College of Horticulture and Landscape Architecture, Southwest University, Chongqing, 400715, China.
Chongqing Academy of Agricultural Sciences, Chongqing, 401329, China.
BMC Genomics. 2022 Nov 8;23(1):745. doi: 10.1186/s12864-022-08965-z.
Plums are one of the most important economic crops of the Rosaceae family and are produced all over the world. China has many local varieties, but the genomic information is limited for genetic studies. Here, we first sequenced, assembled, and analyzed the plastomes of twelve plum cultivars and developed molecular markers to distinguish them.
The twelve plastomes of plum cultivars have a circular structure of 157,863-157,952 bp containing a large single-copy region (LSC) of 86,109-86,287 bp, a small copy region (SSC) of 18,927-19,031 bp, and two inverted repeats (IR) of 26,353-26,387 bp each. The plastomes of plum cultivars encode 131 genes, including 86 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. We detected 50, 54, 54, 53, 53, 50, 54, 54, 54, 49, 50, 54 SSRs in the twelve analyzed varieties, respectively. For repeat sequences, we identified 553 tandem repeats, 204 direct repeats, and 270 palindromic repeats. We also analyzed the expansion/contraction of IR regions. The genes rpl22, rps19, rpl2, ycf1, ndhF, and the trnH span on or near the boundary of IR and single-copy regions. Phylogenetic analysis showed that the twelve cultivars were clustered with the P. salicina and P. domestica. We developed eight markers LZ01 to LZ08 based on whole plastomes and nuclear genes and validated them successfully with six repetitions.
The results obtained here could fill in the blanks of the plastomes of these twelve plum cultivars and provide a wider perspective based on the basis of the plastomes of Prunus to the molecular identification and phylogenetic construction accurately. The analysis from this study provides an important and valuable resource for studying the genetic basis for agronomic and adaptive differentiation of the Prunus species.
李属植物是蔷薇科最重要的经济作物之一，在世界各地均有生产。中国有许多地方品种，但遗传研究的基因组信息有限。在这里，我们首次对 12 个李属品种的质体进行了测序、组装和分析，并开发了分子标记来区分它们。
12 个李属品种的质体具有圆形结构，大小为 157863-157952bp，包含一个大小为 86109-86287bp 的大单拷贝区（LSC）、一个大小为 18927-19031bp 的小拷贝区（SSC）和两个大小各为 26353-26387bp 的反向重复区（IR）。李属品种的质体编码 131 个基因，包括 86 个蛋白质编码基因、37 个 tRNA 基因和 8 个 rRNA 基因。我们在 12 个分析品种中分别检测到 50、54、54、53、53、50、54、54、54、49、50、54 个 SSRs。对于重复序列，我们鉴定了 553 个串联重复序列、204 个直接重复序列和 270 个回文重复序列。我们还分析了 IR 区域的扩张/收缩。rpl22、rps19、rpl2、ycf1、ndhF 和 trnH 基因位于或靠近 IR 和单拷贝区域的边界。系统发育分析表明，这 12 个品种与李和桃聚为一簇。我们基于全质体和核基因开发了 8 个标记 LZ01 到 LZ08，并成功地用 6 次重复验证了它们。
本研究结果填补了这 12 个李属品种质体的空白，为基于李属质体对准确的分子鉴定和系统发育构建提供了更广泛的视角。本研究的分析为研究李属物种的农艺和适应性分化的遗传基础提供了重要而有价值的资源。
