aff001;  Yuanzheng Yue aff001;  Yajie Hua aff001;  Die Hu aff001;  Tingting Shi aff001;  Zhaojing Chang aff001;  Xiulian Yang aff001;  Lianggui Wang aff001
Působiště autorů: College of Landscape Architecture, Nanjing Forestry University, Nanjing, Jiangsu, China aff001;  College of Forestry, Nanjing Forestry University, Nanjing, Jiangsu, China aff002
Vyšlo v časopise: PLoS ONE 14(11)
Kategorie: Research Article
doi: 10.1371/journal.pone.0225451

Souhrn

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.

Klíčová slova:

Alleles – DNA – Microsatellite loci – Plant breeding – RNA sequencing – Sequence motif analysis – Shannon index – Transcriptome analysis


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2019 Číslo 11