College of Landscape Architecture and Life Science, Chongqing University of Arts and Sciences, Chongqing 402160, China.
College of Biology and Food Engineering, Chongqing Three Gorges University, Chongqing 404000, China.
Genes (Basel). 2023 Nov 27;14(12):2136. doi: 10.3390/genes14122136.
'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 'Hongyang' cultivated in China was sequenced using de novo technology in this study. '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 'Hongyang' were biased towards the use of codons containing A/U, and the non-protein coding regions in the '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 plants, with small expansions and contractions of the boundaries. Furthermore, phylogenetic tree indicated that 'Hongyang' was the closest relative to . This research provides a useful basis for future genetic and evolutionary studies of 'Hongyang', and enriches the biological information of species.
“红阳”，又称红心猕猴桃，是原产于中国的藤本果树，具有重要的营养价值和经济价值。然而，其遗传多样性和系统发育的信息仍然非常有限。本研究首次采用从头测序技术对中国栽培的“红阳”进行了叶绿体（cp）基因组测序。“红阳”的 cp 基因组大小为 156267bp，GC 含量为 37.20%。共注释了 132 个基因，其中 85 个为蛋白质编码基因，39 个转移 RNA（tRNA）基因，8 个核糖体 RNA（rRNA）基因。共检测到 49 个微卫星序列（SSR），主要为单核苷酸重复，大多由 A 或 T 碱基重复组成。与 14 个其他物种相比，“红阳”的 cp 基因组更倾向于使用含有 A/U 的密码子，且“红阳”cpDNA 中非编码区的变异大于编码区。核苷酸多态性分析（Pi）得到了 9 个高度可变区热点，大多数位于大单拷贝（LSC）区。cp 基因组边界分析显示，15 种植物 cp 基因组的反向重复区（IRs）的基因排列具有保守性，边界有小的扩张和收缩。此外，系统发育树表明“红阳”与亲缘关系最近。本研究为“红阳”的遗传和进化研究提供了有用的基础，丰富了猕猴桃属物种的生物学信息。
