Large-scale phylogenomics reveals ancient introgression in Asian Hepatica and new insights into the origin of the insular endemic Hepatica maxima

Abstract

Hepatica maxima is native to Ulleungdo, which is one of the oceanic islands in Korea, and it likely originated via anagenetic speciation from the Korean mainland species H. asiatica. However, the relationships among the Asian lineages remain unresolved. Phylogenomics based on plant genomes can provide new insights into the evolutionary history of plants. We first generated plastid, mitochondrial and transcriptome sequences of the insular endemic species H. maxima. Using the genomic data for H. maxima, we obtained a phylogenomic dataset consisting of 76 plastid, 37 mitochondrial and 413 nuclear genes from Asian Hepatica and two outgroups. Coalescent- and concatenation-based methods revealed cytonuclear and organellar discordance in the lineage. The presence of gynodioecy with cytoplasmic male sterility in Asian Hepatica suggests that the discordance is correlated with potential disruption of linkage disequilibrium between the organellar genomes. Species network analyses revealed a deep history of hybridization and introgression in Asian Hepatica. We discovered that ancient and recent introgression events occurred throughout the evolutionary history of the insular endemic species H. maxima. The introgression may serve as an important source of genetic variation to facilitate adaptation to the Ulleungdo environment.

Breaking the limits - multichromosomal structure of an early eudicot Pulsatilla patens mitogenome reveals extensive RNA-editing, longest repeats and chloroplast derived regions among sequenced land plant mitogenomes

“…The hypothesis is also supported by the presence of features usually found in other species with linear single or multi-chromosomal mitochondrial genome: a terminal inverted repeat and the genes of RNA and DNA polymerases [16,17]. The multi-chromosomal, linear mitogenomes were not previously reported in early eudicots, since Aconitum, Anemone and Nelumbo support the master circular chromosome hypothesis [18,19].…”

“…High number of editing sites in CDS of P. patens mitogenome can not be explained by the type of the tissue used for RNA extraction, since leaf (as in case of our study) and root tissues are considered as less frequently edited than flower tissues [56]. The lower number of predicted RNA-editing sites was given for Hepatica maxima [18] due to presence of two genes missing in P. patens (rpl10 and sdh4). However, predicting-based estimation of RNA-editing sites usually overstates the amount of RNA-seq verified editing sites [57].…”

“…The length of the longest MTPT is unusual, since the most of previously identified chloroplast-derived regions fall within 200-4,000 bp range [50] and the largest, 12.6 kbp long MTPT was found in Zea mays mitogenome [51]. In the other known mitogenome of Ranunculales, Hepatica maxima, the MTPT fragments are up tp 7.1 kbp long, with total length of 16 kbp [18] The presence of an almost complete IR region in P. patens mitogenome suggests that it was derived from single transfer that was subsequently split and partially duplicated by rearrangement. Similar scenario was described in Silene conica, where 35 kbp region was transferred in a single event, but Fig.…”

Complete sequence and comparative analysis of the mitochondrial genome of the rare and endangered Clematis acerifolia, the first clematis mitogenome to provide new insights into the phylogenetic evolutionary status of the genus

“…For example, animal mitogenomes are usually only 15-17 kb, algal mitochondria are slightly larger and can reach 13-96 kb, while angiosperm mitogenome size is usually in the range of 200-700 kb (Gualberto and Newton, 2017), Silene conica (11.3 Mb) is the largest plant mitogenome found so far (Sloan et al, 2012). C. acerifolia mitogenome size is between that of A. kusnezoffii (440, 720bp) and A. maxima (1, 122, 546) of the Ranunculaceae (Park and Park, 2020;Li et al, 2021). Although plant mitogenomes are very large, they do not contain many coding genes, typically 50-60 (Kitazaki and Kubo, 2010).…”

Two Korean Endemic Clematis Chloroplast Genomes: Inversion, Reposition, Expansion of the Inverted Repeat Region, Phylogenetic Analysis, and Nucleotide Substitution Rates

“…In addition, the phylogenetic relationship and genomic structure of Aconitum spp. [ 33 , 34 ], Hepatica [ 35 ], and Pulsatilla [ 36 ] have been analyzed. However, there is still a need for in-depth research at the genus level.…”