With respect to the importance of TALEs in the Rice-
We identified and characterized TalD and TalI as two African
Cysteine-rich receptor-like-kinases (
- Award ID(s):
- 2038872
- NSF-PAR ID:
- 10364403
- Publisher / Repository:
- Nature Publishing Group
- Date Published:
- Journal Name:
- Scientific Reports
- Volume:
- 12
- Issue:
- 1
- ISSN:
- 2045-2322
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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Abstract Background Xanthomonas oryzae pv.oryzae (Xoo ) causes bacterial leaf blight, a devastating disease of rice. Among the type-3 effectors secreted byXoo to support pathogen virulence, the Transcription Activator-Like Effector (TALE) family plays a critical role. Some TALEs are major virulence factors that activate susceptibility (S ) genes, overexpression of which contributes to disease development. Host incompatibility can result from TALE-induced expression of so-called executor (E ) genes leading to a strong and rapid resistance response that blocks disease development. In that context, the TALE functions as an avirulence (Avr) factor. To date no such avirulence factors have been identified in African strains ofXoo .Results Xoo pathosystem, we aimed at identifying those that may act as Avr factor within AfricanXoo . We screened 86 rice accessions, and identified 12 that were resistant to two African strains while being susceptible to a well-studied Asian strain. In a gain of function approach based on the introduction of each of the ninetal genes of the avirulent African strain MAI1 into the virulent Asian strain PXO99A, four were found to trigger resistance on specific rice accessions. Loss-of-function mutational analysis further demonstrated theavr activity of two of them,talD andtalI, on the rice varieties IR64 and CT13432 respectively. Further analysis of TalI demonstrated the requirement of its activation domain for triggering resistance in CT13432. Resistance in 9 of the 12 rice accessions that were resistant against AfricanXoo specifically, including CT13432, could be suppressed or largely suppressed by trans-expression of the truncTALEtal2h , similarly to resistance conferred by theXa1 gene which recognizes TALEs generally independently of their activation domain.Conclusion Xoo TALEs with avirulence activity on IR64 and CT13432 respectively. Resistance of CT13432 against AfricanXoo results from the combination of two mechanisms, one relying on the TalI-mediated induction of an unknown executor gene and the other on anXa1 -like gene or allele. -
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Abstract Zinc finger (Zf)-BED proteins are a novel superfamily of transcription factors that controls numerous activities in plants including growth, development, and cellular responses to biotic and abiotic stresses. Despite their important roles in gene regulation, little is known about the specific functions of Zf-BEDs in land plants. The current study identified a total of 750 Zf-BED-encoding genes in 35 land plant species including mosses, bryophytes, lycophytes, gymnosperms, and angiosperms. The gene family size was somewhat proportional to genome size. All identified genes were categorized into 22 classes based on their specific domain architectures. Of these, class I (Zf-BED_DUF-domain_Dimer_Tnp_hAT) was the most common in the majority of the land plants. However, some classes were family-specific, while the others were species-specific, demonstrating diversity at different classification levels. In addition, several novel functional domains were also predicated including WRKY and nucleotide-binding site (NBS). Comparative genomics, transcriptomics, and proteomics provided insights into the evolutionary history, duplication, divergence, gene gain and loss, species relationship, expression profiling, and structural diversity of Zf-BEDs in land plants. The comprehensive study of Zf-BEDs in
Gossypium sp., (cotton) also demonstrated a clear footprint of polyploidization. Overall, this comprehensive evolutionary study of Zf-BEDs in land plants highlighted significant diversity among plant species. -
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Summary Cultivated cotton (
