1
|
Yang Y, Liu M, Huang Z. Genomic and Expression Analysis of Cassava ( Manihot esculenta Crantz) Chalcone Synthase Genes in Defense against Tetranychus cinnabarinus Infestation. Genes (Basel) 2024; 15:336. [PMID: 38540395 PMCID: PMC10970205 DOI: 10.3390/genes15030336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Revised: 02/23/2024] [Accepted: 02/28/2024] [Indexed: 06/14/2024] Open
Abstract
Cassava is susceptible to mites, especially Tetranychus cinnabarinus. Secondary metabolism products such as flavonoids play an important role as antimicrobial metabolites protecting plants against biotic stressors including fungal, pathogen, bacterial, and pest defense. The chalcone synthase (CHS) is the initial step of the phenylpropanoid pathway for producing flavonoids and is the gatekeeper of the pathway. Until recently, the CHS genes family has not been systematically studied in cassava. Thirty-nine CHS genes were identified from the cassava genome database. Based on phylogenetic and sequence composition analysis, these CHSs were divided into 3 subfamilies. Within the same subfamily, the gene structure and motif compositions of these CHS genes were found to be quite conserved. Duplication events, particularly segmental duplication of the cassava CHS genes, were identified as one of the main driving force of its expansion. Various cis-elements contained in the promoter might regulate the gene expression patterns of MeCHS. Protein-protein interaction (PPI) network analysis showed that MeCHS1 and MeCHS10 protein are more closely related to other family members. The expression of MeCHS genes in young leaves was higher than that in other tissues, and their expression varies even within the same tissue. Coincidentally, these CHS genes of most LAP subclasses were highly expressed in young leaves. The verified MeCHS genes showed consistent with the real-time reverse transcription quantitative PCR (RT-qPCR) and proteomic expression in protected and affected leaves respectively, indicating that these MeCHS genes play crucial roles in the response to T. cinnabarinus. This study is the first to comprehensively expatiate the information on MeCHS family members. These data will further enhance our understanding both the molecular mechanisms and the effects of CHS genes. In addition, the results will help to further clarify the effects on T. cinnabarinus and provide a theoretical basis for the potential functions of the specific CHS gene in resistance to mites and other biotic stress.
Collapse
Affiliation(s)
- Yanni Yang
- Guangxi Key Laboratory of Plant Functional Phytochemicals and Sustainable Utilization, Guangxi Institute of Botany, Guangxi Zhuang Autonomous Region and Chinese Academy of Sciences, Guilin 541006, China;
- College of Agronomy, Guangxi University, Nanning 530004, China
| | - Ming Liu
- Guangxi Key Laboratory of Plant Functional Phytochemicals and Sustainable Utilization, Guangxi Institute of Botany, Guangxi Zhuang Autonomous Region and Chinese Academy of Sciences, Guilin 541006, China;
| | - Zenghui Huang
- Nanning New Technology Entrepreneur Center, Nanning 530007, China;
| |
Collapse
|
2
|
Ahn JY, Subburaj S, Yan F, Yao J, Chandrasekaran A, Ahn KG, Lee GJ. Molecular Evaluation of the Effects of FLC Homologs and Coordinating Regulators on the Flowering Responses to Vernalization in Cabbage ( Brassica oleracea var. capitata) Genotypes. Genes (Basel) 2024; 15:154. [PMID: 38397144 PMCID: PMC10887945 DOI: 10.3390/genes15020154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 01/08/2024] [Accepted: 01/20/2024] [Indexed: 02/25/2024] Open
Abstract
The flowering loci of cabbage must be understood to boost their productivity. In this study, to clarify the flowering mechanisms of cabbage, we examined the three flowering repressors BoFLC1, 2 and 3, and the flowering regulators BoGI, BoCOOLAIR, and BoVIN3 of early (CAB1), middle (CAB3), and late (CAB5) flowering cabbage genotypes. Analysis of allele-specifically amplified genomic DNA and various sequence alignments demonstrated that maximal insertions and deletions influenced cabbage flowering behavior, notably in CAB3 and CAB5. Phylogenetic studies showed that BoFLC1, 2, and 3 in the CAB1, 3, and 5 genotypes had the highest homologies to other Brassica species, with CAB3 and 5 the most similar. Although CAB3 and CAB5 have comparable genetic patterns, flowering repressors and flowering regulators were investigated individually with and without vernalization to determine their minor flowering differences. The expression investigation revealed that vernalized CAB5 downregulated all BoFLC genes compared to CAB3 and, in contrast, CAB3 exhibited upregulated BoCOOLAIR. We hypothesized that the CAB3 BoFLC locus' additional insertions may have led to BoCOOLAIR overexpression and BoFLC downregulation. This study sheds light on cabbage genotypes-particularly those of CAB1 and CAB5-and suggests that structural variations in BoFLC2 and 3 bind flowering regulators, such as COOLAIR, which may affect cabbage flowering time.
Collapse
Affiliation(s)
- Ju-Young Ahn
- Department of Horticulture, Chungnam National University, Daejeon 34134, Republic of Korea; (J.-Y.A.); (S.S.); (A.C.)
| | - Saminathan Subburaj
- Department of Horticulture, Chungnam National University, Daejeon 34134, Republic of Korea; (J.-Y.A.); (S.S.); (A.C.)
| | - Fanzhuang Yan
- Department of Smart Agriculture Systems, Chungnam National University, Daejeon 34134, Republic of Korea; (F.Y.); (J.Y.)
| | - Jian Yao
- Department of Smart Agriculture Systems, Chungnam National University, Daejeon 34134, Republic of Korea; (F.Y.); (J.Y.)
| | - Ajithan Chandrasekaran
- Department of Horticulture, Chungnam National University, Daejeon 34134, Republic of Korea; (J.-Y.A.); (S.S.); (A.C.)
- Department of Smart Agriculture Systems, Chungnam National University, Daejeon 34134, Republic of Korea; (F.Y.); (J.Y.)
| | - Kyoung-Gu Ahn
- Joen Seed Co., Ltd., Goesan 28051, Republic of Korea;
| | - Geung-Joo Lee
- Department of Horticulture, Chungnam National University, Daejeon 34134, Republic of Korea; (J.-Y.A.); (S.S.); (A.C.)
