Our understanding of plastid transcriptomes is limited to a few model plants whose plastid genomes (plastomes) have a highly conserved gene order. Consequently, little is known about how gene expression changes in response to genomic rearrangements in plastids. This is particularly important in the highly rearranged conifer plastomes. We sequenced and reported the plastomes and plastid transcriptomes of six conifer species, representing all six extant families. Strand-specific RNAseq data show a nearly full transcription of both plastomic strands and detect C-to-U RNA-editing sites at both sense and antisense transcripts. We demonstrate that the expression of plastid coding genes is strongly functionally dependent among conifer species. However, the strength of this association declines as the number of plastomic rearrangements increases. This finding indicates that plastomic rearrangement influences gene expression. Our data provide the first line of evidence that plastomic rearrangements not only complicate the plastomic architecture but also drive the dynamics of plastid transcriptomes in conifers.

中文翻译：

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针叶树质体组中基因组重排与基因表达的紧密联系

我们对质体转录组的了解仅限于其质体基因组（质体组）具有高度保守的基因顺序的一些模型植物。因此，人们对质体中基因表达如何响应基因组重排而知之甚少。这在高度重排的针叶树质塑料组中尤其重要。我们测序并报告了代表所有六个现存科的六个针叶树种的质体组和质体转录组。链特异性RNAseq数据显示出质体链几乎全部转录，并在有义和反义转录本上检测到C到U的RNA编辑位点。我们证明了针叶树种之间的质体编码基因的表达是强烈的功能依赖性。但是，这种关联的强度随着质体重排数目的增加而下降。这一发现表明，质体重排影响基因表达。我们的数据提供了第一线证据，质体重排不仅使质体结构复杂化，而且还驱动了针叶树质体转录组的动力学。