Ruhlman Tracey A, Zhang Jin, Blazier John C, Sabir Jamal S M, Jansen Robert K
Department of Integrative Biology, University of Texas at Austin, Austin, Texas 78712 USA
Department of Integrative Biology, University of Texas at Austin, Austin, Texas 78712 USA.
Am J Bot. 2017 Apr;104(4):559-572. doi: 10.3732/ajb.1600453. Epub 2017 Apr 11.
There is a misinterpretation in the literature regarding the variable orientation of the small single copy region of plastid genomes (plastomes). The common phenomenon of small and large single copy inversion, hypothesized to occur through intramolecular recombination between inverted repeats (IR) in a circular, single unit-genome, in fact, more likely occurs through recombination-dependent replication (RDR) of linear plastome templates. If RDR can be primed through both intra- and intermolecular recombination, then this mechanism could not only create inversion isomers of so-called single copy regions, but also an array of alternative sequence arrangements.
We used Illumina paired-end and PacBio single-molecule real-time (SMRT) sequences to characterize repeat structure in the plastome of (Geraniaceae). We used OrgConv and inspected nucleotide alignments to infer ancestral nucleotides and identify gene conversion among repeats and mapped long (>1 kb) SMRT reads against the unit-genome assembly to identify alternative sequence arrangements.
Although lacks the canonical IR, we found that large repeats (>1 kilobase; kb) represent ∼22% of the plastome nucleotide content. Among the largest repeats (>2 kb), we identified GC-biased gene conversion and mapping filtered, long SMRT reads to the unit-genome assembly revealed alternative, substoichiometric sequence arrangements.
We offer a model based on RDR and gene conversion between long repeated sequences in the plastome and provide support that both intra-and intermolecular recombination between large repeats, particularly in repeat-rich plastomes, varies unit-genome structure while homogenizing the nucleotide sequence of repeats.
关于质体基因组（质体基因组）小单拷贝区域的可变方向，文献中存在误解。小单拷贝和大单拷贝倒置的常见现象，假设是通过环状单单元基因组中反向重复序列（IR）之间的分子内重组发生的，实际上更可能是通过线性质体基因组模板的重组依赖性复制（RDR）发生的。如果RDR可以通过分子内和分子间重组引发，那么这种机制不仅可以产生所谓单拷贝区域的倒置异构体，还可以产生一系列替代序列排列。
我们使用Illumina双端测序和PacBio单分子实时（SMRT）序列来表征老鹳草科植物质体基因组中的重复结构。我们使用OrgConv并检查核苷酸比对，以推断祖先核苷酸并识别重复序列之间的基因转换，并将长（>1 kb）的SMRT读数与单单元基因组组装进行比对，以识别替代序列排列。
尽管老鹳草科植物缺乏典型的IR，但我们发现大重复序列（>1千碱基；kb）占质体基因组核苷酸含量的约22%。在最大的重复序列（>2 kb）中，我们识别出GC偏向的基因转换，并且将过滤后的长SMRT读数映射到老鹳草科植物单单元基因组组装上，揭示了替代的、亚化学计量的序列排列。
我们提出了一个基于RDR和老鹳草科植物质体基因组中长重复序列之间基因转换的模型，并提供了支持，即大重复序列之间的分子内和分子间重组，特别是在富含重复序列的质体基因组中，会改变单单元基因组结构，同时使重复序列的核苷酸序列同质化。
