College of Life Sciences, Henan Normal University, Xinxiang, 453007, China.
SanQuan Medical College, Xinxiang Medical University, Xinxiang, 453003, China.
BMC Plant Biol. 2019 Aug 16;19(1):361. doi: 10.1186/s12870-019-1975-8.
The transfer of chloroplast DNA into nuclear genome is a common process in plants. These transfers form nuclear integrants of plastid DNAs (NUPTs), which are thought to be driving forces in genome evolution, including sex chromosome evolution. In this study, NUPTs in the genome of a dioecious plant Asparagus officinalis L. were systematically analyzed, in order to investigate the characteristics of NUPTs in the nuclear genome and the relationship between NUPTs and sex chromosome evolution in this species.
A total of 3155 NUPT insertions were detected, and they represented approximated 0.06% of the nuclear genome. About 45% of the NUPTs were organized in clusters. These clusters were derived from various evolutionary events. The Y chromosome contained the highest number and largest proportion of NUPTs, suggesting more accumulation of NUPTs on sex chromosomes. NUPTs were distributed widely in all of the chromosomes, and some regions preferred these insertions. The highest density of NUPTs was found in a 47 kb region in the Y chromosome; more than 75% of this region was occupied by NUPTs. Further cytogenetic and sequence alignment analysis revealed that this region was likely the centromeric region of the sex chromosomes. On the other hand, the male-specific region of the Y chromosome (MSY) and the adjacent regions did not have NUPT insertions.
These results indicated that NUPTs were involved in shaping the genome of A. officinalis through complicated process. NUPTs may play important roles in the centromere shaping of the sex chromosomes of A. officinalis, but were not implicated in MSY formation.
叶绿体 DNA 向核基因组的转移是植物中常见的过程。这些转移形成了质体 DNA 的核整合体（NUPTs），它们被认为是基因组进化的驱动力，包括性染色体进化。在这项研究中，系统分析了雌雄异株植物天门冬属（Asparagus officinalis L.）基因组中的 NUPTs，以研究 NUPTs 在核基因组中的特征以及它们与该物种性染色体进化之间的关系。
共检测到 3155 个 NUPT 插入，它们约占核基因组的 0.06%。大约 45%的 NUPTs 被组织成簇。这些簇来自于各种进化事件。Y 染色体包含数量最多和比例最大的 NUPTs，表明性染色体上有更多的 NUPTs积累。NUPTs 广泛分布在所有染色体上，并且一些区域偏爱这些插入。在 Y 染色体的 47kb 区域中发现了 NUPTs 的最高密度；该区域的 75%以上被 NUPTs 占据。进一步的细胞遗传学和序列比对分析表明，该区域可能是性染色体的着丝粒区域。另一方面，Y 染色体的雄性特异性区域（MSY）及其相邻区域没有 NUPT 插入。
这些结果表明，NUPTs 通过复杂的过程参与了天门冬属基因组的塑造。NUPTs 可能在天门冬属性染色体着丝粒的形成中发挥重要作用，但不参与 MSY 的形成。
