Impact of Whole-Genome and Tandem Duplications in the Expansion and Functional Diversification of the F-Box Family in Legumes (Fabaceae)

Bellieny-Rabelo, Daniel; Oliveira, Antônia Elenir Amâncio; Venancio, Thiago M.

doi:10.1371/journal.pone.0055127

Cited by 30 publications

(17 citation statements)

References 40 publications

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“…However, only 12 pairs were found to be tandem duplicates. This suggests that segmental duplications probably played a bigger role in the expansion of GmFBXs , which is consistent with a recent report on the F-box family in legumes [20]. To date the duplication times and study the selection pressures on amino-acid substitutions among the paralogous genes, the non-synonymous ( K ) value, the synonymous ( K s) value, and the ratios of K a versus K s mutations ( K a/ K s) were calculated (Table S3).…”

Section: Resultssupporting

confidence: 92%

Genome-Wide Analyses of the Soybean F-Box Gene Family in Response to Salt Stress

Jia

Xiao

Wong

et al. 2017

IJMS

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The F-box family is one of the largest gene families in plants that regulate diverse life processes, including salt responses. However, the knowledge of the soybean F-box genes and their roles in salt tolerance remains limited. Here, we conducted a genome-wide survey of the soybean F-box family, and their expression analysis in response to salinity via in silico analysis of online RNA-sequencing (RNA-seq) data and quantitative reverse-transcription polymerase chain reaction (qRT-PCR) to predict their potential functions. A total of 725 potential F-box proteins encoded by 509 genes were identified and classified into 9 subfamilies. The gene structures, conserved domains and chromosomal distributions were characterized. There are 76 pairs of duplicate genes identified, including genome-wide segmental and tandem duplication events, which lead to the expansion of the number of F-box genes. The in silico expression analysis showed that these genes would be involved in diverse developmental functions and play an important role in salt response. Our qRT-PCR analysis confirmed 12 salt-responding F-box genes. Overall, our results provide useful information on soybean F-box genes, especially their potential roles in salt tolerance.

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Section: Resultssupporting

confidence: 92%

Genome-Wide Analyses of the Soybean F-Box Gene Family in Response to Salt Stress

Jia

Xiao

Wong

et al. 2017

IJMS

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“…Further, we found several cases of strong transcriptional divergence between paralogs in these hormonal regulatory pathways, suggesting that gene duplications play important roles in the regulation of germination. Our results also underscore the importance of post-translational regulatory mechanisms via protein phosphorylation and ubiquitination, which may have important contributions from recent duplications and diversification of F-box genes in the soybean lineage78. Taken together, we believe the processes described here shed light on important aspects of the soybean germination and may fuel future biotechnological applications.…”

Section: Resultssupporting

confidence: 57%

Transcriptome analysis uncovers key regulatory and metabolic aspects of soybean embryonic axes during germination

Bellieny-Rabelo

Oliveira

Ribeiro

et al. 2016

Sci Rep

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Soybean (Glycine max) is a major legume crop worldwide, providing a critical source of protein and oil. The release of the soybean genome fuelled several transcriptome projects comprising multiple developmental stages and environmental conditions. Nevertheless, the global transcriptional patterns of embryonic axes during germination remain unknown. Here we report the analysis of ~1.58 billion RNA-Seq reads from soybean embryonic axes at five germination stages. Our results support the early activation of processes that are critical for germination, such as glycolysis, Krebs cycle and cell wall remodelling. Strikingly, only 3 hours after imbibition there is a preferential up-regulation of protein kinases and transcription factors, particularly from the LOB domain family, implying that transcriptional and post-transcriptional regulation play major roles early after imbibition. Lipid mobilization and glyoxylate pathways are also transcriptionally active in the embryonic axes, indicating that the local catabolism of oil reserves in the embryonic axes contributes to energy production during germination. We also present evidence supporting abscisic acid inactivation and the up-regulation of gibberellin, ethylene and brassinosteroid pathways. Further, there is a remarkable differential activation of paralogous genes in these hormone signalling pathways. Taken together, our results provide insights on the regulation and biochemistry of soybean germination.

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“…It is known that TAR genes are enriched for genes functioning in biotic and abiotic stress (Rizzon et al 2006). For disease resistance, there are multiple taxa with an evident impact of TD to trait evolution, including members of Brassicaceae (Leister 2004), Solanaceae (Parniske et al 1999) and Fabaceae (Bellieny-Rabelo et al 2013). In this study, we determine the fraction of tandem- and whole genome duplicate copies among all (re)annotated full-length NB-LRR genes across 12 species in the context of a phylogenomics perspective, based on uniform standards facilitating all comparisons.…”

Section: Introdutionmentioning

confidence: 99%

A Novel Approach for Multi-Domain and Multi-Gene Family Identification Provides Insights into Evolutionary Dynamics of Disease Resistance Genes in Core Eudicot Plants

Hofberger

Zhou

Tang

et al. 2014

Preprint

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Background: Recent advances in DNA sequencing techniques resulted in more than forty sequenced plant genomes representing a diverse set of taxa of agricultural, energy, medicinal and ecological importance. However, gene family curation is often only inferred from DNA sequence homology and lacks insights into evolutionary processes contributing to gene family dynamics. In a comparative genomics framework, we integrated multiple lines of evidence provided by gene synteny, sequence homology and protein-based Hidden Markov Modelling to extract homologous super-clusters composed of multi-domain resistance (R)-proteins of the NB-LRR type (for NUCLEOTIDE BINDING/LEUCINE-RICH REPEATS), that are involved in plant innate immunity. Results: To assess the diversity of R-proteins within and between species, we screened twelve eudicot plant genomes including six major crops and found a total of 2,363 NB-LRR genes. Our curated R-proteins set shows a 50% average for tandem duplicates and a 22% fraction of gene copies retained from ancient polyploidy events (ohnologs). We provide evidence for strong positive selection and show significant differences in molecular evolution rates (Ka/Ks-ratio) among tandem-(mean = 1.59), ohnolog (mean = 1.36) and singleton (mean = 1.22) R-gene duplicates. To foster the process of gene-edited plant breeding, we report species-specific presence/absence of all 140 NB-LRR genes present in the model plant Arabidopsis and describe four distinct clusters of NB-LRR "gatekeeper" loci sharing syntenic orthologs across all analyzed genomes.

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Impact of Whole-Genome and Tandem Duplications in the Expansion and Functional Diversification of the F-Box Family in Legumes (Fabaceae)

Cited by 30 publications

References 40 publications

Genome-Wide Analyses of the Soybean F-Box Gene Family in Response to Salt Stress

Genome-Wide Analyses of the Soybean F-Box Gene Family in Response to Salt Stress

Transcriptome analysis uncovers key regulatory and metabolic aspects of soybean embryonic axes during germination

A Novel Approach for Multi-Domain and Multi-Gene Family Identification Provides Insights into Evolutionary Dynamics of Disease Resistance Genes in Core Eudicot Plants

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