The sugarcane mitochondrial genome: assembly, phylogenetics and transcriptomics
The sugarcane mitochondrial genome: assembly, phylogenetics and transcriptomics
复制标题
DOI：
10.7717/peerj.7558
复制
发表时间：
2019-09-24
期刊：
影响因子：
2.7
通讯作者：
Riano Pachon, Diego M.
中科院分区：
文献类型：
--
作者：
Evans, Dyfed Lloyd;Hlongwane, Thandekile Thandiwe;Riano Pachon, Diego M.
背景：叶绿体基因组提供的系统发育信息不足以区分密切相关的甘蔗品种，因为许多品种的起源较晚，而且叶绿体序列保守。相比之下，植物的线粒体基因组更大，更具可塑性，可能包含更多的系统发育信号。我们用Illumina TruSeq合成长reads和Oxford Nanopore Technologies MinION长reads组装了一致的参考线粒体。在此基础上，我们还分析了甘蔗和高粱的线粒体转录组，并改进了甘蔗线粒体的注释，与其他物种相比。方法：采用诱饵组装法从基因组读取池中组装线粒体基因组。使用BLAST对有丝分裂基因组进行详尽的注释，并在使用Integrated Genome Viewer进行分析之前使用HISAT2绘制转录本数据集。结果：甘蔗线粒体由两条独立的染色体组成，不存在重组的迹象。在SP80-3280的基础上，对另外4个甘蔗品种（R570、LCP85-384、RB72343和SP70-1143）的有丝分裂基因组进行了组装（SP70-1143的组装利用了基因组和转录组学数据）。我们证明甘蔗质体是完全转录的，我们仅使用转录组数据组装了SP80-3280的叶绿体基因组。利用有丝分裂基因组进行系统基因组分析，可以区分近亲甘蔗品种，并支持Saccharum officinarum和Saccharum cultum作为现代甘蔗母本的区分。通过对整个叶绿体的比较，我们证明了现代甘蔗起源于有限数量的Saccharum栽培女性创始人。转录组学和剪接体分析表明，甘蔗线粒体的两条染色体在转录水平上是结合的，剪接位点在基因编码区域内比在基因编码区域外更频繁地发生。我们在甘蔗线粒体中发现了一个确认的和一个潜在的细胞质雄性不育（CMS）因子，这两个因子都是转录的。结论：甘蔗线粒体的转录加工是高度复杂的，剪接事件多种多样，大多数剪接事件跨越两条染色体。PolyA诱导的转录本与使用聚腺苷酸化降解转录本是一致的。我们首次在甘蔗线粒体内标注了两个CMS因子，并证明甘蔗具有CMS和救援所需的所有分子机制。提出了一种基于向导rna的跨染色体剪接机制。我们还证明有丝分裂基因组可以用于甘蔗品种的系统基因组研究。
Background: Chloroplast genomes provide insufficient phylogenetic information to distinguish between closely related sugarcane cultivars, due to the recent origin of many cultivars and the conserved sequence of the chloroplast. In comparison, the mitochondrial genome of plants is much larger and more plastic and could contain increased phylogenetic signals. We assembled a consensus reference mitochondrion with Illumina TruSeq synthetic long reads and Oxford Nanopore Technologies MinION long reads. Based on this assembly we also analyzed the mitochondrial transcriptomes of sugarcane and sorghum and improved the annotation of the sugarcane mitochondrion as compared with other species.Methods: Mitochondrial genomes were assembled from genomic read pools using a bait and assemble methodology. The mitogenome was exhaustively annotated using BLAST and transcript datasets were mapped with HISAT2 prior to analysis with the Integrated Genome Viewer.Results: The sugarcane mitochondrion is comprised of two independent chromosomes, for which there is no evidence of recombination. Based on the reference assembly from the sugarcane cultivar SP80-3280 the mitogenomes of four additional cultivars (R570, LCP85-384, RB72343 and SP70-1143) were assembled (with the SP70-1143 assembly utilizing both genomic and transcriptomic data). We demonstrate that the sugarcane plastome is completely transcribed and we assembled the chloroplast genome of SP80-3280 using transcriptomic data only. Phylogenomic analysis using mitogenomes allow closely related sugarcane cultivars to be distinguished and supports the discrimination between Saccharum officinarum and Saccharum cultum as modern sugarcane's female parent. From whole chloroplast comparisons, we demonstrate that modern sugarcane arose from a limited number of Saccharum cultum female founders. Transcriptomic and spliceosomal analyses reveal that the two chromosomes of the sugarcane mitochondrion are combined at the transcript level and that splice sites occur more frequently within gene coding regions than without. We reveal one confirmed and one potential cytoplasmic male sterility (CMS) factor in the sugarcane mitochondrion, both of which are transcribed.Conclusion: Transcript processing in the sugarcane mitochondrion is highly complex with diverse splice events, the majority of which span the two chromosomes. PolyA baited transcripts are consistent with the use of polyadenylation for transcript degradation. For the first time we annotate two CMS factors within the sugarcane mitochondrion and demonstrate that sugarcane possesses all the molecular machinery required for CMS and rescue. A mechanism of cross-chromosomal splicing based on guide RNAs is proposed. We also demonstrate that mitogenomes can be used to perform phylogenomic studies on sugarcane cultivars.