NEWS 2020

Complete chloroplast genomes of Liliaceae (s.l.) species: comparative genomic and phylogenetic analyses

Ruixue SHE1, Peng ZHAO1, Huijuan ZHOU2, Ming YUE3, Feng YAN1, Guojia HU1, Xiaoxiao GAO1, Shuoxin ZHANG2
Nordic Journal of Botany (2020)
1Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest Univ., No. 229, Street Taibaibei, Xi’an, CN-710069 Shaanxi, PR China
2College of Forestry, Northwest A & F Univ., Yangling, Shaanxi, PR China
3Xi’an Botanical Garden of Shaanxi Province, Xi’an, Shaanxi, PR China.

She et al. 2019


We first report the complete chloroplast (cp) genome of Fritillaria taipaiensisem> and determine its characteristics, sequence divergence and phylogenetic relationships by comparing it with complete cp genomes of Liliaceae s.l. (including e.g. Nartheciaceae, Amaryllidaceae and Asparagaceae) species obtained from NCBI Genbank. We show that the ycf1, ycf15 and infA genes have become pseudogenes or are lost in some of the seventeen Liliaceae species, and that dispersed repeats are prevailing among the four types of repeats (dispersed, palindromic, complement and tandem repeats). The number of simple sequence repeats ranged from 53 to 84 in the seventeen species, with mononucleotide repeats being the most abundant, followed by dinucleotides. A total of nine genes with positive selection sites were identified (atpB, atpE, ndhF, ndhH, petB, rpl2, rpl20, rpl22 and ycf2). Furthermore, we examined 19 mutational hotspot regions, including three coding regions (rps16, infA and rpl22) and sixteen non-coding regions. A phylogenetic analysis of the complete cp genomes and protein-coding sequences showed that Fritillaria is most closely related to Lilium. Moreover, Asparagus and Polygonatum, Hosta and Yucca are closely related to the Liliaceae. These results will contribute to further study of evolutionary patterns and phylogenetic relationships in Liliaceae s.l.

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