<i>At<scp>BUD</scp>13</i> affects pre‐<scp>mRNA</scp> splicing and is essential for embryo development in Arabidopsis

Xiong, Feng; Ren, Jing‐Jing; Yu, Qin; Wang, Yu‐Yi; Kong, Lan‐Jing; Otegui, Marisa S.; Wang, Xiuling

doi:10.1111/tpj.14268

Cited by 25 publications

(22 citation statements)

References 61 publications

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“…Of special interest, the bud-site selection protein 31 ( BUD31 ) was found to be highly upregulated (logFC = 7.22) in resistant plants in the absence of herbicide, whereas its homologue BUD13 was highly significantly downregulated in resistant individuals in the presence of herbicide (logFC = −11.39). BUD13 is involved in pre-mRNA splicing in embryos and is critical for early embryo development (63).…”

Section: Resultsmentioning

confidence: 99%

Inter-chromosomal linkage disequilibrium and linked fitness cost loci associated with selection for herbicide resistance

Gupta

Harkess

Soble

et al. 2021

Preprint

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The adaptation of weedy plants to herbicide is both a significant problem in agriculture and a model for the study of rapid adaptation under regimes of strong selection. Despite recent advances in our understanding of simple genetic changes that lead to resistance, a significant gap remains in our knowledge of resistance controlled by many loci and the evolutionary factors that influence the maintenance of resistance over time. Here, we perform a multi-level analysis involving whole genome sequencing and assembly, resequencing, and gene expression analysis to both uncover putative loci involved in nontarget herbicide resistance and to examine evolutionary forces underlying the maintenance of resistance in natural populations. We found loci involved in herbicide detoxification, stress sensing, and alterations in the shikimate acid pathway to be under selection, and confirmed that detoxification is responsible for glyphosate resistance using a functional assay. Furthermore, we found interchromosomal linkage disequilibrium (ILD), most likely associated with epistatic selection, to influence NTSR loci found on separate chromosomes thus potentially mediating resistance through generations. Additionally, by combining the selection screen, differential expression, and LD analysis, we identified fitness cost loci that are strongly linked to resistance alleles, indicating the role of genetic hitchhiking in maintaining the cost. Overall, our work strongly suggests that NTSR glyphosate resistance in I. purpurea is conferred by multiple genes which are maintained through generations via ILD and that the fitness cost associated with resistance in this species is a by-product of genetic-hitchhiking.

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Section: Resultsmentioning

confidence: 99%

Inter-chromosomal linkage disequilibrium and linked fitness cost loci associated with selection for herbicide resistance

Gupta

Harkess

Soble

et al. 2021

Preprint

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“…In humans, YTHDC1 mediates pre-mRNA splicing by interacting with splicing factor [26]. Pre-mRNA splicing is involved in the regulation of plant development, sexual reproduction, and abiotic stress responses [27][28][29][30][31][32][33][34][35]. Thus, the functions of plant YTHDCs in pre-mRNA splicing merit further study.…”

Section: Discussionmentioning

confidence: 99%

Genome-wide identification and expression analysis of YTH domain-containing RNA-binding protein family in common wheat

et al. 2020

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Background: N6-Methyladenosine (m6A) is the most widespread RNA modification that plays roles in the regulation of genes and genome stability. YT521-B homology (YTH) domain-containing RNA-binding proteins are important RNA binding proteins that affect the fate of m6A-containing RNA by binding m6A. Little is known about the YTH genes in common wheat (Triticum aestivum L.), one of the most important crops for humans. Results: A total of 39 TaYTH genes were identified in common wheat, which are comprised of 13 homologous triads, and could be mapped in 18 out of the 21 chromosomes. A phylogenetic analysis revealed that the TaYTHs could be divided into two groups: YTHDF (TaDF) and YTHDC (TaDC). The TaYTHs in the same group share similar motif distributions and domain organizations, which indicates functional similarity between the closely related TaYTHs. The TaDF proteins share only one domain, which is the YTH domain. In contrast, the TaDCs possess three C3H1-type zinc finger repeats at their N-termini in addition to their central YTH domain. In TaDFs, the predicated aromatic cage pocket that binds the methylysine residue of m6A is composed of tryptophan, tryptophan, and tryptophan (WWW). In contrast, the aromatic cage pocket in the TaDCs is composed of tryptophan, tryptophan, and tyrosine (WWY). In addition to the general aspartic acid or asparagine residue used to form a hydrogen bond with N 1 of m6A, histidine might be utilized in some TaDFb proteins. An analysis of the expression using both online RNA-Seq data and quantitative real-time PCR verification revealed that the TaDFa and TaDFb genes are highly expressed in various tissues/organs compared with that of TaDFcs and TaDCs. In addition, the expression of the TaYTH genes is changed in response to various abiotic stresses. Conclusions: In this study, we identified 39 TaYTH genes from common wheat. The phylogenetic structure, chromosome distribution, and patterns of expression of these genes and their protein structures were analyzed. Our results provide a foundation for the functional analysis of TaYTHs in the future.