- Department of Smart Agriculture Systems, Chungnam National University, Daejeon 34134, Republic of Korea; (F.Y.); (J.Y.)
| |
Collapse
|
3
|
Yu R, Xiong Z, Zhu X, Feng P, Hu Z, Fang R, Zhang Y, Liu Q. RcSPL1-RcTAF15b regulates the flowering time of rose ( Rosa chinensis). HORTICULTURE RESEARCH 2023; 10:uhad083. [PMID: 37323236 PMCID: PMC10266950 DOI: 10.1093/hr/uhad083] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 04/18/2023] [Indexed: 06/17/2023]
Abstract
Rose (Rosa chinensis), which is an economically valuable floral species worldwide, has three types, namely once-flowering (OF), occasional or re-blooming (OR), and recurrent or continuous flowering (CF). However, the mechanism underlying the effect of the age pathway on the duration of the CF or OF juvenile phase is largely unknown. In this study, we observed that the RcSPL1 transcript levels were substantially upregulated during the floral development period in CF and OF plants. Additionally, accumulation of RcSPL1 protein was controlled by rch-miR156. The ectopic expression of RcSPL1 in Arabidopsis thaliana accelerated the vegetative phase transition and flowering. Furthermore, the transient overexpression of RcSPL1 in rose plants accelerated flowering, whereas silencing of RcSPL1 had the opposite phenotype. Accordingly, the transcription levels of floral meristem identity genes (APETALA1, FRUITFULL, and LEAFY) were significantly affected by the changes in RcSPL1 expression. RcTAF15b protein, which is an autonomous pathway protein, was revealed to interact with RcSPL1. The silencing and overexpression of RcTAF15b in rose plants led to delayed and accelerated flowering, respectively. Collectively, the study findings imply that RcSPL1-RcTAF15b modulates the flowering time of rose plants.
Collapse
Affiliation(s)
- Rui Yu
- Department of Ornamental Horticulture, College of Horticulture, China Agricultural University, Beijing 100193, China
| | - Zhiying Xiong
- Department of Ornamental Horticulture, College of Horticulture, China Agricultural University, Beijing 100193, China
| | - Xinhui Zhu
- Department of Ornamental Horticulture, College of Horticulture, China Agricultural University, Beijing 100193, China
| | - Panpan Feng
- Department of Ornamental Horticulture, College of Horticulture, China Agricultural University, Beijing 100193, China
| | - Ziyi Hu
- Department of Ornamental Horticulture, College of Horticulture, China Agricultural University, Beijing 100193, China
| | - Rongxiang Fang
- National Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, and National Plant Gene Research Center, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 101408, China
| | | | | |
Collapse
|
4
|
Artz O, Ackermann A, Taylor L, Koo PK, Pedmale UV. Light and temperature regulate m 6A-RNA modification to regulate growth in plants. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.17.524395. [PMID: 36711495 PMCID: PMC9882139 DOI: 10.1101/2023.01.17.524395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
N6-methyladenosine is a highly dynamic, abundant mRNA modification which is an excellent potential mechanism for fine tuning gene expression. Plants adapt to their surrounding light and temperature environment using complex gene regulatory networks. The role of m6A in controlling gene expression in response to variable environmental conditions has so far been unexplored. Here, we map the transcriptome-wide m6A landscape under various light and temperature environments. Identified m6A-modifications show a highly specific spatial distribution along transcripts with enrichment occurring in 5'UTR regions and around transcriptional end sites. We show that the position of m6A modifications on transcripts might influence cellular transcript localization and the presence of m6A-modifications is associated with alternative polyadenylation, a process which results in multiple RNA isoforms with varying 3'UTR lengths. RNA with m6A-modifications exhibit a higher preference for shorter 3'UTRs. These shorter 3'UTR regions might directly influence transcript abundance and localization by including or excluding cis-regulatory elements. We propose that environmental stimuli might change the m6A landscape of plants as one possible way of fine tuning gene regulation through alternative polyadenylation and transcript localization.
Collapse
Affiliation(s)
- Oliver Artz
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, 11724. USA
| | - Amanda Ackermann
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, 11724. USA
| | - Laura Taylor
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, 11724. USA
| | - Peter K. Koo
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, 11724. USA
| | - Ullas V. Pedmale
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, 11724. USA
| |
Collapse
|
5
|
Soorni A, Karimi M, Al Sharif B, Habibi K. Genome-wide screening and characterization of long noncoding RNAs involved in flowering/bolting of Lactuca sativa. BMC PLANT BIOLOGY 2023; 23:3. [PMID: 36588159 PMCID: PMC9806901 DOI: 10.1186/s12870-022-04031-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 12/28/2022] [Indexed: 06/17/2023]
Abstract
BACKGROUND Lettuce (Lactuca sativa L.) is considered the most important vegetable in the leafy vegetable group. However, bolting affects quality, gives it a bitter taste, and as a result makes it inedible. Bolting is an event induced by the coordinated effects of various environmental factors and endogenous genetic components. Although bolting/flowering responsive genes have been identified in most sensitive and non-sensitive species, non-coding RNA molecules like long non-coding RNAs (lncRNAs) have not been investigated in lettuce. Hence, in this study, potential long non-coding RNAs that regulate flowering /bolting were investigated in two lettuce strains S24 (resistant strain) and S39 (susceptible strain) in different flowering times to better understand the regulation of lettuce bolting mechanism. For this purpose, we used two RNA-seq datasets to discover the lncRNA transcriptome profile during the transition from vegetative to reproductive phase. RESULTS For identifying unannotated transcripts in these datasets, a 7-step pipeline was employed to filter out these transcripts and terminate with 293 novel lncRNAs predicted by PLncPRO and CREMA. These transcripts were then utilized to predict cis and trans flowering-associated targets and Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis. Computational predictions of target gene function showed the involvement of putative flowering-related genes and enrichment of the floral regulators FLC, CO, FT, and SOC1 in both datasets. Finally, 17 and 18 lncRNAs were proposed as competing endogenous target mimics (eTMs) for novel and known lncRNA miRNAs, respectively. CONCLUSION Overall, this study provides new insights into lncRNAs that control the flowering time of plants known for bolting, such as lettuce, and opens new windows for further study.
