The complete chloroplast genome of Fissidens nobilis Griff. (Fissidentaceae, Bryophyta)

Abstract

We presented a complete chloroplast genome of Fissidens nobilis which is 124,962 bp long and has four subregions: 86,122 bp of large single-copy (LSC) and 18,708 bp of small single-copy (SSC) regions are separated by 10,066 bp of inverted repeat (IR) regions including 127 genes (82 protein-coding genes, 8 rRNAs, and 37 tRNAs). The overall GC content is 29.2% and those in the LSC, SSC, and IR regions are 26.6%, 26.0%, and 43.5%, respectively. Phylogenetic trees show that the phylogenetic position of F. nobilis is congruent with the previous phylogenetic study of moss species.

The complete chloroplast genome of Leucobryum juniperoideum (brid.) C. Müll. (Leucobryaceae, Bryophyta)

“…Phylogenetic trees present genus Leucobryum is clustered with genus Fissidens, which is incongruent of phylogenetic relationship among three genera, Leucobryum, Fissidens, and Syntrichia (Liu et al 2019;Kwon et al 2019; Figure 1). In addition, two basal moss species, Sphagnum palustre (Jonathan Shaw et al 2016) and Takakia lepidozioides, are clustered (Figure 1), which is same to the result of previous study (Kwon et al 2019) but incongruent with another phylogentic study (Liu et al 2019). Taken together, it indicates additional moss chloroplast genomes are required to clarify phylogenetic relationship of these species.…”

“…Genome sequencing was performed using HiSeqX at Macrogen Inc., Korea, and de novo assembly and conformation 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 Fissidens nobilis chloroplast genome (MK876184; Kwon et al 2019) L. juniperoideum chloroplast genome (Genbank accession is MK952779), the first chloroplast genome of family Leucobryaceae, is 124,649 bp long (GC ratio is 30.5%) and has four subregions: 86,309 bp of large single copy (28.1%) and 18,696 bp of small single copy (26.8%) regions are separated by 9,882 bp of inverted repeat (IR; 44.5%). It is shorter than that of neighbor species, Fissidens nobilis, by 184 bp (Kwon et al 2019).…”

“…Geneious R11 11.0.5 (Biomatters Ltd., Auckland, New Zealand) was used for chloroplast genome annotation based on Fissidens nobilis chloroplast genome (MK876184; Kwon et al 2019) L. juniperoideum chloroplast genome (Genbank accession is MK952779), the first chloroplast genome of family Leucobryaceae, is 124,649 bp long (GC ratio is 30.5%) and has four subregions: 86,309 bp of large single copy (28.1%) and 18,696 bp of small single copy (26.8%) regions are separated by 9,882 bp of inverted repeat (IR; 44.5%). It is shorter than that of neighbor species, Fissidens nobilis, by 184 bp (Kwon et al 2019). It contains 127 genes (82 protein-coding genes, eight rRNAs, and 37 tRNAs); nine genes (four rRNAs and five tRNAs) are duplicated in IR regions.…”

“…Ten complete chloroplast genomes including L. juniperoideum 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) and IQ-TREE (Nguyen et al 2015), respectively, after aligning whole chloroplast genome sequences using MAFFT 7.388 (Katoh and Standley 2013). Phylogenetic trees present genus Leucobryum is clustered with genus Fissidens, which is incongruent of phylogenetic relationship among three genera, Leucobryum, Fissidens, and Syntrichia (Liu et al 2019;Kwon et al 2019; Figure 1). In addition, two basal moss species, Sphagnum palustre (Jonathan Shaw et al 2016) and Takakia lepidozioides, are clustered (Figure 1), which is same to the result of previous study (Kwon et al 2019) but incongruent with another phylogentic study (Liu et al 2019).…”

“…Geneious R11 11.0.5 (Biomatters Ltd., Auckland, New Zealand) was used for chloroplast genome annotation based on Fissidens nobilis chloroplast genome (MK876184; Kwon et al. 2019 )…”