College of Life and Environmental Science, Wenzhou University, Wenzhou, 325035, China.
Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China.
Sci Rep. 2024 Sep 30;14(1):22686. doi: 10.1038/s41598-024-73941-4.
The small genera Allaeanthus and Malaisia within the Moraceae have important edible, medicinal, and economic value. However, complete plastome blueprints and a well-resolved evolutionary history of these two genera are still lack, thereby limiting their conservation and application. The recent discovery of a new distribution of Allaeanthus kurzii in Hainan, China, marked by the collection of two unique samples, alongside three samples of Malaisia scandens, has opened new avenues for research. This study aimed to compare the Allaeanthus and Malaisia plastomes of Hainan Province samples with those of samples from other regions, focusing on plastome structure, codon usage bias, natural selection, and the evolutionary history of A. kurzii and M. scandens. The results showed that both species had a quadripartite plastome structure, with sizes ranging from 162,134 to 162,170 bp for A. kurzii and 161,235 to 162,134 bp for M. scandens. Both species displayed loss of the infA gene and reduction of the rpl22 gene. Two highly variable regions (petD-trnD-GUC and rpl20-clpP) and three highly variable genes (rpl20, petB, and rpl16) were identified in A. kurzii, while two highly variable regions (ycf2-ndhB and ccsA-ndhE) and three highly variable genes (psbT, rpl36, and ycf2) were found in M. scandens. The protein-coding sequences (CDSs) of the Allaeanthus and Malaisia plastomes exhibited similar patterns of adaptive indices and codon usage frequencies. The genes associated with photosynthesis underwent strong purifying selection. Phylogenetic analysis revealed that Allaeanthus, Broussonetia, and Malaisia constituted a monophyletic group, with Malaisia being more closely related to Broussonetia. Broussonetia diversified approximately 19.78 million years ago, Malaisia approximately 4.74 million years ago, and Allaeanthus approximately 16.18 million years ago. These new plastome-based discoveries will guide conservation planners and medicinal plant breeders and genetic resource development for these species in the region.
小果野麻属（Allaeanthus）和拟赤杨属（Malaisia）隶属于桑科（Moraceae），具有重要的食用、药用和经济价值。然而，这两个属的完整质体蓝图和清晰的进化历史仍然缺乏，从而限制了它们的保护和应用。最近在中国海南发现了一个新的小果野麻属（Allaeanthus）的分布区，采集到了两个独特的样本，以及三个拟赤杨属（Malaisia）的样本，为研究开辟了新的途径。本研究旨在比较海南省小果野麻属（Allaeanthus）和拟赤杨属（Malaisia）的质体图谱，并与其他地区的样本进行比较，重点关注质体结构、密码子使用偏好、自然选择以及 A. kurzii 和 M. scandens 的进化历史。结果表明，两个物种的质体均为四分体结构，大小分别为 A. kurzii 的 162,134-162,170bp 和 M. scandens 的 161,235-162,134bp。两个物种都丢失了 infA 基因，rpl22 基因减少。在 A. kurzii 中鉴定出两个高度可变区（petD-trnD-GUC 和 rpl20-clpP）和三个高度可变基因（rpl20、petB 和 rpl16），而在 M. scandens 中鉴定出两个高度可变区（ycf2-ndhB 和 ccsA-ndhE）和三个高度可变基因（psbT、rpl36 和 ycf2）。质体蛋白编码序列（CDS）表现出相似的适应性指数和密码子使用频率模式。与光合作用相关的基因经历了强烈的纯化选择。系统发育分析表明，小果野麻属（Allaeanthus）、构树属（Broussonetia）和拟赤杨属（Malaisia）构成一个单系群，拟赤杨属（Malaisia）与构树属（Broussonetia）的亲缘关系更近。构树属（Broussonetia）约在 1978 万年前分化，拟赤杨属（Malaisia）约在 474 万年前分化，小果野麻属（Allaeanthus）约在 1618 万年前分化。这些基于新质体的发现将为该地区的这些物种的保护规划者、药用植物培育者和遗传资源开发者提供指导。
