The complete chloroplast genome sequence of Dodonaea viscosa: comparative and phylogenetic analyses

Abstract

The plant chloroplast (cp) genome is a highly conserved structure which is beneficial for evolution and systematic research. Currently, numerous complete cp genome sequences have been reported due to high throughput sequencing technology. However, there is no complete chloroplast genome of genus Dodonaea that has been reported before. To better understand the molecular basis of Dodonaea viscosa chloroplast, we used Illumina sequencing technology to sequence its complete genome. The whole length of the cp genome is 159,375 base pairs (bp), with a pair of inverted repeats (IRs) of 27,099 bp separated by a large single copy (LSC) 87,204 bp, and small single copy (SSC) 17,972 bp. The annotation analysis revealed a total of 115 unique genes of which 81 were protein coding, 30 tRNA, and four ribosomal RNA genes. Comparative genome analysis with other closely related Sapindaceae members showed conserved gene order in the inverted and single copy regions. Phylogenetic analysis clustered D. viscosa with other species of Sapindaceae with strong bootstrap support. Finally, a total of 249 SSRs were detected. Moreover, a comparison of the synonymous (Ks) and nonsynonymous (Ka) substitution rates in D. viscosa showed very low values. The availability of cp genome reported here provides a valuable genetic resource for comprehensive further studies in genetic variation, taxonomy and phylogenetic evolution of Sapindaceae family. In addition, SSR markers detected will be used in further phylogeographic and population structure studies of the species in this genus.

Comparative Genomics of the Balsaminaceae Sister Genera Hydrocera triflora and Impatiens pinfanensis

“…Based on sequence similarity among the IR, SSC and LSC regions, the IR region was more conserved. This is in agreement with previous reports that found out that IR region diverged at a slower rate than the LSC and SSC regions as a result of frequent recombinant events taking place in IR region leading to selective constraints on sequence homogeneity [ 50 , 51 ].…”

The Complete Chloroplast Genome Sequence of Tree of Heaven (Ailanthus altissima (Mill.) (Sapindales: Simaroubaceae), an Important Pantropical Tree

“…In all the seven species, mononucleotide repeats were more abundant with A/T repeats being the most common repeats. This result is consistent with earlier studies in [ 31 , 35 , 46 ] which revealed that many angiosperm chloroplast genomes are rich in poly A and poly T. Moreover, in the seven analyzed species, hexanucleotide repeats were not detected, whereas Azadirachta indica , Dodonaea viscosa and Leitneria floridana had no pentanucleotide repeats.…”

“…The collinear blocks of the genes including ribosomal RNA, tRNA, and protein coding genes revealed that all the seven genomes were relatively conserved with no gene rearrangement ( Figure 3 ). Some other studies have revealed homology in genome organization and no gene rearrangements, thus our findings support their conclusions [ 31 , 39 , 40 ].…”

“…The overall guanine-cytosine (GC) content of the whole genome is 37.6%, while the average adenine-thymine A + T content is 62.36%. The relatively higher IR GC content and A + T bias in this chloroplast have been previously reported in genomes of relative species in order Sapindales [ 31 ]. The GC content of the LSC, SSC and IR regions are 35.7, 32.2 and 42.6% respectively.…”

Chloroplast Genome of the Folk Medicine and Vegetable Plant Talinum paniculatum (Jacq.) Gaertn.: Gene Organization, Comparative and Phylogenetic Analysis

“…As previously reported, leucine and isoleucine are the more commonly seen amino acids in the cp genomes of Angiosperms [ 33 , 50 , 51 , 52 , 53 ]. Likewise, like in earlier studies about repeats and SSRs, mononucleotide repeats are more abundant with A/T repeats, which is consistent with AT richness in Angiosperm chloroplast genomes [ 54 , 55 , 56 ]. Complement repeats were rarely found in T. paniculatum and C. gigantea [ 24 ].…”