A Tale of Two Families: Whole Genome and Segmental Duplications Underlie Glutamine Synthetase and Phosphoenolpyruvate Carboxylase Diversity in Narrow-Leafed Lupin (Lupinus angustifolius L.)

Abstract

Narrow-leafed lupin (Lupinus angustifolius L.) has recently been supplied with advanced genomic resources and, as such, has become a well-known model for molecular evolutionary studies within the legume family—a group of plants able to fix nitrogen from the atmosphere. The phylogenetic position of lupins in Papilionoideae and their evolutionary distance to other higher plants facilitates the use of this model species to improve our knowledge on genes involved in nitrogen assimilation and primary metabolism, providing novel contributions to our understanding of the evolutionary history of legumes. In this study, we present a complex characterization of two narrow-leafed lupin gene families—glutamine synthetase (GS) and phosphoenolpyruvate carboxylase (PEPC). We combine a comparative analysis of gene structures and a synteny-based approach with phylogenetic reconstruction and reconciliation of the gene family and species history in order to examine events underlying the extant diversity of both families. Employing the available evidence, we show the impact of duplications on the initial complement of the analyzed gene families within the genistoid clade and posit that the function of duplicates has been largely retained. In terms of a broader perspective, our results concerning GS and PEPC gene families corroborate earlier findings pointing to key whole genome duplication/triplication event(s) affecting the genistoid lineage.

Photoperiod and Vernalization Control of Flowering-Related Genes: A Case Study of the Narrow-Leafed Lupin (Lupinus angustifolius L.)

“…L. angustifolius genome contains two FTa and two FTc genes, which putatively arose from single copies by lineage-specific duplication, whereas the whole FTb subclade is absent (Ksiażkiewicz et al, 2016). Indeed, L. angustifolius was recently used as a reference species in several phylogenetic studies addressing the influence of wholegenome and local duplications on the evolutionary fate of selected legume-specific and plant-wide gene clades (Przysiecka et al, 2015;Narożna et al, 2017;Szczepaniak et al, 2018;Czyż et al, 2020). The differences in the expression profiles for FTa and FTc genes, as established in the present study, provided novel evidence supporting the hypothesis on a functional divergence of particular duplicates.…”

Identification of the glutamine synthetase (GS) gene family in four wheat species and functional analysis of Ta4D.GSe in Arabidopsis thaliana

“…Liu et al ( 2018 ) identified six GS genes from Gracilariopsis lemaneiformis genome through transcriptome data and all of these genes were divided into three clusters, and found that GSII might have a key role in the process of nitrogen metabolism. Moreover, Czyż et al ( 2020 ) studied the complex characterization of narrow-leafed lupin GS gene family with advanced genomic resources and pointed out that sub-functionalization and/or regulatory rewiring played an important role in shaping the primary metabolic pathways of the extant carbon and nitrogen in some lineages. However, very little information about GS from Ta and its relatives is available.…”

Innovative transcriptome‐based genotyping highlights environmentally responsive genes for phenology, growth and yield in a non‐model grain legume

“…It has a relatively low chromosome number (2n = 40) and small genome size (2C = 1.89 pg), as compared with other lupins (Naganowska, Wolko, Sliwińska, & Kaczmarek, 2003). L. angustifolius is a diploid and self‐pollinating species, which putatively experienced lineage‐specific whole‐genome duplications or a triplication during its evolution, highlighted by the presence of numerous genes and collinear blocks in three copies (Czyż et al, 2020; Hane et al, 2017; Kamphuis et al, 2015; Kroc, Koczyk, Święcicki, Kilian, & Nelson, 2014; Narożna et al, 2017). During its domestication process, numerous agronomic traits were selected by traditional breeding approaches (Święcicki & Święcicki, 1995).…”