Abstract
The chloroplast genomes of liverworts, an early land plant lineage, exhibit stable structure and gene content, however the known resources are very limited. The newly sequenced plastomes of Conocephalum, Riccia and Sphaerocarpos species revealed an increase of simple sequence repeats during the diversification of complex thalloid liverwort lineage. The presence of long TA motifs forced applying the long-read nanopore sequencing method for proper and dependable plastome assembly, since the length of dinucleotide repeats overcome the length of Illumina short reads. The accumulation of SSRs (simple sequence repeats) enabled the expansion of inverted repeats by the incorporation of rps12 and rps7 genes, which were part of large single copy (LSC) regions in the previously sequenced plastomes. The expansion of inverted repeat (IR) at the genus level is reported for the first time for non-flowering plants. Moreover, comparative analyses with remaining liverwort lineages revealed that the presence of SSR in plastomes is specific for simple thalloid species. Phylogenomic analysis resulted in trees confirming monophyly of Marchantiidae and partially congruent with previous studies, due to dataset-dependent results of Dumortiera-Reboulia relationships. Despite the lower evolutionary rate of Marchantiales plastomes, significant barcoding gap was detected, even for recently divergent holarctic Conocephalum species. The sliding window analyses revealed the presence of 18 optimal (500 bp long) barcodes that enable the molecular identification of all studied species.
Highlights
The plastid genomes are the most frequently used molecules in evolutionary studies on plants, including phylogenetics, phylogeography, and population genetics [1,2,3]
The result of our study revealed the increase of SSR during the diversification of complex thalloid liverworts, which, in the case of SSRs located near inverted repeat (IR)-large single copy (LSC) boundaries, leads to the expansion of
The newly sequenced genomes confirmed the stable structure of liverwort plastomes, with one exception for Conocephalum salebrosum, where the significant expansion of IRs was detected for the first time
Summary
The plastid genomes are the most frequently used molecules in evolutionary studies on plants, including phylogenetics, phylogeography, and population genetics [1,2,3]. They serve as barcoding resources for most of the taxonomic groups [4], with only a few exceptions when plastid-derived. In contrast to vascular plants, where plastome structure variation is observed at the family or even at genus level [7,8], in bryophytes the gene content and order seem to be very stable across evolutionary lineages. The mosses, phylogenetically sister to liverworts, are known from at least two different conformations [13] of chloroplast genome due to LSC inversion in Funariaceae [14], the gene content of IRs, LSC, and SSC regions remained unchanged
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