Phylogenetic analysis, structural evolution and functional divergence of the 12-oxo-phytodienoate acid reductase gene family in plants

Li, Wenyan; Liu, Bing; Yu, Lujun; Feng, Dan; Wang, Hongbin; Wang, Jinfa

doi:10.1186/1471-2148-9-90

Cited by 100 publications

(70 citation statements)

References 83 publications

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“…Although several models of the genome evolution have been proposed from comparative genomic analyses of model organisms [54-56], little attention has been paid to the structural evolution of duplicated gene families [57]. In fact, exon/intron diversification of gene family members has played an important role in the evolution of multiple gene families through three main types of mechanism: exon/intron gain/loss, exonization/pseudoexonization, and insertion/deletion [51].…”

Section: Discussionmentioning

confidence: 99%

Genome-wide identification, evolutionary and expression analysis of the aspartic protease gene superfamily in grape

Guo

Carole

et al. 2013

BMC Genomics

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BackgroundAspartic proteases (APs) are a large family of proteolytic enzymes found in almost all organisms. In plants, they are involved in many biological processes, such as senescence, stress responses, programmed cell death, and reproduction. Prior to the present study, no grape AP gene(s) had been reported, and their research on woody species was very limited.ResultsIn this study, a total of 50 AP genes (VvAP) were identified in the grape genome, among which 30 contained the complete ASP domain. Synteny analysis within grape indicated that segmental and tandem duplication events contributed to the expansion of the grape AP family. Additional analysis between grape and Arabidopsis demonstrated that several grape AP genes were found in the corresponding syntenic blocks of Arabidopsis, suggesting that these genes arose before the divergence of grape and Arabidopsis. Phylogenetic relationships of the 30 VvAPs with the complete ASP domain and their Arabidopsis orthologs, as well as their gene and protein features were analyzed and their cellular localization was predicted. Moreover, expression profiles of VvAP genes in six different tissues were determined, and their transcript abundance under various stresses and hormone treatments were measured. Twenty-seven VvAP genes were expressed in at least one of the six tissues examined; nineteen VvAPs responded to at least one abiotic stress, 12 VvAPs responded to powdery mildew infection, and most of the VvAPs responded to SA and ABA treatments. Furthermore, integrated synteny and phylogenetic analysis identified orthologous AP genes between grape and Arabidopsis, providing a unique starting point for investigating the function of grape AP genes.ConclusionsThe genome-wide identification, evolutionary and expression analyses of grape AP genes provide a framework for future analysis of AP genes in defining their roles during stress response. Integrated synteny and phylogenetic analyses provide novel insight into the functions of less well-studied genes using information from their better understood orthologs.

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Section: Discussionmentioning

confidence: 99%

Genome-wide identification, evolutionary and expression analysis of the aspartic protease gene superfamily in grape

Guo

Carole

et al. 2013

BMC Genomics

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“…The various physiological and morphological adaptations to land were likely associated with expansion of gene families involved in signalling pathways, such as those for auxin, ABA and cytokinin Rensing et al, 2008;De Smet et al, 2011). Morphological innovations and the evolution of morphological complexity in land plants have been linked with increased gene family complexity of several genes including actin , MADS box genes (Henschel et al, 2002;Tanabe et al, 2005), homeobox genes (Mukherjee et al, 2009) and OPR genes (Li et al, 2009). Expansion of the glutaredoxins gene family (enzymes implicated in oxidative stress response) in land plants likely resulted in genes with novel functions in development and pathogenesis response (Ziemann et al, 2009).…”

Section: Genetic Codes and The Translational Apparatus In Green Sementioning

confidence: 99%

Phylogeny and Molecular Evolution of the Green Algae

Leliaert

Smith

Moreau

et al. 2012

Critical Reviews in Plant Sciences

750

655

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“…For example, several genes that were thought to be important in the evolution of land plants [80] may have true orthologs with similar function in the Coleochaetophyceae and/or Zygnematophyceae [72,86]. The diversification of embryophytes and the evolution of complex plants was associated with expansion of numerous gene families, including MADS box genes [87], homeobox genes [88], OPR genes [89] and genes involved in signalling pathways, such as auxin, ABA and cytokinin [85,86,90]. Expansion of the glutaredoxins gene family likely resulted in proteins with novel functions, such as in development and the pathogenesis response [91].…”

Section: Glossarymentioning

confidence: 99%

Into the deep: New discoveries at the base of the green plant phylogeny

2011

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Recent data have provided evidence for an unrecognised ancient lineage of green plants that persists in marine deep-water environments. The green plants are a major group of photosynthetic eukaryotes that have played a prominent role in the global ecosystem for millions of years. A schism early in their evolution gave rise to two major lineages, one of which diversified in the world's oceans and gave rise to a large diversity of marine and freshwater green algae (Chlorophyta) while the other gave rise to a diverse array of freshwater green algae and the land plants (Streptophyta). It is generally believed that the earliest-diverging Chlorophyta were motile planktonic unicellular organisms, but the discovery of an ancient group of deep-water seaweeds has challenged our understanding of the basal branches of the green plant phylogeny. In this review, we discuss current insights into the origin and diversification of the green plant lineage.

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Phylogenetic analysis, structural evolution and functional divergence of the 12-oxo-phytodienoate acid reductase gene family in plants

Abstract: Background: The 12-oxo-phytodienoic acid reductases (OPRs) are enzymes that catalyze the reduction of double-

Cited by 100 publications

References 83 publications

Genome-wide identification, evolutionary and expression analysis of the aspartic protease gene superfamily in grape

Genome-wide identification, evolutionary and expression analysis of the aspartic protease gene superfamily in grape

Phylogeny and Molecular Evolution of the Green Algae

Into the deep: New discoveries at the base of the green plant phylogeny

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