Conifers are a group of cone-bearing seed plants.They comprise ca. 630 species in two clades, Pinaceae (conifers I clade) and cupressophytes (conifers II clade, consisting of five families). 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 .
Plastid gene transcription is a complex process, involving both prokaryotic- and eukaryotic-type systems . Most plastid genes are presumably transcribed as polycistronic mRNAs which then undergo various post-transcriptional modifications . These processes generate tremendously elaborate transcriptomes with an unprecedented diversity of non-coding RNAs , multiple loci for transcriptional initiation and termination [5, 6], a full or nearly full transcription of the genome [7, 8], and varying frequencies of RNA-editing sites .
Plastid genomes (plastomes) of land plants are highly conserved in their gene content and order. Functionally related genes are commonly found in clusters and are likely co-transcribed as operons . These operons may be conserved due to selective constraints rather than slow rates of neutral chromosomal rearrangements . However, mounting evidence indicates that many taxa, including conifers (the largest group of gymnosperms), have highly rearranged plastomes [12–14]. Some of these rearrangements resulted in disruption of canonical operons and creation of novel co-transcriptional units. An example is the disruption of rps2 operons in Sciadopitys and Callitris [15, 16]. We have long been puzzled by these findings because it is then unclear whether plastomic rearrangements affect plastid gene transcription. If they do, what are the underlying mechanisms and consequences of such changes?
In this study, we sequenced both plastomic DNA and RNA from one representative genus in each of the six extant conifer families. Strand-specific RNA libraries have the advantage of allowing for the discrimination of sense and antisense transcripts . We took advantage of this to (1) investigate the full transcription capability of both plastomic strands, (2) estimate the relative number of plastid coding and antisense transcripts, and (3) identify plastid C-to-U RNA-editing sites separately at sense and antisense transcripts in conifers. We also compared plastid gene expression levels among conifers and demonstrated a strong association between gene expression and plastomic rearrangements. We discuss possible mechanisms underlying this association.