Comparative And Phylogenomic Analyses Of Nymphoides And Menyanthes(Menyanthaceae)

The Menyanthaceae is a family consisting of six genera namely;Nephrophyllidium,Nymphoides,Liparophyllum,Menyanthes,Ornduffia and Villarsia genera of aquatic flowering plants with diverse leaf and floral traits,leading to uncertainty about taxonomic,phylogenetic and evolutionary relationships within this family.They have dimorphic heterostyly structure of flowers which enable diverse sexual reproduction conditions.The plants are widely distributed across the world.Nymphoides is the largest genus while Menyanthes trifoliata is a mono genus.In order to study the molecular evolution and phylogeny within Menyanthaceae,we sequenced six representative species from Nymphoides and genus Menyanthes.In our study,the chloroplast genomes sizes ranged from 151,985 bp for Nymphoides coronata to 154,313 bp for Menyanthes trifoliata L.in length.Large Single-Copy(LSC),Small Single-Copy(SSC)and Inverted Repeat regions(IRs)portrayed normal length similar to most reported angiosperms.Menyanthaceae family chloroplast genomes possess a typical quadripartite structure,conserved in genomic structure and gene order.The size of the cp genome for the seven Menyanthaceae species consistently encoded 112 to 113 unique genes,including 79 to 80 protein-coding genes,29 transfer RNA(tRNAs),and four ribosomal RNAs(rRNAs),17 genes were duplicated in the inverted repeat region(IR)in both Nymphoides to 18 genes in Menyanthes respectively.Comparative analysis of the chloroplast genomes showed that Nymphoides species have lost the rpl2 intron and that the common ancestor of this family lacks the rpl2 intron.Phylogenetic analyses were conducted using 70 protein-coding genes in other families in order Asterales.Menyanthaceae divided into two clades with robust support.The genus Nymphoides resolved to a monophyletic lineage and was closely related to Menyanthes.Generally,the gene synteny,order and organization assumed a similar pattern for this family especially the small single copy,(SSC)region,which was strongly conserved in gene order and content within this family.The overall GC content was 37.1 comprised of(42.9%)in IR regions slightly higher than that of LSC(35.2%)and SSC region(31%).The IR borders for most Nymphoides were similar except for N.crenata which had an overlap of 2bp between genes ndhF and ?ycfland Menyanthes IR's consisted of(rpl2)gene which was absent in Nymphoides.In all studied chloroplast genomes,30 codons had relative synonymous codon usage RSCU>1(higher preference),29 codons had RSCU<1(low preference).Most RNA editing site changed from Serine to Leucine.The largest nucleotide diversity(Pi)was found in genes ccsA,rpl22,matK,and rps16 in CDS region and trnK-UUU-rpsl6,trnG-GCC-trnR-UCU,accD-psaI,psbK-psbI,trnH-psbA,and rpl32-trnL-UAG,in the IGS region.Palindromic and Forward repeats dominated among dispersed repeats while most simple sequence repeats like in other reported angiosperms were mononucleotides ending with A/T in all cp genomes.We recommend that,more complete chloroplast genomes for Menyanthaceae to be sequenced,that would be excellent to solve the family relationship.