Collapse
Affiliation(s)
- Aboozar Soorni
- Department of Biotechnology, College of Agriculture, Isfahan University of Technology, Isfahan, Iran.
| | | | - Batoul Al Sharif
- Department of Biotechnology, College of Agriculture, Isfahan University of Technology, Isfahan, Iran
| | - Khashayar Habibi
- Department of Biotechnology, College of Agriculture, Isfahan University of Technology, Isfahan, Iran
| |
Collapse
|
6
|
Li W, Chen Y, Wang Y, Zhao J, Wang Y. Gypsy retrotransposon-derived maize lncRNA GARR2 modulates gibberellin response. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 110:1433-1446. [PMID: 35368126 DOI: 10.1111/tpj.15748] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 03/15/2022] [Accepted: 03/22/2022] [Indexed: 05/09/2023]
Abstract
Long non-coding RNAs (lncRNAs) mediate diverse biological events mainly through the modulation of transcriptional hierarchy. The phytohormone gibberellin (GA) is essential for various aspects of plant growth and development. However, the roles of lncRNAs in the regulation of the GA response remain largely unknown. Through sequencing multiple strand-specific and ribosomal-depleted RNA libraries, we delineated the landscape of lncRNAs in maize (Zea mays). Out of identified lncRNAs, 445 GIBBERELLIN-RESPONSIVE lncRNAs (GARRs) were differentially expressed upon GA application. By the intersection of GARRs from normal-height and dwarf plants from an advanced backcross population, four shared GARRs (GARR1 to GARR4) were identified. Out of these four shared GARRs, GARR2 was derived from a Gypsy LTR retrotransposon. GA-responsive element P-boxes were identified upstream of GARR2. GARR2-edited lines exhibited a GA-induced phenotype. Editing of GARR2 resulted in changes in the transcriptional abundance of GA pathway components and endogenous GA contents. Besides GA, GARR2 affected the primary auxin response. An RNA pull-down assay revealed the HECT ubiquitin-protein ligase family member ZmUPL1 as a potential interaction target of GARR2. GARR2 influenced the abundance of ZmUPL1 in the GA response. Our study uncovers lncRNA players involved in the modulation of the GA response and guides the development of plant height ideotype driven by knowledge of the phytohormone GA.
Collapse
Affiliation(s)
- Wei Li
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou, 225009, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, 225009, China
| | - Yudong Chen
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou, 225009, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, 225009, China
| | - Yali Wang
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou, 225009, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, 225009, China
| | - Jia Zhao
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou, 225009, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, 225009, China
| | - Yijun Wang
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou, 225009, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, 225009, China
| |
Collapse
|
7
|
Liu H, Jia Y, Chai Y, Wang S, Chen H, Zhou X, Huang C, Guo S, Chen D. Whole-transcriptome analysis of differentially expressed genes between ray and disc florets and identification of flowering regulatory genes in Chrysanthemum morifolium. FRONTIERS IN PLANT SCIENCE 2022; 13:947331. [PMID: 35991433 PMCID: PMC9388166 DOI: 10.3389/fpls.2022.947331] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 06/29/2022] [Indexed: 05/13/2023]
Abstract
Chrysanthemum morifolium has ornamental and economic values. However, there has been minimal research on the morphology of the chrysanthemum florets and related genes. In this study, we used the leaves as a control to screen for differentially expressed genes between ray and disc florets in chrysanthemum flowers. A total of 8,359 genes were differentially expressed between the ray and disc florets, of which 3,005 were upregulated and 5,354 were downregulated in the disc florets. Important regulatory genes that control flower development and flowering determination were identified. Among them, we identified a TM6 gene (CmTM6-mu) that belongs to the Class B floral homeotic MADS-box transcription factor family, which was specifically expressed in disc florets. We isolated this gene and found it was highly similar to other typical TM6 lineage genes, but a single-base deletion at the 3' end of the open reading frame caused a frame shift that generated a protein in which the TM6-specific paleoAP3 motif was missing at the C terminus. The CmTM6-mu gene was ectopically expressed in Arabidopsis thaliana. Petal and stamen developmental processes were unaffected in transgenic A. thaliana lines; however, the flowering time was earlier than in the wild-type control. Thus, the C-terminal of paleoAP3 appears to be necessary for the functional performance in regulating the development of petals or stamens and CmTM6-mu may be involved in the regulation of flowering time in chrysanthemum. The results of this study will be useful for future research on flowering molecular mechanisms and for the breeding of novel flower types.
Collapse
Affiliation(s)
- Hua Liu
- Institute of Grassland, Flowers and Ecology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Yin Jia
- College of Landscape Architecture, Sichuan Agricultural University, Chengdu, China
| | - Yuhong Chai
- Institute of Grassland, Flowers and Ecology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- School of Horticulture and Landscape Architecture, Henan Institute of Science and Technology, Xinxiang, China
| | - Sen Wang
- Institute of Grassland, Flowers and Ecology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Haixia Chen
- Institute of Grassland, Flowers and Ecology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Xiumei Zhou
- School of Horticulture and Landscape Architecture, Henan Institute of Science and Technology, Xinxiang, China
| | - Conglin Huang
- Institute of Grassland, Flowers and Ecology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- *Correspondence: Conglin Huang,
| | - Shuang Guo
- Chengdu Park City Construction Development Research Institute, Chengdu, China
- *Correspondence: Conglin Huang,
| | - Dongliang Chen
- Institute of Grassland, Flowers and Ecology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- *Correspondence: Conglin Huang,
| |
Collapse
|
8
|
Zhang L, Wang R, Xing Y, Xu Y, Xiong D, Wang Y, Yao S. Separable regulation of POW1 in grain size and leaf angle development in rice. PLANT BIOTECHNOLOGY JOURNAL 2021; 19:2517-2531. [PMID: 34343399 PMCID: PMC8633490 DOI: 10.1111/pbi.13677] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 07/27/2021] [Accepted: 07/28/2021] [Indexed: 05/27/2023]
Abstract
Leaf angle is one of the key factors that determines rice plant architecture. However, the improvement of leaf angle erectness is often accompanied by unfavourable changes in other traits, especially grain size reduction. In this study, we identified the pow1 (put on weight 1) mutant that leads to increased grain size and leaf angle, typical brassinosteroid (BR)-related phenotypes caused by excessive cell proliferation and cell expansion. We show that modulation of the BR biosynthesis genes OsDWARF4 (D4) and D11 and the BR signalling gene D61 could rescue the phenotype of leaf angle but not grain size in the pow1 mutant. We further demonstrated that POW1 functions in grain size regulation by repressing the transactivation activity of the interacting protein TAF2, a highly conserved member of the TFIID transcription initiation complex. Down-regulation of TAF2 rescued the enlarged grain size of pow1 but had little effect on the increased leaf angle phenotype of the mutant. The separable functions of the POW1-TAF2 and POW1-BR modules in grain size and leaf angle control provide a promising strategy for designing varieties with compact plant architecture and increased grain size, thus promoting high-yield breeding in rice.
