Abstract
The early vascular plants in the genus Selaginella, which is the sole genus of the Selaginellaceae family, have an important place in evolutionary history, along with ferns, as such plants are valuable resources for deciphering plant evolution. In this study, we sequenced and assembled the plastid genome (plastome) sequences of two Selaginella tamariscina individuals, as well as Selaginella stauntoniana and Selaginella involvens. Unlike the inverted repeat (IR) structures typically found in plant plastomes, Selaginella species had direct repeat (DR) structures, which were confirmed by Oxford Nanopore long-read sequence assembly. Comparative analyses of 19 lycophytes, including two Huperzia and one Isoetes species, revealed unique phylogenetic relationships between Selaginella species and related lycophytes, reflected by structural rearrangements involving two rounds of large inversions that resulted in dynamic changes between IR and DR blocks in the plastome sequence. Furthermore, we present other uncommon characteristics, including a small genome size, drastic reductions in gene and intron numbers, a high GC content, and extensive RNA editing. Although the 16 Selaginella species examined may not fully represent the genus, our findings suggest that Selaginella plastomes have undergone unique evolutionary events yielding genomic features unparalleled in other lycophytes, ferns, or seed plants.
Highlights
Chloroplasts, representing the most typical form of plastids, are semiautonomous cellular organelles found in photosynthetic plants and algae that contain their own genomes.Plastid genomes are typically 120–160 kb long, with a quadripartite architecture comprising one long single-copy (LSC) region and a short single-copy (SSC) region separated by two inverted repeats (IRA and IRB ) [1]
As of February 2019, 2364 complete plastome sequences of land plants were registered in National Center for Biotechnology Information (NCBI), with an average size of 151,167 ± 34,672 bp
The canonical quadripartite plastid genomic structure was retained in these Selaginella species, directional change occurred in most Selaginella species with SSC expansion and LSC contraction
Summary
Chloroplasts, representing the most typical form of plastids, are semiautonomous cellular organelles found in photosynthetic plants and algae that contain their own genomes. The near or complete loss of IRs has been reported in some plant lineages of conifers and Fabaceae [4,5], the two repeats are inversely oriented as IRA and IRB in most plastomes [37,38]. RNA editing have been detected in flowering plant plastomes, more than 3400 C-to-U RNA editing events were discovered in S. uncinata plastomes [32] This extensive RNA editing is thought to be related to the high GC bias due to a combination of the reduced AT-mutation pressure and the high number of C-to-U RNA editing sites in the Selaginella genus [31]. This analysis uncovered remarkably dynamic features of the plasand gene losses This analysis uncovered remarkably dynamic features of the plastomes of tomes of plants of the Selaginella genus in the Division Lycopodiophyta.
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