Complete chloroplast and mitochondrial genomes of Ditrichum rhynchostegium Kindb. (Ditrichaceae, Bryophyta).

The moss family Pottiaceae is one of the most diverse lineages of the subclass Dicranidae (haplolepideous mosses). Nevertheless, the phylogenetic relationships of Pottiaceae with other Dicranidae families remain unclear. To better understand the ancestral genomic structure and evolution of the Pottiaceae, herein, we present the chloroplast and mitochondrial genomes of Ditrichum rhynchostegium (Ditrichaceae, Bryophyta). The chloroplast genome is 124,628 bp long and displayed a circular structure composed of a large single-copy region, a small single-copy region, and a pair of inverted repeats. It has 118 genes, including 82 protein-coding genes, 32 tRNA genes, and four rRNA genes. The mitochondrial genome is 106,246 bp long and has a circular structure. It contains 67 genes, including 40 protein-coding genes, 24 tRNA genes, and three rRNA genes. Phylogenetic trees based on the coding sequences strongly support the sister relationship of D. rhynchostegium with all Pottiaceous accessions, and the dextrosely arranged operculum cells suggest its affinity for Pottiaceae. This study also demonstrates that long-read sequencing employing the Nanopore platform facilitates the repair of unassembled or misassembled organellar genomic regions.

The complete chloroplast genome of Callicarpa dichotoma (Lour.) K.Koch (Lamiaceae).

Callicarpa dichotoma (Lour.) K.Koch is a shrub species with distribution from East Asia to Southeast Asia. We assembled and annotated for the first time the complete chloroplast (cp) genome of C. dichotoma. The cp genome of C. dichotoma is 154,110 bp long with the GC content of 38.09% and consists of four subregions: a large single-copy (LSC) region of 84,915 bp, a small single-copy (SSC) region of 17,783 bp and a pair of inverted repeats (IRs) of 25,706 bp each. The cp genome of C. dichotoma encodes a total of 114 unique genes, comprising 80 protein-coding genes, 30 tRNA genes, and four rRNA genes. Phylogenetic trees based on the coding sequences strongly support the position of C. dichotoma within the genus Callicarpa, confirming the previously reported monophyly of the genus.

The complete chloroplast and mitochondrial genomes of Scopelophila cataractae (Mitt.) Broth. (Pottiaceae, Bryophyta).

The complete chloroplast and mitochondrial genome sequences of Scopelophila cataractae (Pottiaceae, Bryophyta) are determined. The chloroplast genome is 122,290 bp with 118 genes and the mitochondrial genome is 105,607 bp with 67 genes, both genomes are circular. This study showed the S. cataractae plastome contains the smallest genome size, and a functional trnP GGG gene, relative to other pottiaceous species. Phylogenetic inferences support the sister relationship of S. cataractae to all other pottiaceous accessions.

The complete chloroplast genome of Petasites japonicus (Siebold & Zucc.) Maxim. (Asteraceae).

The complete chloroplast (cp) genome sequence of Petasites japonicus (Asteraceae) was determined. The cp genome is 150,445 bp and consists of a large single-copy region (82,910 bp), a small single-copy region (17,907 bp), and a pair of inverted repeats (24,814 bp). It encodes a set of 114 genes, consisting of 80 protein-coding genes, 30 tRNA genes, and four rRNA genes. Phylogenetic inference confirmed that P. japonicus is sister to the genus Ligularia in the tribe Senecioneae of Asteraceae.

The complete plastid genome sequence of the enigmatic moss, Takakia lepidozioides (Takakiopsida, Bryophyta): evolutionary perspectives on the largest collection of genes in mosses and the intensive RNA editing.

KEY MESSAGE: Complete chloroplast genome sequence of a moss, Takakia lepidozioides (Takakiopsida) is reported. The largest collection of genes in mosses and the intensive RNA editing were discussed from evolutionary perspectives. We assembled the entire plastid genome sequence of Takakia lepidozioides (Takakiopsida), emerging from the first phylogenetic split among extant mosses. The genome sequences were assembled into a circular molecule 149,016 bp in length, with a quadripartite structure comprising a large and a small single-copy region separated by inverted repeats. It contained 88 genes coding for proteins, 32 for tRNA, four for rRNA, two open reading frames, and at least one pseudogene (tufA). This is the largest number of genes of all sequenced plastid genomes in mosses and Takakia is the only moss that retains the seven coding genes ccsA, cysA, cysT, petN rpoA, rps16 and trnPGGG. Parsimonious interpretation of gene loss suggests that the last common ancestor of bryophytes had all seven genes and that mosses lost at least three of them during their diversification. Analyses of the plastid transcriptome identified the extraordinary frequency of RNA editing with more than 1100 sites. We indicated a close correlation between the monoplastidy of vegetative tissue and the intensive RNA editing sites in the plastid genome in land plant lineages. Here, we proposed a hypothesis that the small population size of plastids in each vegetative cell of some early diverging land plants, including Takakia, might cause the frequent fixation of mutations in plastid genome through the intracellular genetic drift and that deleterious mutations might be continuously compensated by RNA editing during or following transcription.

Molecular phylogeny of the genus Fissidens (Fissidentaceae, Bryophyta) and a refinement of the infrageneric classification.

The genus Fissidens (ca. 440 spp.) is one of the phylogenetically poorly studied groups of mosses (Bryophyta). While various classifications of this genus have been proposed, no attempt at a classification of the genus based on combined molecular and morphological evidence has been made. Here, we present for the first time a comprehensive phylogenetic tree consisting of 50 representatives of Fissidens, reconstructed using sequence data from chloroplast rbcL and rps4 genes. Ancestral state reconstructions provide three clear apomorphies within Fissidens: peristome teeth, limbidium and chromosome number. Based on the phylogeny and morphological reassessment, we recognize three subgenera, Pachyfissidens, Neoamblyothallia, and Fissidens. Subgenus Neoamblyothallia consists of two sections: Neoamblyothallia and Crispidium. Subgenus Fissidens consists of five sections: Fissidens, Polypodiopsis, Aloma, Areofissidens, and Semilimbidium. High diversity of the most derived sect. Semilimbidium in the tropics suggests that the evolutionary history of the genus is through adaptation and diversification in tropical regions.