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

Abstract

The family Balsaminaceae, which consists of the economically important genus Impatiens and the monotypic genus Hydrocera, lacks a reported or published complete chloroplast genome sequence. Therefore, chloroplast genome sequences of the two sister genera are significant to give insight into the phylogenetic position and understanding the evolution of the Balsaminaceae family among the Ericales. In this study, complete chloroplast (cp) genomes of Impatiens pinfanensis and Hydrocera triflora were characterized and assembled using a high-throughput sequencing method. The complete cp genomes were found to possess the typical quadripartite structure of land plants chloroplast genomes with double-stranded molecules of 154,189 bp (Impatiens pinfanensis) and 152,238 bp (Hydrocera triflora) in length. A total of 115 unique genes were identified in both genomes, of which 80 are protein-coding genes, 31 are distinct transfer RNA (tRNA) and four distinct ribosomal RNA (rRNA). Thirty codons, of which 29 had A/T ending codons, revealed relative synonymous codon usage values of >1, whereas those with G/C ending codons displayed values of <1. The simple sequence repeats comprise mostly the mononucleotide repeats A/T in all examined cp genomes. Phylogenetic analysis based on 51 common protein-coding genes indicated that the Balsaminaceae family formed a lineage with Ebenaceae together with all the other Ericales.

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

“…The results showed that the bias was significant in usage of synonymous codons except tryptophan and methionine in T. paniculatum as well as A/T ending rich in cp genome. These results revealed that the RSCU and codon usage exsited biased codon usage, which was consistent with previous reports in cp genomes of higher plants [ 32 , 33 ].…”

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

“…Of 22,964 codons, leucine (Leu) being the most abundant amino acid had a frequency of 10.56%, then isoleucine (Ile) with 8.54%, while cysteine (Cys) was rare with a proportion of 1.12% ( Tables S1 and S2 , Figure 4 ). Our study species genome is like other previously reported genomes which showed that leucine and isoleucine are more common [ 41 , 42 , 43 , 44 , 45 ]. Furthermore, comparable to other angiosperm chloroplast genomes, our results followed the trend of codon preference towards A/T ending which was observed in plastomes of two Aristolochia species [ 46 ], Scutellaria baicalensis [ 47 ], Decaisnea insignis [ 34 ], Papaver rhoeas and Papaver orientale [ 48 ] Cinnamomum camphora [ 49 ], and Forsythia suspensa [ 41 ].…”

Two-Step Contractions of Inverted Repeat Region and <em>Psa</em>i Gene Duplication from the Plastome of <em>Croton Tiglium</em> (Euphorbiaceae)

“…Among them, the numbers of penta-SSRs and mono-SSRs were 123 and 87, respectively, and accounted for 77% of the entire SSRs ( Figure 5A). These results are in sharp contrast to previous results regarding other taxa, in which mono-SSRs were the most abundant and penta-SSRs were rarely present [19,41,[43][44][45][46][47]. The largest number of SSRs was located in the LSC (232), followed by the SSC (37) and the IR (3) ( Figure 4B).…”