Collapse
Affiliation(s)
- Li Zhang
- State Key Laboratory of Plant GenomicsInstitute of Genetics and Developmental BiologyThe Innovative Academy of Seed DesignChinese Academy of SciencesBeijingChina
- College of Advanced Agricultural SciencesUniversity of Chinese Academy of SciencesBeijingChina
| | - Ruci Wang
- State Key Laboratory of Plant GenomicsInstitute of Genetics and Developmental BiologyThe Innovative Academy of Seed DesignChinese Academy of SciencesBeijingChina
| | - Yide Xing
- State Key Laboratory of Plant GenomicsInstitute of Genetics and Developmental BiologyThe Innovative Academy of Seed DesignChinese Academy of SciencesBeijingChina
- College of Advanced Agricultural SciencesUniversity of Chinese Academy of SciencesBeijingChina
| | - Yufang Xu
- State Key Laboratory of Plant GenomicsInstitute of Genetics and Developmental BiologyThe Innovative Academy of Seed DesignChinese Academy of SciencesBeijingChina
- College of Advanced Agricultural SciencesUniversity of Chinese Academy of SciencesBeijingChina
- College of Life ScienceHenan Agricultural UniversityZhengzhouChina
| | - Dunping Xiong
- State Key Laboratory of Plant GenomicsInstitute of Genetics and Developmental BiologyThe Innovative Academy of Seed DesignChinese Academy of SciencesBeijingChina
- College of Advanced Agricultural SciencesUniversity of Chinese Academy of SciencesBeijingChina
| | - Yueming Wang
- State Key Laboratory of Plant GenomicsInstitute of Genetics and Developmental BiologyThe Innovative Academy of Seed DesignChinese Academy of SciencesBeijingChina
| | - Shanguo Yao
- State Key Laboratory of Plant GenomicsInstitute of Genetics and Developmental BiologyThe Innovative Academy of Seed DesignChinese Academy of SciencesBeijingChina
| |
Collapse
|
9
|
Zhu P, Lister C, Dean C. Cold-induced Arabidopsis FRIGIDA nuclear condensates for FLC repression. Nature 2021; 599:657-661. [PMID: 34732891 PMCID: PMC8612926 DOI: 10.1038/s41586-021-04062-5] [Citation(s) in RCA: 65] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 09/27/2021] [Indexed: 11/09/2022]
Abstract
Plants use seasonal temperature cues to time the transition to reproduction. In Arabidopsis thaliana, winter cold epigenetically silences the floral repressor locus FLOWERING LOCUS C (FLC) through POLYCOMB REPRESSIVE COMPLEX 2 (PRC2)1. This vernalization process aligns flowering with spring. A prerequisite for silencing is transcriptional downregulation of FLC, but how this occurs in the fluctuating temperature regimes of autumn is unknown2-4. Transcriptional repression correlates with decreased local levels of histone H3 trimethylation at K36 (H3K36me3) and H3 trimethylation at K4 (H3K4me3)5,6, which are deposited during FRIGIDA (FRI)-dependent activation of FLC7-10. Here we show that cold rapidly promotes the formation of FRI nuclear condensates that do not colocalize with an active FLC locus. This correlates with reduced FRI occupancy at the FLC promoter and FLC repression. Warm temperature spikes reverse this process, buffering FLC shutdown to prevent premature flowering. The accumulation of condensates in the cold is affected by specific co-transcriptional regulators and cold induction of a specific isoform of the antisense RNA COOLAIR5,11. Our work describes the dynamic partitioning of a transcriptional activator conferring plasticity in response to natural temperature fluctuations, thus enabling plants to effectively monitor seasonal progression.
Collapse
Affiliation(s)
- Pan Zhu
- John Innes Centre, Norwich Research Park, Norwich, UK
| | - Clare Lister
- John Innes Centre, Norwich Research Park, Norwich, UK
| | - Caroline Dean
- John Innes Centre, Norwich Research Park, Norwich, UK.
| |
Collapse
|
10
|
Yuan X, Wang Q, Yan B, Zhang J, Xue C, Chen J, Lin Y, Zhang X, Shen W, Chen X. Single-Molecule Real-Time and Illumina-Based RNA Sequencing Data Identified Vernalization-Responsive Candidate Genes in Faba Bean ( Vicia faba L.). Front Genet 2021; 12:656137. [PMID: 34290734 PMCID: PMC8287337 DOI: 10.3389/fgene.2021.656137] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Accepted: 06/07/2021] [Indexed: 12/05/2022] Open
Abstract
Faba bean (Vicia faba L.) is one of the most widely grown cool season legume crops in the world. Winter faba bean normally has a vernalization requirement, which promotes an earlier flowering and pod setting than unvernalized plants. However, the molecular mechanisms of vernalization in faba bean are largely unknown. Discovering vernalization-related candidate genes is of great importance for faba bean breeding. In this study, the whole transcriptome of faba bean buds was profiled by using next-generation sequencing (NGS) and single-molecule, real-time (SMRT) full-length transcriptome sequencing technology. A total of 29,203 high-quality non-redundant transcripts, 21,098 complete coding sequences (CDS), 1,045 long non-coding RNAs (lncRNAs), and 12,939 simple sequence repeats (SSRs) were identified. Furthermore, 4,044 differentially expressed genes (DEGs) were identified through pairwise comparisons. By Gene Ontology (GO) enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis, these differentially expressed transcripts were found to be enriched in binding and transcription factor activity, electron carrier activity, rhythmic process, and receptor activity. Finally, 50 putative vernalization-related genes that played important roles in the vernalization of faba bean were identified; we also found that the levels of vernalization-responsive transcripts showed significantly higher expression levels in cold-treated buds. The expression of VfSOC1, one of the candidate genes, was sensitive to vernalization. Ectopic expression of VfSOC1 in Arabidopsis brought earlier flowering. In conclusion, the abundant vernalization-related transcripts identified in this study will provide a basis for future researches on the vernalization and faba bean breeding and established a reference full-length transcriptome for future studies on faba bean.
