Comparative and Phylogenetic Analysis of Complete Chloroplast Genomes of Five Mangifera Species

Abstract

Background/Objectives: Mango, which is known as the "King of Tropical Fruits", is an evergreen plant belonging to the Anacardiaceae family. It belongs to the genus Mangifera, which comprises 69 species of plants found in tropical and subtropical regions, including India, Indonesia, the Malay Peninsula, Thailand, and South China. However, research on the structural information of complete chloroplast genomes of Mangifera is limited. Methods: The rapid advancement of high-throughput sequencing technology enables the acquisition of the entire chloroplast (cp) genome sequence, providing a molecular foundation for phylogenetic research. This work sequenced the chloroplast genomes of six Mangifera samples, performed a comparative analysis of the cp genomes, and investigated the evolutionary relationships within the Mangifera genus. Results: All six Mangifera samples showed a single circular molecule with a quadripartite structure, ranging from 157,604 bp to 158,889 bp in length. The number of RNA editing sites ranged from 60 to 61, with ndhB exhibiting the highest number of RNA editing sites across all species. Seven genes-namely, atpB, cemA, clpP, ndhD, petB, petD, and ycf15-exhibited a Ka/Ks value > 1, suggesting they may be under positive selection. Phylogenetic analysis revealed that Mangifera siamensis showed a close relationship between Mangifera indica and Mangifera sylvatica. Conclusions: Our comprehensive analysis of the whole cp genomes of the five Mangifera species offers significant insights regarding their phylogenetic reconstruction. Moreover, it elucidates the evolutionary processes of the cp genome within the Mangifera genus.

Keywords: Illumina; Mangifera; chloroplast genome; phylogenetic analysis; polymorphism analysis.

Figure 1

A gene map of the chloroplast genome for six Mangifera samples. Genes are transcribed in a clockwise direction on the outer circle and counterclockwise on the inner circle. Functional gene groups are color-coded for clarity. Variations in shading on the inner circle represent the GC content (darker gray) and AT content (lighter gray) of the chloroplast genome. SSC, small single copy. LSC, long single copy. IR, inverted repeat.

Figure 2

RSCU of chloroplast genes in Mangifera indica CH.

Figure 3

Number of RNA editing sites of chloroplast genes in seven Mangifera samples. The cp genome sequence of M. longipes (MN917210) was obtained from GenBank.

Figure 4

Value of Ka/Ks of chloroplast genes in seven Mangifera samples. The red dashed line indicates the neutral evolution threshold (Ka/Ks = 1).

Figure 5

Analysis of simple sequence repeats (A) and long repeats (B) in the chloroplast genomes of seven Mangifera samples. P, palindromic repeats; F, forward repeats. The cp genome sequence of M. longipes (MN917210) was obtained from GenBank.

Figure 6

Comparison of junctions between four regions across chloroplast genomes of 7 Mangifera samples. JLB, the junction line between LSC and IRb; JSB, the junction line between IRb and SSC; JSA, the junction line between SSC and IRa; JLA, the junction line between IRa and LSC. Ψ, pseudogene.

Figure 7

Global alignment of 7 chloroplast genomes of Mangifera using mVISTA. The Y-axis indicates the range of identity (50–100%). Alignment was performed using M. indica TH as a reference. Various colors differentiate between exons, introns, untranslated regions (UTRs), and conserved non-coding sequences (CNSs). The cp genome sequence of M. longipes (MN917210) was obtained from GenBank.

Figure 8

Nucleotide variability (Pi) values across chloroplast genomes of 7 Mangifera samples (window length: 600 bp; step size: 200 bp). The cp genome sequence of M. longipes (MN917210) was obtained from GenBank.

Figure 9

Preliminary phylogenetic tree of six Mangifera samples and their related species based on chloroplast genomes (A) and protein-coding genes of chloroplast genomes (B). Chloroplast genome sequences were downloaded from GenBank.