Coleanthus subtilis (Tratt.) Seidel (Poaceae) is a rare grass in the monotypic genus Coleanthus Seidl. It has been protected in many countries because of the extremely short life cycle, strict habitat and breeding conditions, and habitat destruction, such as the Czech Republic, North America, and China. In addition, C. subtilis has a remarkable ability to reappear in its previous habitats after long time intervals.

In March 2021, researchers collected it on the beaches of the Yangtze River, and subsequently it was discovered by researchers from Wuhan Botanical Garden in the Songhua River basin in Harbin, which is nearly 100 years after its last appearance in China. Interestingly, its distribution has never been recorded along the Yangtze River before, and the factors responsible for this particular distribution are unclear. The phylogenetic position of C. subtilis and the composition of the subtribe Coleanthinae are controversial, and the absence of information on the chloroplast genome greatly limits the comprehensive understanding of its phylogeny.

Researchers from Wuhan Botanical Garden sequenced and assembled the chloroplast genome of C. subtilis for the first time, and did a comparative and phylogenetic analysis with other species in the family Poaceae.

The chloroplast (cp) genome of C. subtilis exhibited a tetrad structure of 135915 bp in length, which is similar to the length and structural characteristics of cp genomes of other Poaceae species. The accD gene and the introns of both clpP and rpoC1 genes have been lost within the cp genomes of C. subtilis, while ycf1, ycf2, ycf15 and ycf68 were pseudogenes, which is a relatively common phenomenon in Poaceae.

Although the cp genome structure of C. subtilis was relatively conserved, 26 SSRs (simple sequence repeats) and 13 highly variable loci were detected, which could be developed as important genetic markers for the Poaceae. Furthermore, the results of the phylogenetic analysis strongly supported that Coleanthus and Phippsia were sister taxa to each other and enlightened the relationships between Coleanthus, Zingeria and Colpodium.

This study presents the initial chloroplast genome report of C. subtilis, which provides an essential data reference for further research on its origin and has implications for population genetics and conservation of this species.

The research was published in the journal Frontiers in Plant Science under the title "Comparative and phylogenetic analysis based on the chloroplast genome of Coleanthus subtilis (Tratt.) Seidel, a protected rare species of monotypic genus".

Master student REN Jing was the first author. Prof. HU Guangwan from Wuhan Botanical Garden and Associate Prof. CAI Xiuzhen from Hunan Normal University were the co-corresponding authors. This work was supported by grants from the National Science & Technology Fundamental Resources Investigation Program of China and National Natural Science Foundation of China.

Chloroplast genome map of C. subtilis (Image by REN Jing)

Phylogenetic trees were generated based on the 76 shared protein-coding sequences of 53 species using maximum likelihood and Bayesian methods (Image by REN Jing)