Explosive Tandem and Segmental Duplications of Multigenic Families in Eucalyptus grandis

Abstract

Plant organisms contain a large number of genes belonging to numerous multigenic families whose evolution size reflects some functional constraints. Sequences from eight multigenic families, involved in biotic and abiotic responses, have been analyzed in Eucalyptus grandis and compared with Arabidopsis thaliana. Two transcription factor families APETALA 2 (AP2)/ethylene responsive factor and GRAS, two auxin transporter families PIN-FORMED and AUX/LAX, two oxidoreductase families (ascorbate peroxidases [APx] and Class III peroxidases [CIII Prx]), and two families of protective molecules late embryogenesis abundant (LEA) and DNAj were annotated in expert and exhaustive manner. Many recent tandem duplications leading to the emergence of species-specific gene clusters and the explosion of the gene numbers have been observed for the AP2, GRAS, LEA, PIN, and CIII Prx in E. grandis, while the APx, the AUX/LAX and DNAj are conserved between species. Although no direct evidence has yet demonstrated the roles of these recent duplicated genes observed in E. grandis, this could indicate their putative implications in the morphological and physiological characteristics of E. grandis, and be the key factor for the survival of this nondormant species. Global analysis of key families would be a good criterion to evaluate the capabilities of some organisms to adapt to environmental variations.

Genome-wide identification, structural and gene expression analysis of the bZIP transcription factor family in sweet potato wild relative Ipomoea trifida

“…The amplification of gene family in plant evolution is mainly carried out by genome duplication [42,43]. To investigate possible relationships among the ItfbZIP genes and potential gene duplication type, we performed collinear analysis.…”

Global analysis of non-animal peroxidases provides insights into the evolutionary basis of this gene family in green lineage

“…The number of CIII Prx genes has largely increased along the green lineage (from 0 in Chlorophyceae to 191 E. grandis , Figure 2 and Table 1). The late diverging plants contain more CIII Prxs copies than early diverging plants due to explosive and recent duplications (tandem (TDs), segmental (SDs) and whole genome duplications (WGDs), (Li et al , 2015), which make the size of CIII family quite variable (Figure 2). Since Streptophytes are the only mitochondria containing organisms lacking CcP, and because CI and CIII Prxs present high level of homology and several conserved key residues, we raise a hypothesis that the ancestral CIII Prx was derived from the ancestral CcP sequence.…”

CsWAKL08, a pathogen-induced wall-associated receptor-like kinase in sweet orange, confers resistance to citrus bacterial canker via ROS control and JA signaling

“…Plant antipathogen responses often depend on the production of excess ROS, which will induce oxidative damage to pathogens or plant apoptotic cell death [30][31][32][33] . To determine whether ROS homeostasis was involved in CsWAKL08-mediated resistance to Xcc, we analyzed the relative ROS levels in the CK and transgenic plants.…”

“…CsWAKL searches were performed using all 27 WAK and WAKL genes previously reported in A. thaliana as the BLAST query 15 . Exhaustive data mining and annotation were executed via a semiautomated three-step expert process that should avoid the errors inherent in fully automated predictive methods 32,46 . During the annotation process, the gene reannotation tool Fgenesh++ 47 , Citrus genomic variation database (CitGVD) 48 , as well as the protein functional domain analysis tools Pfam V32 49 and SMART 50 , were used for the functional reannotation, while Scipio 51 was used to retrieve CsWAKLs misannotated by the automated processes.…”