Comparative Analysis of Four Calypogeia Species Revealed Unexpected Change in Evolutionarily-Stable Liverwort Mitogenomes

Abstract

Liverwort mitogenomes are considered to be evolutionarily stable. A comparative analysis of four Calypogeia species revealed differences compared to previously sequenced liverwort mitogenomes. Such differences involve unexpected structural changes in the two genes, cox1 and atp1, which have lost three and two introns, respectively. The group I introns in the cox1 gene are proposed to have been lost by two-step localized retroprocessing, whereas one-step retroprocessing could be responsible for the disappearance of the group II introns in the atp1 gene. These cases represent the first identified losses of introns in mitogenomes of leafy liverworts (Jungermanniopsida) contrasting the stability of mitochondrial gene order with certain changes in the gene content and intron set in liverworts.

The complete mitochondrial genome of Taxus cuspidata (Taxaceae): eight protein-coding genes have transferred to the nuclear genome

“…Retroprocessing, also known as a reverse transcriptase-mediated model, is the most frequently reported mechanism for the removal of introns [65][66][67][68]. Under this model, introns located at the 3′ ends of genes are more likely to be lost than those at the 5′ ends [63,65,69]. However, introns have been lost from the start or center of the genes nad1, nad2 and nad7 in Taxus, which is similar to the finding for cox1 in Calypogeia [63].…”

“…Previous studies suggested some possible mechanisms for intron loss, including genomic deletion, exonization, gene conversion, EGT, and retroprocessing [63]. Deletion can be ruled out because all introns in the Taxus and Welwitschia mitogenomes are precisely removed.…”

“…Under this model, introns located at the 3′ ends of genes are more likely to be lost than those at the 5′ ends [63,65,69]. However, introns have been lost from the start or center of the genes nad1, nad2 and nad7 in Taxus, which is similar to the finding for cox1 in Calypogeia [63]. A mutational mechanism (e.g., internally primed reverse transcription) or selective pressure to maintain introns near the 5′ and 3′ ends of genes could explain this pattern of intron loss [70].…”

Exploring the plastid genome disparity of liverworts

“…Future studies could focus in particular on the reduction of the plastome length in adaptation to epiphyllic habitats because taxa with this life strategy show evidence of enhanced reduction of the plastid genome length. Another intriguing question is whether the conservatism observed in plastid genomes of liverworts coincides with the conservatism of the mitochondrial genomes (Ślipiko et al, ) and perhaps also the nuclear genome. Furthermore, the evolution of the plastid genome structure of liverworts in arguably the majority of land plants does not reflect recent changes in the diversification rates of these plants (Laenen et al, ).…”

Recombination Events Involving the atp9 Gene Are Associated with Male Sterility of CMS PET2 in Sunflower

“…In recent years, mitochondrial DNAs have been sequenced to answer several questions [ 33 , 34 , 35 , 36 , 37 ]. Some mitochondrial genome sequences have been successfully used to identify CMS-specific open reading frames [ 38 , 39 , 40 ], whereas in other studies no clear answers regarding the CMS mechanism were obtained like in wheat [ 41 ] or in pigeonpea [ 42 ].…”