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Xiang X, Deng Q, Zheng Y, He Y, Ji D, Vejlupkova Z, Fowler JE, Zhou L. Genome-wide investigation of the LARP gene family: focus on functional identification and transcriptome profiling of ZmLARP6c1 in maize pollen. BMC PLANT BIOLOGY 2024; 24:348. [PMID: 38684961 PMCID: PMC11057080 DOI: 10.1186/s12870-024-05054-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Accepted: 04/19/2024] [Indexed: 05/02/2024]
Abstract
BACKGROUND The La-related proteins (LARPs) are a superfamily of RNA-binding proteins associated with regulation of gene expression. Evidence points to an important role for post-transcriptional control of gene expression in germinating pollen tubes, which could be aided by RNA-binding proteins. RESULTS In this study, a genome-wide investigation of the LARP proteins in eight plant species was performed. The LARP proteins were classified into three families based on a phylogenetic analysis. The gene structure, conserved motifs, cis-acting elements in the promoter, and gene expression profiles were investigated to provide a comprehensive overview of the evolutionary history and potential functions of ZmLARP genes in maize. Moreover, ZmLARP6c1 was specifically expressed in pollen and ZmLARP6c1 was localized to the nucleus and cytoplasm in maize protoplasts. Overexpression of ZmLARP6c1 enhanced the percentage pollen germination compared with that of wild-type pollen. In addition, transcriptome profiling analysis revealed that differentially expressed genes included PABP homologous genes and genes involved in jasmonic acid and abscisic acid biosynthesis, metabolism, signaling pathways and response in a Zmlarp6c1::Ds mutant and ZmLARP6c1-overexpression line compared with the corresponding wild type. CONCLUSIONS The findings provide a basis for further evolutionary and functional analyses, and provide insight into the critical regulatory function of ZmLARP6c1 in maize pollen germination.
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Affiliation(s)
- Xiaoqin Xiang
- College of Agronomy and Biotechnology, Maize Research Institute, Southwest University, Beibei, Chongqing, 400715, China
| | - Qianxia Deng
- College of Agronomy and Biotechnology, Maize Research Institute, Southwest University, Beibei, Chongqing, 400715, China
| | - Yi Zheng
- College of Agronomy and Biotechnology, Maize Research Institute, Southwest University, Beibei, Chongqing, 400715, China
| | - Yi He
- College of Agronomy and Biotechnology, Maize Research Institute, Southwest University, Beibei, Chongqing, 400715, China
| | - Dongpu Ji
- College of Agronomy and Biotechnology, Maize Research Institute, Southwest University, Beibei, Chongqing, 400715, China
| | - Zuzana Vejlupkova
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, 97331, USA
| | - John E Fowler
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, 97331, USA
| | - Lian Zhou
- College of Agronomy and Biotechnology, Maize Research Institute, Southwest University, Beibei, Chongqing, 400715, China.
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Chongqing, 400715, China.
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2
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Chettoor AM, Yang B, Evans MMS. Control of cellularization, nuclear localization, and antipodal cell cluster development in maize embryo sacs. Genetics 2023; 225:iyad101. [PMID: 37232380 DOI: 10.1093/genetics/iyad101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 03/30/2023] [Accepted: 05/15/2023] [Indexed: 05/27/2023] Open
Abstract
The maize female gametophyte contains four cell types: two synergids, an egg cell, a central cell, and a variable number of antipodal cells. In maize, these cells are produced after three rounds of free-nuclear divisions followed by cellularization, differentiation, and proliferation of the antipodal cells. Cellularization of the eight-nucleate syncytium produces seven cells with two polar nuclei in the central cell. Nuclear localization is tightly controlled in the embryo sac. This leads to precise allocation of the nuclei into the cells upon cellularization. Nuclear positioning within the syncytium is highly correlated with their identity after cellularization. Two mutants are described with extra polar nuclei, abnormal antipodal cell morphology, and reduced antipodal cell number, as well as frequent loss of antipodal cell marker expression. Mutations in one of these genes, indeterminate gametophyte2 encoding a MICROTUBULE ASSOCIATED PROTEIN65-3 homolog, shows a requirement for MAP65-3 in cellularization of the syncytial embryo sac as well as for normal seed development. The timing of the effects of ig2 suggests that the identity of the nuclei in the syncytial female gametophyte can be changed very late before cellularization.