Collapse
Affiliation(s)
- Xingxing Yuan
- College of Life Sciences, Nanjing Agricultural University, Nanjing, China.,Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Qiong Wang
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Bin Yan
- College of Life Sciences, Nanjing Agricultural University, Nanjing, China.,Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Jiong Zhang
- College of Life Sciences, Nanjing Agricultural University, Nanjing, China.,Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Chenchen Xue
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Jingbin Chen
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Yun Lin
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Xiaoyan Zhang
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Wenbiao Shen
- College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Xin Chen
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| |
Collapse
|
11
|
Liu C, Zhang Q, Zhu H, Cai C, Li S. Characterization of Mungbean CONSTANS-LIKE Genes and Functional Analysis of CONSTANS-LIKE 2 in the Regulation of Flowering Time in Arabidopsis. FRONTIERS IN PLANT SCIENCE 2021; 12:608603. [PMID: 33613600 PMCID: PMC7890258 DOI: 10.3389/fpls.2021.608603] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Accepted: 01/11/2021] [Indexed: 05/05/2023]
Abstract
CONSTANS-LIKE (COL) genes play important roles in the regulation of plant growth and development, and they have been analyzed in many plant species. However, few studies have examined COL genes in mungbean (Vigna radiata). In this study, we identified and characterized 31 mungbean genes whose proteins contained B-Box domains. Fourteen were designated as VrCOL genes and were distributed on 7 of the 11 mungbean chromosomes. Based on their phylogenetic relationships, VrCOLs were clustered into three groups (I, II, and III), which contained 4, 6, and 4 members, respectively. The gene structures and conserved motifs of the VrCOL genes were analyzed, and two duplicated gene pairs, VrCOL1/VrCOL2 and VrCOL8/VrCOL9, were identified. A total of 82 cis-acting elements were found in the VrCOL promoter regions, and the numbers and types of cis-acting elements in each VrCOL promoter region differed. As a result, the expression patterns of VrCOLs varied in different tissues and throughout the day under long-day and short-day conditions. Among these VrCOL genes, VrCOL2 showed a close phylogenetic relationship with Arabidopsis thaliana CO and displayed daily oscillations in expression under short-day conditions but not long-day conditions. In addition, overexpression of VrCOL2 accelerated flowering in Arabidopsis under short-day conditions by affecting the expression of the flowering time genes AtFT and AtTSF. Our study lays the foundation for further investigation of VrCOL gene functions.
Collapse
Affiliation(s)
- Chenyang Liu
- Key Laboratory of Plant Biotechnology in Universities of Shandong Province, College of Life Sciences, Qingdao Agricultural University, Qingdao, China
| | - Qianqian Zhang
- Key Laboratory of Plant Biotechnology in Universities of Shandong Province, College of Life Sciences, Qingdao Agricultural University, Qingdao, China
| | - Hong Zhu
- College of Agronomy, Qingdao Agricultural University, Qingdao, China
| | - Chunmei Cai
- Key Laboratory of Plant Biotechnology in Universities of Shandong Province, College of Life Sciences, Qingdao Agricultural University, Qingdao, China
| | - Shuai Li
- Key Laboratory of Plant Biotechnology in Universities of Shandong Province, College of Life Sciences, Qingdao Agricultural University, Qingdao, China
- *Correspondence: Shuai Li,
| |
Collapse
|
12
|
Molecular cloning and expression analysis of sucrose phosphate synthase genes in cassava (Manihot esculenta Crantz). Sci Rep 2020; 10:20707. [PMID: 33244128 PMCID: PMC7692556 DOI: 10.1038/s41598-020-77669-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2019] [Accepted: 11/13/2020] [Indexed: 11/09/2022] Open
Abstract
Sucrose phosphate synthase (SPS), a key rate-limiting enzyme in the sucrose biosynthesis pathway in plants, is encoded by a multi-gene family. Until recently, the identification and characterization of the SPS gene family have been performed for dozens of plant species; however, few studies have involved a comprehensive analysis of the SPS family members in tropical crops, such as cassava (Manihot esculenta Crantz). In the current study, five SPS genes (MeSPS1, MeSPS2, MeSPS3, MeSPS4, and MeSPS5) were isolated from cassava, and their sequence characteristics were comprehensively characterized. These MeSPS genes were found distributed on five chromosomes (Chr2, Chr14, Chr15, Chr16, and Chr18). Phylogenetic analysis showed that the MeSPS protein sequences were clustered into three families, together with other SPS sequences from both dicot and monocot species (families A, B, and C). The spatio-temporal expression pattern analysis of MeSPS genes showed a tissue-specific and partially overlapping expression pattern, with the genes mainly expressed in source tissues during cassava growth and development. Correlation analysis revealed that the expression of MeSPS genes correlated positively with root starch content, indicating that the expression of MeSPS genes might accelerate the rate of starch accumulation in the roots of cassava plants.
Collapse
|
13
|
Huang T, Luo X, Fan Z, Yang Y, Wan W. Genome-wide identification and analysis of the sucrose synthase gene family in cassava (Manihot esculenta Crantz). Gene 2020; 769:145191. [PMID: 33007377 DOI: 10.1016/j.gene.2020.145191] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 09/11/2020] [Accepted: 09/24/2020] [Indexed: 11/29/2022]
Abstract
Sucrose synthase (SUS), a key enzyme of the sucrose metabolism pathway, is encoded by a multi-gene family in plants. To date, dozens of SUS gene families have been characterized in various plant genomes. However, only a few studies have performed comprehensive analyses in tropical crops like cassava (Manihot esculenta Crantz). In the present study, seven non-redundant members of the SUS gene family (MeSUS1-7) were identified and characterized from the cassava genome. The MeSUS genes were distributed on five chromosomes (Chr1, Chr2, Chr3, Chr14, and Chr16) and the encoded proteins could be classified into three major groups with other SUS proteins from both dicot and monocot species (SUS I, SUS II, and SUS III). The spatio-temporal expression profiles of MeSUS genes showed a developmental stage-dependent, partially overlapping pattern, mainly expressed in the source and sink tissues. Cold and drought treatments significantly induced the expressions of MeSUS2, MeSUS4, MeSUS6, and MeSUS7 and the activities of the encoded enzymes, indicating that these genes may play crucial roles in resistance against abiotic stresses. These results provide new insights into the multifaceted role of the SUS gene family members in various physiological processes, especially sucrose transport and starch accumulation in cassava roots.
