Complete chloroplast genomes and phylogeny in three Euterpe palms (E. edulis, E. oleracea and E. precatoria) from different Brazilian biomes

Abstract

The Brazilian palm fruits and hearts-of-palm of Euterpe edulis, E. oleracea and E. precatoria are an important source for agro-industrial production, due to overexploitation, conservation strategies are required to maintain genetic diversity. Chloroplast genomes have conserved sequences, which are useful to explore evolutionary questions. Besides the plastid DNA, genome skimming allows the identification of other genomic resources, such as single nucleotide polymorphisms (SNPs), providing information about the genetic diversity of species. We sequenced the chloroplast genome and identified gene content in the three Euterpe species. We performed comparative analyses, described the polymorphisms among the chloroplast genome sequences (repeats, indels and SNPs) and performed a phylogenomic inference based on 55 palm species chloroplast genomes. Finally, using the remaining data from genome skimming, the nuclear and mitochondrial reads, we identified SNPs and estimated the genetic diversity among these Euterpe species. The Euterpe chloroplast genomes varied from 159,232 to 159,275 bp and presented a conserved quadripartite structure with high synteny with other palms. In a pairwise comparison, we found a greater number of insertions/deletions (indels = 93 and 103) and SNPs (284 and 254) between E. edulis/E. oleracea and E. edulis/E. precatoria when compared to E. oleracea/E. precatoria (58 indels and 114 SNPs). Also, the phylogeny indicated a closer relationship between E. oleracea/E. precatoria. The nuclear and mitochondrial genome analyses identified 1,077 SNPs and high divergence among species (FST = 0.77), especially between E. edulis and E. precatoria (FST = 0.86). These results showed that, despite the few structural differences among the chloroplast genomes of these Euterpe palms, a differentiation between E. edulis and the other Euterpe species can be identified by point mutations. This study not only brings new knowledge about the evolution of Euterpe chloroplast genomes, but also these new resources open the way for future phylogenomic inferences and comparative analyses within Arecaceae.

Fig 1. Gene map of the Euterpe edulis, E. oleracea and E. precatoria chloroplast genomes.

Genes represented inside the large circle are oriented clockwise and the ones outside are oriented counter clockwise. The different colors represent functional groups, and the darker gray in the inner circle indicates the GC content. The quadripartite structure is also reported as: LSC = Large Single Copy, SSC = Small Single Copy, IRA/IRB = Inverted Repeats A and B.

Fig 2. Synteny and divergence in the SSC size detected in Arecaceae chloroplast genomes using the Mauve multiple-genome alignment program.

A sample of nine different chloroplast genomes is shown. Color bars indicate syntenic blocks and the lines indicate the correspondence between them. Blocks on the top row are in the same orientation, while blocks on the bottom row are in inverse orientation.

Fig 3. Comparison of the IRA and IRB borders among Brazilian palms from the Arecoideae species.

The numbers indicate the lengths of IGSs, genes, and spacers between IR-LSC and IR-SSC junctions. The ycf1* and rps19* genes have incomplete CDSs.

Fig 4. Distribution and classification of SSR and dispersed repeats in the chloroplast genomes of Euterpe edulis, E. oleracea and E. precatoria.

(A) Proportion of coding and non-coding regions containing SSRs; (B) Proportion of different types of SSR present in the chloroplast genomes; (C) Proportion of regions containing repeats; (D) Frequency distribution of different types of repeats: F = Forward, P = Palindrome, R = Reverse and C = Complement. CDS = Coding sequence, IGS = Intergenic spacer.

Fig 5. Indels and single nucleotide polymorphisms (SNPs) detected in comparisons between Euterpe chloroplast genomes.

(A) Proportion of indels in different coding and non-coding regions; (B) Comparison of the number of SNPs found in the alignment (C) Proportion of SNPs in different coding and non-coding regions of the chloroplast genomes.

Fig 6. Sliding window analysis of the alignment from the chloroplast genome of Euterpe edulis, E. oleracea and E. precatoria chloroplast genomes.

The regions with high nucleotide variability (Pi > 0.02) are indicated. Pi is the nucleotide diversity of each window, and the window length was 200 bp with 50 bp step sizes.

Fig 7. Majority-rule consensus tree of 30,000 trees obtained from a Bayesian inference analysis of chloroplast protein coding genes of 55 taxa.

Posterior probabilities (PP) for each are indicated above branches. Co = Coryphoideae, Ar = Arecoideae, Ny = Nypoideae, Ce = Ceroxyloideae, Ca = Calamoideae.