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Affiliation(s)
- Antony M Chettoor
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA 94305, USA
| | - Bing Yang
- Donald Danforth Plant Science Center, St. Louis, MO 63132, USA
- Division of Plant Science and Technology, Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA
| | - Matthew M S Evans
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA 94305, USA
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3
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Singh R, Shankar R, Yadav SK, Kumar V. Transcriptome analysis of ovules offers early developmental clues after fertilization in Cicer arietinum L.. 3 Biotech 2023; 13:177. [PMID: 37188294 PMCID: PMC10175530 DOI: 10.1007/s13205-023-03599-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 04/29/2023] [Indexed: 05/17/2023] Open
Abstract
Chickpea (Cicer arietinum L.) seeds are valued for their nutritional scores and limited information on the molecular mechanisms of chickpea fertilization and seed development is available. In the current work, comparative transcriptome analysis was performed on two different stages of chickpea ovules (pre- and post-fertilization) to identify key regulatory transcripts. Two-staged transcriptome sequencing was generated and over 208 million reads were mapped to quantify transcript abundance during fertilization events. Mapping to the reference genome showed that the majority (92.88%) of high-quality Illumina reads were aligned to the chickpea genome. Reference-guided genome and transcriptome assembly yielded a total of 28,783 genes. Of these, 3399 genes were differentially expressed after the fertilization event. These involve upregulated genes including a protease-like secreted in CO(2) response (LOC101500970), amino acid permease 4-like (LOC101506539), and downregulated genes MYB-related protein 305-like (LOC101493897), receptor like protein 29 (LOC101491695). WGCNA analysis and pairwise comparison of datasets, successfully constructed four co-expression modules. Transcription factor families including bHLH, MYB, MYB-related, C2H2 zinc finger, ERF, WRKY and NAC transcription factor were also found to be activated after fertilization. Activation of these genes and transcription factors results in the accumulation of carbohydrates and proteins by enhancing their trafficking and biosynthesis. Total 17 differentially expressed genes, were randomly selected for qRT-PCR for validation of transcriptome analysis and showed statistically significant correlations with the transcriptome data. Our findings provide insights into the regulatory mechanisms underlying changes in fertilized chickpea ovules. This work may come closer to a comprehensive understanding of the mechanisms that initiate developmental events in chickpea seeds after fertilization. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-023-03599-8.
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Affiliation(s)
- Reetu Singh
- Department of Botany, School of Basic Sciences, Central University of Punjab, Bathinda, 151001 India
| | - Rama Shankar
- Department of Paediatrics and Human Development, Michigan State University, Grand Rapids, MI 49503 USA
| | | | - Vinay Kumar
- Department of Botany, School of Basic Sciences, Central University of Punjab, Bathinda, 151001 India
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4
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Birchler JA, Yang H. The multiple fates of gene duplications: Deletion, hypofunctionalization, subfunctionalization, neofunctionalization, dosage balance constraints, and neutral variation. THE PLANT CELL 2022; 34:2466-2474. [PMID: 35253876 PMCID: PMC9252495 DOI: 10.1093/plcell/koac076] [Citation(s) in RCA: 84] [Impact Index Per Article: 42.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 02/17/2022] [Indexed: 05/13/2023]
Abstract
Gene duplications have long been recognized as a contributor to the evolution of genes with new functions. Multiple copies of genes can result from tandem duplication, from transposition to new chromosomes, or from whole-genome duplication (polyploidy). The most common fate is that one member of the pair is deleted to return the gene to the singleton state. Other paths involve the reduced expression of both copies (hypofunctionalization) that are held in duplicate to maintain sufficient quantity of function. The two copies can split functions (subfunctionalization) or can diverge to generate a new function (neofunctionalization). Retention of duplicates resulting from doubling of the whole genome occurs for genes involved with multicomponent interactions such as transcription factors and signal transduction components. In contrast, these classes of genes are underrepresented in small segmental duplications. This complementary pattern suggests that the balance of interactors affects the fate of the duplicate pair. We discuss the different mechanisms that maintain duplicated genes, which may change over time and intersect.
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Affiliation(s)
- James A Birchler
- Division of Biological Sciences, University of Missouri, Columbia, Missouri 65211, USA
| | - Hua Yang
- Division of Biological Sciences, University of Missouri, Columbia, Missouri 65211, USA
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5
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Xu Q, Wu L, Luo Z, Zhang M, Lai J, Li L, Springer NM, Li Q. DNA demethylation affects imprinted gene expression in maize endosperm. Genome Biol 2022; 23:77. [PMID: 35264226 PMCID: PMC8905802 DOI: 10.1186/s13059-022-02641-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 02/23/2022] [Indexed: 11/28/2022] Open
Abstract
Background DNA demethylation occurs in many species and is involved in diverse biological processes. However, the occurrence and role of DNA demethylation in maize remain unknown. Results We analyze loss-of-function mutants of two major genes encoding DNA demethylases. No significant change in DNA methylation has been detected in these mutants. However, we detect increased DNA methylation levels in the mutants around genes and some transposons. The increase in DNA methylation is accompanied by alteration in gene expression, with a tendency to show downregulation, especially for the genes that are preferentially expressed in endosperm. Imprinted expression of both maternally and paternally expressed genes changes in F1 hybrid with the mutant as female and the wild-type as male parental line, but not in the reciprocal hybrid. This alteration in gene expression is accompanied by allele-specific DNA methylation differences, suggesting that removal of DNA methylation of the maternal allele is required for the proper expression of these imprinted genes. Finally, we demonstrate that hypermethylation in the double mutant is associated with reduced binding of transcription factor to its target, and altered gene expression. Conclusions Our results suggest that active removal of DNA methylation is important for transcription factor binding and proper gene expression in maize endosperm.
