Comparative analysis of the complete mitogenome of Geoffroea decorticans: a native tree surviving in the Atacama Desert

Abstract

Chañar (Geoffroea decorticans (Gill., ex Hook. & Arn.) Burkart) has been highly significant for indigenous people in the Atacama Desert for over 3,000 years. Through evolutionary processes, the G. decorticans mitogenome likely underwent changes facilitating its adaptation to the extreme conditions of the Atacama Desert. Here, we compare the mitochondrial genome of G. decorticans with those of other Papilionoideae family species. The complete mitogenome of G. decorticans was sequenced and assembled, making it the first in the genus Geoffroea. The mitogenome contained 383,963 base pairs, consisting of 33 protein coding genes, 21 transfer RNA genes, and 3 ribosomal RNA genes. The Chañar mitogenome is relatively compact, and has two intact genes (sdh4 and nad1) which were not observed in most other species. Additionally, Chañar possessed the highest amount of mitochondrial DNA of plastid origin among angiosperm species. The phylogenetic analysis of the mitogenomes of Chañar and 12 other taxa displayed a high level of consistency in taxonomic classification, when compared to those of the plastid genome. Atp8 was subjected to positive selection, while the ccmFc and rps1 were subjected to neutral selection. This study provides valuable information regarding its ability to survive the extreme environmental conditions of the Atacama Desert.

Keywords: Atacama Desert; Geoffroea decorticans; extremophiles; fabaceae; mitochondrial genome; stress tolerance.

FIGURE 1

Mitochondrial maps of Geoffroea decorticans (size: 383,969 bp).

FIGURE 2

Maximum likelihood phylogeny of thirteen Fabaceae mitogenome based on nucleotide datasets of 33 protein-coding genes (left), and with plastid genomes (right). Bootstrap values are place on the nodes. Scale indicates number of nucleotide substitutions per site.

FIGURE 3

Box-and-whisker plots of Ka/Ks value of 25 protein-coding genes in G. decorticans and ten Papilionoideae species. Each box (with whiskers) shows the variation of the Ka/Ks values of a gene, among the 11 species studied using G. decorticans as a reference. Box plots show the median (central line), mean (dot on the box plot) and outliers.