Abstract
BackgroundOur 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.ResultsWe 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.ConclusionsOur 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.
Highlights
Our understanding of plastid transcriptomes is limited to a few model plants whose plastid genomes have a highly conserved gene order
We discuss possible mechanisms underlying this association. Both plastomic strands are fully transcribed in conifers The six newly assembled plastomes are illustrated as linear molecules to facilitate pairwise comparisons (Fig. 1a)
A plastomic inversion was detected in the sampled K. davidiana individual when it was compared to the conspecific reference (NC_011930; Fig. S1a)
Summary
Our understanding of plastid transcriptomes is limited to a few model plants whose plastid genomes (plastomes) have a highly conserved gene order. Little is known about how gene expression changes in response to genomic rearrangements in plastids. This is important in the highly rearranged conifer plastomes. Conifers are a group of cone-bearing seed plants. Conifers dominate temperate forests, especially in the Northern hemisphere, and significantly contribute to photosynthesis and biomass production. They provide shelters for wildlife and important resources for humans, such as solid wood fuel, valuable timber, edible seeds, and essential oils [1]. Most plastid genes are presumably transcribed as polycistronic mRNAs which undergo various post-
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