Legume isoflavone synthase genes have evolved by whole-genome and local duplications yielding transcriptionally active paralogs

Legume Cytosolic and Plastid Acetyl-Coenzyme—A Carboxylase Genes Differ by Evolutionary Patterns and Selection Pressure Schemes Acting before and after Whole-Genome Duplications

“…Here, we demonstrated that L. angustifolius cytosolic ACCase duplicates Lan_ACC1 and Lan_ACC2 as well as plastid ACCase subunit duplicates of accA ( Lan_accA1 , Lan_accA2 and Lan_accA3 ), accB ( Lan_accB2a/b and Lan_accB2c ) and accC ( Lan _accC1 and Lan_accC2 ) originated from lineage-specific WGD, whereas the pair of genes Lan_accB2a and Lan_accB2b evolved by local tandem duplication. It was well-evidenced by cytogenetic and comparative mapping that WGD shaped the evolution of numerous L. angustifolius genes, including genes from phenylpropanoid pathway (chalcone isomerase, chalcone isomerase like, fatty acid binding protein and isoflavone synthase) [ 35 , 37 ], phosphatidylethanolamine binding protein family [ 36 ] as well as genes involved in symbiotic interactions and nitrogen fixation (early nodulin, nodulin 26-like, phosphoenolpyruvate carboxylase, and glutamine synthetase genes) [ 33 ].…”

“…Putatively due to these whole-genome duplication(s), numerous lupin genes are present in several copies, regardless of their relatively low copy number in other legumes. Such observations were done for genes encoding phosphatidyl ethanolamine-binding proteins, chalcone isomerase-fold proteins, isoflavone synthase, as well as for some genes encoding enzymes required for symbiosome activity during nitrogen fixation process [ 33 , 35 , 36 , 37 ]. Due to such considerable uniqueness of lupins, accompanied by a well-developed molecular tool-box, we have selected L. angustifolius as a reference genome to study the evolutionary conserved group of genes encoding acetyl-coenzyme A carboxylases.…”

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

“…During the early divergence of some downstream lineages, dated to roughly~30-55 mya, additional independent WGD events probably occurred, affecting Mimosoideae-Cassiinae-Caesalpinieae, Detarieae, Cercideae, and Lupinus clades [75]. Large-scale duplication and/or triplication in the L. angustifolius genome has been well-evidenced by recent studies involving linkage and comparative mapping [17,36] and microsynteny analysis of selected gene families [30,31,34,62,63]. These WGD events apparently contributed to multiplication of the gene copy number of L. angustifolius GS and PEPC genes because hypothetical duplicates were found in sister branches of the phylogenetic tree and the genome regions harboring these genes shared common collinearity links.…”

“…Hane et al estimated the Papilionoideae radiation at 58 mya with genistoid lineage separation from the other Papilionoideae legumes at 54.6 mya, followed by whole-genome triplication in the genistoid lineage at 24.6 mya [11]. Additionally, the ancient polyploidy event has been confirmed based on an analysis of several genes, such as chalcone isomerases (CHI) [62], phosphatidylethanolamine binding proteins (PEBP) [30], isoflavone synthetases (IFS) [63], and cytosolic and plastid acetyl-coenzyme A carboxylases (ACCase) [64]. All listed genes are present in the narrow-leafed lupin genome in multiple variants and evolved by WGDs, evidenced by shared synteny and Bayesian phylogenetic inference.…”

“…Usually, genes encoding enzymes located at the top of the metabolic pathway are under stronger purifying selection than downstream ones [87]. An association between the selective pressure acting on a gene and the position of an encoded enzyme in the pathway was revealed in a wide metabolic context [88,89], including L. angustifolius genes encoding isoflavone synthase and acetyl-coenzyme A carboxylase [63,64]. A higher selection pressure acts on central and highly connected enzymes, enzymes with high metabolic flux, and enzymes catalyzing reactions that are difficult to bypass through alternative pathways [88].…”