Coordinated Functional Divergence of Genes after Genome Duplication in <i>Arabidopsis thaliana</i>

Smet, Riet De; Sabaghian, Ehsan; Li, Zhen; Saeys, Yvan; Peer, Yves Van de

doi:10.1105/tpc.17.00531

Cited by 53 publications

(41 citation statements)

References 107 publications

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“…Third, the expression patterns of EXO70A1 and EXO70A2 alternate between the sporophyte-specific and pollenspecific, respectively. This is in agreement with the hypothesis suggesting that after a whole-genome duplication in plants, genes directly linked to cell polarity tend to diverge in their expression patterns to sporophyte-specific and to those enriched in tip-growing cells, especially in the male gametophyte (De Smet et al, 2017). In general, about 10% of essential housekeeping genes evolved their pollen specific paralogs to sustain the specific requirements for tip growth (Becker and Feijó, 2007).…”

Section: Discussionsupporting

confidence: 90%

EXO70A2 is critical for the exocyst complex function in Arabidopsis pollen

Marković

Cvrčková

Potocký

et al. 2019

Preprint

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Pollen development, pollen grain germination and pollen tube elongation are crucial biological processes in angiosperm plants that need precise regulation to deliver sperm cells to fertilize ovules. Pollen grains undergo two major developmental switches: dehydration characterized by metabolic quiescent state, and rehydration upon pollination that leads to extraordinary metabolic and membrane trafficking activity, resulting in germination and rapid tip growth of pollen tubes. To sustain these processes, many plant housekeeping genes evolved their pollen-specific paralogs. Highly polarized secretion at a growing pollen tube tip requires the exocyst tethering complex responsible for specific targeting of secretory vesicles to the plasma membrane. Here, we describe that EXO70A2 (At5g52340) is the main exocyst EXO70 isoform in Arabidopsis pollen, which governs the conventional secretory function of the exocyst, analogically to EXO70A1 (At5g03540) in the sporophyte. Our analysis of a CRISPR-generated exo70a2 mutant revealed that EXO70A2 is essential for efficient pollen maturation, pollen grain germination and pollen tube growth. GFP:EXO70A2 was localized similarly to other exocyst subunits to the apical domain in growing pollen tube tips characterized by intensive exocytosis. Moreover, EXO70A2 could substitute for the EXO70A1 function in the sporophyte, indicating functional redundancy of these two closely related isoforms. Phylogenetic analysis revealed that the ancient duplication of EXO70A to two (or more) paralogs, one of which is highly expressed in pollen, occurred independently in monocots and dicots. In summary, EXO70A2 is a crucial component of the exocyst complex in the Arabidopsis pollen required for efficient plant sexual reproduction. KEY WORDSexocyst, EXO70A2, EXO70A1, pollen development, pollen tube, tip growth, polarized secretion ABBREVIATIONS CDS -coding sequence GFP -green fluorescent protein NBT -nitroblue tetrazolium PM -plasma membrane PME -pectin methylesterases ROS -reactive oxygen species WT -wild type

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Section: Discussionsupporting

confidence: 90%

EXO70A2 is critical for the exocyst complex function in Arabidopsis pollen

Marković

Cvrčková

Potocký

et al. 2019

Preprint

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“…The natural variant of rice DEP1 harbors Δ625 bp that confers erect panicles and increased grain yield (Huang et al 2009 ), and the spontaneous deletions in maize WAXY gene alter starch composition of the grains (Wessler et al 1990 ). Genomic deletions also play major roles in plant evolution (De Smet et al 2017 ; Soltis et al 2014 ). Divergence in the function of the duplicated genes could occur upon deletions in the genes (Haberer et al 2004 ; Liu et al 2011 ).…”