Supplementary Information The online version contains supplementary material available at 10.1186/s13059-022-02641-x.
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Affiliation(s)
- Qiang Xu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Leiming Wu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Zhixiang Luo
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Mei Zhang
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Nanxincun 20, Fragrant Hill, Beijing, 100093, China
| | - Jinsheng Lai
- State Key Laboratory of Plant Physiology and Biochemistry and National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100094, China
| | - Lin Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Nathan M Springer
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, MN, 55108, USA
| | - Qing Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China. .,Hubei Hongshan Laboratory, Wuhan, 430070, China.
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6
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Abstract
Flowering plants alternate between multicellular haploid (gametophyte) and diploid (sporophyte) generations. Pollen actively transcribes its haploid genome, providing phenotypic diversity even among pollen grains from a single plant. In this study, we used allele-specific RNA sequencing of single pollen precursors to follow the shift to haploid expression in maize pollen. We observed widespread biallelic expression for 11 days after meiosis, indicating that transcripts synthesized by the diploid sporophyte persist long into the haploid phase. Subsequently, there was a rapid and global conversion to monoallelic expression at pollen mitosis I, driven by active new transcription from the haploid genome. Genes showed evidence of increased purifying selection if they were expressed after (but not before) pollen mitosis I. This work establishes the timing during which haploid selection may act in pollen.
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Affiliation(s)
- Brad Nelms
- Department of Plant Biology, University of Georgia, Athens, GA 30606, USA
| | - Virginia Walbot
- Department of Biology, Stanford University, Stanford, CA 94305, USA
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7
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Williams JH. Consequences of whole genome duplication for 2n pollen performance. PLANT REPRODUCTION 2021; 34:321-334. [PMID: 34302535 DOI: 10.1007/s00497-021-00426-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 07/17/2021] [Indexed: 06/13/2023]
Abstract
The vegetative cell of the angiosperm male gametophyte (pollen) functions as a free-living, single-celled organism that both produces and transports sperm to egg. Whole-genome duplication (WGD) should have strong effects on pollen because of the haploid to diploid transition and because of both genetic and epigenetic effects on cell-level phenotypes. To disentangle historical effects of WGD on pollen performance, studies can compare 1n pollen from diploids to neo-2n pollen from diploids and synthetic autotetraploids to older 2n pollen from established neo-autotetraploids. WGD doubles both gene number and bulk nuclear DNA mass, and a substantial proportion of diploid and autotetraploid heterozygosity can be transmitted to 2n pollen. Relative to 1n pollen, 2n pollen can exhibit heterosis due to higher gene dosage, higher heterozygosity and new allelic interactions. Doubled genome size also has consequences for gene regulation and expression as well as epigenetic effects on cell architecture. Pollen volume doubling is a universal effect of WGD, whereas an increase in aperture number is common among taxa with simultaneous microsporogenesis and pored apertures, mostly eudicots. WGD instantly affects numerous evolved compromises among mature pollen functional traits and these are rapidly shaped by highly diverse tissue interactions and pollen competitive environments in the early post-WGD generations. 2n pollen phenotypes generally incur higher performance costs, and the degree to which these are met or evolve by scaling up provisioning and metabolic vigor needs further study.
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Affiliation(s)
- Joseph H Williams
- Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, TN, 37996, USA.
