Abstract
Inverted repeat (IR) regions in the plastomes from land plants induce homologous recombination, generating isomeric plastomes. While the plastomes of Taxaceae species often lose one of the IR regions, considerable isomeric plastomes were created in Taxaceae species with a hitherto unclarified mechanism. To investigate the detailed mechanism underpinning the IR-independent genesis of plastomic diversity, we sequenced four Taxaceae plastomes, including Taxus cuspidata Siebold & Zuccarini, Taxus fauna Nan Li & R. R. Mill, and two individuals of Taxus wallichiana Zuccarini. Then we compared these structures with those of previously reported Taxaceae plastomes. Our analysis identified four distinct plastome forms that originated from the rearrangements of two IR-flanking inverted fragments. The presence of isomeric plastomes was then verified in T. cuspidata individuals. Both rearrangement analyses and phylogenetic results indicated that Taxaceae were separated into two clades, one including Taxus and Pseudotaxus and another formed by Amentotaxus and Torreya. Our reconstructed scenario suggests that the minimum number of inversion events required for the transformation of the plastome of Cephalotaxus oliveri Masters into the diversified Taxaceae plastomes ranged from three to six. To sum up, our study reveals a distinct pattern and the mechanism driving the structural diversification of Taxaceae plastomes, which will advance our understanding of the maintenance of plastomic diversity and complexity in conifers.
Highlights
Chloroplast is the organelle responsible for photosynthesis and providing energy for plants and photosynthetic algae (Dyall et al, 2004)
In this study, using a comparative plastome profiling, we revealed that the plastomes of all the 12 species from four different genera of Taxaceae contained an rpl23-rps3 cluster that is located downstream of the inverted repeat region B (IRB), demonstrating that Taxaceae plastomes lack inverted repeat region A (IRA) (Figure 1)
We revealed four new forms of organization in Taxaceae plastomes, which have possibly been generated by the rearrangements of two large inverted fragments (R1: infA-rps12 and R2: trnQ-Inverted repeat (IR)) that are flanked by specific short repeats (Figure 5 and Table 2)
Summary
Chloroplast (cp) is the organelle responsible for photosynthesis and providing energy for plants and photosynthetic algae (Dyall et al, 2004). The plastomes of most land plants and algae are composed of four parts, namely, two copies of large inverted repeats (IRs) that contain four ribosomal RNA genes (rrn, rrn, rrn4.5, and rrn5), a large single copy (LSC) and a small single copy (SSC) region (Wang et al, 2008; Wicke et al, 2011; Davis et al, 2014). Gymnosperms are generally categorized into five groups, namely, cycads, ginkgo, gnetophytes, Pinaceae (conifers I), and cupressophytes (conifers II) (Chaw et al, 1997; Rai et al, 2008). While the plastomes of cycads, ginkgo, and gnetophytes are known to be quadripartite, recent comparative analyses of conifer plastomes have revealed that Pinaceae and cupressophyte species possess reduced IR copies. Comparative analysis have demonstrated that the Pinaceae have lost inverted repeat region B (IRB) and the cupressophytes have lost inverted repeat region A (IRA), suggesting the IR loss is homoplasious rather than synapomorphic (Wu et al, 2011; Wu and Chaw, 2014)
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