- 131 genes were identified in the plastome out of which 113 are unique and 18 were repeated in IR region. - The analysis of long repeat showed all types of repeats were present in the plastome and palindromic has the highest frequency. - In addition high variation is observed in the intergenic spacer region than the coding region. - The analysis of sequence divergence in the protein coding genes indicates that the following genes undergo positive selection (atpF, petD, psbZ, rpl20, petB, rpl16, rps16, rpoC, rps7, rpl32 and ycf3).. - The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. - Presl is among the largest family in the order Lamiales with ca. - The family is close to Bignoniaceae family in the Lamiales order [3]. - The main centres of distribution of the species in the family are Africa, Central America and Asian continent particularly Malaysia, Indonesia and Brazil [4]. - In an effort to resolve taxonomic issues of the family and its species, researchers for the past decades works extensively in delimiting the family [7–10], identifying major clades in the family [11–14]. - prionitis contained 113 different genes out of which 18 are dupli- cated in the IRA and IRB region, totaling 131 genes. - The number of rRNA genes, tRNA genes and protein-coding genes in the genome are 4, 30 and 80, respectively (Fig. - Four rRNA, seven protein cod- ing and tRNA genes are located in the pair of the inverted repeat region of the plastome whereas the large single copy region harbored 62 protein-coding sequence and 22 tRNA genes, the remaining one tRNA and 12 pro- tein coding genes are located in the single copy region.. - prionitis is found to have intron in some of the genes, like in other species in the Lamiales order [36, 37]. - Four of the genes with. - 1 Gene map of the B. - Known functional genes are indicated in the colored bar. - The GC and AT content are denotes by the dark grey and light grey colour in the inner circle respectively. - Table 1 Nucleotide composition in the complete plastome sequence of B. - Table 2 Genes present in the chloroplast genome of B. - Table 3 Genes with intron in the B. - intron viz.: ndhB, trnA-UGC, trnI-GAU and rpl2 are sit- uated in the inverted repeat region and the other 12 in the large single copy region. - trnK-UUU is the gene with longest intron with 2460 bp because of the situation of matK in the gene.. - The frequency of the codon usage present in the plastome of B. - prionitis was computed using the nu- cleotide sequence of protein-coding genes and tRNA genes 100,319 bp, the result is presented in Table 4, the results showed the genes in the plastome are encoded by 33, 436 codons. - for the amino acids Leucine appears more frequently in the genome Fig. - 2), comparable to that of Ailanthus altisssima and the ones coding for Trp have the lowest in the plastid se- quence. - The result of the analysis show that there is low codon usage bias in the plastome sequence of B.prionitis (Table 4).. - The prediction of RNA editing sites present in the plastome sequence of B. - The results as shown in (Table 5) showed that most of the conversions in the codon posi- tions are from Serine to Leucine. - Generally, the editing sites observed in the plastome were 61 which are distrib- uted between the 19 protein-coding genes. - Nine (9) RNA editing site in ndhB has been confirmed in the plastome of other spe- cies [41–43]. - Conversions of proline to serine were ob- served, which involves the changing of the amino acids in the RNA editing site from apolar to polar group.. - Repeat sequence in the chloroplast genome of B. - prioni- tis were screen using REPuter programme with default settings, the programme revealed that only three types of repeats were present in the genome viz. - In the first location, 65.30% of the repeats are contained in the non coding region. - Eight repeats were located in the tRNA (16.32. - situated in the protein coding genes in particular rpl2, ndhA, ycf1, ndhC, and ycf2. - The rate of repeats among eight Acanthoideae plas- tomes was compared, the results indicates that comple- ment, palindromic, reverse and forward type of repeats occurred in the plastome of J. - breedlovei, whereas no comple- ment repeats detected in the cp genomes of B. - pani- culata have15 forward repeats in their plastome and the frequency of reverse repeats is identical in the plastome of A. - knappiae and is the least repeat in the plastome of J. - In this research, a total number of 98 microsatellites were identified in the chloroplast genome of B. - Most of the microsatellites in the plastome are mononucleotide (83.67%) and majority of them are polythymine 58.53%. - followed by poly A (polyadenine) 40.24%, only one Poly G (polyguanine (1.21%) is present where as no poly C detected in the genome. - ATTG and only one penta AAATGG/ATTTCC were detected in the genome (Fig. - Table 5 Predicted RNA editing site in the B. - The majority of the microsatellites are found in the intergenic spacer region (Fig. - The majority of the repeats were located in the large single copy region (70.40%) and the single copy region contained the lowest frequency of repeat (9.18%) in the plastome.. - Pentanucleotides were not found in the plastome of B. - The comparison between the invterted repats and single copy regions boundries in the eight plastome of Acanthaceae (B. - There is a little