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.

The Complete Chloroplast Genome Sequence of a Relict Conifer Glyptostrobus pensilis: Comparative Analysis and Insights into Dynamics of Chloroplast Genome Rearrangement in Cupressophytes and Pinaceae

“…pensilis cp genome. Although different algorithms and criteria were used for SSR identification, their characteristics and distribution were similar to those reported for other conifer cp genomes [51, 66], 14 monocot cp genomes [67] and 30 asterid cp genomes [50]. The SSRs we have identified in the G .…”

“…The GC content at the first, second and third codon positions of protein-coding genes is 45.94, 36.82 and 27.50%, respectively (Table 1). This trend of decreasing GC content at the three codon positions and the bias toward a lower GC content at the third codon position has been observed in many other sequenced plant cp genomes, and this pattern contributes to the relatively high AT content throughout the cp genome [47–51]. With regard to amino acid and codon usage, the most- and least-frequently coded amino acids are leucine (2660, 10.83%) and cysteine (279, 1.14%), respectively, whearea AAA (1176, 4.79%) and CGG (77, 0.31%) are the most and least used, respectively (S2 Fig and S7 Table).…”

“…pensilis cp genome lacks the typical quadripartite structure (S1 Fig) because of the loss of one IR copy, which has also been observed in other conifer cp genomes from Pinaceae [22, 45] and cupressophytes [51, 60]. Since cp genomes of these two conifer clades lost different IR copies [23, 44], comparsion of cp genome structure were performed to confirm which one IR copy were lost in the G .…”

Chloroplast Genome Sequence of Pigeonpea (Cajanus cajan (L.) Millspaugh) and Cajanus scarabaeoides (L.) Thouars: Genome Organization and Comparison with Other Legumes

“…Here too leucine (2264 codons, 9.05%) is the most abundant amino acid and cysteine (416 codons, 1.66%) is the least abundant amino acid (Supplementary Tables S2, S3). Leucine and cysteine are reported as the most and least abundant amino acids respectively in other cp genomes also (Chen et al, 2015; Curci et al, 2015; Redwan et al, 2015). It has been suggested in previous studies that there is a significant relationship between codon usage bias and gene expression level (Iannacone et al, 1997; Rouwendal et al, 1997), therefore it implies that there is a strong natural selection pressure on highly expressed genes to optimize their translation efficiency by using major codons (Bulmer, 1988).…”

The complete chloroplast genome of the spring ephemeral plant Alyssum desertorum and its implications for the phylogenetic position of the tribe Alysseae within the Brassicaceae

“…As more seed plant cp genomes are sequenced and deposited in GenBank, several studies have used partial or whole cp genomes in phylogenetic analyses to gain new insights into the relationships among and evolution of plant species or populations (Cahoon et al 2010, Bennett and Triemer 2015, Chen et al 2015. It is also worth noting that the cp genome of Lobularia maritima was sequenced and used in a phylogenetic study of Raphanus (Jeong et al 2014).…”