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Background Handeliodendron  Rehder and  Eurycorymbus  Hand.-Mazz. are the monotypic genera in the Sapindaceae family. The phylogenetic relationship of these endangered species  Handeliodendron bodinieri  (Lévl.) Rehd. and  Eurycorymbus cavaleriei  (Lévl.) Rehd. et Hand.-Mazz. with other members of Sapindaceae s.l. is not well resolved. A previous study concluded that the genus  Aesculus  might be paraphyletic because  Handeliodendron  was nested within it based on small DNA fragments. Thus, their chloroplast genomic information and comparative genomic analysis with other Sapindaceae species are necessary and crucial to understand the circumscription and plastome evolution of this family. Results The chloroplast genome sizes of  Handeliodendron bodinieri  and  Eurycorymbus cavaleriei  are 151,271 and 158,690 bp, respectively. Results showed that a total of 114 unique genes were annotated in  H. bodinieri  and  E. cavaleriei , and the  ycf1  gene contained abundant SSRs in both genomes. Comparative analysis revealed that gene content, PCGs, and total GC content were remarkably similar or identical within 13 genera from Sapindaceae, and the chloroplast genome size of four genera was generally smaller within the family, including  Acer ,  Dipteronia ,  Aesculus , and  Handeliodendron . IR boundaries of the  H. bodinieri  showed a significant contraction, whereas it presented a notable expansion in  E. cavaleriei  cp genome.  Ycf1 ,  ndhC-trnV-UAC , and  rpl32-trnL-UAG-ccsA  were remarkably divergent regions in the Sapindaceae species. Analysis of selection pressure showed that there are a few positively selected genes. Phylogenetic analysis based on different datasets, including whole chloroplast genome sequences, coding sequences, large single-copy, small single-copy, and inverted repeat regions, consistently demonstrated that  H. bodinieri  was sister to the clade consisting of  Aesculus chinensis  and  A. wangii  and strongly support  Eurycorymbus cavaleriei  as sister to  Dodonaea viscosa . Conclusion This study revealed that the cp genome size of the Hippocastanoideae was generally smaller compared to the other subfamilies within Sapindaceae, and three highly divergent regions could be used as the specific DNA barcodes within Sapindaceae. Phylogenetic results strongly support that the subdivision of four subfamilies within Sapindaceae, and  Handeliodendron  is not nested within the genus  Aesculus .

bmc genomics

Comparative genomics and phylogenetic relationships of two endemic and endangered species (Handeliodendron bodinieri and Eurycorymbus cavaleriei) of two monotypic genera within Sapindales