Incarvillea Juss. is an herbaceous genus comprising only 16 species of the Bignoniaceae family. Here, we investigated Incarvillea potaninii Batalin in Mongolia, using conservation assessments, distribution modeling, taxonomic treatment, and comparative plastome analysis. Although previously found in Mongolia and China, we confirmed that it currently occurs only in Mongolia. Globally, I. potaninii is considered vulnerable. Its plastome is 154,003 bp long, containing a large single-copy (LSC) region of 81,790 bp and a small single-copy (SSC) region of 10,037 bp, separated by a pair of inverted repeats (IRs) of 31,088 bp. The genome comprises 111 unique genes, including 77 protein-coding genes, 30 tRNA genes, and four rRNA genes, and the ndhA gene was lost. Compared to typical angiosperm plastomes, Incarvillea shows several large-scale inversions, translocations, accD gene loss in genus, IR expansion, and SSC contraction. The IR region, integrated with one to thirteen genes of the SSC region, showed great variation in size, order, and content. Phylogenetic analysis revealed that I. potaninii is closely related to I. sinensis and I. semiretschenskia. We determined the current and future distributions of I. potaninii using MaxEnt. Under current climatic conditions, the potential habitat of I. potaninii spans approximately 19,655.54 km², with highly suitable areas concentrated in southern Mongolia. Although the total suitable habitat area is projected to remain stable, the area of extreme suitability will decline markedly in future. Under the SSP126 scenario, extreme suitability areas may decrease by 67.83% by 2070. Key predictors of distribution include temperature seasonality, precipitation during the driest quarter, and soil pH. We provide descriptions, taxonomic notes, and distribution of I. potaninii.
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