Comparative analysis of chloroplast genomes in Vasconcellea pubescens A.DC. and Carica papaya L

Abstract

The chloroplast genome is an integral part of plant genomes in a species along with nuclear and mitochondrial genomes, contributing to adaptation, diversification, and evolution of plant lineages. In the family Caricaceae, only the Carica papaya chloroplast genome and its nuclear and mitochondrial genomes were sequenced, and no chloroplast genome-wide comparison across genera was conducted. Here, we sequenced and assembled the chloroplast genome of Vasconcellea pubescens A.DC. using Oxford Nanopore Technology. The size of the genome is 158,712 bp, smaller than 160,100 bp of the C. papaya chloroplast genome. And two structural haplotypes, LSC_IRa_SSCrc_IRb and LSC_IRa_SSC_IRb, were identified in both V. pubescens and C. papaya chloroplast genomes. The insertion-deletion mutations may play an important role in Ycf1 gene evolution in family Caricaceae. Ycf2 is the only one gene positively selected in the V. pubescens chloroplast genome. In the C. papaya chloroplast genome, there are 46 RNA editing loci with an average RNA editing efficiency of 63%. These findings will improve our understanding of the genomes of these two crops in the family Caricaceae and will contribute to crop improvement.

Figure 1

Gene map of the Vasconcellea pubescens. Thick lines indicate the extent of the inverted repeat regions (IRa and IRb), which separate the genome into small (SSC) and large (LSC) single copy regions. Genes drawn inside the circle are transcribed clockwise, and those outside are transcribed counter clockwise. Different colors represent different functional groups of Genes.

Figure 2

Comparison of the borders of LSC, SSC, and IR regions of chloroplast genomes of Vasconcellea pubescens and Carica papaya.

Figure 3

Repeats and SSRs number comparison of Vasconcellea pubescens (Vp) and Carica papaya (Cp) chloroplast genome.

Figure 4

RNA editing efficiency plot of Carica papaya chloroplast RNA. Different colors respect for different Region of chloroplast genome, red for LSC, green for IRa, yellow for SSC and blue for IRb region. X axis represent RNA efficiency, and the number after the gene name in the Y axis represent the editing site.

Figure 5

Vasconcellea pubescens chloroplast genome codon usage pattern related plot. (A) GC content of different codon sites. (B) Neutrality plot (GC12 against GC3). (C) The codon adaptation index (CAI) value of different function gene sets. (D) Relationship between GC3 and effective number of codons (ENC) (ENC-plot).

Figure 6

Stucture haplotypes plot. The number of Nanopore reads that supported the two structure haplotypes of Carica papaya and Vasconcellea pubescens chloroplast genome, respectively (A). Two different structure haplotypes of the chloroplast genome detected in this study, the dashed line with different colors illustrated Nanopore reads with different lengths which covered different regions of the two haplotypes chloroplast molecular (B).