Jia Xiaowen, Li Hanyu, Han Ying, Wang Lu, Lai Chanjuan, Liu Xi, Li Pan, Lei Zupei, Zhang Yonghua
School of Life and Environmental Science, Wenzhou University, Wenzhou, Zhejiang, 325035, China.
Zhejiang Wuyanling National Nature Reserve Management Bureau, Wenzhou, Zhejiang, 325500, China.
BMC Genomics. 2025 Jan 22;26(1):61. doi: 10.1186/s12864-025-11238-0.
Broussonetia papyrifera, B. monoica, and B. kaempferi belong to the genus Broussonetia (Moraceae). These three species hold significant economic and research values. However, few molecular markers have been effectively utilized for resource development and molecular genetic breeding of these species. Sequencing of their genomes allowed us to develop genomic markers (e.g. simple sequence repeats (SSRs)) and construct a high-density physical map.
A total of 369,557, 332,627, and 276,245 SSRs were identified in 13 high-quality assembled pseudochromosomes and their unassembled scaffolds for B. papyrifera, B. monoica, and B. kaempferi, respectively. Among the identified genomic SSRs across the three species, short repeat sequences were more abundant, while long repeat sequences constituted a smaller proportion. Additionally, the predominant repeat motifs in the SSRs of the three Broussonetia species were composed of 'A' and 'T' repeats. Using B. papyrifera genome as a reference, 4,419 common SSRs were identified among these three species, while 2,048 SSRs were specific to B. kaempferi, and 4,285 SSRs were specific to B. monoica. Distribution analysis indicated a notable similarity in the distribution patterns of SSRs across the pseudochromosomes of these three species. Furthermore, of the identified SSRs, 28%, 31%, and 24% were mapped to genes in B. papyrifera, B. kaempferi, and B. monoica, respectively. Genic-mapped SSRs may regulate biological processes by influencing gene activity and protein function. To verify SSRs polymorphism, we selected 30 ones from 10,752 potentially polymorphic SSRs loci for PCR amplification among these three species, all of which were successfully amplified and exhibited polymorphism across these three species.
These findings are helpful for further research on the origin, evolution, and migration of Broussonetia species and also laid the foundation for the precise identification, systematic evaluation, and efficient utilization of the germplasm resources of Broussonetia species.
构树、小构树和光叶楮属于构属（桑科）。这三个物种具有重要的经济和研究价值。然而，很少有分子标记被有效地用于这些物种的资源开发和分子遗传育种。对它们的基因组进行测序使我们能够开发基因组标记（如简单序列重复（SSR））并构建高密度物理图谱。
分别在构树、小构树和光叶楮的13条高质量组装假染色体及其未组装支架中鉴定出369,557、332,627和276,245个SSR。在这三个物种中鉴定出的基因组SSR中，短重复序列更为丰富，而长重复序列所占比例较小。此外，这三种构属物种的SSR中主要的重复基序由“A”和“T”重复组成。以构树基因组为参考，在这三个物种中鉴定出4,419个共同的SSR，而2,048个SSR是光叶楮特有的，4,285个SSR是小构树特有的。分布分析表明，这三个物种的假染色体上SSR的分布模式具有显著相似性。此外，在鉴定出的SSR中，分别有28%、31%和24%被定位到构树、光叶楮和小构树的基因中。基因定位的SSR可能通过影响基因活性和蛋白质功能来调节生物学过程。为了验证SSR的多态性，我们从10,752个潜在多态性SSR位点中选择了30个在这三个物种中进行PCR扩增，所有这些位点均成功扩增并在这三个物种中表现出多态性。
这些发现有助于进一步研究构属物种的起源、进化和迁移，也为构属物种种质资源的精确鉴定、系统评价和高效利用奠定了基础。