variation in the boundaries of the IR-SSC and IR-LSC of the plastomes (Fig. - In the SSC/IRb border of the eight plastomes, ycf1 and ndhF genes are found.. - Table 6 Repeat sequences present in the B. - Positioning of ycf2 gene in the IRb/LCS border is ob- served only in the genome of R. - The gene ndhF was found to have 36 bp, 109 bp, 40 bp and 41 in the IRb region in B. - The size of the genome in all the studied species is rele- vant to variation in the LSC region. - cusia which has trnH-GUG in the inverted repeat regions and ycf2 in the large single copy [52]. - Some of the genes in the cp genome of B. - Most of the repeats were located in the non coding region and ycf genes (ycf1 and ycf2), this has been com- monly observed in plastome of angiosperms [58].. - cp microsatellites analysis, reveal total number of 98 SSRs in the cp gen- ome of B. - Poly A and T are reported to be the most Table 7 Simple sequence repeats in the chloroplast genome of B. - Most of the cpSSRs are located in the non coding region whereas few are located in the protein coding genes re- gion. - Contraction and expansion in IRs region were ob- served in the cp genome B. - paniculata, one of the duplicated rpl2 is located in the LSC region while the other is in the IRb region whereas only 1 rps19 is present in the LSC. - attenuatus, here the two rps19 are located in the inverted repeat regions (IRa and IRb) and the rpl22 gene is located in the LSC region.. - cusia and is characterized by having trnH-GUG duplicated in the inverted region.. - Type IV has no genes in the IRb/LSC border and was only found in R. - In type V which is observed in the genome J. - flava, some part of the rps19 gene are located in the inverted repeat region while some are lo- cated in single copy region, another remarkable observa- tion is that the two rps19 are of unequal length. - ciliaris and is characterized by having rps19 in the LSC region and rpl2 in the IRb region. - All the genomes have ndhF in the IRb/SSC border as well as ycf1 in the SSC/IRa border. - In addition, the stop codon is absent in the ycf1 gene sequence and this result to the differences in the distribution of genes in single copy and inverted repeat. - c Number of different SSR type in the eight chloroplast genome of Acanthoideae. - The result of the comparative genome analysis using mVISTA revealed that the genome is relatively conserved with some degree of variation, which mostly occurs in the non coding region as a result of insertion and deletion. - The results of the alignment showed no considerable structural rearrangements, like gene reloca- tion or inversion were detected in the plastomes. - The structural rearrangement was detected in the cp genome of S. - DNA barcodes are sequences in the genome unique to particular taxa and are used as reliable tools for identification of plants and resolving phylogenetic re- lationship [65, 66]. - These regions will be used as makers for identification of the sampled Acanthaceae species as well as resolving phylogetic relationships in the family.. - Most of the variable regions are located in the single. - Synonymous (dS) and non synonymous (dN) substitu- tion rate as well as dN/dS ration were calculated to evaluate sequence divergence and purifying selection in the protein coding genes. - 5 Sequence alignment of eight chloroplast genome in the Acanthaceae family performed with mVISTA using annotation of B. - The x-axis represents the coordinates in the cp genome while y- axis represents percentage identity within 50 – 100%. - Andrographideae and Barlerieae were placed in the tribe Justiceae as sub. - The numbers in the branch nodes represent bootstrap percentage (BP)/posterior probability (PP). - studies of the family Acanthaceae. - Alzahrani, the voucher speci- men was deposited in the herbarium of King Abdulaziz University, Jeddah, Saudi Arabia, with voucher specimen number KAU22534. - PREP suite [80] with cutoff value of 8.0 was used to predict the RNA editing sites in the plastome.. - prionitis as reference in the Shuffle- LAGAN mode [83].. - For phylogenomic analysis, the cp genomes of Acanthoi- deae species deposited in the GenBank were recovered (Table 8). - Table 8 Accession numbers of plastomes analysed in the study. - All data generated or analysed during this study are included in this published article and the complete chloroplast genome sequence of Barleria prionitis is deposited in the genbank with I. - Synoptical Classification of the Lamiales. - Relationships in the Acanthaceae and related families as suggested by cladistic analysis of rbcL nucleotides equences. - Corolla ontogeny and aestivation in the Acanthaceae. - PCR-RFLP analysis of cpDNA and mtDNA in the genus Houttuynia in some areas of China.. - Dynamics and evolution of the inverted repeat-large single copy junctions in the chloroplast genomes of monocots. - The chloroplast genome sequence of the medicinal plant Andrographis paniculata.. - Phylogenetic studies and comparative chloroplast genome analyses elucidate the basal position of halophyte Nitraria sibirica (Nitrariaceae) in the Sapindales.. - Complete chloroplast genome of the multifunctional crop globe artichoke and. - The role of insertions/deletions in the evolution of the intergenic region between psbA and trnH in the chloroplast genome
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