Journal of Integrative Agriculture

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甘蔗线粒体基因组的构象多样性及遗传进化

  

  • 修回日期:2025-02-17

Multiple chromosomal configurations and phylogenetic implications in Saccharum mitochondrial genomes

Guilong Lu1,2, Chang Zhang2, Qibin Wu2, Tingting Sun2, Shaolin Yang2, Erya Wei1, Junhui Li1, Youxiong Que2#   

  1. 1 School of Horticulture and Landscape Architecture, Henan Institute of Science and Technology, Xinxiang 453003, China

    2 National Key Laboratory for Tropical Crop Breeding, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences / Yunnan Academy of Agricultural Sciences, Sanya 572024 / Kaiyuan 661600, China

  • Revised:2025-02-17
  • About author: Guilong Lu, E-mail: luguilong666@126.com; #Correspondence Youxiong Que, E-mail: queyouxiong@126.com
  • Supported by:

    This work was supported by the Chinese Academy of Tropical Agricultural Sciences for Science and Technology Innovation Team of National Tropical Agricultural Science Center (CATASCXTD202402), National Key Research and Development Program of China (2022YFD2301100), National Key Laboratory for Tropical Crop Breeding (NKLTCB20230305, Hainan; NKLTCB-YAAS-2024-S01, Yunnan), the Agriculture Research System of China (CARS-17), and the Scientific Research Start-up Fund for High-level Introduced Talents of Henan Institute of Science and Technology (103020224001/073).

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摘要：

线粒体在植物生长发育、配子育性和生态适应性方面扮演着重要角色。甘蔗（Saccharum spp. hybrids）是世界上最为重要的糖料和能源作物，割手密（S. Spontaneum）和斑茅（S. arundinaceum）是改良甘蔗品种特性和拓宽遗传基础的优异种质资源，但其线粒体基因组及相关研究却鲜有报道。我们的研究对斑茅1-6，割手密2-2和甘蔗杂交种GT42、GT44、LC05-136、LC1541与YZ08-1609的线粒体基因组进行了组装和深入解析。结果表明，这些基因组全长445,578-533,662 bp，编码33个蛋白编码基因（protein coding genes, PCGs），GC含量为43.43%-43.82%。斑茅、割手密和甘蔗杂交种的线粒体基因组主结构分别为三环、单环+线性和双环类型，且由重复序列介导重组产生多种潜在构象。基于线粒体基因的内含子序列开发了可区分斑茅、割手密和甘蔗杂交种的分子标记SAnad4i3。在这些物种的PCGs中鉴定到了540-581个C到U的RNA编辑位点，其中在斑茅中有6个编辑与创造起始或终止密码子有关，而在割手密和甘蔗杂交种中只鉴定到5个相关位点。进一步，在线粒体基因组中鉴定到了30-37个叶绿体基因组同源片段，其中以割手密数量最多、斑茅最少。进化分析显示，甘蔗在长期进化中可能经历了多次基因组重组和基因转移事件，并丢失了8个PCGs。以上研究揭示了“甘蔗复合体”线粒体基因组的遗传多样性和复杂性，为物种分类和高倍体作物遗传进化研究提供了科学基础。

Abstract:

Mitochondria influence plant growth, fertility, and adaptation. Sugarcane (Saccharum hybrids) is the most important sugar and energy crop worldwide, and S. spontaneum and S. arundinaceum are excellent parental germplasm. However, few studies have been conducted on the mitochondrial genomes of sugarcane and related species. In this study, the mitogenomes of one S. arundinaceum, one S. spontaneum, and five sugarcane cultivars were assembled. The results showed that the sizes of these mitogenomes, encoding 33 protein-coding genes (PCGs), were between 445,578 and 533,662 bp, with a GC content of 43.43%-43.82%. The major structures of S. arundinaceum comprised three small rings, S. spontaneum had one ring and one linear structure, and sugarcane had two rings; there were multiple potential conformations due to repeat-mediated recombination. Furthermore, we developed an intron marker SAnad4i3 that can distinguish these species. Between 540 and 581 and from C to U RNA editing sites were identified in the PCGs, with six RNA editing sites were associated with the creation of start or stop codons in S. arundinaceum, and five sites each in S. spontaneum and the sugarcane hybrids were observed. Notably, 30-37 fragments homologous to chloroplast DNA were identified, with the highest number found in S. spontaneum. During evolution, these mitogenomes may have undergone multiple genomic reorganization and gene transfer events and lost eight PCGs. Collectively, this study reveals the genetic diversity and complexity of the Saccharum complex by providing a scientific basis for further germplasm identification and evolutionary research.

Key words: Saccharum , mitogenome ,  germplasm classification ,  RNA editing ,  gene transfer