Sequencing of organellar genomes of Gymnomitrion concinnatum (Jungermanniales) revealed the first exception in the structure and gene order of evolutionary stable liverworts mitogenomes

Abstract

BackgroundComparative analyses of chloroplast and mitochondrial genomes have shown that organelle genomes in bryophytes evolve slowly. However, in contrast to seed plants, the organellar genomes are yet poorly explored in bryophytes, especially among liverworts. Discovering another organellar genomes of liverwort species by sequencing provides new conclusions on evolution of bryophytes.ResultsIn this work, the organellar genomes of Gymnomitrion concinnatum liverwort were sequenced, assembled and annotated for the first time. The chloroplast genome displays, typical for most plants, quadripartite structure containing large single copy region (81,701 bp), two inverted repeat regions (8704 bp each) and small single copy region (20,179 bp). The gene order and content of chloroplast are very similar to other liverworts with minor differences observed. A total number of 739 and 222 RNA editing sites were predicted in chloroplast and mitochondrial genes of G. concinnatum. The mitochondrial genome gene content is also in accordance with liverworts except few alterations such as: intron loss in cox1 and atp1 genes. Nonetheless the analysis revealed that G. concinnatum mitogenome structure and gene order are rearranged in comparison with other mitogenomes of liverworts. The causes underlying such mitogenomic rearrangement were investigated and the probable model of recombination was proposed.ConclusionsThis study provide the overview of mitochondrial and chloroplast genome structure and gene order diversity of Gymnomitrion concinnatum against the background of known organellar genomes of liverworts. The obtained results cast doubt on the idea that mitogenome structure of early land plants is highly conserved as previous studies suggested. In fact is the very first case of recombination within, evolutionary stable, mitogenomes of liverworts.Electronic supplementary materialThe online version of this article (10.1186/s12870-018-1558-0) contains supplementary material, which is available to authorized users.

Molecular delimitation of European leafy liverworts of the genus Calypogeia based on plastid super-barcodes

“…The GC content of Calypogeia plastome is 34.6% and is almost the same like in Gymnomitrion concinnatum (34.5%), the leafy liverwort species for which the complete chloroplast genome was sequenced most recently [48]. The GC content in Calypogeia plastid genome falls in the range of values known for other liverwort species, from 28.8% for Marchantia paleacea [39] to 40.6% for Aneura mirabilis [52].…”

“…The length of chloroplast genomes seems to be variable not only at the genus level, but also at the species and even at the individual level. Plastome of Calypogeia is 824-1, 366 bp shorter than the longest known leafy liverwort chloroplast genome of Gymnomitrion concinnatum [48] and 1, 880-2, 422 bp shorter than the longest known thalloid liverwort chloroplast genome of Dumortiera hirsuta [49]. Calypogeia species also varied in plastid genome length similarily to Aneura pinguis cryptic species [32].…”

Potential of Transcript Editing Across Mitogenomes of Early Land Plants Shows Novel and Familiar Trends

“…The RNA editing process is known in most currently living plant lineages [17,18,19], including the early land plants—bryophytes [16,20,21,22]. Bryophytes comprise three lineages, hornworts, liverworts, and mosses that share a common haploid-dominant life cycle.…”

Molecular delimitation of European leafy liverworts of the genus Calypogeia based on plastid super-barcodes

“…The length of chloroplast genomes seems to be variable not only at the genus level, but also at the species and even at the individual level. Plastome of Calypogeia is 824-1, 366 bp shorter than the longest known leafy liverwort chloroplast genome of Gymnomitrion concinnatum [48] and 1, 880-2, 422 bp shorter than the longest known thalloid liverwort chloroplast genome of Dumortiera hirsuta [49]. Calypogeia species also varied in plastid genome length similarily to Aneura pinguis cryptic species [32].…”