Collapse
Affiliation(s)
- Tangwei Huang
- College of Agriculture, Guangxi University, Nanning 530004, China
| | - Xinglu Luo
- College of Agriculture, Guangxi University, Nanning 530004, China; State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Nanning 530004, China.
| | - Zhupeng Fan
- College of Agriculture, Guangxi University, Nanning 530004, China
| | - Yanni Yang
- College of Agriculture, Guangxi University, Nanning 530004, China
| | - Wen Wan
- College of Agriculture, Guangxi University, Nanning 530004, China
| |
Collapse
|
14
|
Gipson AB, Giloteaux L, Hanson MR, Bentolila S. Arabidopsis RanBP2-Type Zinc Finger Proteins Related to Chloroplast RNA Editing Factor OZ1. PLANTS 2020; 9:plants9030307. [PMID: 32121603 PMCID: PMC7154859 DOI: 10.3390/plants9030307] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 02/20/2020] [Accepted: 02/21/2020] [Indexed: 01/01/2023]
Abstract
OZ1, an RNA editing factor that controls the editing of 14 cytidine targets in Arabidopsis chloroplasts, contains two RanBP2-type zinc finger (Znf) domains. The RanBP2 Znf is a C4-type member of the broader zinc finger family with unique functions and an unusually diverse distribution in plants. The domain can mediate interactions with proteins or RNA and appears in protein types such as proteases, RNA editing factors, and chromatin modifiers; however, few characterized Arabidopsis proteins containing RanBP2 Znfs have been studied specifically with the domain in mind. In humans, RanBP2 Znf-containing proteins are involved in RNA splicing, transport, or transcription initiation. We present a phylogenetic overview of Arabidopsis RanBP2 Znf proteins and the functional niches that these proteins occupy in plants. OZ1 and its four-member family represent a branch of this family with major impact on the RNA biology of chloroplasts and mitochondria in Arabidopsis. We discuss what is known about other plant proteins carrying the RanBP2 Znf domain and point out how phylogenetic information can provide clues to functions of uncharacterized Znf proteins.
Collapse
|
15
|
Yan Z, Shi H, Liu Y, Jing M, Han Y. KHZ1 and KHZ2, novel members of the autonomous pathway, repress the splicing efficiency of FLC pre-mRNA in Arabidopsis. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:1375-1386. [PMID: 31701139 PMCID: PMC7031081 DOI: 10.1093/jxb/erz499] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Accepted: 11/06/2019] [Indexed: 05/03/2023]
Abstract
As one of the most important events during the life cycle of flowering plants, the floral transition is of crucial importance for plant propagation and requires the precise coordination of multiple endogenous and external signals. There have been at least four flowering pathways (i.e. photoperiod, vernalization, gibberellin, and autonomous) identified in Arabidopsis. We previously reported that two Arabidopsis RNA-binding proteins, KHZ1 and KHZ2, redundantly promote flowering. However, the underlying mechanism was unclear. Here, we found that the double mutant khz1 khz2 flowered late under both long-day and short-day conditions, but responded to vernalization and gibberellin treatments. The late-flowering phenotype was almost completely rescued by mutating FLOWERING LOCUS C (FLC) and fully rescued by overexpressing FLOWERING LOCUS T (FT). Additional experiments demonstrated that the KHZs could form homodimers or interact to form heterodimers, localized to nuclear dots, and repressed the splicing efficiency of FLC pre-mRNA. Together, these data indicate that the KHZs could promote flowering via the autonomous pathway by repressing the splicing efficiency of FLC pre-mRNA.
Collapse
Affiliation(s)
- Zongyun Yan
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Huiying Shi
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Yanan Liu
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Meng Jing
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Yuzhen Han
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, China
- Correspondence:
| |
Collapse
|
16
|
B-box Proteins in Arachis duranensis: Genome-Wide Characterization and Expression Profiles Analysis. AGRONOMY-BASEL 2019. [DOI: 10.3390/agronomy10010023] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
B-box (BBX) proteins are important factors involved in plant growth and developmental regulation, and they have been identified in many species. However, information on the characteristics and transcription patterns of BBX genes in wild peanut are limited. In this study, we identified and characterized 24 BBX genes from a wild peanut, Arachis duranensis. Many characteristics were analyzed, including chromosomal locations, phylogenetic relationships, and gene structures. Arachis duranensis B-box (AdBBX) proteins were grouped into five classes based on the diversity of their conserved domains: I (3 genes), II (4 genes), III (4 genes), IV (9 genes), and V (4 genes). Fifteen distinct motifs were found in the 24 AdBBX proteins. Duplication analysis revealed the presence of two interchromosomal duplicated gene pairs, from group II and IV. In addition, 95 kinds of cis-acting elements were found in the genes’ promoter regions, 53 of which received putative functional predictions. The numbers and types of cis-acting elements varied among different AdBBX promoters, and, as a result, AdBBX genes exhibited distinct expression patterns in different tissues. Transcriptional profiling combined with synteny analysis suggests that AdBBX8 may be a key factor involved in flowering time regulation. Our study will provide essential information for further functional investigation of AdBBX genes.
Collapse
|
17
|
Jin H, Tang X, Xing M, Zhu H, Sui J, Cai C, Li S. Molecular and transcriptional characterization of phosphatidyl ethanolamine-binding proteins in wild peanuts Arachis duranensis and Arachis ipaensis. BMC PLANT BIOLOGY 2019; 19:484. [PMID: 31706291 PMCID: PMC6842551 DOI: 10.1186/s12870-019-2113-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2019] [Accepted: 10/31/2019] [Indexed: 05/10/2023]
Abstract
BACKGROUND Phosphatidyl ethanolamine-binding proteins (PEBPs) are involved in the regulation of plant architecture and flowering time. The functions of PEBP genes have been studied in many plant species. However, little is known about the characteristics and expression profiles of PEBP genes in wild peanut species, Arachis duranensis and Arachis ipaensis, the diploid ancestors of cultivated peanuts. RESULTS In this study, genome-wide identification methods were used to identify and characterize a total of 32 peanut PEBP genes, 16 from each of the two wild peanut species, A. duranensis and A. ipaensis. These PEBP genes were classified into 3 groups (TERMINAL FLOWER1-like, FLOWERING LOCUS T-like, and MOTHER OF FT AND TFL1-like) based on their phylogenetic relationships. The gene structures, motifs, and chromosomal locations for each of these PEBPs were analyzed. In addition, 4 interchromosomal duplications and 1 tandem duplication were identified in A. duranensis, and 2 interchromosomal paralogs and 1 tandem paralog were identified in A. ipaensis. Ninety-five different cis-acting elements were identified in the PEBP gene promoter regions and most genes had different numbers and types of cis-elements. As a result, the transcription patterns of these PEBP genes varied in different tissues and under long day and short day conditions during different growth phases, indicating the functional diversities of PEBPs in different tissues and their potential functions in plant photoperiod dependent developmental pathways. Moreover, our analysis revealed that AraduF950M/AraduWY2NX in A. duranensis, and Araip344D4/Araip4V81G in A. ipaensis are good candidates for regulating plant architecture, and that Aradu80YRY, AraduYY72S, and AraduEHZ9Y in A. duranensis and AraipVEP8T in A. ipaensis may be key factors regulating flowering time. CONCLUSION Sixteen PEBP genes were identified and characterized from each of the two diploid wild peanut genomes, A. duranensis and A. ipaensis. Genetic characterization and spatio-temporal expression analysis support their importance in plant growth and development. These findings further our understanding of PEBP gene functions in plant species.