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8
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Su H, Liang J, Abou-Elwafa SF, Cheng H, Dou D, Ren Z, Xie J, Chen Z, Gao F, Ku L, Chen Y. ZmCCT regulates photoperiod-dependent flowering and response to stresses in maize. BMC PLANT BIOLOGY 2021; 21:453. [PMID: 34615461 PMCID: PMC8493678 DOI: 10.1186/s12870-021-03231-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Accepted: 09/23/2021] [Indexed: 05/30/2023]
Abstract
BACKGROUND Appropriate flowering time is very important to the success of modern agriculture. Maize (Zea mays L.) is a major cereal crop, originated in tropical areas, with photoperiod sensitivity. Which is an important obstacle to the utilization of tropical/subtropical germplasm resources in temperate regions. However, the study on the regulation mechanism of photoperiod sensitivity of maize is still in the early stage. Although it has been previously reported that ZmCCT is involved in the photoperiod response and delays maize flowering time under long-day conditions, the underlying mechanism remains unclear. RESULTS Here, we showed that ZmCCT overexpression delays flowering time and confers maize drought tolerance under LD conditions. Implementing the Gal4-LexA/UAS system identified that ZmCCT has a transcriptional inhibitory activity, while the yeast system showed that ZmCCT has a transcriptional activation activity. DAP-Seq analysis and EMSA indicated that ZmCCT mainly binds to promoters containing the novel motifs CAAAAATC and AAATGGTC. DAP-Seq and RNA-Seq analysis showed that ZmCCT could directly repress the expression of ZmPRR5 and ZmCOL9, and promote the expression of ZmRVE6 to delay flowering under long-day conditions. Moreover, we also demonstrated that ZmCCT directly binds to the promoters of ZmHY5, ZmMPK3, ZmVOZ1 and ZmARR16 and promotes the expression of ZmHY5 and ZmMPK3, but represses ZmVOZ1 and ZmARR16 to enhance stress resistance. Additionally, ZmCCT regulates a set of genes associated with plant development. CONCLUSIONS ZmCCT has dual functions in regulating maize flowering time and stress response under LD conditions. ZmCCT negatively regulates flowering time and enhances maize drought tolerance under LD conditions. ZmCCT represses most flowering time genes to delay flowering while promotes most stress response genes to enhance stress tolerance. Our data contribute to a comprehensive understanding of the regulatory mechanism of ZmCCT in controlling maize flowering time and stress response.
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Affiliation(s)
- Huihui Su
- Synergetic Innovation Center of Henan Grain Crops and National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, 450046, Henan, China
| | - Jiachen Liang
- Synergetic Innovation Center of Henan Grain Crops and National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, 450046, Henan, China
| | | | - Haiyang Cheng
- Synergetic Innovation Center of Henan Grain Crops and National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, 450046, Henan, China
| | - Dandan Dou
- Synergetic Innovation Center of Henan Grain Crops and National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, 450046, Henan, China
| | - Zhenzhen Ren
- Synergetic Innovation Center of Henan Grain Crops and National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, 450046, Henan, China
| | - Jiarong Xie
- Synergetic Innovation Center of Henan Grain Crops and National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, 450046, Henan, China
| | - Zhihui Chen
- Synergetic Innovation Center of Henan Grain Crops and National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, 450046, Henan, China
| | - Fengran Gao
- Synergetic Innovation Center of Henan Grain Crops and National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, 450046, Henan, China
| | - Lixia Ku
- Synergetic Innovation Center of Henan Grain Crops and National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, 450046, Henan, China.
| | - Yanhui Chen
- Synergetic Innovation Center of Henan Grain Crops and National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, 450046, Henan, China.
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9
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Rutley N, Poidevin L, Doniger T, Tillett RL, Rath A, Forment J, Luria G, Schlauch KA, Ferrando A, Harper JF, Miller G. Characterization of novel pollen-expressed transcripts reveals their potential roles in pollen heat stress response in Arabidopsis thaliana. PLANT REPRODUCTION 2021; 34:61-78. [PMID: 33459869 PMCID: PMC7902599 DOI: 10.1007/s00497-020-00400-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Accepted: 11/17/2020] [Indexed: 05/27/2023]
Abstract
Arabidopsis pollen transcriptome analysis revealed new intergenic transcripts of unknown function, many of which are long non-coding RNAs, that may function in pollen-specific processes, including the heat stress response. The male gametophyte is the most heat sensitive of all plant tissues. In recent years, long noncoding RNAs (lncRNAs) have emerged as important components of cellular regulatory networks involved in most biological processes, including response to stress. While examining RNAseq datasets of developing and germinating Arabidopsis thaliana pollen exposed to heat stress (HS), we identified 66 novel and 246 recently annotated intergenic expressed loci (XLOCs) of unknown function, with the majority encoding lncRNAs. Comparison with HS in cauline leaves and other RNAseq experiments indicated that 74% of the 312 XLOCs are pollen-specific, and at least 42% are HS-responsive. Phylogenetic analysis revealed that 96% of the genes evolved recently in Brassicaceae. We found that 50 genes are putative targets of microRNAs and that 30% of the XLOCs contain small open reading frames (ORFs) with homology to protein sequences. Finally, RNAseq of ribosome-protected RNA fragments together with predictions of periodic footprint of the ribosome P-sites indicated that 23 of these ORFs are likely to be translated. Our findings indicate that many of the 312 unknown genes might be functional and play a significant role in pollen biology, including the HS response.
