Phylogenomic and Microsynteny Analysis Provides Evidence of Genome Arrangements of High-Affinity Nitrate Transporter Gene Families of Plants

Abstract

Nitrate transporter 2 (NRT2) and NRT3 or nitrate-assimilation-related 2 (NAR2) proteins families form a two-component, high-affinity nitrate transport system, which is essential for the acquisition of nitrate from soils with low N availability. An extensive phylogenomic analysis across land plants for these families has not been performed. In this study, we performed a microsynteny and orthology analysis on the NRT2 and NRT3 genes families across 132 plants (Sensu lato) to decipher their evolutionary history. We identified significant differences in the number of sequences per taxonomic group and different genomic contexts within the NRT2 family that might have contributed to N acquisition by the plants. We hypothesized that the greater losses of NRT2 sequences correlate with specialized ecological adaptations, such as aquatic, epiphytic, and carnivory lifestyles. We also detected expansion on the NRT2 family in specific lineages that could be a source of key innovations for colonizing contrasting niches in N availability. Microsyntenic analysis on NRT3 family showed a deep conservation on land plants, suggesting a high evolutionary constraint to preserve their function. Our study provides novel information that could be used as guide for functional characterization of these gene families across plant lineages.

Identity and functional characterisation of the transporter supporting the Na+‐dependent high‐affinity NO3− uptake in Zostera marina L.

“…However, the latter appears to be the case for the nitrate uptake mechanism in this species. Thus, contrasted with terrestrial plants, where several members of both the NRT2 and NAR2 families are present (Zoghbi‐Rodríguez et al, 2021), the two‐component model for the high‐affinity NO 3 − uptake seems to be simplified in Z. marina , perhaps a result of its adaptation to the marine environment. ZosmaNRT2 is separated on the phylogenetic lineage from A. thaliana NRT2 proteins, except for AtNRT2.5.…”

“…where several members of both the NRT2 and NAR2 families are present (Zoghbi-Rodríguez et al, 2021), the two-component model for the high-affinity NO 3 − uptake seems to be simplified in Z. marina, perhaps a result of its adaptation to the marine environment.…”

Highly differentiated genomic properties underpin the different cell walls of Poaceae and eudicots

“…In this regard, the differentiation of syntenic genomic contexts seemed to have played a major role. The fact that differentially organized genomic gene contexts can facilitate the functional diversification of plant genes, leading to phenotypic adaptations, has been amply discussed, as for the MADS-box ( Zhao et al 2017 ), APETALA2 ( Kerstens et al 2020 ), LEA ( Artur et al 2019 ), or NRT plant gene families ( Zoghbi-Rodríguez et al 2021 ). Typically, different genomic contexts can differentiate the modes of gene function, for example, by determining different patterns of gene expression or by favoring gene diversification and subfunctionalization ( Dewey 2011 ).…”

LjNRT2.3 plays a hierarchical role in the control of high affinity transport system for root nitrate acquisition in Lotus japonicus

“…The distribution of NRT2 families in land plants is very patchy with a number of members that does not linearly fits with the level of ploidy and overall genome size in different monocot and dicot plants. The number of NRT2 genes spans from 33 in Triticum aestivum , 17 in Brassica napus , 7 in A. thaliana , 5 in O. sativa , 6 in Populus trichocarpa , 6 in Manihot esculenta , 4 in Hordeum vulgare , 4 in Solanum lycopersicon , 2 in Cucumis sativus , 9 in Physcomitrella patens ( Zoghbi-Rodrìguez et al., 2021 ; Akbubak et al., 2022 ). The situation is even more intriguing in legumes where the reported number of NRT2 genes is generally low: 3 in L. japonicus ( Misawa et al., 2022 ), 3 in M. truncatula ( Pellizzaro et al., 2015 ), 5 in Glycine soya ( You et al., 2020 ), 1 in Pisum sativum ( Gu et al., 2022 ).…”