Collapse
Affiliation(s)
- Hanqi Jin
- College of Life Sciences, Key Lab of Plant Biotechnology in Universities of Shandong Province, Qingdao Agricultural University, Qingdao, 266109 China
| | - Xuemin Tang
- College of Life Sciences, Key Lab of Plant Biotechnology in Universities of Shandong Province, Qingdao Agricultural University, Qingdao, 266109 China
| | - Mengge Xing
- College of Life Sciences, Key Lab of Plant Biotechnology in Universities of Shandong Province, Qingdao Agricultural University, Qingdao, 266109 China
| | - Hong Zhu
- College of Agronomy, Qingdao Agricultural University, Qingdao, 266109 China
| | - Jiongming Sui
- College of Agronomy, Qingdao Agricultural University, Qingdao, 266109 China
| | - Chunmei Cai
- College of Life Sciences, Key Lab of Plant Biotechnology in Universities of Shandong Province, Qingdao Agricultural University, Qingdao, 266109 China
| | - Shuai Li
- College of Life Sciences, Key Lab of Plant Biotechnology in Universities of Shandong Province, Qingdao Agricultural University, Qingdao, 266109 China
| |
Collapse
|
18
|
Wilhelmsson PKI, Chandler JO, Fernandez-Pozo N, Graeber K, Ullrich KK, Arshad W, Khan S, Hofberger JA, Buchta K, Edger PP, Pires JC, Schranz ME, Leubner-Metzger G, Rensing SA. Usability of reference-free transcriptome assemblies for detection of differential expression: a case study on Aethionema arabicum dimorphic seeds. BMC Genomics 2019; 20:95. [PMID: 30700268 PMCID: PMC6354389 DOI: 10.1186/s12864-019-5452-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Accepted: 01/14/2019] [Indexed: 12/31/2022] Open
Abstract
Background RNA-sequencing analysis is increasingly utilized to study gene expression in non-model organisms without sequenced genomes. Aethionema arabicum (Brassicaceae) exhibits seed dimorphism as a bet-hedging strategy – producing both a less dormant mucilaginous (M+) seed morph and a more dormant non-mucilaginous (NM) seed morph. Here, we compared de novo and reference-genome based transcriptome assemblies to investigate Ae. arabicum seed dimorphism and to evaluate the reference-free versus -dependent approach for identifying differentially expressed genes (DEGs). Results A de novo transcriptome assembly was generated using sequences from M+ and NM Ae. arabicum dry seed morphs. The transcripts of the de novo assembly contained 63.1% complete Benchmarking Universal Single-Copy Orthologs (BUSCO) compared to 90.9% for the transcripts of the reference genome. DEG detection used the strict consensus of three methods (DESeq2, edgeR and NOISeq). Only 37% of 1533 differentially expressed de novo assembled transcripts paired with 1876 genome-derived DEGs. Gene Ontology (GO) terms distinguished the seed morphs: the terms translation and nucleosome assembly were overrepresented in DEGs higher in abundance in M+ dry seeds, whereas terms related to mRNA processing and transcription were overrepresented in DEGs higher in abundance in NM dry seeds. DEGs amongst these GO terms included ribosomal proteins and histones (higher in M+), RNA polymerase II subunits and related transcription and elongation factors (higher in NM). Expression of the inferred DEGs and other genes associated with seed maturation (e.g. those encoding late embryogenesis abundant proteins and transcription factors regulating seed development and maturation such as ABI3, FUS3, LEC1 and WRI1 homologs) were put in context with Arabidopsis thaliana seed maturation and indicated that M+ seeds may desiccate and mature faster than NM. The 1901 transcriptomic DEG set GO-terms had almost 90% overlap with the 2191 genome-derived DEG GO-terms. Conclusions Whilst there was only modest overlap of DEGs identified in reference-free versus -dependent approaches, the resulting GO analysis was concordant in both approaches. The identified differences in dry seed transcriptomes suggest mechanisms underpinning previously identified contrasts between morphology and germination behaviour of M+ and NM seeds. Electronic supplementary material The online version of this article (10.1186/s12864-019-5452-4) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Per K I Wilhelmsson
- Plant Cell Biology, Faculty of Biology, University of Marburg, 35043, Marburg, Germany
| | - Jake O Chandler
- School of Biological Sciences, Royal Holloway University of London, Egham, Surrey, TW20 0EX, UK
| | - Noe Fernandez-Pozo
- Plant Cell Biology, Faculty of Biology, University of Marburg, 35043, Marburg, Germany
| | - Kai Graeber
- School of Biological Sciences, Royal Holloway University of London, Egham, Surrey, TW20 0EX, UK
| | - Kristian K Ullrich
- Plant Cell Biology, Faculty of Biology, University of Marburg, 35043, Marburg, Germany.,Present Address: Max Planck Institute for Evolutionary Biology, August-Thienemann-Straße 2, 24306, Ploen, Germany
| | - Waheed Arshad
- School of Biological Sciences, Royal Holloway University of London, Egham, Surrey, TW20 0EX, UK
| | - Safina Khan
- School of Biological Sciences, Royal Holloway University of London, Egham, Surrey, TW20 0EX, UK
| | - Johannes A Hofberger
- Biosystematics Group, Wageningen University, Wageningen, 6708 PB, The Netherlands
| | - Karl Buchta
- Plant Cell Biology, Faculty of Biology, University of Marburg, 35043, Marburg, Germany
| | - Patrick P Edger
- Department of Horticulture, Michigan State University, East Lansing, MI, 48864, USA
| | - J Chris Pires
- Division of Biological Sciences, University of Missouri, Columbia, MO, 65211, USA
| | - M Eric Schranz
- Biosystematics Group, Wageningen University, Wageningen, 6708 PB, The Netherlands
| | - Gerhard Leubner-Metzger
- School of Biological Sciences, Royal Holloway University of London, Egham, Surrey, TW20 0EX, UK. .,Laboratory of Growth Regulators, Centre of the Region Haná for Biotechnological and Agricultural Research, Palacký University and Institute of Experimental Botany, Academy of Sciences of the Czech Republic, 78371, Olomouc, Czech Republic.
| | - Stefan A Rensing
- Plant Cell Biology, Faculty of Biology, University of Marburg, 35043, Marburg, Germany. .,BIOSS Centre for Biological Signalling Studies, University of Freiburg, Freiburg, Germany.