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Affiliation(s)
- Nicholas Rutley
- The Mina and Everard Goodman Faculty of Life Sciences, Bar Ilan University, 5290002, Ramat-Gan, Israel
| | - Laetitia Poidevin
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Cient́́if́icas-Universitat Politècnica de València, Valencia, Spain
| | - Tirza Doniger
- The Mina and Everard Goodman Faculty of Life Sciences, Bar Ilan University, 5290002, Ramat-Gan, Israel
| | - Richard L Tillett
- Department of Biochemistry and Molecular Biology, University of Nevada at Reno, Reno, NV, 89557, USA
- Nevada INBRE Bioinformatics Core, University of Nevada at Reno, Reno, NV, 89557, USA
| | - Abhishek Rath
- The Mina and Everard Goodman Faculty of Life Sciences, Bar Ilan University, 5290002, Ramat-Gan, Israel
| | - Javier Forment
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Cient́́if́icas-Universitat Politècnica de València, Valencia, Spain
| | - Gilad Luria
- The Mina and Everard Goodman Faculty of Life Sciences, Bar Ilan University, 5290002, Ramat-Gan, Israel
| | - Karen A Schlauch
- Institute of Health Innovation, Desert Research Institute, Department of Pharmacology, University of Nevada at Reno, Reno, NV, 89557, USA
| | - Alejandro Ferrando
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Cient́́if́icas-Universitat Politècnica de València, Valencia, Spain
| | - Jeffery F Harper
- Department of Biochemistry and Molecular Biology, University of Nevada at Reno, Reno, NV, 89557, USA
| | - Gad Miller
- The Mina and Everard Goodman Faculty of Life Sciences, Bar Ilan University, 5290002, Ramat-Gan, Israel.
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10
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Stephan OOH. Implications of ionizing radiation on pollen performance in comparison with diverse models of polar cell growth. PLANT, CELL & ENVIRONMENT 2021; 44:665-691. [PMID: 33124689 DOI: 10.1111/pce.13929] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 10/21/2020] [Accepted: 10/22/2020] [Indexed: 06/11/2023]
Abstract
Research concerning the effects of ionizing radiation (IR) on plant systems is essential for numerous aspects of human society, as for instance, in terms of agriculture and plant breeding, but additionally for elucidating consequences of radioactive contamination of the ecosphere. This comprehensive survey analyses effects of x- and γ-irradiation on male gametophytes comprising primarily in vitro but also in vivo data of diverse plant species. The IR-dose range for pollen performance was compiled and 50% inhibition doses (ID50 ) for germination and tube growth were comparatively related to physiological characteristics of the microgametophyte. Factors influencing IR-susceptibility of mature pollen and polarized tube growth were evaluated, such as dose-rate, environmental conditions, or species-related variations. In addition, all available reports suggesting bio-positive IR-effects particularly on pollen performance were examined. Most importantly, for the first time influences of IR specifically on diverse phylogenetic models of polar cell growth were comparatively analysed, and thus demonstrated that the gametophytic system of pollen is extremely resistant to IR, more than plant sporophytes and especially much more than comparable animal cells. Beyond that, this study develops hypotheses regarding a molecular basis for the extreme IR-resistance of the plant microgametophyte and highlights its unique rank among organismal systems.
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Affiliation(s)
- Octavian O H Stephan
- Department of Biology, Friedrich-Alexander University of Erlangen-Nuremberg, Erlangen, Germany
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11
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Zhou L, Vejlupkova Z, Warman C, Fowler JE. A Maize Male Gametophyte-Specific Gene Encodes ZmLARP6c1, a Potential RNA-Binding Protein Required for Competitive Pollen Tube Growth. FRONTIERS IN PLANT SCIENCE 2021; 12:635244. [PMID: 33719310 PMCID: PMC7947365 DOI: 10.3389/fpls.2021.635244] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 02/08/2021] [Indexed: 06/12/2023]
Abstract
Members of the La-related protein family (LARPs) contain a conserved La module, which has been associated with RNA-binding activity. Expression of the maize gene GRMZM2G323499/Zm00001d018613, a member of the LARP family, is highly specific to pollen, based on both transcriptomic and proteomic assays. This suggests a pollen-specific RNA regulatory function for the protein, designated ZmLARP6c1 based on sequence similarity to the LARP6 subfamily in Arabidopsis. To test this hypothesis, a Ds-GFP transposable element insertion in the ZmLarp6c1 gene (tdsgR82C05) was obtained from the Dooner/Du mutant collection. Sequencing confirmed that the Ds-GFP insertion is in an exon, and thus likely interferes with ZmLARP6c1 function. Tracking inheritance of the insertion via its endosperm-expressed GFP indicated that the mutation was associated with reduced transmission from a heterozygous plant when crossed as a male (ranging from 0.5 to 26.5% transmission), but not as a female. Furthermore, this transmission defect was significantly alleviated when less pollen was applied to the silk, reducing competition between mutant and wild-type pollen. Pollen grain diameter measurements and nuclei counts showed no significant differences between wild-type and mutant pollen. However, in vitro, mutant pollen tubes were significantly shorter than those from sibling wild-type plants, and also displayed altered germination dynamics. These results are consistent with the idea that ZmLARP6c1 provides an important regulatory function during the highly competitive progamic phase of male gametophyte development following arrival of the pollen grain on the silk. The conditional, competitive nature of the Zmlarp6c1::Ds male sterility phenotype (i.e., reduced ability to produce progeny seed) points toward new possibilities for genetic control of parentage in crop production.