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“…Furthermore, mutations in genes that are components of the RNA splicing machinery (spliceosome) affect gametophyte function and embryogenesis. For example, mutations such as gfa1/clotho , rtf2 , sus2/prp8 , or bud13 cause severely reduced transmission of the mutant alleles via the female gametophyte and cause embryo lethality in Arabidopsis 10 – 14 .…”

Section: Introductionmentioning

confidence: 99%

The integral spliceosomal component CWC15 is required for development in Arabidopsis

Slane

Lee

Kolb

et al. 2020

Sci Rep

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Efficient mRNA splicing is a prerequisite for protein biosynthesis and the eukaryotic splicing machinery is evolutionarily conserved among species of various phyla. At its catalytic core resides the activated splicing complex Bact consisting of the three small nuclear ribonucleoprotein complexes (snRNPs) U2, U5 and U6 and the so-called NineTeen complex (NTC) which is important for spliceosomal activation. CWC15 is an integral part of the NTC in humans and it is associated with the NTC in other species. Here we show the ubiquitous expression and developmental importance of the Arabidopsis ortholog of yeast CWC15. CWC15 associates with core components of the Arabidopsis NTC and its loss leads to inefficient splicing. Consistent with the central role of CWC15 in RNA splicing, cwc15 mutants are embryo lethal and additionally display strong defects in the female haploid phase. Interestingly, the haploid male gametophyte or pollen in Arabidopsis, on the other hand, can cope without functional CWC15, suggesting that developing pollen might be more tolerant to CWC15-mediated defects in splicing than either embryo or female gametophyte. Angiosperms are the predominant group of land plants. A hallmark of this dominance in the course of evolution is the establishment of a reduced haploid phase (called gametophyte) in the life cycle of flowering plants. In free-living gametophytes of mosses, the gametophytic generation forms independently recognizable plants that can even be the dominant structure. In contrast, the gametophyte of flowering plants is reduced to a small dependent structure with an almost minimal number of cells and a short lifetime 1. In Arabidopsis, the female gametophyte is deeply embedded in sporophytic tissue, whereas the male gametophyte or pollen has to be released from the sporophytic anther tissue for pollination to occur. Upon successful pollen-stigma interaction, the pollen tube grows inside the transmitting tract towards the ovule. Recent research has revealed that several signaling molecules including peptides play a role in the guidance of the pollen tube, attraction by the female gametophyte and burst of the pollen tube tip within one of the two synergid cells. If any of the aforementioned processes is disrupted, fertilization does not take place. Several mutants with disruptions in these processes have been isolated in the past 1-3. Upon successful fertilization, the Arabidopsis zygote initiates a precise developmental program, which results in a heart-shaped embryo already comprising all major seedling organs: two primary leaves or cotyledons, a shoot meristem, a hypocotyl, and a primary root with a root meristem 4. This invariant embryo patterning and development is impaired in mutants defective for various cellular response pathways e.g. responses to phytohormones, small RNA pathways, vesicular trafficking, cytoskeletal structure, and cell cycle control 5-9. Furthermore, mutations in genes that are components of the RNA splicing machinery (spliceosome) affect gametophyte function and embryoge...

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AtBUD13 affects pre‐mRNA splicing and is essential for embryo development in Arabidopsis

Cited by 25 publications

References 61 publications

Inter-chromosomal linkage disequilibrium and linked fitness cost loci associated with selection for herbicide resistance

Inter-chromosomal linkage disequilibrium and linked fitness cost loci associated with selection for herbicide resistance

Genome-wide identification and expression analysis of YTH domain-containing RNA-binding protein family in common wheat

The integral spliceosomal component CWC15 is required for development in Arabidopsis

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