Comparative Analyses And Phylogenetic Relationships Of Complete Chloroplast Genomes From The Genus Trapa In China

Trapa L.,a member of Trapaceae,is a floating-leaved aquatic plant with important economic and ecological values.However,species identification and phylogenetic relationship are still unresolved for Trapa.In this study,complete chloroplast genomes of nine wild species/taxa and five cultivated species/taxa in Trapa were sequenced and annotated.Combined with obtained sequences of the other seven species from our lab(six wild and one cultivated species/taxa),comparative analysis of cp genomes were first performed on the 15 wild and six cultivated species/taxa,respectively.The results were as follows:The 15 complete chloroplast genomes of wild species/taxa exhibited quadripartite structures with medium size of 155,453?155,559 bp.IR/SC junctions were conservative with no obvious change found.Long repetitive repeats and SSRs were mostly detected in the intergenic and LSC regions,providing useful plastid markers for species and relationship identification.MP,ML and BI,three phylogenetic analysesconsistently showed two branches within Trapa,including small-and large-seed species/taxa,respectively.The 13 large-seed species/taxa was divided into three clusters:(1)T.quadrispinosa Roxb.,T.bispinosa Roxb.and T.macropoda var.bispinosa W.H.Wan.;(2)T.japonica Flerow,T.mammillifera Miki,T.potaninii V.Vassil,T.pseudoincisa Nakai,T.arcuata S.H.Li et Y.L.Chang,T.natans var.baidangensis;(3)T.litwinowii V.Vassil,T.manshurica Flerow,T.kozhevnikovirum Pshennikova and T.sibirica Flerow.The 12 complete chloroplast genomes of 6 cultivated species/taxa showed a little difference in their cp genome sizes,with 155,534?155,539 bp.The IR/SC junctions of12 individuals showed no change,suggesting that complete chloroplast genomes of cultivated species/taxa were more conservative than those of the wild species/taxa.Similarly,most long repetitive repeats and SSRs were detected in intergenic and LSC regions of cultivated complete chloroplast genomes.Phylogenetic analyses exhibited that all Trapa species/taxa were separated into three branches: firstly,the two small-seed species(T.incisa Sieb.et Zucc.and T.maximowiczii Korsh.)were separated from other Trapa species/taxa;secondly,all large-seed wild species/taxa clustered into a branch;finally,all cultivated individuals of Trapa species/taxa clustered together.And two clusters were included in the cultivated species/taxa:(1)the two escaped taxa of cultivated species;(2)four common cultivated species(T.bicornis var.cochinchinensis,T.bicornis Osbeck,T.acornis and T.bicornis var.Taiwanensis).This study provided basic genetic information for species identification and evolutionary relationships in Trapa,which laid a foundation for the genealogical geography of the genus.The results of this study will promote the effective management and sustainable utilization of genetic resources of Trapa.