Sequence diversity of two chloroplast genes: rps4 and tRNAGly (UCC), in the liverwort Marchantia polymorpha, an emerging plant model system

Abstract

<p>The primary purpose of this study is to evaluate the sequence variation for two regions of chloroplast DNA in a collection of 27 taxonomically well-annotated clonal lines of <em>Marchantia polymorpha</em> sensu lato derived from European populations. We attempted to develop molecular markers so as to identify three taxa usually recognized as subspecies. We sequenced two regions: the <em>rps4</em> gene along with the <em>rps4-trnT</em> intergenic spacer and an intron of the tRNA<sup>Gly</sup> (UCC) gene. Samples of <em>Marchantia paleacea</em> ssp. <em>diptera</em> from Japan were used for comparative purposes.</p><p>Three haplotypes (MA, MB, and MC) were identified for the species, and almost all sequence divergence between subspecies was found to occur at the level of 0.0023–0.0032 substitutions per site. The sequence divergence between <em>M. polymorpha</em> and <em>M. paleacea</em> was tenfold greater (0.0331–0.0340). We did not detect any differences between <em>M. paleacea</em> and homologous sequences from the reference chloroplast genome of <em>M. polymorpha</em> obtained from the GeneBank (NC_001319). It was confirmed that the cell suspension line A-18 used for the sequencing of the full chloroplast genome in 1986 was incorrectly taxonomically annotated.</p>

Evolutionary History of the Marchantia polymorpha Complex

“…This treatment has been questioned by Schuster (1992) and Damsholt (2002) arguing that the taxa are morphologically differentiated, having largely non-overlapping distribution areas. Kijak et al (2018) came to the same conclusion based on data from two cpDNA regions. Whether to recognize the taxa at species or subspecies level depend to some extent on the species concept chosen and this will be discussed in another context.…”

Construction of DNA Tools for Hyperexpression in Marchantia Chloroplasts

“…We conducted this assembly to resolve a taxonomic misidentification of the source of the reference plastid genome (Genbank accession NC_001319.1), which likely originated from the related species Marchantia paleacea . 16 The plastid genome of M. polymorpha Cam1/2 is 120,314 bp and contains 123 annotated genes, 17 which are mainly involved in photosynthesis, electron transport, transcription, and translation. A small number of genes with more specific functions are also present, such as the chl L gene involved in chlorophyll biosynthesis.…”

“…We previously generated a high-quality plastid genome assembly for the M. polymorpha Cam1/2 isolates using next generation sequencing data (Genbank accession: MH635409) (Figure S1a). We conducted this assembly to resolve a taxonomic misidentification of the source of the reference plastid genome (Genbank accession NC_001319.1), which likely originated from the related species Marchantia paleacea . The plastid genome of M. polymorpha Cam1/2 is 120,314 bp and contains 123 annotated genes, which are mainly involved in photosynthesis, electron transport, transcription, and translation.…”

The renaissance and enlightenment ofMarchantiaas a model system

“…For a more detailed history of nomenclature and rationale for considering them as three species or three subspecies see Bowman et al (2016) . Recent analyses indicate that the three subspecies have unique chloroplast and mitochondrial haplotypes ( Kijak et al, 2018 ; Linde et al, 2020 ), but that their nuclear genomes exhibit evidence of hybridization and introgression when subspecies are sympatric ( Linde et al, 2020 ). However, based on examination of three to five individuals of each subspecies collected primarily from Sweden, only limited genomic regions were detected to be exchanged between subspecies in each hybridization event, with different genomic regions susceptible to varying levels of introgression ( Linde et al, 2020 ).…”