Section: Discussionmentioning

confidence: 99%

Dual-targeting by CRISPR/Cas9 leads to efficient point mutagenesis but only rare targeted deletions in the rice genome

et al. 2019

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The present study investigated the efficiency of CRISPR/Cas9 in creating genomic deletions as the basis of its application in removing selection marker genes or the intergenic regions. Three loci, representing a transgene and two rice genes, were targeted at two sites each, in separate experiments, and the deletion of the defined fragments was investigated by PCR and sequencing. Genomic deletions were found at a low rate among the transformed callus lines that could be isolated, cultured, and regenerated into plants harboring the deletion. However, randomly regenerated plants showed mixed genomic effects, and generally did not harbor heritable genomic deletions. To determine whether point mutations occurred at each targeted site, a total of 114 plants consisting of primary transgenic lines and their progeny were analyzed. Ninety-three plants showed targeting, 60 of which were targeted at both sites. The presence of point mutations at both sites was correlated with the guide RNA efficiency. In summary, genomic deletions through dual-targeting by the paired-guide RNAs were generally observed in callus, while de novo point mutations at one or both sites occurred at high rates in transgenic plants and their progeny, generating a variety of insertion–deletions or single-nucleotide variations. In this study, point mutations were exceedingly favored over genomic deletions; therefore, for the recovery of plant lines harboring targeted deletions, identifying early transformed clones harboring the deletions, and isolating them for plant regeneration is recommended.

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“…Subsequently, it is also evident from our result that the number of paralogs originated via WGD in A. thaliana (12.9%) is nearly half to the paralogs in B. rapa (23.5%) which re ects the effects of extra round of genome duplication in B. rapa. This result is also echoed in a previous study on A. thaliana hypothesized that many of the identi ed duplicated gene pairs evolving by WGD mechanism might function in cell wall integrity pathways, growth and stress tolerance [42]. Unlike small-scale gene duplications, whole-genome duplications copy entire pathways or networks, thus play an important role in the evolution of novel traits and increased biological complexity [43][44][45].…”

Section: Discussionmentioning

confidence: 60%

Enrichment of Intrinsically Disordered Residues in Ohnologs Facilitate Abiotic Stress Resilience in Brassica Rapa

Laha

Saha

Ghosh

et al. 2020

Preprint

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Background: Arabidopsis thaliana and Brassica rapa shared a common evolutionary clade but Brassica species experienced an extra whole genome triplication (WGT) event compared with the model plant A. thaliana. This extra round of WGT confers B. rapa more abiotic stress resistant. The study aims to unravel how the consequences of whole genome duplication steer the variation in stress adaptation competency between the two species.Result: Comparing the duplication status between abiotic stress resistant (ASR) genes in the two species, significant increase in the number of paralogs in ASR genes of B. rapa than A. thaliana was found. Investigation on the proteomic features suggests that the ohnologs pairs in both species are more enriched with intrinsically disordered residues (IDRs) than other duplicated pairs but IDRs only in B. rapa have showed a significant positive correlation with functional divergence between the duplicated pairs. The functional divergence helps to mediate more stress adaptation functions in the ohnologs of B. rapa than that of A. thaliana. Moreover, domain ontology analysis has revealed that the new domains with stress functions are significantly more enriched in the ohnologs of B. rapa. Interestingly, majority of these stress tolerant domains are found to be present in the intrinsically disordered regions of the proteins. Statistical analysis along with these observations make it reasonable to speculate that IDRs expedite stress adaption potentiality in B. rapa by enriching more stress related functions and accommodating stress specific domains in ohnologs of this plant species.Conclusion: With the occurrence of WGT in the Brassica species the stress resilience features of B. rapa as compared to A. thaliana is less studied. This study unveils the role of intrinsically disordered residues (IDRs) of ohnologs in optimizing more stress resilience in B. rapa than A. thaliana. Thus, it will open new avenues in understanding the mechanism of succeeding stress adaptation potentiality in B. rapa over evolutionary time.

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Coordinated Functional Divergence of Genes after Genome Duplication in Arabidopsis thaliana

Cited by 53 publications

References 107 publications

EXO70A2 is critical for the exocyst complex function in Arabidopsis pollen

EXO70A2 is critical for the exocyst complex function in Arabidopsis pollen

Dual-targeting by CRISPR/Cas9 leads to efficient point mutagenesis but only rare targeted deletions in the rice genome

Enrichment of Intrinsically Disordered Residues in Ohnologs Facilitate Abiotic Stress Resilience in Brassica Rapa

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