| |
Collapse
|
19
|
Wilhelmsson PKI, Chandler JO, Fernandez-Pozo N, Graeber K, Ullrich KK, Arshad W, Khan S, Hofberger JA, Buchta K, Edger PP, Pires JC, Schranz ME, Leubner-Metzger G, Rensing SA. Usability of reference-free transcriptome assemblies for detection of differential expression: a case study on Aethionema arabicum dimorphic seeds. BMC Genomics 2019. [PMID: 30700268 DOI: 10.1186/s12864-019-5452-5454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/10/2023] Open
Abstract
BACKGROUND RNA-sequencing analysis is increasingly utilized to study gene expression in non-model organisms without sequenced genomes. Aethionema arabicum (Brassicaceae) exhibits seed dimorphism as a bet-hedging strategy - producing both a less dormant mucilaginous (M+) seed morph and a more dormant non-mucilaginous (NM) seed morph. Here, we compared de novo and reference-genome based transcriptome assemblies to investigate Ae. arabicum seed dimorphism and to evaluate the reference-free versus -dependent approach for identifying differentially expressed genes (DEGs). RESULTS A de novo transcriptome assembly was generated using sequences from M+ and NM Ae. arabicum dry seed morphs. The transcripts of the de novo assembly contained 63.1% complete Benchmarking Universal Single-Copy Orthologs (BUSCO) compared to 90.9% for the transcripts of the reference genome. DEG detection used the strict consensus of three methods (DESeq2, edgeR and NOISeq). Only 37% of 1533 differentially expressed de novo assembled transcripts paired with 1876 genome-derived DEGs. Gene Ontology (GO) terms distinguished the seed morphs: the terms translation and nucleosome assembly were overrepresented in DEGs higher in abundance in M+ dry seeds, whereas terms related to mRNA processing and transcription were overrepresented in DEGs higher in abundance in NM dry seeds. DEGs amongst these GO terms included ribosomal proteins and histones (higher in M+), RNA polymerase II subunits and related transcription and elongation factors (higher in NM). Expression of the inferred DEGs and other genes associated with seed maturation (e.g. those encoding late embryogenesis abundant proteins and transcription factors regulating seed development and maturation such as ABI3, FUS3, LEC1 and WRI1 homologs) were put in context with Arabidopsis thaliana seed maturation and indicated that M+ seeds may desiccate and mature faster than NM. The 1901 transcriptomic DEG set GO-terms had almost 90% overlap with the 2191 genome-derived DEG GO-terms. CONCLUSIONS Whilst there was only modest overlap of DEGs identified in reference-free versus -dependent approaches, the resulting GO analysis was concordant in both approaches. The identified differences in dry seed transcriptomes suggest mechanisms underpinning previously identified contrasts between morphology and germination behaviour of M+ and NM seeds.
Collapse
Affiliation(s)
- Per K I Wilhelmsson
- Plant Cell Biology, Faculty of Biology, University of Marburg, 35043, Marburg, Germany
| | - Jake O Chandler
- School of Biological Sciences, Royal Holloway University of London, Egham, Surrey, TW20 0EX, UK
| | - Noe Fernandez-Pozo
- Plant Cell Biology, Faculty of Biology, University of Marburg, 35043, Marburg, Germany
| | - Kai Graeber
- School of Biological Sciences, Royal Holloway University of London, Egham, Surrey, TW20 0EX, UK
| | - Kristian K Ullrich
- Plant Cell Biology, Faculty of Biology, University of Marburg, 35043, Marburg, Germany
- Present Address: Max Planck Institute for Evolutionary Biology, August-Thienemann-Straße 2, 24306, Ploen, Germany
| | - Waheed Arshad
- School of Biological Sciences, Royal Holloway University of London, Egham, Surrey, TW20 0EX, UK
| | - Safina Khan
- School of Biological Sciences, Royal Holloway University of London, Egham, Surrey, TW20 0EX, UK
| | - Johannes A Hofberger
- Biosystematics Group, Wageningen University, Wageningen, 6708 PB, The Netherlands
| | - Karl Buchta
- Plant Cell Biology, Faculty of Biology, University of Marburg, 35043, Marburg, Germany
| | - Patrick P Edger
- Department of Horticulture, Michigan State University, East Lansing, MI, 48864, USA
| | - J Chris Pires
- Division of Biological Sciences, University of Missouri, Columbia, MO, 65211, USA
| | - M Eric Schranz
- Biosystematics Group, Wageningen University, Wageningen, 6708 PB, The Netherlands
| | - Gerhard Leubner-Metzger
- School of Biological Sciences, Royal Holloway University of London, Egham, Surrey, TW20 0EX, UK.
- Laboratory of Growth Regulators, Centre of the Region Haná for Biotechnological and Agricultural Research, Palacký University and Institute of Experimental Botany, Academy of Sciences of the Czech Republic, 78371, Olomouc, Czech Republic.
| | - Stefan A Rensing
- Plant Cell Biology, Faculty of Biology, University of Marburg, 35043, Marburg, Germany.
- BIOSS Centre for Biological Signalling Studies, University of Freiburg, Freiburg, Germany.
| |
Collapse
|
20
|
Qi HD, Lin Y, Ren QP, Wang YY, Xiong F, Wang XL. RNA Splicing of FLC Modulates the Transition to Flowering. FRONTIERS IN PLANT SCIENCE 2019; 10:1625. [PMID: 31921267 PMCID: PMC6928127 DOI: 10.3389/fpls.2019.01625] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Accepted: 11/19/2019] [Indexed: 05/10/2023]
Abstract
Flowering is a critical stage of plant development and is closely correlated with seed production and crop yield. Flowering transition is regulated by complex genetic networks in response to endogenous and environmental signals. FLOWERING LOCUS C (FLC) is a central repressor in the flowering transition of Arabidopsis thaliana. The regulation of FLC expression is well studied at transcriptional and post-transcriptional levels. A subset of antisense transcripts from FLC locus, collectively termed cold-induced long antisense intragenic RNAs (COOLAIR), repress FLC expression under cold exposure. Recent studies have provided important insights into the alternative splicing of COOLAIR and FLC sense transcripts in response to developmental and environmental cues. Herein, at the 20th anniversary of FLC functional identification, we summarise new research advances in the alternative splicing of FLC sense and antisense transcripts that regulates flowering.
Collapse
Affiliation(s)
- Hao-Dong Qi
- National Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, China
| | - Yi Lin
- National Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, China
| | - Qiu-Ping Ren
- College of Agronomy, Liaocheng University, Liaocheng, China
| | - Yu-Yi Wang
- National Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, China
| | - Feng Xiong
- National Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, China
| | - Xiu-Ling Wang
- National Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, China
- *Correspondence: Xiu-Ling Wang,
| |
Collapse
|