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细胞器衍生核 DNA 在小麦族物种中的进化轨迹。

Evolutionary trajectory of organelle-derived nuclear DNAs in the Triticum/Aegilops complex species.

机构信息

Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun 130024, China.

Jilin Academy of Vegetable and Flower Science, Changchun 130033, China.

出版信息

Plant Physiol. 2024 Jan 31;194(2):918-935. doi: 10.1093/plphys/kiad552.

DOI:10.1093/plphys/kiad552
PMID:37847157
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC10828211/
Abstract

Organelle-derived nuclear DNAs, nuclear plastid DNAs (NUPTs), and nuclear mitochondrial DNAs (NUMTs) have been identified in plants. Most, if not all, genes residing in NUPTs/NUMTs (NUPGs/NUMGs) are known to be inactivated and pseudogenized. However, the role of epigenetic control in silencing NUPGs/NUMGs and the dynamic evolution of NUPTs/NUMTs with respect to organismal phylogeny remain barely explored. Based on the available nuclear and organellar genomic resources of wheat (genus Triticum) and goat grass (genus Aegilops) within Triticum/Aegilops complex species, we investigated the evolutionary fates of NUPTs/NUMTs in terms of their epigenetic silencing and their dynamic occurrence rates in the nuclear diploid genomes and allopolyploid subgenomes. NUPTs and NUMTs possessed similar genomic atlas, including (i) predominantly located in intergenic regions and preferential integration to gene regulation regions and (ii) generating sequence variations in the nuclear genome. Unlike nuclear indigenous genes, the alien NUPGs/NUMGs were associated with repressive epigenetic signals, namely high levels of DNA methylation and low levels of active histone modifications. Phylogenomic analyses suggested that the species-specific and gradual accumulation of NUPTs/NUMTs accompanied the speciation processes. Moreover, based on further pan-genomic analyses, we found significant subgenomic asymmetry in the NUPT/NUMT occurrence, which accumulated during allopolyploid wheat evolution. Our findings provide insight into the dynamic evolutionary fates of organelle-derived nuclear DNA in plants.

摘要

细胞器衍生核 DNA、核质体 DNA（NUPTs）和核线粒体 DNA（NUMTs）已在植物中被鉴定出来。已知大多数（如果不是全部）位于 NUPTs/NUMTs（NUPGs/NUMGs）中的基因失活和假基因化。然而，表观遗传控制在 NUPGs/NUMGs 沉默中的作用以及 NUPTs/NUMTs 相对于生物体系统发育的动态进化仍几乎未被探索。基于小麦（属 Triticum）和山羊草（属 Aegilops）在 Triticum/Aegilops 复合体物种中的核和细胞器基因组资源，我们研究了 NUPTs/NUMTs 的进化命运，包括它们的表观遗传沉默以及它们在核二倍体基因组和异源多倍体亚基因组中的动态发生频率。NUPTs 和 NUMTs 具有相似的基因组图谱，包括（i）主要位于基因间区域，优先整合到基因调控区域，以及（ii）在核基因组中产生序列变异。与核本土基因不同，外来的 NUPGs/NUMGs 与抑制性表观遗传信号相关，即高水平的 DNA 甲基化和低水平的活性组蛋白修饰。系统基因组分析表明，物种特异性和逐渐积累的 NUPTs/NUMTs 伴随着物种形成过程。此外，基于进一步的泛基因组分析，我们发现 NUPT/NUMT 发生的亚基因组不对称性显著，这在异源多倍体小麦进化过程中积累。我们的研究结果为植物中线粒体衍生核 DNA 的动态进化命运提供了新的见解。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/051d/10828211/1c3a052bcf92/kiad552f8.jpg
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