State Key Laboratory of Silkworm Genome Biology, Institute of Sericulture and Systems Biology, Southwest University, Chongqing 400716, China.
Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China.
Genomics Proteomics Bioinformatics. 2022 Dec;20(6):1119-1137. doi: 10.1016/j.gpb.2022.08.005. Epub 2022 Aug 30.
Multiple plant lineages have independently evolved sex chromosomes and variable karyotypes to maintain their sessile lifestyles through constant biological innovation. Morus notabilis, a dioecious mulberry species, has the fewest chromosomes among Morus spp., but the genetic basis of sex determination and karyotype evolution in this species has not been identified. In this study, three high-quality genome assemblies were generated for Morus spp. [including dioecious M. notabilis (male and female) and Morus yunnanensis (female)] with genome sizes of 301-329 Mb and were grouped into six pseudochromosomes. Using a combination of genomic approaches, we found that the putative ancestral karyotype of Morus species was close to 14 protochromosomes, and that several chromosome fusion events resulted in descending dysploidy (2n = 2x = 12). We also characterized a ∼ 6.2-Mb sex-determining region on chromosome 3. Four potential male-specific genes, a partially duplicatedDNA helicase gene (named MSDH) and three Ty3_Gypsy long terminal repeat retrotransposons (named MSTG1/2/3), were identified in the Y-linked area and considered to be strong candidate genes for sex determination or differentiation. Population genomic analysis showed that Guangdong accessions in China were genetically similar to Japanese accessions of mulberry. In addition, genomic areas containing selective sweeps that distinguish domesticated mulberry from wild populations in terms of flowering and disease resistance were identified. Our study provides an important genetic resource for sex identification research and molecular breeding in mulberry.
多个植物谱系独立进化出性染色体和可变的染色体组型，通过不断的生物创新来维持其固着的生活方式。桑树是雌雄异株的物种，其中桑树的染色体数目最少，但该物种的性别决定和染色体组型进化的遗传基础尚未确定。在这项研究中，我们为桑树属[包括雌雄异株的 M. notabilis（雄性和雌性）和 M. yunnanensis（雌性）]生成了三个高质量的基因组组装，基因组大小为 301-329 Mb，并将其分组为六个假染色体。通过结合基因组方法，我们发现桑树属的假定祖先染色体组接近于 14 个原染色体，并且发生了几次染色体融合事件，导致染色体数目下降（2n=2x=12）。我们还对 3 号染色体上的一个约 6.2-Mb 的性别决定区域进行了特征描述。在 Y 连锁区域中鉴定出四个潜在的雄性特异性基因，一个部分重复的 DNA 解旋酶基因（命名为 MSDH）和三个 Ty3_Gypsy 长末端重复反转录转座子（命名为 MSTG1/2/3），它们被认为是性别决定或分化的候选基因。群体基因组分析表明，中国广东的桑树种质与日本的桑树具有相似的遗传关系。此外，还鉴定出了区分驯化桑和野生种群在开花和抗病性方面的基因组选择性清除区域。我们的研究为桑树的性别鉴定研究和分子育种提供了重要的遗传资源。
