Xu Xiaoxiang, Zhang Le, Bi Changwei, Qin Meiling, Wang Shouchang, Li Dong, He Ningjia, Zeng Qiwei
State Key Laboratory of Resource Insects, Institute of Sericulture and Systems Biology, Southwest University, 216 Tiansheng Road, Beibei District, Chongqing 400716, China.
State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Tree Genetics and Silvicultural Sciences of Jiangsu Province, Nanjing Forestry University, Nanjing 210037, China.
Plants (Basel). 2025 Aug 18;14(16):2570. doi: 10.3390/plants14162570.
The internal transcribed spacer (ITS) is one of the most extensively utilized in the taxonomy of the genus due to its generally concerted evolution. Although non-concerted evolution of nuclear ribosomal DNA (nrDNA) has been reported in some species, genome-wide nrDNA characteristics in the genus remain poorly understood. In this study, 158 single-nucleotide polymorphisms (SNPs) and 15 insertions and deletions (InDels) were identified within the nrDNA regions of 542 mulberry accessions representing sixteen species. These wide occurrences of heterogeneous SNPs and InDels revealed the intra-individual polymorphism within the nrDNA region of , indicating the incomplete concerted evolution of nrDNA. Notably, 66 out of 158 SNPs and 13 out of 15 InDels were localized within the ITS regions (ITS1-5.8S-ITS2), indicating a high degree of polymorphism in the ITS, which was further validated through classical cloning and Sanger sequencing methodologies. The 13/16 bp InDel located in the ITS1 region was utilized to develop a rapid and reliable cleaved amplified polymorphic sequence (CAPS) marker-based method for distinguishing . and from other species, eliminating the need for a clone-based sequencing step or comparative phenotypic analysis. Phylogenetic analysis based on nrDNA SNPs from 542 mulberry accessions revealed six distinct clades, corresponding to the six species. These findings offer novel new insights into the taxonomy, conservation, and breeding improvement of species.
由于其通常的协同进化，内部转录间隔区（ITS）是该属分类学中应用最广泛的区域之一。尽管在一些物种中已报道了核糖体DNA（nrDNA）的非协同进化，但该属全基因组的nrDNA特征仍知之甚少。在本研究中，在代表16个桑种的542份桑种质的nrDNA区域内鉴定出158个单核苷酸多态性（SNP）和15个插入缺失（InDel）。这些广泛存在的异质SNP和InDel揭示了桑属nrDNA区域内的个体内多态性，表明nrDNA的协同进化不完全。值得注意的是，158个SNP中的66个和15个InDel中的13个位于ITS区域（ITS1-5.8S-ITS2），表明ITS具有高度多态性，这通过经典克隆和桑格测序方法进一步得到验证。位于ITS1区域的13/16 bp InDel被用于开发一种基于快速可靠的酶切扩增多态性序列（CAPS）标记的方法，用于区分鲁桑和白桑与其他桑种，无需基于克隆的测序步骤或比较表型分析。基于542份桑种质nrDNA SNP的系统发育分析揭示了六个不同的分支，对应于六个桑种。这些发现为桑种的分类学、保护和育种改良提供了新的见解。
