The extraordinary variation of the organellar genomes of the Aneura pinguis revealed advanced cryptic speciation of the early land plants

Abstract

Aneura pinguis is known as a species complex with several morphologically indiscernible species, which are often reproductively isolated from each other and show distinguishable genetic differences. Genetic dissimilarity of cryptic species may be detected by genomes comparison. This study presents the first complete sequences of chloroplast and mitochondrial genomes of six cryptic species of A. pinguis complex: A. pinguis A, B, C, E, F, J. These genomes have been compared to each other in order to reconstruct phylogenetic relationships and to gain better understanding of the evolutionary process of cryptic speciation in this complex. The chloroplast genome with the nucleotide diversity 0.05111 and 1537 indels is by far more variable than mitogenome with π value 0.00233 and number of indels 1526. Tests of selection evidenced that on about 36% of chloroplast genes and on 10% of mitochondrial genes of A. pinguis acts positive selection. It suggests an advanced speciation of species. The phylogenetic analyses based on genomes show that A. pinguis is differentiated and forms three distinct clades. Moreover, on the cpDNA trees, Aneura mirabilis is nested among the cryptic species of A. pinguis. This indicates that the A. pinguis cryptic species do not derive directly from one common ancestor.

Chloroplast phylogenomics of liverworts: a reappraisal of the backbone phylogeny of liverworts with emphasis on Ptilidiales

“…These remarkable improvements include that liverworts were strongly supported as sister to mosses in recent phylogenomic studies (Wickett et al, 2014;Puttick et al, 2018;de Sousa et al, 2018) than the alternative hypothesis of this group as the earliest lineage of land plants (Qiu et al, 1998(Qiu et al, , 2006. These findings, consistent with those of the first chloroplast phylogenomic analysis (Nishiyama et al, 2004), not only provide new insights into the deepest diverging events of land plants, but also enable us to reappraise hypotheses on the evolution of key innovative morphological characters (e.g. stomata) and evolutionary events, based-hitherto--on early land plant fossils Puttick et al, 2018).…”

“…0.48% of liverwort species diversity), representing 33 families (42% of family diversity) and 13 orders (87% of order diversity). The chloroplast genome data for 31 liverwort species were newly generated as part of our project on the diversity of liverwort chloroplast genomes (see, also, Yu et al., unpublished) and four were extracted from previously published studies: Aneura pinguis (Myszczyński et al., ), Marchantia polymorpha (Ohyama et al., ), Apopellia endiviifolia (Grosche et al., ) and Ptilidium pulcherrimum (Forrest et al., ). Specimen information and accession numbers are listed in Table .…”

Exploring the plastid genome disparity of liverworts

“…As a consequence, the evolutionary history of plastid genomes during the colonization of land by plants is still poorly understood. The few available bryophyte plastomes suggest evolutionary conservatism of the genome structures, especially among liverworts (Wickett et al, 2008;Forrest et al, 2011;Wicke et al, 2011;Grosche et al, 2012;Myszczyński et al, 2017), although some gene deletions were found in the nonphotosynthetic liverwort A. mirabilis (Wickett et al, 2008;Myszczyński et al, 2017). Thus, liverworts may diverge from vascular plants and even mosses by the absence of evidence supporting major structural reorganization as a major process in the plastid genome evolution (Wicke et al, 2011;Mower & Vickrey, 2018).…”

The second complete chloroplast genome sequence of Nymphaea alba L. (Nymphaeaceae) to investigate inner-species variations

“…Interestingly, four SNPs near to 3' end of psbA gene are surrounded by 14 bp IRs. Number of sequence variations in N. alba reflects low level of genetic diversity in comparison to other studies (Young et al 2011;Myszczy nski et al 2017).…”