Comparative Analysis of Apopellia endiviifolia Plastomes Reveals a Strikingly High Level of Differentiation between Its Terrestrial and Water Form

Abstract

The simple thalloid liverwort Apopellia endiviifolia is a widespread Holarctic species belonging to the family Pelliaceae. European populations of this species comprise two distinct evolutionary lineages named “species A”, known also as water form, and typical, mainly terrestrial forms named “species B”. Newly sequenced, assembled and annotated chloroplast genomes of six European specimens belonging to the two cryptic lineages occupying different microhabitats, revealed the structure typical for liverworts and previously sequenced reference. The plastomes of A. endiviifolia are 120,537–120,947 bp long with a structure typical for most plants, including a pair of IR regions (each of 9092–9207 bp) separated by LSC (82,506–82,609 bp) and SSC (19,854–19,924 bp) regions and consist of 121 unique genes, including 81 protein-coding genes, 6 genes of unknown function (ycf genes), 4 ribosomal RNAs and 30 transfer RNAs. Comparative analysis of typical, terrestrial and water forms revealed 4971 molecular diagnostic characters (MDCs), which exceeds numbers found in many well recognized liverworts taxa. Moreover, beside the presence of evolutionary hotspots like ycf1 and ycf2 genes and several intergenic spacer like ndhB-psbM, rps4-ndhJ and ndhC-atpE, the molecular identification of Apopellia cryptic species was possible by almost 98% of 500 bp long frames simulating mini barcodes. The different ecological niches can be driven by different pressures of positive selection, which was detected in nine genes including ccsA, ndhD, ndhF, petA, psbB, psbC, rpoB, ycf1 and ycf2. Despite clearly genetic differences and ecological preferences, the current observation of morphological differentiation does not no allow to separate terrestrial and water forms into taxonomic species.

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

“…Phylogenetic placement of Pelliidae based on plastid sequence is mostly congruent with previous studies 28 , 35 , 70 . One minor difference is the position of Conocephalum conicum , which in the work of Dong et al was resolved as an unusual clade, probably due to plastome misassembly (GB accession number MK645816).…”

“…However, plastome length in Pellidae doesn’t correlate with gene losses, while the second largest plastome of Pallavicinia (124,103 bp) and the smallest of Pellia neesiana (115,875 bp) have identical gene content, whereas plastomes of Apopellia with complete gene sets (120,537–120,947 bp), are smaller than Pallavicinia without cys A and cys T genes. Independently of gene loss, plastome reduction was also found in leafy Cephaloziineae, which plastomes ranged between 118,571 and 114,423 bp, despite identical gene sets 28 , 64 . Plastid gene losses are scattered along different evolutionary lineages including loss of cys A and cys T genes in Ptilidium pulcherrimum and Cheilolejeunea xanthocarpa 33 , 35 and additional four genes ( ndh F, rpl 21, rps 32 and ccs A) in Cololejeunea lanciloba 66 .…”

“…Plastomes of the Pellia genus lost two genes ( cys A and cys T), but gene order remains stable. These genes are present in the sister genera Apopellia, Makinoa and Moerckia 19 , 28 , but in the remaining genera of Pelliidae ( Fossombronia , Pallavicinia, Pellia ) are pseudogenised, as well as in many other leafy liverworts 19 . Further gene losses include trn S(GCU)- psb I- trn S(GCA) in Makinoa and Fossombronia .…”

“…The reduction or increase of mitogenome length in leafy liverworts is often caused by indels between genes nad 3 and rpl 10. This region contains the pseudogenized (with exception of Haplomitrium and Treubia where nad 7 is functional) nad 7 gene and three tRNAs: trn V-UAC, trn D-GUC, trn S-GCU and is a main source of mitogenome size variation among Nowellia and Scapania species 28 . Comparative analyses of Pelliidae mitogenomes also confirmed this observation revealing over 11 kbp difference in nad 3- rpl 10 region between Makinoa and Fossombronia species, with differ by 8 kbp in total mitogenome length ( Makinoa contains two more cox 1 introns).…”

“…Despite recent advances in liverwort organellar genomics, the simply thalloid Pelliidae are poorly explored in that field. Chloroplast genome of Apopellia endiviifolia was among the first sequenced liverwort plastomes 27 , but since then only plastomes of Fossombronia cristula , Makinoa crispata , Pallavicinia lyellii 19 and water form of A. endiviifolia 28 have been sequenced. The mitogenomic resources of Pelliidae were limited to three species of Fossombroniales: F. cristula , F. foveolata and M. crispata 29 , 30 and mitogenomes of orders Pelliales and Pallaviciniales remain unexplored.…”