Chloroplast Genome Analysis,Comparison And Phylogenetic Analysis Of Xerophyta Spekei From Kenya

Xerophyta is a monocotyledonous genus from the family Velloziaceae distributed in Africa mainland,Madagascar and Arabian Peninsula;with 45 species,25 species and 1 species respectively.They are mostly confined to xeric environments having specific substrates requirements on inselberg and rocky outcrops.Several studies carried out on this genus have mainly focused on desiccation tolerance nature of its species.However,there have been few studies on the complete chloroplast genome of this genus to provide insights into the evolution,phylogeny and solve the species delimitation at lower taxonomic levels.In this study focus was on X.spekei Baker,an important economical and medicinal plant,widely distributed in Kenya,Tanzania,Zambia,Zimbabwe,and Ethiopia.The complete chloroplast genome of Xerophyta spekei was sequenced,analyzed and compared to other species in the order pandanales:(1)The chloroplast genome of X.spekei exhibits a circular DNA molecule of 155,235bp in length,with a typical quadripartite structure.It consists of two inverted repeat regions(IRa and IRb)of 27,109bp each,separated by large(LSC)and small(S SC)single-copy regions of 83,629bp and 17,388bp,respectively.The overall GC content of X.spekei was 37.6%,while those of LSC,SSC and IR regions had 35.5%,31.8%and 42.5%respectively.The chloroplast genome had 112 unique genes,of which 78 were protein-coding genes,30 tRNA genes and 4 rRNA genes.The gene content and organization of X.spekei chloroplast genome were similar to those of other Pandanales.Obvious codon preferences were also shown in almost all protein-coding cpDNA and amino acid sequences.The repeat analysis indicates that the genome contained only the palindromic and the Forward repeats.(2)We identified 36 simple sequence repeats(SSRs)of which majority are mononucleotides A/T.(3)Analysis of the phylogenetic relationships among the 11 species indicated that Acanthochlamys bracteata was sister to the Xerophyta and the close relationship supported their placement in the same family Velloziaceae.The clade that consists of Xerophyta and A.bracteata was clustered with other species of the order Pandanales in a big clade with a strong bootstrap support,supporting the placement of Velloziaceae in the order of Pandanales.The availability of cp genome reported here provides a valuable genetic resource for comprehensive further studies in genetic variation,taxonomy and phylogenetic evolution of Order Pandanales.In addition,SSR markers detected will be used in further phylogeographic and population structure studies of the species in this genus.