Chloroplast genome study of Gueldenstaedtia monophylla (Fabaceae): unique genome within Chesneyeae

Gueldenstaedtia Fisch. is the smallest genus of the Fabaceae and contains only four species. In higher classification, this genus belonging to tribe Chesneyeae, together with Chesneya Lindl. ex Endl. and Tibetia (Ali) H.P. Tsui. However, the phylogenetic position and comparative genetic relationships between species remain unresolved due to the scarcity of available genetic data. In this study, we utilized high-throughput sequencing of complete chloroplast genomes of Gueldenstaedtia monophylla Fisch. and conducted comparative analyses with related species within the tribe. The complete chloroplast genome of G. monophylla is 118,980 bp in length and smallest genome within the tribe. It belongs to the inverted repeat-lacking clade (IRLC) of legumes and encodes 110 genes, including 76 protein-coding genes, 30 tRNAs, and 4 rRNAs. As typical of IRLC legumes, the rpl22 and rps16 genes were completely lost and the clpP and rps12 genes each lost one intron. Gueldenstaedtia plastid genomes exhibited several large-scale rearrangements that distinguish them from other genera within the tribe. Furthermore, G. monophylla retains some ancestral genomic architecture compared to rest of the genus. Phylogenetic analysis showed that G. monophylla exhibited a distinct position within the genus, with an estimated divergence time of 7.21 MYA. In addition, codon usage pattern and selective pressure analysis of protein-coding genes supported the evolutionary distinctiveness of G. monophylla within the genus. This reflects a unique evolutionary history and adaptive divergence in core genes, highlighting the importance of G. monophylla for understanding the origin and diversification of the genus.