Chloroplast Genome Comparison and Phylogenetic Analysis of the Commercial Variety Actinidia chinensis 'Hongyang'

Abstract

Actinidia chinensis 'Hongyang', also known as red yangtao (red heart kiwifruit), is a vine fruit tree native to China possessing significant nutritional and economic value. However, information on its genetic diversity and phylogeny is still very limited. The first chloroplast (cp) genome of A. chinensis 'Hongyang' cultivated in China was sequenced using de novo technology in this study. A. chinensis 'Hongyang' possesses a cp genome that spans 156,267 base pairs (bp), exhibiting an overall GC content of 37.20%. There were 132 genes that were annotated, with 85 of them being protein-coding genes, 39 transfer RNA (tRNA) genes, and 8 ribosomal RNA (rRNA) genes. A total of 49 microsatellite sequences (SSRs) were detected, mainly single nucleotide repeats, mostly consisting of A or T base repeats. Compared with 14 other species, the cp genomes of A. chinensis 'Hongyang' were biased towards the use of codons containing A/U, and the non-protein coding regions in the A. chinensis 'Hongyang' cpDNA showed greater variation than the coding regions. The nucleotide polymorphism analysis (Pi) yielded nine highly variable region hotspots, most in the large single copy (LSC) region. The cp genome boundary analysis revealed a conservative order of gene arrangement in the inverted repeats (IRs) region of the cp genomes of 15 Actinidia plants, with small expansions and contractions of the boundaries. Furthermore, phylogenetic tree indicated that A. chinensis 'Hongyang' was the closest relative to A. indochinensis. This research provides a useful basis for future genetic and evolutionary studies of A. chinensis 'Hongyang', and enriches the biological information of Actinidia species.

Keywords: A. chinensis ‘Hongyang’; chloroplast genome; comparative analysis; phylogeny.

Figure 1

The cp genomes of A. chinensis ‘Hongyang’ are depicted in the gene map. The genes located inside the circular structure are transcribed in a clockwise manner, whereas the genes situated outside the circle are transcribed in an anticlockwise manner. Gray arrows represent the direction of gene transcription. Genes with diverse functional groups are visually distinguished by colors. The inner loop of the map, represented by a darker gray color, indicates the GC content. The map displays SSC, LSC, and IR sequences.

Figure 2

RSCU analysis in cp genes of Actinidia plants. (A): Preference for codon usage and the proportion of amino acids in the PCGs of the 15 Actinidia cp genomes. (B): The histogram above each amino acid on the X-axis corresponds to the order of the 15 species.

Figure 3

Type and number of SSR nucleotides in the cpDNA of A. chinensis ‘Hongyang’.

Figure 4

The mVISTA was utilized to analyze and compare the cp genomes of fifteen samples. The gene orientation and the positions of IRs were indicated by gray arrows and bold black lines, respectively. The Y-scale depicted the percentage of identity, ranging from 50% to 100%. To enhance clarity, different genomic regions were color-coded, with protein-coding sequences (exons) shown in blue, rRNA in cyan, and a conserved non-coding sequence (CNS) in pink.

Figure 5

Comparison of nucleotide variability (Pi) values among fifteen different species’cp genomes. The Pi values are depicted on the Y-axis, and the genes exhibiting high Pi values are plotted on the X-axis.

Figure 6

Comparison of the boundaries of LSC, SSC, and IR regions across fifteen cp genomes.

Figure 7

The molecular phylogenetic trees were reconstructed of the genus Actinidia using the PCGs data. (A): ML tree. (B): BI tree. The red pentagrams represent the newly sequenced species in this study. Bootstrap values are indicated by numbers positioned above the branches. Lei: section Leiocarpae Dunn; Ste: section Stellatae; Mac: section Maculatae; Str: section Strigosae.