Plant responses to the environment are shaped by external stimuli and internal signaling pathways. In both the model plant
Identifying genes that interact to confer a biological function to an organism is one of the main goals of functional genomics. High‐throughput technologies for assessment and quantification of genome‐wide gene expression patterns have enabled systems‐level analyses to infer pathways or networks of genes involved in different functions under many different conditions. Here, we leveraged the publicly available, information‐rich RNA‐Seq datasets of the model plant
- Award ID(s):
- 1932639
- NSF-PAR ID:
- 10445953
- Publisher / Repository:
- Wiley Blackwell (John Wiley & Sons)
- Date Published:
- Journal Name:
- Plant Direct
- Volume:
- 6
- Issue:
- 4
- ISSN:
- 2475-4455
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
More Like this
-
more » « less
Abstract Arabidopsis thaliana (Arabidopsis ) and crop species, circadian clock factors are critical for growth, flowering, and circadian rhythms. Outside ofArabidopsis, however, little is known about the molecular function of clock gene products. Therefore, we sought to compare the function ofBrachypodium distachyon (Brachypodium ) andSetaria viridis (Setaria ) orthologs ofEARLY FLOWERING 3,Arabidopsis . To identify both cycling genes and putativeELF 3Setaria , a circadianRNA ‐seq dataset and online query tool (Diel Explorer) were generated to explore expression profiles ofSetaria genes under circadian conditions. The function ofELF 3Arabidopsis, Brachypodium, andSetaria was tested for complementation of anelf3 mutation inArabidopsis . We find that both monocot orthologs were capable of rescuing hypocotyl elongation, flowering time, and arrhythmic clock phenotypes. Using affinity purification and mass spectrometry, our data indicate that BdELF 3 and SvELF 3 could be integrated into similar complexesin vivo as AtELF 3. Thus, we find that, despite 180 million years of separation,Bd andELF 3Sv can functionally complement loss ofELF 3ELF 3 -
more » « less
Summary The flowering plant
Arabidopsis thaliana is a dicot model organism for research in many aspects of plant biology. A comprehensive annotation of its genome paves the way for understanding the functions and activities of all types of transcripts, includingmRNA , the various classes of non‐codingRNA , and smallRNA . TheTAIR 10 annotation update had a profound impact on Arabidopsis research but was released more than 5 years ago. Maintaining the accuracy of the annotation continues to be a prerequisite for future progress. Using an integrative annotation pipeline, we assembled tissue‐specificRNA ‐Seq libraries from 113 datasets and constructed 48 359 transcript models of protein‐coding genes in eleven tissues. In addition, we annotated various classes of non‐codingRNA including microRNA , long intergenicRNA , small nucleolarRNA , natural antisense transcript, small nuclearRNA , and smallRNA using published datasets and in‐house analytic results. Altogether, we identified 635 novel protein‐coding genes, 508 novel transcribed regions, 5178 non‐codingRNA s, and 35 846 smallRNA loci that were formerly unannotated. Analysis of the splicing events andRNA ‐Seq based expression profiles revealed the landscapes of gene structures, untranslated regions, and splicing activities to be more intricate than previously appreciated. Furthermore, we present 692 uniformly expressed housekeeping genes, 43% of whose human orthologs are also housekeeping genes. This updated Arabidopsis genome annotation with a substantially increased resolution of gene models will not only further our understanding of the biological processes of this plant model but also of other species. -
more » « less
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. -
more » « less
Summary Maize (
Zea mays L.), a model species for genetic studies, is one of the two most important crop species worldwide. The genome sequence of the reference genotype, B73, representative of the stiff stalk heterotic group was recently updated (AGP v4) using long‐read sequencing and optical mapping technology. To facilitate the use ofAGP v4 and to enable functional genomic studies and association of genotype with phenotype, we determined expression abundances for replicatedmRNA ‐sequencing datasets from 79 tissues and five abiotic/biotic stress treatments revealing 36 207 expressed genes. Characterization of the B73 transcriptome across six organs revealed 4154 organ‐specific and 7704 differentially expressed (DE) genes following stress treatment. Gene co‐expression network analyses revealed 12 modules associated with distinct biological processes containing 13 590 genes providing a resource for further association of gene function based on co‐expression patterns. Presence−absence variants (PAV s) previously identified using whole genome resequencing data from 61 additional inbred lines were enriched in organ‐specific and stress‐induced DE genes suggesting thatPAV s may function in phenological variation and adaptation to environment. Relative to core genes conserved across the 62 profiled inbreds,PAV s have lower expression abundances which are correlated with their frequency of dispersion across inbreds and on average have significantly fewer co‐expression network connections suggesting that a subset ofPAV s may be on an evolutionary path to pseudogenization. To facilitate use by the community, we developed the Maize Genomics Resource website (maize.plantbiology.msu.edu) for viewing and data‐mining these resources and deployed two new views on the maize electronic Fluorescent Pictograph Browser (bar.utoronto.ca/efp_maize). -
more » « less
Abstract With the high variability of natural growth environments, plants exhibit flexibility and resilience in regard to the strategies they employ to maintain overall fitness, including maximizing light use for photosynthesis, while simultaneously limiting light‐associated damage. We measured distinct parameters of photosynthetic performance of
Arabidopsis thaliana