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Affiliation(s)
- Lian Zhou
- Maize Research Institute, College of Agronomy and Biotechnology, Southwest University, Chongqing, China
| | - Zuzana Vejlupkova
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States
| | - Cedar Warman
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States
| | - John E Fowler
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States
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12
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Beaudry FE, Rifkin JL, Barrett SC, Wright SI. Evolutionary Genomics of Plant Gametophytic Selection. PLANT COMMUNICATIONS 2020; 1:100115. [PMID: 33367268 PMCID: PMC7748008 DOI: 10.1016/j.xplc.2020.100115] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 10/17/2020] [Accepted: 10/22/2020] [Indexed: 05/26/2023]
Abstract
It has long been recognized that natural selection during the haploid gametophytic phase of the plant life cycle may have widespread importance for rates of evolution and the maintenance of genetic variation. Recent theoretical advances have further highlighted the significance of gametophytic selection for diverse evolutionary processes. Genomic approaches offer exciting opportunities to address key questions about the extent and effects of gametophytic selection on plant evolution and adaptation. Here, we review the progress and prospects for integrating functional and evolutionary genomics to test theoretical predictions, and to examine the importance of gametophytic selection on genetic diversity and rates of evolution. There is growing evidence that selection during the gametophyte phase of the plant life cycle has important effects on both gene and genome evolution and is likely to have important pleiotropic effects on the sporophyte. We discuss the opportunities to integrate comparative population genomics, genome-wide association studies, and experimental approaches to further distinguish how differential selection in the two phases of the plant life cycle contributes to genetic diversity and adaptive evolution.
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Affiliation(s)
- Felix E.G. Beaudry
- Department of Ecology and Evolutionary Biology, The University of Toronto, 25 Willcocks Street, Toronto, ON M5S 3B2, Canada
| | - Joanna L. Rifkin
- Department of Ecology and Evolutionary Biology, The University of Toronto, 25 Willcocks Street, Toronto, ON M5S 3B2, Canada
| | - Spencer C.H. Barrett
- Department of Ecology and Evolutionary Biology, The University of Toronto, 25 Willcocks Street, Toronto, ON M5S 3B2, Canada
| | - Stephen I. Wright
- Department of Ecology and Evolutionary Biology, The University of Toronto, 25 Willcocks Street, Toronto, ON M5S 3B2, Canada
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13
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Stable unmethylated DNA demarcates expressed genes and their cis-regulatory space in plant genomes. Proc Natl Acad Sci U S A 2020; 117:23991-24000. [PMID: 32879011 DOI: 10.1073/pnas.2010250117] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The genomic sequences of crops continue to be produced at a frenetic pace. It remains challenging to develop complete annotations of functional genes and regulatory elements in these genomes. Chromatin accessibility assays enable discovery of functional elements; however, to uncover the full portfolio of cis-elements would require profiling of many combinations of cell types, tissues, developmental stages, and environments. Here, we explore the potential to use DNA methylation profiles to develop more complete annotations. Using leaf tissue in maize, we define ∼100,000 unmethylated regions (UMRs) that account for 5.8% of the genome; 33,375 UMRs are found greater than 2 kb from genes. UMRs are highly stable in multiple vegetative tissues, and they capture the vast majority of accessible chromatin regions from leaf tissue. However, many UMRs are not accessible in leaf, and these represent regions with potential to become accessible in specific cell types or developmental stages. These UMRs often occur near genes that are expressed in other tissues and are enriched for binding sites of transcription factors. The leaf-inaccessible UMRs exhibit unique chromatin modification patterns and are enriched for chromatin interactions with nearby genes. The total UMR space in four additional monocots ranges from 80 to 120 megabases, which is remarkably similar considering the range in genome size of 271 megabases to 4.8 gigabases. In summary, based on the profile from a single tissue, DNA methylation signatures provide powerful filters to distill large genomes down to the small fraction of putative functional genes and regulatory elements.
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14
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Zhou P, Li Z, Magnusson E, Gomez Cano F, Crisp PA, Noshay JM, Grotewold E, Hirsch CN, Briggs SP, Springer NM. Meta Gene Regulatory Networks in Maize Highlight Functionally Relevant Regulatory Interactions. THE PLANT CELL 2020; 32:1377-1396. [PMID: 32184350 PMCID: PMC7203921 DOI: 10.1105/tpc.20.00080] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Revised: 03/06/2020] [Accepted: 03/16/2020] [Indexed: 05/22/2023]
Abstract
The regulation of gene expression is central to many biological processes. Gene regulatory networks (GRNs) link transcription factors (TFs) to their target genes and represent maps of potential transcriptional regulation. Here, we analyzed a large number of publically available maize (Zea mays) transcriptome data sets including >6000 RNA sequencing samples to generate 45 coexpression-based GRNs that represent potential regulatory relationships between TFs and other genes in different populations of samples (cross-tissue, cross-genotype, and tissue-and-genotype samples). While these networks are all enriched for biologically relevant interactions, different networks capture distinct TF-target associations and biological processes. By examining the power of our coexpression-based GRNs to accurately predict covarying TF-target relationships in natural variation data sets, we found that presence/absence changes rather than quantitative changes in TF gene expression are more likely associated with changes in target gene expression. Integrating information from our TF-target predictions and previous expression quantitative trait loci (eQTL) mapping results provided support for 68 TFs underlying 74 previously identified trans-eQTL hotspots spanning a variety of metabolic pathways. This study highlights the utility of developing multiple GRNs within a species to detect putative regulators of important plant pathways and provides potential targets for breeding or biotechnological applications.
