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Abstract Camelina (Camelina sativa), an allohexaploid species, is an emerging aviation biofuel crop that has been the focus of resurgent interest in recent decades. To guide future breeding and crop improvement efforts, the community requires a deeper comprehension of subgenome dominance, often noted in allopolyploid species, “alongside an understanding of the genetic diversity” and population structure of material present within breeding programs. We conducted population genetic analyses of a C. sativa diversity panel, leveraging a new genome, to estimate nucleotide diversity and population structure, and analyzed for patterns of subgenome expression dominance among different organs. Our analyses confirm that C. sativa has relatively low genetic diversity and show that the SG3 subgenome has substantially lower genetic diversity compared to the other two subgenomes. Despite the low genetic diversity, our analyses identified 13 distinct subpopulations including two distinct wild populations and others putatively representing founders in existing breeding populations. When analyzing for subgenome composition of long non-coding RNAs, which are known to play important roles in (a)biotic stress tolerance, we found that the SG3 subgenome contained significantly more lincRNAs compared to other subgenomes. Similarly, transcriptome analyses revealed that expression dominance of SG3 is not as strong as previously reported and may not be universal across all organ types. From a global analysis, SG3 “was only significant higher expressed” in flower, flower bud, and fruit organs, which is an important discovery given that the crop yield is associated with these organs. Collectively, these results will be valuable for guiding future breeding efforts in camelina. 

Abstract Nondestructive plant phenotyping forms a key technique for unraveling molecular processes underlying plant development and response to the environment. While the emergence of high-throughput phenotyping facilities can further our understanding of plant development and stress responses, their high costs greatly hinder scientific progress. To democratize high-throughput plant phenotyping, we developed sets of low-cost image- and weight-based devices to monitor plant shoot growth and evapotranspiration. We paired these devices to a suite of computational pipelines for integrated and straightforward data analysis. The developed tools were validated for their suitability for large genetic screens by evaluating a cowpea (Vigna unguiculata) diversity panel for responses to drought stress. The observed natural variation was used as an input for a genome-wide association study, from which we identified nine genetic loci that might contribute to cowpea drought resilience during early vegetative development. The homologs of the candidate genes were identified in Arabidopsis (Arabidopsis thaliana) and subsequently evaluated for their involvement in drought stress by using available T-DNA insertion mutant lines. These results demonstrate the varied applicability of this low-cost phenotyping system. In the future, we foresee these setups facilitating the identification of genetic components of growth, plant architecture, and stress tolerance across a wide variety of plant species. 

Summary Among many mRNA modifications, adenine methylation at the N⁶position (N⁶‐methyladenosine, m⁶A) is known to affect mRNA biology extensively. The influence of m⁶A has yet to be assessed under drought, one of the most impactful abiotic stresses.We show thatArabidopsis thaliana(L.) Heynh. (Arabidopsis) plants lacking mRNA ADENOSINE METHYLASE (MTA) are drought‐sensitive. Subsequently, we comprehensively assess the impacts of MTA‐dependent m⁶A changes during drought on mRNA abundance, stability, and translation in Arabidopsis.During drought, there is a global trend toward hypermethylation of many protein‐coding transcripts that does not occur inmta. We also observe complex regulation of m⁶A at a transcript‐specific level, possibly reflecting compensation by other m⁶A components. Importantly, a subset of transcripts that are hypermethylated in an MTA‐dependent manner exhibited reduced turnover and translation inmta, compared with wild‐type (WT) plants, during drought. Additionally, MTA impacts transcript stability and translation independently of m⁶A. We also correlate drought‐associated deposition of m⁶A with increased translation of modulators of drought response, such asRD29A,COR47,COR413,ALDH2B,ERD7, andABF4in WT, which is impaired inmta.m⁶A is dynamic during drought and, alongside MTA, promotes tolerance by regulating drought‐responsive changes in transcript turnover and translation. 

