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1. Desert-adapted tomato Solanum pennellii exhibit unique regulatory elements and stress-ready transcriptome patterns to drought

   https://doi.org/10.1371/journal.pone.0324724  

   Contreras-Riquelme, J Sebastián; Contreras, Miguel; Moyano, Tomas C; Sjoberg, Rachid; Jimenez-Gomez, José; Alvarez, José M (May 2025, PLOS One)

   Irfan, Mohammad (Ed.)

   Drought is a significant environmental stressor that severely impairs plant growth and agricultural productivity. Unraveling the molecular mechanisms underlying plant responses to drought is crucial for developing crops with enhanced resilience. In this study, we investigated the transcriptomic responses of cultivated tomato (Solanum lycopersicum) and its drought-tolerant wild relative,Solanum pennellii, to identify “stress-ready” gene expression patterns associated with pre-adaptation to arid environments. Through RNA-seq analysis, we identified orthologous genes between the two species and compared their transcriptomic profiles under both control and drought conditions. Approximately 43% of the orthologous genes exhibited species-specific expression patterns, while nearly 20% were classified as stress-ready. These stress-ready genes were significantly enriched for functions related to nucleosome assembly, RNA metabolism, and transcriptional regulation. Furthermore, transcription factor binding motif analysis revealed a marked enrichment of ERF family motifs, emphasizing their role in both stress-ready and species-specific responses. Our findings indicate that regulatory mechanisms, particularly those mediated by ERF transcription factors, are pivotal to the drought resilience ofS. pennellii, providing a foundation for future crop improvement strategies. 

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2. Evolutionary characteristics of intergenic transcribed regions indicate rare novel genes and widespread noisy transcription in the Poaceae

   https://doi.org/10.1038/s41598-019-47797-y  

   Lloyd, John_P; Bowman, Megan_J; Azodi, Christina_B; Sowers, Rosalie_P; Moghe, Gaurav_D; Childs, Kevin_L; Shiu, Shin-Han (August 2019, Scientific Reports)

   Abstract Extensive transcriptional activity occurring in intergenic regions of genomes has raised the question whether intergenic transcription represents the activity of novel genes or noisy expression. To address this, we evaluated cross-species and post-duplication sequence and expression conservation of intergenic transcribed regions (ITRs) in four Poaceae species. Among 43,301 ITRs across the four species, 34,460 (80%) are species-specific. ITRs found across species tend to be more divergent in expression and have more recent duplicates compared to annotated genes. To assess if ITRs are functional (under selection), machine learning models were established inOryza sativa(rice) that could accurately distinguish between phenotype genes and pseudogenes (area under curve-receiver operating characteristic = 0.94). Based on the models, 584 (8%) and 4391 (61%) rice ITRs are classified as likely functional and nonfunctional with high confidence, respectively. ITRs with conserved expression and ancient retained duplicates, features that were not part of the model, are frequently classified as likely-functional, suggesting these characteristics could serve as pragmatic rules of thumb for identifying candidate sequences likely to be under selection. This study also provides a framework to identify novel genes using comparative transcriptomic data to improve genome annotation that is fundamental for connecting genotype to phenotype in crop and model systems. 

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3. Long-read transcriptome and other genomic resources for the angiosperm Silene noctiflora

   https://doi.org/10.1093/g3journal/jkab189  

   Williams, Alissa M; Itgen, Michael W; Broz, Amanda K; Carter, Olivia G; Sloan, Daniel B (January 2021, G3 Genes|Genomes|Genetics)

