Zheng Enting, Yisilam Gulbar, Li Chuanning, Jiao Fangfang, Ling Yulan, Lu Shuhua, Wang Qiuyan, Tian Xinmin
Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Ministry of Education) & Guangxi Key Laboratory of Landscape Resources Conservation and Sustainable Utilization in Lijiang River Basin, Guangxi Normal University, Guilin, 541006, China.
Guangxi University Engineering Research Center of Bioinformation and Genetic Improvement of Specialty Crops, Guangxi Normal University, Guilin, 541006, China.
BMC Genomics. 2025 May 9;26(1):463. doi: 10.1186/s12864-025-11581-2.
Pitaya is an important tropical fruit highly favoured by consumers owing to its good and juicy characteristics. It contains a large amount of betacyanin, which is a natural food-colouring agent, in the peel and pulp. However, few studies have focused on the pitaya chloroplast (cp) genomes.
To explore the genetic differences and phylogenetic relationships among the cp genomes of the six pitaya cultivars, we assembled, annotated, and performed a comparative genomic analysis. The cp genomes of the six cultivars exhibited a typical circular structure, ranging in length from 133,146 to 133,617 bp, with a GC content of 36.4%. All individual cp genomes were annotated with 123 genes, including 80 protein-coding genes, 38 tRNA genes, four rRNA genes, and one pseudogene (ycf68). Six mutated hotspot regions (trnF-GAA-rbcL, trnM-CAU-accD, rpl20-psbB, accD, rpl22, ycf1) were detected, which could be considered potential molecular markers for population genetics and molecular phylogeny studies. Phylogenetic analysis showed that pitaya cultivars clustered into a single branch in the phylogenetic tree of the Cactaceae family. Furthermore, the observed phylogenetic patterns suggest a complex genetic basis for colour variation among pitaya cultivars.
The study findings expand our understanding of the cp genome of pitaya and the phylogenetic relationships among different cultivars. The genomic data obtained provide important information for the breeding and genetic improvement of pitaya.
火龙果是一种重要的热带水果，因其口感良好且多汁而深受消费者喜爱。其果皮和果肉中含有大量的甜菜色素，这是一种天然食用色素。然而，很少有研究关注火龙果叶绿体（cp）基因组。
为了探究六个火龙果品种cp基因组之间的遗传差异和系统发育关系，我们进行了组装、注释和比较基因组分析。六个品种的cp基因组呈现典型的环状结构，长度在133,146至133,617 bp之间，GC含量为36.4%。所有个体cp基因组均注释了123个基因，包括80个蛋白质编码基因、38个tRNA基因、4个rRNA基因和1个假基因（ycf68）。检测到六个突变热点区域（trnF-GAA-rbcL、trnM-CAU-accD、rpl20-psbB、accD、rpl22、ycf1），这些区域可被视为群体遗传学和分子系统发育研究的潜在分子标记。系统发育分析表明，火龙果品种在仙人掌科系统发育树中聚为一个单分支。此外，观察到的系统发育模式表明火龙果品种间颜色变异具有复杂的遗传基础。
该研究结果扩展了我们对火龙果cp基因组以及不同品种间系统发育关系的理解。所获得的基因组数据为火龙果的育种和遗传改良提供了重要信息。