Gossypium hirsutum ) is the most important fibre crop in the world. Cotton leaf curl disease (CLC uD) is the major limiting factor and a threat to textile industry in India and Pakistan. All the local cotton cultivars exhibit moderate to no resistance againstCLC uD. In this study, we evaluated an exotic cotton accession Mac7 as a resistance source toCLC uD by challenging it with viruliferous whiteflies and performingqPCR to evaluate the presence/absence and relative titre ofCLC uD‐associated geminiviruses/betasatellites. The results indicated that replication of pathogenicity determinant betasatellite is significantly attenuated in Mac7 and probably responsible for resistance phenotype. Afterwards, to decipher the genetic basis ofCLC uD resistance in Mac7, we performedRNA sequencing onCLC uD‐infested Mac7 and validatedRNA ‐Seq data withqPCR on 24 independent genes. We performed co‐expression network and pathway analysis for regulation of geminivirus/betasatellite‐interacting genes. We identified nine novel modules with 52 hubs of highly connected genes in network topology within the co‐expression network. Analysis of these hubs indicated the differential regulation of auxin stimulus and cellular localization pathways in response toCLC uD. We also analysed the differential regulation of geminivirus/betasatellite‐interacting genes in Mac7. We further performed the functional validation of selected candidate genes via virus‐induced gene silencing (VIGS ). Finally, we evaluated the genomic context of resistance responsive genes and found that these genes are not specific to A or D sub‐genomes ofG. hirsutum . These results have important implications in understandingCLC uD resistance mechanism and developing a durable resistance in cultivated cotton. -
Sindhu Sareen (Ed.)Potassium (K+) is the most abundant cation that plays a crucial role in various cellular processes in plants. Plants have developed an efficient mechanism for the acquisition of K+ when grown in K+ deficient or saline soils. A total of 47 K+ transport gene homologs (27 HAKs, 4 HKTs, 2 KEAs, 9 AKTs, 2 KATs, 2 TPCs, and 1 VDPC) have been identified in Sorghum bicolor. Of 47 homologs, 33 were identified as K+ transporters and the remaining 14 as K+ channels. Chromosome 2 has been found as the hotspot of K+ transporters with 9 genes. Phylogenetic analysis revealed the conservation of sorghum K+ transport genes akin to Oryza sativa. Analysis of regulatory elements indicates the key roles that K+ transport genes play under different biotic and abiotic stress conditions. Digital expression data of different developmental stages disclosed that expressions were higher in milk, flowering, and tillering stages. Expression levels of the genes SbHAK27 and SbKEA2 were higher during milk, SbHAK17, SbHAK11, SbHAK18, and SbHAK7 during flowering, SbHAK18, SbHAK10, and 23 other gene expressions were elevated during tillering inferring the important role that K+ transport genes play during plant growth and development. Differential transcript expression was observed in different tissues like root, stem, and leaf under abiotic stresses such as salt, drought, heat, and cold stresses. Collectively, the in-depth genome-wide analysis and differential transcript profiling of K+ transport genes elucidate their role in ion homeostasis and stress tolerance mechanisms.more » « less
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Abstract As a model organism for studies of cell and environmental biology, the free‐living and cosmopolitan ciliate
Euplotes vannus shows intriguing features like dual genome architecture (i.e., separate germline and somatic nuclei in each cell/organism), “gene‐sized” chromosomes, stop codon reassignment, programmed ribosomal frameshifting (PRF) and strong resistance to environmental stressors. However, the molecular mechanisms that account for these remarkable traits remain largely unknown. Here we report a combined analysis of de novo assembled high‐quality macronuclear (MAC; i.e., somatic) and partial micronuclear (MIC; i.e., germline) genome sequences forE. vannus , and transcriptome profiling data under varying conditions. The results demonstrate that: (a) the MAC genome contains more than 25,000 complete “gene‐sized” nanochromosomes (~85 Mb haploid genome size) with the N50 ~2.7 kb; (b) although there is a high frequency of frameshifting at stop codons UAA and UAG, we did not observe impaired transcript abundance as a result of PRF in this species as has been reported for other euplotids; (c) the sequence motif 5′‐TA‐3′ is conserved at nearly all internally‐eliminated sequence (IES) boundaries in the MIC genome, and chromosome breakage sites (CBSs) are duplicated and retained in the MAC genome; (d) by profiling the weighted correlation network of genes in the MAC under different environmental stressors, including nutrient scarcity, extreme temperature, salinity and the presence of ammonia, we identified gene clusters that respond to these external physical or chemical stimulations, and (e) we observed a dramatic increase in HSP70 gene transcription under salinity and chemical stresses but surprisingly, not under temperature changes; we link this temperature‐resistance to the evolved loss of temperature stress‐sensitive elements in regulatory regions. Together with the genome resources generated in this study, which are available online atEuplotes vannus Genome Database (http://evan.ciliate.org ), these data provide molecular evidence for understanding the unique biology of highly adaptable microorganisms.
