The Y-segment of novel cold dehydrin genes is conserved and codons in the PR-10 genes are under positive selection in Oxytropis (Fabaceae) from contrasting climates

Abstract

While the arctic flora is particularly threatened by climate changes, the molecular aspects allowing colonization of this harsh environment remain largely enigmatic. Genes with a likely functional or evolutive role for arctic Oxytropis (Fabaceae) were previously discovered given a sharp differential expression between arctic and temperate species, but the evolutionary forces in action were unknown within the respective species. Here, we analyze gene duplication patterns and positive and negative selection between genes from species of contrasting environments, which can reveal potential gene functions. Genes were amplified and sequenced from two arctic (Oxytropis arctobia and O. maydelliana) and two temperate (O. campestris subsp. johannensis and O. splendens) species. Detection of codons under positive or negative selection and phylogenetic analyses were used to further elucidate pathogenesis-related class 10 (PR-10), ripening-related proteins, cold dehydrins gene families and light-harvesting complex (lhcaIII and lhcbI) genes from Oxytropis. Overall, results showed that the three gene families duplicated in tandem prior to the Oxytropis genus diversification; that genes overexpressed in arctic species evolve under higher constraints at the sequence level in these species; that evolving novel protein variants in PR-10 genes were required for initial adaptation to the Arctic, and that Oxytropis cold dehydrins are of a novel (K-like-Y(4)-K-S) structure, where the Y-segment is under stringent evolutive constraints in the arctic species. This suggests a scenario not previously described for arctic plants, where tandem duplications precede gene recruitment that later become both highly expressed and under stringent constraints in the arctic species.

De Novo Regulatory Motif Discovery Identifies Significant Motifs in Promoters of Five Classes of Plant Dehydrin Genes

“…The gene products of the other dehydrin classes do not have any such domains. In addition, there are evolutive constraints on the Y-segment in a dehydrin from arctic Oxytropis species compared with temperate species [ 126 ], suggesting that the Y-segment might carry an important function that differentiates Y n SK n from SK n dehydrins. Some of the published data shows that Y n SK n dehydrins are not expressed in response to cold [ 3 , 5 ], however there is evidence that after a period of acclimation they do accumulate in Red-Osier Dogwood ( Cornus sericea L.) [ 127 ] and apple trees [ 128 ].…”

Characterization of dehydrin AhDHN from Mediterranean saltbush (Atriplex halimus)

“…Moreover, certain plant species can possess multiple DHN class architectures, e.g., poplar (Kim et al, 2012), soybean (Yamasaki et al, 2013), and tea (Paul and Kumar, 2013). In a study of DHNs in Oxytropis spp., Archambault and Strömvik (2012) reported tandem duplications of the Y-segment, which can lead to high gene expression in Arctic plant species. Nonetheless, no single Y-segment (DEYGNP) could be detected in the herein described AhDHN nor in its homolog, AcDHN (Figure 3).…”

The plastome of ArcticOxytropis arctobia(Fabaceae) is significantly different from that ofO. splendensand other related species

“…were assembled and compared. These plants have been previously investigated for molecular variations that may impact their adaptation to Arctic conditions (Archambault and Strömvik 2011, 2012a, 2012b. 10X Genomics sequence reads obtained from genomic DNA samples of the two species of Oxytropis were assembled into complete circular sequences using an in-house de novo assembly pipeline (Achakkagari et al 2020).…”