Haikou Experimental Station, Chinese Academy of Tropical Agricultural Sciences, Haikou, China.
College of Agriculture, Yunnan University, Yunnan, China.
PLoS One. 2019 Sep 18;14(9):e0221827. doi: 10.1371/journal.pone.0221827. eCollection 2019.
Chloroplasts significantly influence species phylogenies because of their maternal inheritance and the moderate evolutionary rate of their genomes. Avocado, which is a member of the family Lauraceae, has received considerable attention from botanists, likely because of its position as a basal angiosperm. However, there is relatively little avocado genomic information currently available. In this study, six complete avocado chloroplast genomes from three ecological races were assembled to examine the sequence diversity among the three avocado ecological races. A comparative genomic analysis revealed that 515 simple sequence repeat loci and 176 repeats belonging to four other types were polymorphic across the six chloroplast genomes. Three highly variable regions (trnC-GCA-petN, petN-psbM, and petA-psbJ) were identified as highly informative markers. A phylogenetic analysis based on 79 common protein-coding genes indicated that the six examined avocado accessions from three ecological races form a monophyletic clade. The other three genera belonging to the Persea group clustered to form a sister clade with a high bootstrap value. These chloroplast genomes provide important genetic information for future attempts at identifying avocado races and for the related biological research.
叶绿体由于其母系遗传和基因组的中等进化速度，对物种系统发育有很大的影响。鳄梨是樟科的一员，受到植物学家的广泛关注，可能是因为它处于被子植物的基部。然而，目前鳄梨的基因组信息相对较少。在这项研究中，我们组装了来自三个生态型的六个完整的鳄梨叶绿体基因组，以研究三个鳄梨生态型之间的序列多样性。比较基因组分析表明，六个叶绿体基因组中有 515 个简单序列重复序列和 176 个属于其他四种类型的重复序列是多态的。三个高度可变区域（trnC-GCA-petN、petN-psbM 和 petA-psbJ）被鉴定为高度信息性标记。基于 79 个常见的蛋白质编码基因的系统发育分析表明，来自三个生态型的六个被检测的鳄梨品系形成一个单系分支。其他三个属于 Persea 组的属聚类形成一个具有高自举值的姐妹分支。这些叶绿体基因组为未来识别鳄梨品种和相关生物学研究提供了重要的遗传信息。
