Key Laboratory of Plant Resources Conservation and Sustainable Utilization / Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China.
South China National Botanical Garden, Guangzhou, 510650, China.
BMC Plant Biol. 2023 Apr 26;23(1):218. doi: 10.1186/s12870-023-04217-8.
Avena longiglumis Durieu (2n = 2x = 14) is a wild relative of cultivated oat (Avena sativa, 2n = 6x = 42) with good agronomic and nutritional traits. The plant mitochondrial genome has a complex organization and carries genetic traits of value in exploiting genetic resources, not least male sterility alleles used to generate F hybrid seeds. Therefore, we aim to complement the chromosomal-level nuclear and chloroplast genome assemblies of A. longiglumis with the complete assembly of the mitochondrial genome (mitogenome) based on Illumina and ONT long reads, comparing its structure with Poaceae species.
The complete mitochondrial genome of A. longiglumis can be represented by one master circular genome being 548,445 bp long with a GC content of 44.05%. It can be represented by linear or circular DNA molecules (isoforms or contigs), with multiple alternative configurations mediated by long (4,100-31,235 bp) and medium (144-792 bp) size repeats. Thirty-five unique protein-coding genes, three unique rRNA genes, and 11 unique tRNA genes are identified. The mitogenome is rich in duplications (up to 233 kb long) and multiple tandem or simple sequence repeats, together accounting for more than 42.5% of the total length. We identify homologous sequences between the mitochondrial, plastid and nuclear genomes, including the exchange of eight plastid-derived tRNA genes, and nuclear-derived retroelement fragments. At least 85% of the mitogenome is duplicated in the A. longiglumis nuclear genome. We identify 269 RNA editing sites in mitochondrial protein-coding genes including stop codons truncating ccmFC transcripts.
Comparative analysis with Poaceae species reveals the dynamic and ongoing evolutionary changes in mitochondrial genome structure and gene content. The complete mitochondrial genome of A. longiglumis completes the last link of the oat reference genome and lays the foundation for oat breeding and exploiting the biodiversity in the genus.
长穗燕麦（Avena longiglumis Durieu，2n=2x=14）是栽培燕麦（Avena sativa，2n=6x=42）的野生近缘种，具有良好的农艺和营养特性。植物线粒体基因组具有复杂的结构，并携带具有利用遗传资源价值的遗传特征，尤其是用于产生 F1 杂种种子的雄性不育等位基因。因此，我们旨在基于 Illumina 和 ONT 长读长，用完整的线粒体基因组（mitogenome）补充长穗燕麦的染色体水平核基因组和叶绿体基因组组装，并比较其与禾本科物种的结构。
长穗燕麦的完整线粒体基因组可以用一个主环基因组来表示，该基因组长 548445bp，GC 含量为 44.05%。它可以用线性或圆形 DNA 分子（同种型或连续体）来表示，这些分子通过长（4100-31235bp）和中（144-792bp）大小重复来介导多种替代构型。鉴定出 35 个独特的蛋白质编码基因、3 个独特的 rRNA 基因和 11 个独特的 tRNA 基因。线粒体基因组富含重复序列（长达 233kb）和多个串联或简单序列重复，占总长度的 42.5%以上。我们在线粒体、质体和核基因组之间鉴定了同源序列，包括 8 个质体衍生的 tRNA 基因和核衍生的反转录元件片段的交换。至少 85%的线粒体基因组在长穗燕麦的核基因组中发生了重复。我们在线粒体蛋白编码基因中鉴定了 269 个 RNA 编辑位点，包括终止密码子截断 ccmFC 转录物的位点。
与禾本科物种的比较分析揭示了线粒体基因组结构和基因含量的动态和持续进化变化。长穗燕麦完整的线粒体基因组完成了燕麦参考基因组的最后一环，为燕麦的选育和利用燕麦属的生物多样性奠定了基础。
