Sequencing of Organellar Genomes of Nowellia curvifolia (Cephaloziaceae Jungermanniales) Revealed the Smallest Plastome with Complete Gene Set and High Intraspecific Variation Suggesting Cryptic Speciation

Abstract

The leafy liverwort Nowellia curvifolia is a widespread Holarctic species belonging to the family Cephaloziaceae. It is made up of a newly sequenced, assembled and annotated organellar genomes of two European specimens, which revealed the structure typical for liverworts, but also provided new insights into its microevolution. The plastome of N. curvifolia is the second smallest among photosynthetic liverworts, with the shortest known inverted repeats. Moreover, it is the smallest liverwort genome with a complete gene set, since two smaller genomes of Aneura mirabilis and Cololejeunea lanciloba are missing six and four protein-coding genes respectively. The reduction of plastome size in leafy liverworts seems to be mainly impacted by deletion within specific region between psbA and psbD genes. The comparative intraspecific analysis revealed single SNPs difference among European individuals and a low number of 35 mutations differentiating European and North American specimens. However, the genetic resources of Asian specimen enabled to identify 1335 SNPs in plastic protein-coding genes suggesting an advanced cryptic speciation within N. curvifolia or the presence of undescribed morphospecies in Asia. Newly sequenced mitogenomes from European specimens revealed identical gene content and structure to previously published and low intercontinental differentiation limited to one substitution and three indels. The RNA-seq based RNA editing analysis revealed 17 and 127 edited sites in plastome and mitogenome respectively including one non-canonical editing event in plastid chiL gene. The U to C editing is common in non-seed plants, but in liverwort plastome is reported for the first time.

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

“…However, the comparative analyses of European Calypogeia species revealed a low level of intraspecific variation, limited to few SNPs [49]. Analysis of the complete chloroplast genomes of leafy Nowellia curvifolia from Europe revealed only one SNP, but the European and North American specimens differed by 35 SNPs [28]. Considering currently available complete genome sequences of liverworts, low interspecific differentiation of complex thalloid plastomes does not reflect infraspecific variation, which seems to be comparable to simple thalloid and leafy liverworts plastomes.…”

“…Despite recent advances in sequencing and assembly liverwort plastomes [22,23,26,49,64,65] the information about intraspecific variation of these molecules is still limited and only few species, excluding cryptic species of Aneura pinguis [26] and Nowellia curvifolia [28], have two or more complete chloroplast genome sequences available. However, based on the results of this and previous studies, the liverworts plastome variation at intraspecific level seem to be rather low [27,49,66] in comparison to vascular plants [19,67,68].…”

“…Chloroplast genome of Apopellia endiviifolia was among the first sequenced liverworts plastomes [25]; however, up to date, detailed comparative study of plastomes of cryptic lineages within it was not performed. The recent advances in the next generation sequencing provided better datasets to study cryptic speciation of liverworts [26][27][28] and enabled detailed view into plastomes divergence between cryptic evolutionary lineages.…”

Investigation of the Copper Requirements of the Metallophyte Liverworts Cephaloziella nicholsonii Douin and C. massalongoi (Spruce) Müll.Frib

“…are inadequate; the authors suggest a full taxonomic revision of the genus [79]. Cryptic speciation may be widespread in liverworts [80][81][82] and this could explain differences in ecological preferences among populations, such as those observed in this study. Our findings support the view that a fresh investigation of the genus Cephaloziella-combining morphological and molecular techniques-is urgently needed.…”

Are the Organellar Genomes Useful for Fine Scale Population Structure Analysis of Endangered Plants?—A Case Study of Pulsatilla patens (L.) Mill

“…However, the comparative mitogenomic data at the intraspecific level is still very limited. Only one SNP and three InDels were found between two European and North American mitogenomes of Nowellia curvifolia, while European accessions were identical [47]. Analysis of complex plant mitogenomes is challenging, but the latest advances in long-read sequencing enabled assembling complex, large mitogenomes [48], but studies focus mainly on high-ranked taxa.…”