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.

The chloroplast genome inheritance pattern of the Deli-Nigerian prospection material (NPM) × Yangambi population of Elaeis guineensis Jacq

“…All four repeat types (palindrome, forward, reverse and complementary) are present in the chloroplast genome. The results are consistent with repeat types of three other palm family of genus Euterpe ( Francisconi et al, 2022 ) in which palindrome repeat has the highest number, followed by forward repeat, reverse repeat and finally complementary repeat. This revealed high conservation of gene structure in palm species specifically among genus Euterpe and Elaeis species.…”

“…Both studies ( Uthaipaisanwong et al, 2012 ; Yao et al, 2023 ) showed the gene content and arrangement in chloroplast genome are highly conserved in the palm family. Comparative analysis of chloroplast genomes was done between three different palm species from Brazil ( Francisconi et al, 2022 ). This study showed these three species’ nucleotide sequences are significantly varied from each other in term of insertion/deletion (InDels) and single nucleotide polymorphisms (SNPs).…”

Complete chloroplast genomes of six Neotropical palm tree species: genome structure comparison, identification of repeats sequences and evolutionary dynamic patterns

“…In all species, the mononucleotide A/T was the most frequent motif. This characteristic was also reported in other palm complete chloroplast genomes 30,31,33 . Plastid SSR markers, especially combined with nuclear markers, can improve the e ciency of studies of structure, diversity and gene ow in natural populations 37 .…”

“…2) 31 . As already pointed out, a signi cant dissimilarity among the species of the subfamily Arecoideae that occurs in Brazil can be identi ed in the length of the LSC, between 40,000 and 50,000 bp 33 . Furthermore, between the species C. alba and C. prunifera of the subfamily Coryphoideae, it was also possible to observe a reduction in LSC size (Table 1, Fig.…”

“…Although they are considered highly conserved structures for stabilizing chloroplast genomes structure 36 , uctuations caused by contractions/expansions of the IRs have already been reported in palms 30,33 . The most surprising case was the total loss of one IR in the species Tahina spectabilis, instead of rearrangement, as this structure was considered canonical in monocots 28 .…”