Comparative chloroplast genomics provides insights into the genealogical relationships of endangered Tetraena mongolica and the chloroplast genome evolution of related Zygophyllaceae species

Abstract

A comprehensive understanding of genetic background for rare species will provide an important theoretical basis for the future species management, monitoring and conservation. Tetraena mongolica is restrictedly distributed in the western Ordos plateau of China and has been listed as a national protected plant. We generated 13 chloroplast (cp) genomes of T. mongolica (size range of 106,062–106,230 bp) and conducted a series of comparative analyses of six Zygophyllaceae cp genomes. T. mongolica cp genome exhibited a quadripartite structure with drastically reduced inverted repeats (IRs, 4,315 bp) and undergone the loss of a suit of ndh genes and a copy of rRNAs. Furthermore, all the T. mongolica populations were divided into two genetic groups based on complete cp phylogenomics. In addition, notably variable genome size, gene order and structural changes had been observed among the six Zygophyllaceae cp genomes. Overall, our findings provide insights into the cp genome evolution mode and intraspecific relationships of T. mongolica, and provide a molecular basis for scientific conservation of this endangered plant.

Assembly and comparative analysis of the complete mitochondrial and chloroplast genome of Cyperus stoloniferus (Cyperaceae), a coastal plant possessing saline-alkali tolerance

“…These are not only important sources of information for developing populations and evolutionary analysis markers but also play an important role in genome plasticity and adaptive evolution [ 55 ]. Additionally, certain noncoding regions of cpDNA exhibit relatively high nucleotide substitution rates that are not only suitable for reconstructing phylogenetic relationships between species but also for studying phylogenetic geography within species [ 56 , 57 ]. Therefore, the organellar genome contributes to genetic diversity, and lineage geography research focused on C. stoloniferus helps to trace the historical origins of existing distribution patterns and elucidates the impact of geological changes on the evolution of C. stoloniferus .…”

Assembly and comparative analysis of the complete mitochondrial and chloroplast genome of Cyperus stoloniferus (Cyperaceae), a coastal plant possessing saline-alkali tolerance

“…These are not only important sources of information for developing populations and evolutionary analysis markers but also play an important role in genome plasticity and adaptive evolution [54]. Additionally, certain noncoding regions of cpDNA exhibit relatively high nucleotide substitution rates that are not only suitable for reconstructing phylogenetic relationships between species but also for studying phylogenetic geography within species [55,56]. Therefore, the organellar genome contributes to genetic diversity, and lineage geography research focused on C. stoloniferus helps to trace the historical origins of existing distribution patterns and elucidates the impact of geological changes on the evolution of C. stoloniferus.…”

“…atp6 and atp9 are located on the inner mitochondrial membrane and are important components of the ATP synthase complex [66]. They are potential drivers of mtDNA evolution and are often used in CMS breeding [55,67]. Similar to the growth environment of C. stoloniferus, it has been observed in mangroves that only the rps7 gene is positively selected [68].…”

Genetic Diversity and Phylogenetic Analysis of Zygophyllum loczyi in Northwest China’s Deserts Based on the Resequencing of the Genome

“…Zygophyllum species grow in stony residual dune slopes, fixed and semi-fixed sands, dry riverbeds, gravelly inter-dune flats, and steep loess walls. These species are exceptionally adapted to arid conditions and provide essential ecosystem services in arid environments such as deserts and steppes in the Gobi [43][44][45]. Zygophyllum serves as a fundamental component in arid environments due to its susceptibility to wind erosion, drought tolerance, salinity tolerance, and the capacity to thrive in infertile soils.…”