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Affiliation(s)
- Peng Zhou
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, Minnesota 55108
| | - Zhi Li
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota 55108
| | - Erika Magnusson
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, Minnesota 55108
| | - Fabio Gomez Cano
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824
| | - Peter A Crisp
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, Minnesota 55108
| | - Jaclyn M Noshay
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, Minnesota 55108
| | - Erich Grotewold
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824
| | - Candice N Hirsch
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota 55108
| | - Steven P Briggs
- Division of Biological Sciences, University of California, San Diego, La Jolla, California 92093
| | - Nathan M Springer
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, Minnesota 55108
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15
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Warman C, Panda K, Vejlupkova Z, Hokin S, Unger-Wallace E, Cole RA, Chettoor AM, Jiang D, Vollbrecht E, Evans MMS, Slotkin RK, Fowler JE. High expression in maize pollen correlates with genetic contributions to pollen fitness as well as with coordinated transcription from neighboring transposable elements. PLoS Genet 2020; 16:e1008462. [PMID: 32236090 PMCID: PMC7112179 DOI: 10.1371/journal.pgen.1008462] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 02/27/2020] [Indexed: 12/20/2022] Open
Abstract
In flowering plants, gene expression in the haploid male gametophyte (pollen) is essential for sperm delivery and double fertilization. Pollen also undergoes dynamic epigenetic regulation of expression from transposable elements (TEs), but how this process interacts with gene expression is not clearly understood. To explore relationships among these processes, we quantified transcript levels in four male reproductive stages of maize (tassel primordia, microspores, mature pollen, and sperm cells) via RNA-seq. We found that, in contrast with vegetative cell-limited TE expression in Arabidopsis pollen, TE transcripts in maize accumulate as early as the microspore stage and are also present in sperm cells. Intriguingly, coordinate expression was observed between highly expressed protein-coding genes and their neighboring TEs, specifically in mature pollen and sperm cells. To investigate a potential relationship between elevated gene transcript level and pollen function, we measured the fitness cost (male-specific transmission defect) of GFP-tagged coding sequence insertion mutations in over 50 genes identified as highly expressed in the pollen vegetative cell, sperm cell, or seedling (as a sporophytic control). Insertions in seedling genes or sperm cell genes (with one exception) exhibited no difference from the expected 1:1 transmission ratio. In contrast, insertions in over 20% of vegetative cell genes were associated with significant reductions in fitness, showing a positive correlation of transcript level with non-Mendelian segregation when mutant. Insertions in maize gamete expressed2 (Zm gex2), the sole sperm cell gene with measured contributions to fitness, also triggered seed defects when crossed as a male, indicating a conserved role in double fertilization, given the similar phenotype previously demonstrated for the Arabidopsis ortholog GEX2. Overall, our study demonstrates a developmentally programmed and coordinated transcriptional activation of TEs and genes in pollen, and further identifies maize pollen as a model in which transcriptomic data have predictive value for quantitative phenotypes.
