Structural Rearrangements And Size Variation Of The Chloroplast Genomes In The Order Alismatales

The aquatic monocot order Alismatales,is an important primary producer in aquatic environments,serving as food for aquatic animals and substrate stabilizers.The order consists of 14 families and ca 166 genera with worldwide distribution.Some species in the families,Hydrocharitaceae,Alismataceae,Butomaceae,and Aponogetonaceae,are economically traded worldwide as aquarium plants and in outdoor gardens.The order is morphologically diverse and often presents taxonomical challenges in identification.Whole chloroplast genome sequence,newly sequenced in 31 chloroplast genomes were reported and compared to 19 plastomes available from online databases.The chloroplast genomes variable and ranged from 143,877 bp in Zostera marina to 179,839 bp in Alisma canaliculatum.In all the plastomes of Alismatales compared,five types of inversion events are revealed in this study,such as the trnV-UAC-rbcL inversion region observed among six families forming a single clade,and the inversion region containing the genes trnQ-UUG to trnS-GCU,unique to Alismataceae family as seen in six species sampled for this study.Minor IR expansion and contractions between 1-2 kb,are typical in the order Alismatales.Moreover,major IR border shifts were also noted,such as in Helantium sp.resulting in a reduced SSC region with only 6 genes,and Thalassia hemprichii IR expansion including 15 genes from LSC and SSC However,both IR copies were maintained in all chloroplast genomes analyzed.Previously,gene loss was reported in Najas flexilis and Z.marina,however,ndhJ and ndhK genes are missing in Posidonia oceanica in this study.There was no gene loss in this study in family Cymodoceaceae,unlike previously reported.Pseugogenization of ycf1 gene caused by IR border shifts in different species in this study was frequent.Also,there are genes presenting stop codons within the reading frame,such as ycf15 and accD are regarded as missing here.Repeat sequences were prevalent in the non-coding regions among the Alismatales,with large repeats being recorded in Araceae.The mononucleotide repeats were highest in frequency among the Alismatales.Hydrocharitaceae was the most rearranged family in this study.However,all Alismatales genome sequences maintained the typical structure of angiosperm plastome.Our results revealed detailed structural rearrangements present in the chloroplast genome sequences of the order Alismatales,crucial for understanding the evolutionary history and phylogenetic relationships within Alismatales plastomes.SSR repeats identified in this study increase the efficacy of marker development for evolutionary and conservation studies among Alismatales.Our research provides the first insight into the extent of genomic rearrangement among Alismatales and gives a better understanding of the relationships within.