The mitochondrial genomes of bryophytes

Abstract

In contrast to the highly variable mitogenomes of vascular plants, the composition and architecture of mitogenomes within the three bryophyte lineages appear stable and invariant. Currently, complete mitogenomes are available from 113 bryophyte accessions of 71 genera and 28 orders. Liverworts and mosses hold a rich mitochondrial (mt) gene repertoire among land plants with 40–42 protein-coding genes, whereas hornworts maintain the smallest functional gene set among land plants, of only around two dozen protein-coding genes, with the majority of ribosomal genes pseudogenized and all cytochrome c maturase genes lost. The rRNA and tRNA genes are also conserved and rich in mosses and liverworts, whereas subject to patchy losses in hornworts. In contrast to the conserved gene set, intron content varies significantly with only one intron shared among the three bryophyte lineages. Bryophytes hold relatively compact mitogenomes with narrow size fluctuations. Among the three bryophyte lineages, intergenic spacers and repeat content are smallest in mosses, largest in hornworts, and intermediate in liverworts, mirroring their size differences and levels of structural dynamics among the three lineages. Mosses, with the least repeated sequences, show the most static genome structure; whereas hornworts, with a relatively large set of repeated sequences, experience 1–4 rearrangements; liverworts, with intermediate repeat levels, see only one structural variant that requires two inversions to gain collinearity with the mitogenome of other liverworts. Repeat sequences were evoked to explain the mt gene order rearrangements in hornwort and liverwort mitogenomes; with the latter also supported by sequencing read evidence, which suggests that the conserved mitogenome structure observed in bryophyte lineages might be shaped by low repeat recombination level, and/or along with the intensified nucleus’ surveillance. Mitochondrial RNA editing is abundant in hornworts, with medium frequency and high variation in liverwort species, and generally limited in mosses, reflecting the diversity of nuclear encoded PPR proteins that are functionally related to RNA editing processes.

The organellar genomes of Pellidae (Marchantiophyta): the evidence of cryptic speciation, conflicting phylogenies and extraordinary reduction of mitogenomes in simple thalloid liverwort lineage

“…In contrast to plastomes, evolutionary losses of mitochondrial introns seem to be common in liverworts, but mainly concern leafy liverwort lineages, while the intron content of thallus liverworts is stable 29 , 30 , 69 . Out of ten intron losses only the loss of trn L could happen once and remaining losses were independent across different evolutionary lineages of leafy liverworts 70 . Unlike previously sequenced genomes of Pelliidae ( Fossombronia cristula and Makinoa crispata ), the mitogenomes of Pellia and Apopellia have introns in the atp 1 gene and in contrast to Fossombronia , keep complete cox 1 intron set 30 , 70 .…”

Target capture and genome skimming for plant diversity studies

“…However, there have been debates in the literature regarding the nonrecombining nature of plastid genes (Gonçalves et al, 2019(Gonçalves et al, , 2020; Doyle, 2022). The generation of organellar genome data for a wider range of plants will reveal the extent of such variation (Wikström and Pryer, 2005;Bouillé et al, 2011;Wang and Lanfear, 2019;Sousa et al, 2020;Dong and Liu, 2021). Similarly, exciting new patterns are emerging from the high volume of nuclear data now available.…”

Super-Mitobarcoding in Plant Species Identification? It Can Work! The Case of Leafy Liverworts Belonging to the Genus Calypogeia

“…It is even more difficult to collect information about the genetic variation of mitogenomes in bryophytes. Most studies report that mitochondrial genomes of bryophytes are invariant, but it refers to their stability at composition and architecture levels [ 39 , 40 , 66 ]. Among liverworts, the level of genetic variation has been determined only for Calypogeia plastomes [ 52 ] and for organelle genomes of cryptic species of the Aneura pinguis complex [ 67 ].…”