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The chloroplast genome of the moss Haplocladium microphyllum, first in family Thuidiaceae.

ABSTRACT: Bryophytes are a highly diverse group containing more than 12,800 species. Haplocladium microphyllum is in a large moss belonging to the family Thuidiaceae. We report the complete chloroplast (124,478 bp) genome sequence of H. microphyllum, it includes a pair of inverted repeat regions (IRs, 9727 bp), one large single-copy (LSC, 86,528 bp) region, and one small single-copy (SSC, 18,496 bp) region. Besides, the complete chloroplast genome contains 134 genes in total, including 88 protein-coding genes, 38 tRNA genes, and eight rRNA genes. Phylogenetic analysis showed that H. microphyllum has the closest relationship with Sanionia uncinata in Amblystegiaceae. Our study lays a foundation for further research like speciation of this species and the phylogeny of the Thuidiaceae family.

SUBMITTER: Mao L

PROVIDER: S-EPMC7781994 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:Bignoniaceae is a Pantropical plant family that is especially abundant in the Neotropics. Members of the Bignoniaceae are diverse in many ecosystems and represent key components of the Tropical flora. Despite the ecological importance of the Bignoniaceae and all the efforts to reconstruct the phylogeny of this group, whole chloroplast genome information has not yet been reported for any members of the family. Here, we report the complete chloroplast genome sequence of Tanaecium tetragonolobum (Jacq.) L.G. Lohmann, which was reconstructed using de novo and referenced-based assembly of single-end reads generated by shotgun sequencing of total genomic DNA in an Illumina platform. The gene order and organization of the chloroplast genome of T. tetragonolobum exhibits the general structure of flowering plants, and is similar to other Lamiales chloroplast genomes. The chloroplast genome of T. tetragonolobum is a circular molecule of 153,776 base pairs (bp) with a quadripartite structure containing two single copy regions, a large single copy region (LSC, 84,612 bp) and a small single copy region (SSC, 17,586 bp) separated by inverted repeat regions (IRs, 25,789 bp). In addition, the chloroplast genome of T. tetragonolobum has 38.3% GC content and includes 121 genes, of which 86 are protein-coding, 31 are transfer RNA, and four are ribosomal RNA. The chloroplast genome of T. tetragonolobum presents a total of 47 tandem repeats and 347 simple sequence repeats (SSRs) with mononucleotides being the most common and di-, tri-, tetra-, and hexanucleotides occurring with less frequency. The results obtained here were compared to other chloroplast genomes of Lamiales available to date, providing new insight into the evolution of chloroplast genomes within Lamiales. Overall, the evolutionary rates of genes in Lamiales are lineage-, locus-, and region-specific, indicating that the evolutionary pattern of nucleotide substitution in chloroplast genomes of flowering plants is complex. The discovery of tandem repeats within T. tetragonolobum and the presence of divergent regions between chloroplast genomes of Lamiales provides the basis for the development of markers at various taxonomic levels. The newly developed markers have the potential to greatly improve the resolution of molecular phylogenies.

Dataset Information

The chloroplast genome of the moss Haplocladium microphyllum, first in family Thuidiaceae.

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