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复杂物种四个线粒体基因组的组装与比较基因组分析

Assembly and comparative genome analysis of four mitochondrial genomes from complex species.

作者信息

Li Sicheng, Yang Cuifang, Wang Zhen, Xu Chaohua, Zhang Gemin, Huang Yuxin, Zhang Baoqing, Zhou Shan, Gao Yijing, Zong Wenyi, Duan Weixing, Yang Xiping

机构信息

Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences/Guangxi Key Laboratory of Sugarcane Genetic Improvement/Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture & Rural Affairs, Nanning, China.

State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, China.

出版信息

Front Plant Sci. 2024 Jul 19;15:1421170. doi: 10.3389/fpls.2024.1421170. eCollection 2024.

DOI:10.3389/fpls.2024.1421170
PMID:39100089
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC11294102/
Abstract

complex includes genera , , , , and . Since the complex/Saccharinae constitutes the gene pool used by sugarcane breeders to introduce useful traits into sugarcane, studying the genomic characterization of the Saccharum complex has become particularly important. Here, we assembled graph-based mitochondrial genomes (mitogenomes) of four Saccharinae species (, E. rockii, , and ) using Illumina and PacBio sequencing data. The total lengths of the mitogenomes of , , and were 549,593 bp, 514,248 bp, 481,576 bp and 513,095 bp, respectively. Then, we performed a comparative mitogenomes analysis of Saccharinae species, including characterization, organelles transfer sequence, collinear sequence, phylogenetics analysis, and gene duplicated/loss. Our results provided the mitogenomes of four species closely related to sugarcane breeding, enriching the mitochondrial genomic resources of the Saccharinae. Additionally, our study offered new insights into the evolution of mitogenomes at the family and genus levels and enhanced our understanding of organelle evolution in the highly polyploid genus.

摘要

该复合体包括属、、、、和。由于复合体/甘蔗亚族构成了甘蔗育种者用于将有用性状导入甘蔗的基因库，研究甘蔗属复合体的基因组特征变得尤为重要。在此，我们利用Illumina和PacBio测序数据组装了四种甘蔗亚族物种（、滇蔗茅、、和）基于图谱的线粒体基因组（线粒体基因组）。、、和的线粒体基因组总长度分别为549,593 bp、514,248 bp、481,576 bp和513,095 bp。然后，我们对甘蔗亚族物种进行了线粒体基因组比较分析，包括特征分析、细胞器转移序列、共线序列、系统发育分析以及基因重复/丢失分析。我们的结果提供了与甘蔗育种密切相关的四个物种的线粒体基因组，丰富了甘蔗亚族的线粒体基因组资源。此外，我们的研究为科和属水平上线粒体基因组的进化提供了新见解，并增强了我们对高度多倍体甘蔗属中细胞器进化的理解。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/58cf/11294102/d40b614578a5/fpls-15-1421170-g007.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/58cf/11294102/eb4fc636c037/fpls-15-1421170-g001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/58cf/11294102/5bc37efa0639/fpls-15-1421170-g002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/58cf/11294102/0c83d8e8083e/fpls-15-1421170-g003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/58cf/11294102/f99dee3195c4/fpls-15-1421170-g004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/58cf/11294102/fb9e51eb1f9b/fpls-15-1421170-g005.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/58cf/11294102/af54e3a951d4/fpls-15-1421170-g006.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/58cf/11294102/d40b614578a5/fpls-15-1421170-g007.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/58cf/11294102/eb4fc636c037/fpls-15-1421170-g001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/58cf/11294102/5bc37efa0639/fpls-15-1421170-g002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/58cf/11294102/0c83d8e8083e/fpls-15-1421170-g003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/58cf/11294102/f99dee3195c4/fpls-15-1421170-g004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/58cf/11294102/fb9e51eb1f9b/fpls-15-1421170-g005.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/58cf/11294102/af54e3a951d4/fpls-15-1421170-g006.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/58cf/11294102/d40b614578a5/fpls-15-1421170-g007.jpg

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本文引用的文献

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The complex polyploid genome architecture of sugarcane.甘蔗复杂的多倍体基因组结构。
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Biomass and energy potential of Erianthus arundinaceus and Saccharum spontaneum-derived novel sugarcane hybrids in rainfed environments.雨养环境下芦竹和野生甘蔗衍生新型甘蔗杂种的生物量和能源潜力。
BMC Plant Biol. 2024 Mar 19;24(1):198. doi: 10.1186/s12870-024-04885-0.
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Genome copy number predicts extreme evolutionary rate variation in plant mitochondrial DNA.基因组拷贝数预测了植物线粒体 DNA 的极端进化速率变化。
Proc Natl Acad Sci U S A. 2024 Mar 5;121(10):e2317240121. doi: 10.1073/pnas.2317240121. Epub 2024 Mar 1.
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Plant organellar genomes: much done, much more to do.植物细胞器基因组：完成了很多，还有更多要做。
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TBtools-II: A "one for all, all for one" bioinformatics platform for biological big-data mining.TBtools-II：一个“一专多能”的生物信息学大数据挖掘平台。
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