The result of the analysis which includes the complete chloroplast genomes features and map of
P. tomentosa and comparison with
C. procera, Cynanchum wilfordii and
Asclepias nivea as well as the presentation of the evolution of
accD gene in Asclepiadoidea
e, Apoceanaceae were discussed.
Genes with Introns
Table 1 is narrating features of genes with introns in
P. tomentosa whole chloroplast genome with
clpP,
accD and
ycf3 both from LSC section of the genome were located at intron 2 and exon 3 respectively. The position of
accD and ycf3 gens agrees with the finding of
Yaradua et al., (2019).
SSR Analysis
Table 2 shows the SSR markers in
P. tomentosa with about 42 repeats sequences which are either palindromic or forward. The findings are similar to the studies by
Huang et al., 2020. The cp genome has a similar variability with the previously reported cp genomes of Asclepiadoideae subfamily such as the
C. wilfordii (KT220733) (
Park, et al., 2018) and
C. procera (NC041440). All the genomes had a quadripartite structure consisting of SSC, SSC regions and inverted repeats.
Genome features analysis of P. tomentosa, C. procera, C. wilfordii and A. nivea
Table 3 Indicates genome features of
P. tomentosa, C. procera, C.wilfordii and
A. nivea, in which the
C. procera genome size is 166,010 bp,
P. tomentosa 164,213 bp,
A. nivea 161,592 bp and
C. wilfordii 161,180 bp (Fig 1). The total number of genes was highest in
C. wilfordii 168,
C. procera 163, while
P. tomentosa and
A. nivea are the least number of genes with 161 each However, the GC content of the genomes showed highest
in A. nivea, C. wilfordii and
P. tomentosa with 38% while
C. procera is the least with 37%. tRNA content is highest in
A. nivea and
P. tomentosa 46% and low in
C. procera and
C. wilfordii 42% each; total rRNA genes were same in all the plants 8 each; the size of the inverted repeats (IR) were highest in
C. procera 26,219bp, followed by A
. nivea 25,472bp,
C. wilfordii 24,637bp and
P. tomentosa 21411bp. For the size of large singe copy (LSC)
C. procera is the highest 94,104bp, then
C. wilfordii 91,976bp,
A. niveae 91,971bp and
P. tomentosa being the least with 80,102bp; Also the size of Small single copy (SSC) of the plants
C. wilfordii has the highest size with 19,930bp, then
C. procera 19,468bp, followed by
A. niveae with 18,771 and
P. tomentosa with 17,022bp.
Comparative genome analysis using Mvista alignment
Comparative genomic analysis in Fig 3 indicate that genes at non-coding regions are more conserved compared to the ones at the coding regions; such as
ycf15,
cemA,
rpl16 and
clpP genes were the most divergent regions observed. Genetic diversity in angiosperm chloroplast genomes has been reported in families such as the Angiosperms such as the Amaranthaceae, Caryophyllaceae, with some showing a character of loss of introns in coding regions
(Daniell et al., 2008). The nature of chloroplast varied as reported by different authors even though are also similar in most angiosperms; in terms of the coding regions sizes, complete gene number, complete tRNA genes and complete protein genes (
Raubeson and Jansen, 2005;
Daniell et al., 2016; Yaradua et al., 2019). Distribution in the number of SSR Fig 2. revealed that non-coding region has higher SSR, followed by the coding region and the cp genome region.
Furthermore, the
accD gene deals with the formation of fatty acids in plants programming the betacarboxyl transferase a derivative of acetyl coA (
Sasaki and Nagano, 2004;
Rousseau-Guetin et al., 2013; Kode et al., 2005). It was also reported that fatty acids contents and metabolic activities in plants are influenced by the
accD gene expression
(Lee et al., 2004; Nakkew et al., 2008); accD gene is a pseudo-gene in some angiosperm
(Xiang et al., 2016) while exist as a complete gene in others
(Ni et al., 2016b) the result of these study indicate about 6 highly conserved regions in the
accD of
P. tomentosa and
A. nivea while two and four highly conserved regions detected on
accD gene of
C. wilfordii and
C. procera, respectively.
IR border junction analysis
Variations exist between the chloroplast genomes of
P. tomentosa. C. procera, A. nivea and
C. wilfordii as seen in Fig 4 where
trnH,
rpl22,
ycf1,
ndhF and
rps19 genes are designated by the junction of IR andSSC regions. Variation was also observed at the SSC section of
A. nivea genome; with
ycf1 and
rps19. Angiosperms chloroplast genome was generally known for its uniqueness and conservative features in structures and topology; even with many evolutionary events there exists slight changes that lead to the variations among members of the same taxonomic groups due to contraction in the borders of the genomes. The comparison between plastome genomes of
P. tomentosa, C. procera, A. nivea and
C. wilfordii reveals some variations in their genome architecture.
Phylogenetic analysis
Phylogenetic inference revealed that the genus
Pergularia is a monophyletic genus (Fig 5) and a sister genus to
Calotropis and
Asclepias. This result agrees with the findings of
Rapini et al., 2012 and
Abba et al., 2020 based on complete chloroplast genome sequences of some species in the subfamily Asclepiadoideae. Therefore, this study highlighted the chloroplast genome architecture in Asclepiadoideae and the variations among the species studied. There is a close resemblance in the genome’s features; identified SSR markers (Fig 2) could be used in population genetics and Phylogenetic studies of the subfamily Asclepiadoideae.
