Barrett Craig F, Ramachandran Dhanushya, Chen Chih-Hui, Corbett Cameron W, Huebner Cynthia D, Sinn Brandon T, Yu Wen-Bin, Suetsugu Kenji
Department of Biology, West Virginia University, 53 Campus Drive, Morgantown, West Virginia, USA 26506.
Endemic Species Research Institute, 1 Ming-Sheng East Road, Jiji, Nantou 552, Taiwan.
bioRxiv. 2023 Feb 11:2023.02.10.527995. doi: 10.1101/2023.02.10.527995.
Plants remain underrepresented among species with sequenced mitochondrial genomes (mitogenomes), due to the difficulty in assembly with short-read technology. Invasive species lag behind crops and other economically important species in this respect, representing a lack of tools for management and land conservation efforts.
The mitogenome of , one of the most damaging invasive plant species in North America, was sequenced and analyzed using long-read data, providing a resource for biologists and managers. We conducted analyses of genome content, phylogenomic analyses among grasses and relatives based on mitochondrial coding regions, and an analysis of mitochondrial single nucleotide polymorphism in this invasive grass species.
The assembly is 478,010 bp in length and characterized by two large, inverted repeats, and a large, direct repeat. However, the genome could not be circularized, arguing against a "master circle" structure. Long-read assemblies with data subsets revealed several alternative genomic conformations, predominantly associated with large repeats. Plastid-like sequences comprise 2.4% of the genome, with further evidence of Class I and Class II transposable element-like sequences. Phylogenetic analysis placed with other species, excluding , but with weak support. Analysis of polymorphic sites across 112 accessions of from the native and invasive ranges revealed a complex invasion history.
We present an in-depth analysis of mitogenome structure, content, phylogenetic relationships, and range-wide genomic variation in invasive US range. The mitogenome of is typical of other andropogonoid grasses, yet mitochondrial sequence variation across the invasive and native ranges is extensive. Our findings suggest multiple introductions to the US over the last century, with subsequent spread, secondary contact, long-distance dispersal, and possibly post-invasion selection on awn phenotypes. Efforts to produce genomic resources for invasive species, including sequenced mitochondrial genomes, will continue to provide tools for their effective management, and to help predict and prevent future invasions.
由于短读长技术在组装方面存在困难，植物在已测序线粒体基因组（线粒体基因组）的物种中所占比例仍然较低。在这方面，入侵物种落后于作物和其他具有经济重要性的物种，这意味着缺乏用于管理和土地保护工作的工具。
对北美最具破坏性的入侵植物物种之一的线粒体基因组进行了测序，并使用长读长数据进行了分析，为生物学家和管理人员提供了一种资源。我们对基因组内容进行了分析，基于线粒体编码区域对禾本科植物及其近缘种进行了系统发育分析，并对这种入侵禾本科植物的线粒体单核苷酸多态性进行了分析。
组装后的长度为478,010碱基对，其特征是有两个大的反向重复序列和一个大的正向重复序列。然而，基因组无法环化，这与“主环”结构相悖。使用数据子集进行的长读长组装揭示了几种替代的基因组构象，主要与大的重复序列相关。类质体序列占基因组的2.4%，还有更多关于I类和II类转座元件样序列的证据。系统发育分析将该物种与其他物种归为一类，但不包括某一物种，且支持力度较弱。对来自原生和入侵范围的112份该物种样本的多态性位点分析揭示了复杂的入侵历史。
我们对美国入侵范围内该物种的线粒体基因组结构、内容、系统发育关系和全范围基因组变异进行了深入分析。该物种的线粒体基因组是其他须芒草类禾本科植物的典型代表，但入侵和原生范围内的线粒体序列变异广泛。我们的研究结果表明，在上个世纪该物种多次被引入美国，随后扩散、二次接触、远距离传播，并可能在芒的表型上进行了入侵后选择。为入侵物种生产基因组资源的努力，包括已测序的线粒体基因组，将继续为其有效管理提供工具，并有助于预测和防止未来的入侵。
