Yanlei Feng , Yukang Wang , Hejun Lu , Jun Li , Delara Akhter , Fang Liu , Ting Zhao , Xingxing Shen , Xiaobo Li , James Whelan , Tianzhen Zhang , Jianping Hu , Ronghui Pan
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Whereas, with only a few mitogenomes assembled in the cotton genus <em>Gossypium</em>, our knowledge about their roles in cotton evolution and speciation is still scarce. To close this gap, here we assembled 20 mitogenomes from 15 cotton species spanning all the cotton clades (A–G, K, and AD genomes) and 5 cotton relatives using short and long sequencing reads. Systematic analyses uncovered a high level of mitochondrial gene sequence conservation, abundant sequence repeats and many insertions of foreign sequences, as well as extensive structural variations in cotton mitogenomes. The sequence repeats and foreign sequences caused significant mitogenome size inflation in <em>Gossypium</em> and its close relative <em>Kokia</em> in general, while there is no significant difference between the lint and fuzz cotton mitogenomes in terms of gene content, RNA editing, and gene expression level. Interestingly, we further revealed the specific presence and expression of two novel mitochondrial open reading frames (ORFs) in lint-fiber cotton species. 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引用次数: 0
摘要
棉花是世界上提供最重要的可再生纺织纤维的主要作物。棉花物种的分类和进化研究受到广泛关注,这不仅是因为棉花的经济价值,还因为棉花是研究多倍体物种起源、进化和栽培的理想模式系统。之前的研究表明,线粒体基因组编辑位点和拷贝数以及线粒体功能参与了棉花纤维的伸长。然而,由于棉属植物棉花的有丝分裂基因组只有少数几个,我们对它们在棉花进化和物种分化中的作用仍然知之甚少。为了填补这一空白,我们利用长短测序读数从 15 个棉花物种(跨越所有棉花支系(A-G、K 和 AD 基因组))和 5 个棉花近缘种中组装了 20 个有丝分裂基因组。系统分析发现,棉花有丝分裂基因组中存在线粒体基因序列高度保守、丰富的序列重复和大量外来序列插入,以及广泛的结构变异。序列重复和外来序列导致棉花及其近亲 Kokia 的有丝分裂基因组体积明显增大,而皮棉和绒毛棉的有丝分裂基因组在基因含量、RNA 编辑和基因表达水平方面没有显著差异。有趣的是,我们进一步揭示了两种新型线粒体开放阅读框(ORF)在皮棉和绒毛棉中的特异性存在和表达。最后,这些结构特征和新型 ORFs 有助于我们从有丝分裂基因组学的角度深入了解棉花进化和多倍体化的历史以及长皮棉物种的起源。
Assembly and phylogenomic analysis of cotton mitochondrial genomes provide insights into the history of cotton evolution
Cotton is a major crop that provides the most important renewable textile fibers in the world. Studies of the taxonomy and evolution of cotton species have received wide attentions, not only due to cotton’s economic value but also due to the fact that Gossypium is an ideal model system to study the origin, evolution, and cultivation of polyploid species. Previous studies suggested the involvement of mitochondrial genome editing sites and copy number as well as mitochondrial functions in cotton fiber elongation. Whereas, with only a few mitogenomes assembled in the cotton genus Gossypium, our knowledge about their roles in cotton evolution and speciation is still scarce. To close this gap, here we assembled 20 mitogenomes from 15 cotton species spanning all the cotton clades (A–G, K, and AD genomes) and 5 cotton relatives using short and long sequencing reads. Systematic analyses uncovered a high level of mitochondrial gene sequence conservation, abundant sequence repeats and many insertions of foreign sequences, as well as extensive structural variations in cotton mitogenomes. The sequence repeats and foreign sequences caused significant mitogenome size inflation in Gossypium and its close relative Kokia in general, while there is no significant difference between the lint and fuzz cotton mitogenomes in terms of gene content, RNA editing, and gene expression level. Interestingly, we further revealed the specific presence and expression of two novel mitochondrial open reading frames (ORFs) in lint-fiber cotton species. Finally, these structural features and novel ORFs help us gain valuable insights into the history of cotton evolution and polyploidization and the origin of species producing long lint fibers from a mitogenomic perspective.
Crop JournalAgricultural and Biological Sciences-Agronomy and Crop Science
CiteScore
9.90
自引率
3.00%
发文量
638
审稿时长
41 days
期刊介绍:
The major aims of The Crop Journal are to report recent progresses in crop sciences including crop genetics, breeding, agronomy, crop physiology, germplasm resources, grain chemistry, grain storage and processing, crop management practices, crop biotechnology, and biomathematics.
The regular columns of the journal are Original Research Articles, Reviews, and Research Notes. The strict peer-review procedure will guarantee the academic level and raise the reputation of the journal. The readership of the journal is for crop science researchers, students of agricultural colleges and universities, and persons with similar academic levels.