The complete chloroplast genome sequence of the relict woody plant Metasequoia glyptostroboides Hu et Cheng

Abstract

Metasequoia glyptostroboides Hu et Cheng is the only species in the genus Metasequoia Miki ex Hu et Cheng, which belongs to the Cupressaceae family. There were around 10 species in the Metasequoia genus, which were widely spread across the Northern Hemisphere during the Cretaceous of the Mesozoic and in the Cenozoic. M. glyptostroboides is the only remaining representative of this genus. Here, we report the complete chloroplast (cp) genome sequence and the cp genomic features of M. glyptostroboides. The M. glyptostroboides cp genome is 131,887 bp in length, with a total of 117 genes comprised of 82 protein-coding genes, 31 tRNA genes and four rRNA genes. In this genome, 11 forward repeats, nine palindromic repeats, and 15 tandem repeats were detected. A total of 188 perfect microsatellites were detected through simple sequence repeat (SSR) analysis and these were distributed unevenly within the cp genome. Comparison of the cp genome structure and gene order to those of several other land plants indicated that a copy of the inverted repeat (IR) region, which was found to be IR region A (IRA), was lost in the M. glyptostroboides cp genome. The five most divergent and five most conserved genes were determined and further phylogenetic analysis was performed among plant species, especially for related species in conifers. Finally, phylogenetic analysis demonstrated that M. glyptostroboides is a sister species to Cryptomeria japonica (L. F.) D. Don and to Taiwania cryptomerioides Hayata. The complete cp genome sequence information of M. glyptostroboides will be great helpful for further investigations of this endemic relict woody plant and for in-depth understanding of the evolutionary history of the coniferous cp genomes, especially for the position of M. glyptostroboides in plant systematics and evolution.

Keywords: Metasequoia glyptostroboides; chloroplast genome; conifer evolution; cupressophytes; inverted repeat; relict plant.

FIGURE 1

Gene map of the Metasequoia glyptostroboides cp genome. Genes shown inside of the circle are transcribed clockwise, whereas genes transcribed counter-clockwise are depicted on the outside. Genes belonging to different functional groups are color-coded. GC content is represented on the inner circle by dark gray bars, and AT content is represented by lighter gray bars.

FIGURE 2

Amino acid frequencies in the M. glyptostroboides cp protein-coding genes. The frequencies of amino acids were calculated for all of the 82 protein-coding genes from the start codon to the stop codon in the M. glyptostroboides cp genome excluding introns.

FIGURE 3

Frequency of repeats by length in the M. glyptostroboides cp protein-coding genes. The cutoff value for tandem repeats was 15 bp and for forward repeat and palindromic repeat was 30 bp.

FIGURE 4

Simple sequence repeat (SSR) analysis in the M. glyptostroboides cp genome. (A) Frequency of identified SSR motifs in different repeat type classes. (B) Location distribution of all of the SSR motifs.

FIGURE 5

Comparisons of cp genomic structure among five land plants, including M. glyptostroboides. Each colored gene segment has the same gene order in the five land plants. Each colored box for each gene order represents different regions [large single-copy (LSC), IRB, SSC, and IR region A (IRA)] in Glycine max (A), Oryza australiensis (B), Nymphaea alba (C), and Ginkgo biloba (D). In M. glyptostroboides (E), the purple and cyan arrows show two duplicated genes, which are trnQ-UUG and trnI-CAU, respectively, and the pink dashed box is believed to correspond to the IRB, which is retained in this species.

FIGURE 6

The maximum parsimony (MP) phylogenetic tree based on 47 protein-coding genes. The MP tree has a length of 21,985, with a consistency index of 0.6723, and a retention index of 0.8701. Numbers below each node are bootstrap support values. G. biloba and Cycas revoluta were set as outgroups.