The Unique Evolutionary Trajectory and Dynamic Conformations of DR and IR/DR- coexisting Plastomes of the Early Vascular Plant Selaginellaceae (Lycophyte)

Abstract

24Both direct repeats (DR) and inverted repeats (IR) are documented in the published 25 plastomes of four Selaginella species indicating the unusual and diverse plastome 26 structure in the family Selaginellaceae. In this study, we newly sequenced complete 27 plastomes of seven species from five main lineages of Selaginellaceae and also re-28 sequenced three species (S. tamariscina, S. uncinata and S. moellendorffii) to explore 29 the evolutionary trajectory of Selaginellaceae plastomes. Our results showed that the 30 plastomes of Selaginellaceae vary remarkably in size, gene contents, gene order and 31 GC contents. Notably, both DR and IR structure existed in the plastomes of 32 Selaginellaceae with DR structure being an early diverged character. The occurrence 33 of DR structure was right after the Permian-Triassic (P-T) extinction (ca. 246 Ma) and 34 remained in most subgenera of Selaginellaceae, whereas IR structure only reoccurred 35 in the most derived subg. Heterostachys (ca. 23 Ma). The presence of a pair of large 36 repeats psbK-trnQ, together with DR/IR region in S. bisulcata, S. pennata, S. uncinata, 37 and S. hainanensis, could frequently mediate diverse homologous recombination and 38 create approximately equal stoichiometric isomers (IR/DR-coexisting) and 39 subgenomes. High proportion of repeats is presumably responsible for the dynamic 40 IR/DR-coexisting plastomes, which possess a lower synonymous substitution rate (dS) 41 compared with DR-possessing plastomes. We propose that the occurrence of DR 42 structure, together with few repeats, is possibly selected to adapt to the 43 environmental upheaval during the P-T crisis and the IR/DR-coexisting plastomes also 44 reached an equilibrium in plastome organization through highly efficient homologous 45 recombination to maintain stability. 46 47 65 conservation in structures and gene order (Mower and Vickrey 2018). A 30 kb inversion 66 (ycf2-psbM) was detected in the large single copy (LSC) of ferns and seed plants 67 plastomes relative to bryophytes and lycophytes, which is a strong evidence showing 68 lycophytes are located at the basal position of vascular plants (Raubeson and Jansen 69 1992). The plastomes of ferns underwent two hypothetical inversions (CE inversion 70 (trnC to trnE) and DE inversion (trnD-trnY)) within rpoB-psbZ (BZ) region from the 71 ancestral gene order in eusporangiates to the derived gene order in core 72

Extreme plastid RNA editing may confound phylogenetic reconstruction: A case study of Selaginella (lycophytes)

“…1 f, Table 1 ). The studies of Zhang et al., 2019 , Zhang et al, 2020 suggested that species in clade E have lower substitution rates and simpler plastome structures, whereas species in clades A–D have higher substitution rates and more complex plastome structures. Our analyses indicate that the frequency of RNA editing in Selaginella plastomes may be positively correlated with the variation in plastome structure and the substitution rate.…”

“…Compared with species in clade D, species in clades A had a relatively lower number of RNA editing sites ( Fig. 1 f, Table 1 ), but more complex plastome structures and an accelerated substitution rate ( Zhang et al., 2019 , Zhang et al, 2020 ). More comprehensive taxon sampling and transcriptomic evidence are needed to illuminate the evolutionary patterns of RNA editing in Selaginella .…”

Phylogenomics of Selaginellaceae with special reference to the enigmatic sanguinolenta group

“…Plastomes of ten species of Selaginella were newly sequenced; three of them were selected from sanguinolenta group (Table S1). Two unpublished plastomes of S. nipponica and S. pallidissima from our group (Kang et al unpublished data) and the previously published fourteen Selaginella plastomes (Mower et al, 2019; Smith, 2009; Tsuji et al, 2007; Xu et al, 2018; Zhang et al, 2019; Zhang et al, 2018) were combined in the following analyses. The Selaginella species were selected to ensure even taxon sampling across subgenera in the genus and covered almost all major lineages (Jermy, 1990; Weststrand and Korall, 2016a, b; Zhou et al, 2016; Zhou and Zhang, 2015).…”

“…Total genomic DNA was isolated from silica gel dried materials with a modified cetyl trimethylammonium bromide (CTAB) method (Li et al, 2013) and sequenced on an Illumina HiSeq 2500 (Illumina, San Diego, California, USA). Plastomes were de novo assembled following the methods in Zhang et al (2019); Zhang et al (2018).…”

“…Nowadays, more and more recalcitrant relationships among families, lineages, or even species can be untangled using genomic (plastid, mitochondria, and nucleus) datasets, which containing unprecedented numbers of informative loci and sites, compared with multi-locus phylogeny (Lu et al, 2015; Ross et al, 2016; Zhang et al, 2016). Studies on whole plastomes of ferns and seed plants (Delsuc et al, 2005; Gao et al, 2010; Morris et al, 2018; Wei et al, 2017; Wickett et al, 2014) have been increasing quickly, whereas scarce phylogenomic studies have been carried out in lycophytes (Zhang et al, 2019). Here, for the first time, we reconstructed the robust phylogenetic framework of Selaginellaceae using plastome data from 26 species representing six out of seven subgenera based on the classification of Weststrand and Korall (2016b).…”