Abstract Various messenger RNA (mRNA) decay mechanisms play major roles in controlling mRNA quality and quantity in eukaryotic organisms under different conditions. While it is known that the recently discovered co‐translational mRNA decay (CTRD), the mechanism that allows mRNAs to be degraded while still being actively translated, is prevalent in yeast, humans, and various angiosperms, the regulation of this decay mechanism is less well studied. Moreover, it is still unclear whether this decay mechanism plays any role in the regulation of specific physiological processes in eukaryotes. Here, by re‐analyzing the publicly available polysome profiling or ribosome footprinting and degradome sequencing datasets, we discovered that highly translated mRNAs tend to have lower co‐translational decay levels. Based on this finding, we then identified Pelota and Hbs1, the translation‐related ribosome rescue factors, as suppressors of co‐translational mRNA decay in Arabidopsis. Furthermore, we found that Pelota and Hbs1 null mutants have lower germination rates compared to the wild‐type plants, implying that proper regulation of co‐translational mRNA decay is essential for normal developmental processes. In total, our study provides further insights into the regulation of CTRD in Arabidopsis and demonstrates that this decay mechanism does play important roles in Arabidopsis physiological processes. 

Abstract Posttranscriptional regulation of mRNA mediated by methylation at the N6 position of adenine (N6-methyladenosine [m6A]) has profound effects on transcriptome regulation in plants. Focused studies across eukaryotes offer glimpses into the processes governed by m6A throughout developmental and disease states. However, we lack an understanding of the dynamics and the regulatory potential of m6A during biotic stress in plants. Here, we provide a comprehensive look into the effects of m6A on both the short-term and long-term responses to pathogen signaling in Arabidopsis (Arabidopsis thaliana). We demonstrate that m6A-deficient plants are more resistant to bacterial and fungal pathogen infections and have altered immune responses. Furthermore, m6A deposition is specifically coordinated on transcripts involved in defense and immunity prior to and proceeding the pathogen signal flagellin. Consequently, the dynamic modulation of m6A on specific stress-responsive transcripts is correlated with changes in abundance and cleavage of these transcripts. Overall, we show that the m6A methylome is regulated prior to and during simulated and active pathogen stress and functions in the coordination and balancing of normal growth and pathogen responses. 

Summary Drought stress substantially impacts crop physiology resulting in alteration of growth and productivity. Understanding the genetic and molecular crosstalk between stress responses and agronomically important traits such as fibre yield is particularly complicated in the allopolyploid species, upland cotton (Gossypium hirsutum), due to reduced sequence variability between A and D subgenomes. To better understand how drought stress impacts yield, the transcriptomes of 22 genetically and phenotypically diverse upland cotton accessions grown under well‐watered and water‐limited conditions in the Arizona low desert were sequenced. Gene co‐expression analyses were performed, uncovering a group of stress response genes, in particular transcription factors GhDREB2A‐A and GhHSFA6B‐D, associated with improved yield under water‐limited conditions in an ABA‐independent manner. DNA affinity purification sequencing (DAP‐seq), as well as public cistrome data from Arabidopsis, were used to identify targets of these two TFs. Among these targets were two lint yield‐associated genes previously identified through genome‐wide association studies (GWAS)‐based approaches,GhABP‐DandGhIPS1‐A. Biochemical and phylogenetic approaches were used to determine thatGhIPS1‐Ais positively regulated by GhHSFA6B‐D, and that this regulatory mechanism is specific toGossypiumspp. containing the A (old world) genome. Finally, an SNP was identified within the GhHSFA6B‐D binding site inGhIPS1‐Athat is positively associated with yield under water‐limiting conditions. These data lay out a regulatory connection between abiotic stress and fibre yield in cotton that appears conserved in other systems such as Arabidopsis. 

Summary Water scarcity, resulting from climate change, poses a significant threat to ecosystems.Syntrichia ruralis, a dryland desiccation‐tolerant moss, provides valuable insights into survival of water‐limited conditions.We sequenced the genome ofS. ruralis, conducted transcriptomic analyses, and performed comparative genomic and transcriptomic analyses with existing genomes and transcriptomes, including with the close relativeS. caninervis. We took a genetic approach to characterize the role of anS. ruralistranscription factor, identified in transcriptomic analyses, inArabidopsis thaliana.The genome was assembled into 12 chromosomes encompassing 21 169 protein‐coding genes. Comparative analysis revealed copy number and transcript abundance differences in known desiccation‐associated gene families, and highlighted genome‐level variation among species that may reflect adaptation to different habitats. A significant number of abscisic acid (ABA)‐responsive genes were found to be negatively regulated by a MYB transcription factor (MYB55) that was upstream of theS. ruralisortholog of ABA‐insensitive 3 (ABI3). We determined that this conserved MYB transcription factor, uncharacterized inArabidopsis, acts as a negative regulator of an ABA‐dependent stress response inArabidopsis.The new genomic resources from this emerging model moss offer novel insights into how plants regulate their responses to water deprivation. 

