The complete chloroplast genome of Riccia fluitans L. (Ricciaceae, Marchantiophyta)

Abstract

Riccia fluitans L. (Marchantiales) is an aquatic liverwort usually found in lentic environments. Here, we presented a complete chloroplast genome of R. fluitans (MK645896) which is 121,682 bp long and has four subregions: 81,626 bp of large single copy (LSC) and 20,254 bp of small single copy (SSC) regions are separated by 9,901 bp of inverted repeat (IR) regions including 131 genes (87 protein-coding genes, 8 rRNAs, and 36 tRNAs). The overall GC content is 29.0% and those in the LSC, SSC, and IR regions are 26.6%, 24.6%, and 42.9%, respectively. Phylogenetic trees show incongruence with Bryophyte taxonomy, requiring intensive researches to find genes causing this incongruence.

Keywords:

• Riccia fluitans
• chloroplast genome
• Ricciaceae
• Marchantiales
• incongruence

Genus Riccia L. covers approximately 150 species, which is the most diverse genus in order Marchantiales (Ayub et al. 2014). Riccia fluitans L, one of the most common species in Riccia, is distributed world widely (Manju et al. 2012). It is a conspicuous aquatic liverwort usually found in lentic environments, characterized by floating thalli which regularly fork into equal branches; however, it is difficult to be distinguished with other species in R. fluitans complex (Berrie 1964). It can also grow in both aquatic and terrestrial habitats with various morphological types along with different habitats (Carter 1935). Recent phylogenetic study presented that Ricciella (Braun) Boulay, the subgenus of R. fluitans, was polyphyletic (Cargill et al. 2016), requiring more information of molecular markers to clarify its phylogenetic position. We completed chloroplast genome of R. fluitans as a fourth representative species of Marchantiales families considering both chloroplast and mitochondrial genomes (Kwon, Kim, et al. 2019b, 2019a, 2019c; Kwon, Min, et al. 2019; Park et al. accepted.

Thallus of R. fluitans was collected in a marsh in Namyangju city, South Korea (Voucher in InfoBoss Cyber Herbarium (IN); W. Kwon, IB-50004) and its DNA was extracted by using a DNeasy Plant Mini Kit (QIAGEN, Hilden, Germany). Genome sequencing was performed using HiSeqX at Macrogen Inc., Korea, and de novo assembly and sequence conformation processes were done by Velvet 1.2.10 (Zerbino and Birney 2008), SOAPGapCloser 1.12 (Zhao et al. 2011), BWA 0.7.17 (Li 2013), and SAMtools 1.9 (Li et al. 2009). Geneious R11 11.0.5 (Biomatters Ltd., Auckland, New Zealand) was used for chloroplast genome annotation based on Marchantia polymorpha subsp. ruderalis chloroplast genome (NC_037507).

Riccia fluitans chloroplast genome (Genbank accession is MK645896) is 121,682 bp (GC ratio is 29.0%) and has four subregions: 81,626 bp of large single copy (26.6%) and 20,254 bp of small single copy (24.6%) regions are separated by 9901 bp of the inverted repeat (IR; 42.9%). It contained 131 genes (87 protein-coding genes, 8 rRNAs, and 36 tRNAs); 9 genes (4 rRNAs and 5 tRNAs) are duplicated in IR regions.

Ten complete chloroplast genomes including R. fluitans were used for constructing neighbor joining (bootstrap repeat is 10,000) and maximum likelihood (bootstrap repeat is 1,000) phylogenic trees using MEGA X (Kumar et al. 2018) after aligning whole chloroplast genomes (named as W-Tree) and 63 conserved protein-coding genes (named as C-Tree) using MAFFT 7.388 (Katoh and Standley 2013). Phylogenetic trees show incongruent with previous phylogenetic study of Marchantiales (Crandall‐Stotler et al. 2016) by showing that Dumortiera hirsutais clustered with Reboulia hemisphaerica from W-Tree or D. hirsutais in the same clade of R. fluitans from C-Tree (Figure 1). This phenomenon has also been observed in ant species (Park et al. 2019b, 2019a). In addition, maximum likelihood tree is also incongruent with neighbor joining tree in this clade (Figure 1). It is similar to the incongruence of each chloroplast gene tree of available Bryophyte species, suggesting intensive researches to find genes causing incongruence with the classical phylogenetic relationship. More Bryophytes chloroplast genomes are required to resolve this incongruence precisely in the near future.

Figure 1. Neighbor joining (bootstrap repeat is 10,000) and maximum likelihood (bootstrap repeat is 1,000) phylogenetic tree of ten complete chloroplast genomes: Riccia fluitans (MK645896 in this study), Reboulia hemisphaerica (MK477551), Marchantia polymorpha subsp. ruderalis (NC_037507), Marchantia paleacea (NC_001319), Dumortiera hirsuta (NC_039590), Pellia endiviifolia (NC_019628), Aneura pinguis (NC_035617), Gymnomitrion concinnatum (NC_040133), Ptilidium pulcherrimum (NC_015402), and Sphagnum palustre (NC_030198) as an outgroup. Black bars in the right side indicate specific clades with labels. Phylogenetic tree was drawn based on neighbour joining tree from alignment of complete chloroplast genomes. The numbers above branches indicate bootstrap support values of neighbor joining and maximum likelihood phylogenetic trees from alignment of complete chloroplast genomes (black color) or 63 conserved genes (dart red color), respectively.

Disclosure statement

The authors declare that they have no competing interests.

Additional information

Funding

This work was supported by InfoBoss Research Grant [IBG-0027].