Chloroplast Genome Comparison and Phylogenetic Analysis of the Commercial Variety Actinidia chinensis ‘Hongyang’
Author:
Liu Han12, Liu Xia1, Sun Chong13, Li Hong-Lei1, Li Zhe-Xin1, Guo Yuan1, Fu Xue-Qian1, Liao Qin-Hong1, Zhang Wen-Lin1, Liu Yi-Qing3
Affiliation:
1. College of Landscape Architecture and Life Science, Chongqing University of Arts and Sciences, Chongqing 402160, China 2. College of Biology and Food Engineering, Chongqing Three Gorges University, Chongqing 404000, China 3. Spice Crops Research Institute, College of Horticulture and Gardening, Yangtze University, Jingzhou 434023, China
Abstract
Actinidia chinensis ‘Hongyang’, also known as red yangtao (red heart kiwifruit), is a vine fruit tree native to China possessing significant nutritional and economic value. However, information on its genetic diversity and phylogeny is still very limited. The first chloroplast (cp) genome of A. chinensis ‘Hongyang’ cultivated in China was sequenced using de novo technology in this study. A. chinensis ‘Hongyang’ possesses a cp genome that spans 156,267 base pairs (bp), exhibiting an overall GC content of 37.20%. There were 132 genes that were annotated, with 85 of them being protein-coding genes, 39 transfer RNA (tRNA) genes, and 8 ribosomal RNA (rRNA) genes. A total of 49 microsatellite sequences (SSRs) were detected, mainly single nucleotide repeats, mostly consisting of A or T base repeats. Compared with 14 other species, the cp genomes of A. chinensis ‘Hongyang’ were biased towards the use of codons containing A/U, and the non-protein coding regions in the A. chinensis ‘Hongyang’ cpDNA showed greater variation than the coding regions. The nucleotide polymorphism analysis (Pi) yielded nine highly variable region hotspots, most in the large single copy (LSC) region. The cp genome boundary analysis revealed a conservative order of gene arrangement in the inverted repeats (IRs) region of the cp genomes of 15 Actinidia plants, with small expansions and contractions of the boundaries. Furthermore, phylogenetic tree indicated that A. chinensis ‘Hongyang’ was the closest relative to A. indochinensis. This research provides a useful basis for future genetic and evolutionary studies of A. chinensis ‘Hongyang’, and enriches the biological information of Actinidia species.
Funder
National Natural Science Foundation of China Science and Technology Research Program of the Chongqing Education Commission, China Chongqing Municipal Science and Technology Commission, China
Subject
Genetics (clinical),Genetics
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