The kinetoplastids are unicellular flagellates that derive their name from the ‘kinetoplast’, a region within their single mitochondrion harboring its organellar genome of high DNA content, called kinetoplast (k) DNA. Some protein products of this mitochondrial genome are encoded as cryptogenes; their transcripts require editing to generate an open reading frame. This happens through RNA editing, whereby small regulatory guide (g)RNAs direct the proper insertion and deletion of one or more uridines at each editing site within specific transcript regions. An accurate perspective of the kDNA expansion and evolution of their unique uridine insertion/deletion editing across kinetoplastids has been difficult to achieve. Here, we resolved the kDNA structure and editing patterns in the early-branching kinetoplastid Trypanoplasma borreli and compare them with those of the well-studied trypanosomatids. We find that its kDNA consists of circular molecules of about 42 kb that harbor the rRNA and protein-coding genes, and 17 different contigs of approximately 70 kb carrying an average of 23 putative gRNA loci per contig. These contigs may be linear molecules, as they contain repetitive termini. Our analysis uncovered a putative gRNA population with unique length and sequence parameters that is massive relative to the editing needs of this parasite. We validated or determined the sequence identity of four edited mRNAs, including one coding for ATP synthase 6 that was previously thought to be missing. We utilized computational methods to show that the T. borreli transcriptome includes a substantial number of transcripts with inconsistent editing patterns, apparently products of non-canonical editing. This species utilizes the most extensive uridine deletion compared to other studied kinetoplastids to enforce amino acid conservation of cryptogene products, although insertions still remain more frequent. Finally, in three tested mitochondrial transcriptomes of kinetoplastids, uridine deletions are more common in the raw mitochondrial reads than aligned to the fully edited, translationally competent mRNAs. We conclude that the organization of kDNA across known kinetoplastids represents variations on partitioned coding and repetitive regions of circular molecules encoding mRNAs and rRNAs, while gRNA loci are positioned on a highly unstable population of molecules that differ in relative abundance across strains. Likewise, while all kinetoplastids possess conserved machinery performing RNA editing of the uridine insertion/deletion type, its output parameters are species-specific.

动质体是单细胞鞭毛虫，它们的名字来源于“动质体”，这是它们单个线粒体内的一个区域，包含其高 DNA 含量的细胞器基因组，称为动质体 (k) DNA。该线粒体基因组的一些蛋白质产物被编码为隐基因；他们的成绩单需要编辑以生成开放阅读框。这是通过 RNA 编辑实现的，其中小的调节指导 (g)RNA 指导在特定转录本区域内的每个编辑位点正确插入和删除一个或多个尿苷。很难准确地了解 kDNA 扩展和它们独特的尿苷插入/删除编辑在动质体中的演变。在这里，我们解决了早期分支动质体中的 kDNA 结构和编辑模式Trypanoplasma borreli并将它们与研究充分的锥虫进行比较。我们发现它的 kDNA 由大约 42 kb 的环状分子组成，其中包含 rRNA 和蛋白质编码基因，以及 17 个大约 70 kb 的不同重叠群，每个重叠群平均携带 23 个假定的 gRNA 位点。这些重叠群可能是线性分子，因为它们包含重复的末端。我们的分析发现了一个推定的 gRNA 群体，其具有独特的长度和序列参数，相对于这种寄生虫的编辑需求而言是巨大的。我们验证或确定了四种编辑过的 mRNA 的序列身份，包括一种以前认为缺失的 ATP 合酶 6 编码。我们利用计算方法表明T. borreli转录组包括大量具有不一致编辑模式的转录本，显然是非规范编辑的产物。与其他研究的动质体相比，该物种利用最广泛的尿苷缺失来加强隐基因产物的氨基酸保护，尽管插入仍然更频繁。最后，在三个测试的动质体线粒体转录组中，尿苷缺失在原始线粒体读数中比与完全编辑的、具有翻译能力的 mRNA 对齐更常见。我们得出结论，kDNA 在已知动质体中的组织代表了编码 mRNA 和 rRNA 的环状分子的分区编码和重复区域的变化，而 gRNA 位点位于高度不稳定的分子群中，这些分子在不同菌株中的相对丰度不同。同样地，虽然所有的动质体都拥有保守的机制来执行尿苷插入/删除类型的 RNA 编辑，但其输出参数是物种特异性的。