Abstract How the noncoding genome affects cellular functions is a key biological question. A particular challenge is to distinguish the effects of noncoding DNA elements from long noncoding RNAs (lncRNAs) that coincide at the same loci. Here, we identified the flowering‐associated intergenic lncRNA (FLAIL) inArabidopsisthrough early floweringflailmutants. Expression ofFLAILRNA from a different chromosomal location in combination with strand‐specific RNA knockdown characterizedFLAILas a trans‐acting RNA molecule.FLAILdirectly binds to differentially expressed target genes that control flowering via RNA–DNA interactions through conserved sequence motifs.FLAILinteracts with protein and RNA components of the spliceosome to affect target mRNA expression through co‐transcriptional alternative splicing (AS) and linked chromatin regulation. In the absence ofFLAIL, splicing defects at the direct FLAIL target flowering gene LACCASE 8 (LAC8) correlated with reduced mRNA expression. Double mutant analyses support a model whereFLAIL‐mediated splicing of LAC8 promotes its mRNA expression and represses flowering. Our study suggests lncRNAs as accessory components of the spliceosome that regulate AS and gene expression to impact organismal development. 

Abstract In contrast to the catalytic subunit of telomerase, its RNA subunit (TR) is highly divergent in size, sequence and biogenesis pathways across eukaryotes. Current views on TR evolution assume a common origin of TRs transcribed with RNA polymerase II in Opisthokonta (the supergroup including Animalia and Fungi) and Trypanosomida on one hand, and TRs transcribed with RNA polymerase III under the control of type 3 promoter, found in TSAR and Archaeplastida supergroups (including e.g. ciliates and Viridiplantae taxa, respectively). Here, we focus on unknown TRs in one of the largest Animalia order - Hymenoptera (Arthropoda) with more than 300 available representative genomes. Using a combination of bioinformatic and experimental approaches, we identify their TRs. In contrast to the presumed type of TRs (H/ACA box snoRNAs transcribed with RNA Polymerase II) corresponding to their phylogenetic position, we find here short TRs of the snRNA type, likely transcribed with RNA polymerase III under the control of the type 3 promoter. The newly described insect TRs thus question the hitherto assumed monophyletic origin of TRs across Animalia and point to an evolutionary switch in TR type and biogenesis that was associated with the divergence of Arthropods. 

Abstract A signaling complex comprising members of the LORELEI (LRE)-LIKE GPI-anchored protein (LLG) and Catharanthus roseus RECEPTOR-LIKE KINASE 1-LIKE (CrRLK1L) families perceive RAPID ALKALINIZATION FACTOR (RALF) peptides and regulate growth, reproduction, immunity, and stress responses in Arabidopsis (Arabidopsis thaliana). Genes encoding these proteins are members of multigene families in most angiosperms and could generate thousands of signaling complex variants. However, the links between expansion of these gene families and the functional diversification of this critical signaling complex as well as the evolutionary factors underlying the maintenance of gene duplicates remain unknown. Here, we investigated LLG gene family evolution by sampling land plant genomes and explored the function and expression of angiosperm LLGs. We found that LLG diversity within major land plant lineages is primarily due to lineage-specific duplication events, and that these duplications occurred both early in the history of these lineages and more recently. Our complementation and expression analyses showed that expression divergence (i.e. regulatory subfunctionalization), rather than functional divergence, explains the retention of LLG paralogs. Interestingly, all but one monocot and all eudicot species examined had an LLG copy with preferential expression in male reproductive tissues, while the other duplicate copies showed highest levels of expression in female or vegetative tissues. The single LLG copy in Amborella trichopoda is expressed vastly higher in male compared to in female reproductive or vegetative tissues. We propose that expression divergence plays an important role in retention of LLG duplicates in angiosperms.