   Abstract The angiosperm genus Silene is a model system for several traits of ecological and evolutionary significance in plants, including breeding system and sex chromosome evolution, host-pathogen interactions, invasive species biology, heavy metal tolerance, and cytonuclear interactions. Despite its importance, genomic resources for this large genus of approximately 850 species are scarce, with only one published whole-genome sequence (from the dioecious species Silene latifolia). Here, we provide genomic and transcriptomic resources for a hermaphroditic representative of this genus (S. noctiflora), including a PacBio Iso-Seq transcriptome, which uses long-read, single-molecule sequencing technology to analyze full-length mRNA transcripts. Using these data, we have assembled and annotated high-quality full-length cDNA sequences for approximately 14,126 S. noctiflora genes and 25,317 isoforms. We demonstrated the utility of these data to distinguish between recent and highly similar gene duplicates by identifying novel paralogous genes in an essential protease complex. Furthermore, we provide a draft assembly for the approximately 2.7-Gb genome of this species, which is near the upper range of genome-size values reported for diploids in this genus and threefold larger than the 0.9-Gb genome of Silene conica, another species in the same subgenus. Karyotyping confirmed that S. noctiflora is a diploid, indicating that its large genome size is not due to polyploidization. These resources should facilitate further study and development of this genus as a model in plant ecology and evolution. 

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4. The vacuolar Ca ²⁺ transporter CATION EXCHANGER 2 regulates cytosolic calcium homeostasis, hypoxic signaling, and response to flooding in Arabidopsis thaliana

   https://doi.org/10.1111/nph.19274  

   Bakshi, Arkadipta; Choi, Won‐Gyu; Kim, Su‐Hwa; Gilroy, Simon (September 2023, New Phytologist)

   Summary Flooding represents a major threat to global agricultural productivity and food security, but plants are capable of deploying a suite of adaptive responses that can lead to short‐ or longer‐term survival to this stress. One cellular pathway thought to help coordinate these responses is via flooding‐triggered Ca²⁺signaling.We have mined publicly available transcriptomic data from Arabidopsis subjected to flooding or low oxygen stress to identify rapidly upregulated, Ca²⁺‐related transcripts. We then focused on transporters likely to modulate Ca²⁺signals. Candidates emerging from this analysis includedAUTOINHIBITED Ca²⁺ATPASE 1andCATION EXCHANGER 2. We therefore assayed mutants in these genes for flooding sensitivity at levels from growth to patterns of gene expression and the kinetics of flooding‐related Ca²⁺changes.Knockout mutants inCAX2especially showed enhanced survival to soil waterlogging coupled with suppressed induction of many marker genes for hypoxic response and constitutive activation of others.CAX2mutants also generated larger and more sustained Ca²⁺signals in response to both flooding and hypoxic challenges.CAX2 is a Ca²⁺transporter located on the tonoplast, and so these results are consistent with an important role for vacuolar Ca²⁺transport in the signaling systems that trigger flooding response. 

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5. IsoSeq transcriptome assembly of C ₃ panicoid grasses provides tools to study evolutionary change in the Panicoideae

   https://doi.org/10.1002/pld3.203  

   Carvalho, Daniel S.; Nishimwe, Aime V.; Schnable, James C. (February 2020, Plant Direct)

   Abstract The number of plant species with genomic and transcriptomic data has been increasing rapidly. The grasses—Poaceae—have been well represented among species with published reference genomes. However, as a result the genomes of wild grasses are less frequently targeted by sequencing efforts. Sequence data from wild relatives of crop species in the grasses can aid the study of domestication, gene discovery for breeding and crop improvement, and improve our understanding of the evolution of C₄photosynthesis. Here, we used long‐read sequencing technology to characterize the transcriptomes of three C₃panicoid grass species:Dichanthelium oligosanthes,Chasmanthium laxum, andHymenachne amplexicaulis. Based on alignments to the sorghum genome, we estimate that assembled consensus transcripts from each species capture between 54.2% and 65.7% of the conserved syntenic gene space in grasses. Genes co‐opted into C₄were also well represented in this dataset, despite concerns that because these genes might play roles unrelated to photosynthesis in the target species, they would be expressed at low levels and missed by transcript‐based sequencing. A combined analysis using syntenic orthologous genes from grasses with published reference genomes and consensus long‐read sequences from these wild species was consistent with previously published phylogenies. It is hoped that these data, targeting underrepresented classes of species within the PACMAD grasses—wild species and species utilizing C₃photosynthesis—will aid in future studies of domestication and C₄evolution by decreasing the evolutionary distance between C₄and C₃species within this clade, enabling more accurate comparisons associated with evolution of the C₄pathway. 

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