The plastome sequence of Bactris gasipaes and evolutionary analysis in tribe Cocoseae (Arecaceae)

Abstract

The family Arecaceae is distributed throughout tropical and subtropical regions of the world. Among the five subfamilies, Arecoideae is the most species-rich and still contains some ambiguous inter-generic relationships, such as those within subtribes Attaleinae and Bactridineae. The hypervariable regions of plastid genomes (plastomes) are interesting tools to clarify unresolved phylogenetic relationships. We sequenced and characterized the plastome of Bactris gasipaes (Bactridinae) and compared it with eight species from the three Cocoseae sub-tribes (Attaleinae, Bactridinae, and Elaeidinae) to perform comparative analysis and to identify hypervariable regions. The Bactris gasipaes plastome has 156,646 bp, with 113 unique genes. Among them, four genes have an alternative start codon (cemA, rps19, rpl2, and ndhD). Plastomes are highly conserved within tribe Cocoseae: 97.3% identity, length variation of ~2 kb, and a single ~4.5 kb inversion in Astrocaryum plastomes. The LSC/IR and IR/SSC junctions vary among the subtribes: in Bactridinae and Elaeidinae the rps19 gene is completely contained in the IR region; in the subtribe Attaleinae the rps19 gene is only partially contained in the IRs. The hypervariable regions selected according to sequence variation (SV%) and frequency of parsimony informative sites (PIS%) revealed plastome regions with great potential for molecular analysis. The ten regions with greatest SV% showed higher variation than the plastid molecular markers commonly used for phylogenetic analysis in palms. The phylogenetic trees based on the plastomes and the hypervariable regions (SV%) datasets had well-resolved relationships, with consistent topologies within tribe Cocoseae, and confirm the monophyly of the subtribes Bactridinae and Attaleinae.

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

“…Taking into account the species relationships from Arecoideae subfamily, and the previous evidence from palms chloroplast genome structures [ 28 , 46 ], we decided to conduct two multiple progressive sequence alignment in Mauve v.2.4.0 [ 47 ]. The first one only included chloroplast genomes from Brazilian native species of subfamily Arecoideae: Euterpe edulis , Euterpe oleracea , Syagrus coronata , Astrocaryum aculeatum , Astrocaryum murumuru and Acrocomia aculeata .…”

Bactris gasipaes Kunth var. gasipaes complete plastome and phylogenetic analysis

“…gasipaes OM047178 , B. gasipaes Kunth var. chichagui NC_058634.1 (Santos da Silva et al 2021 ) , Acrocomia aculeata NC_037084.1, Astrocaryum aculeatum NC_044482.1 (de Santana Lopes et al. 2018 ), Cocos nucifera NC_022417.1 (Huang et al.…”

“… 2015 ; Clement et al. 2017 ; Santos da Silva et al 2021 ) or to understand the genetic relationships and gene flow between both varieties (Couvreur et al. 2006 , Couvreur et al.…”

“…chichagui (the wild variety) was recently published (Santos da Silva et al. 2021 ) and opened the way to explore the origins of its domestication. The goal of this work was (i) to characterize the complete plastome of B. gasipaes var.…”

Pangenomes as a Resource to Accelerate Breeding of Under-Utilised Crop Species

“…Chloroplast DNA for phylogenetic study [188] Macaúba palm transcriptome sequencing [189] RNA-seq of tropical palms [190] Plastome sequence [191] Citrullus colocynthis Desert Watermelon or Wild watermelon…”