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Affiliation(s)
- Cedar Warman
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, United States of America
| | - Kaushik Panda
- Donald Danforth Plant Science Center, St. Louis, Missouri, United States of America
| | - Zuzana Vejlupkova
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, United States of America
| | - Sam Hokin
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California, United States of America
| | - Erica Unger-Wallace
- Department of Genetics Development and Cell Biology, Iowa State University, Ames, Iowa, United States of America
| | - Rex A. Cole
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, United States of America
| | - Antony M. Chettoor
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California, United States of America
| | - Duo Jiang
- Department of Statistics, Oregon State University, Corvallis, Oregon, United States of America
| | - Erik Vollbrecht
- Department of Genetics Development and Cell Biology, Iowa State University, Ames, Iowa, United States of America
- Bioinformatics and Computational Biology, Iowa State University, Ames, Iowa, United States of America
- Interdepartmental Genetics, Iowa State University, Ames, Iowa, United States of America
| | - Matthew M. S. Evans
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California, United States of America
| | - R. Keith Slotkin
- Donald Danforth Plant Science Center, St. Louis, Missouri, United States of America
| | - John E. Fowler
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, United States of America
- Center for Genome Research and Biocomputing, Oregon State University, Corvallis, Oregon, United States of America
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16
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Chai L, Yang Y, Yang H, Zhao Y, Wang H. Transcriptome analysis of genes expressed in the earthworm Eisenia fetida in response to cadmium exposure. CHEMOSPHERE 2020; 240:124902. [PMID: 31563721 DOI: 10.1016/j.chemosphere.2019.124902] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Revised: 09/15/2019] [Accepted: 09/17/2019] [Indexed: 06/10/2023]
Abstract
Eisenia fetida earthworm is an ecotoxicologically important test species to monitor various pollutants. However, there is a little knowledge about the effects of cadmium (Cd) on earthworms at the transcriptional level. Firstly, we exposed E. fetida to soils supplemented with different concentrations (10, 30, 60 mg/kg soil) of Cd. Moreover, we depicted the characterization of gene expressions with E. fetida using high-throughput profiling of gene expression. In addition, a comparison of the gene expression profiles between each Cd treatment group and the control group suggested that differential expressional genes (DEGs) mainly enriched in enzyme activity, metabolism, oxidative stress, regeneration and apoptosis pathways. 8 DEGs from these pathways had been selected randomly to confirm the data of RNA-seq. Among these DEGs, six genes (metallothionein-2, phytochelatin synthase 1a, CuZn superoxide dismutase, sex determining region Y-box 2, sex determining region Y-box 4b, TP53-regulated inhibitor of apoptosis 1-like) up-regulated and 2 genes (beta-1,4-endoglucanase, apoptosis-stimulating of p53 protein 2-like) down-regulated in response to Cd exposure. The alteration of them indicated that earthworms could reduce the toxicity and bioavailability of Cd in polluted soil ecosystems through different pathways. This work lays an important foundation for linking earthworm transcriptional level with the ecological risk of Cd in soil ecosystem.
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Affiliation(s)
- Lihong Chai
- School of Environmental Science and Engineering, Chang'an University, Xi'an, 710054, China; Key Laboratory of Subsurface Hydrology and Ecological Effect in Arid Region of Ministry of Education, Chang'an University, Xi'an, 710054, China; Shaanxi Key Laboratory of Land Consolidation, Xi'an, 710054, China.
| | - Yijie Yang
- School of Environmental Science and Engineering, Chang'an University, Xi'an, 710054, China; Key Laboratory of Subsurface Hydrology and Ecological Effect in Arid Region of Ministry of Education, Chang'an University, Xi'an, 710054, China
| | - Hongyu Yang
- College of Life Sciences, Shaanxi Normal University, Xi'an, 710119, China
| | - Yonghua Zhao
- Shaanxi Key Laboratory of Land Consolidation, Xi'an, 710054, China
| | - Hongyuan Wang
- College of Life Sciences, Shaanxi Normal University, Xi'an, 710119, China
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17
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Kim YJ, Zhang D, Jung KH. Molecular Basis of Pollen Germination in Cereals. TRENDS IN PLANT SCIENCE 2019; 24:1126-1136. [PMID: 31610991 DOI: 10.1016/j.tplants.2019.08.005] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Revised: 07/22/2019] [Accepted: 08/22/2019] [Indexed: 05/22/2023]
Abstract
Understanding the molecular basis of pollen germination in cereals holds great potential to improve yield. Pollen, a highly specialized haploid male gametophyte, transports sperm cells through a pollen tube to the female ovule for fertilization, directly determining grain yield in cereal crops. Although insights into the regulation of pollen germination and gamete interaction have advanced rapidly in the model Arabidopsis thaliana (arabidopsis), the molecular mechanisms in monocot cereals remain largely unknown. Recently, pollen-specific genome-wide and mutant analyses in rice and maize have extended our understanding of monocot regulatory components. We highlight conserved and diverse mechanisms underlying pollen hydration, germination, and tube growth in cereals that provide ideas for translating this research from arabidopsis. Recent developments in gene-editing systems may facilitate further functional genetic research.
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Affiliation(s)
- Yu-Jin Kim
- Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin 17104, Korea
| | - Dabing Zhang
- Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin 17104, Korea; Joint International Research Laboratory of Metabolic and Developmental Sciences, Shanghai Jiao Tong University-University of Adelaide Joint Centre for Agriculture and Health, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China; School of Agriculture, Food, and Wine, University of Adelaide, South Australia 5064, Australia.
| | - Ki-Hong Jung
- Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin 17104, Korea.
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18
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Li Y, Zhai L, Fan J, Ren J, Gong W, Wang X, Huang J. Genome-wide identification, phylogenetic and expression analysis of the maize HECT E3 ubiquitin ligase genes. Genetica 2019; 147:391-400. [PMID: 31741104 DOI: 10.1007/s10709-019-00080-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Accepted: 11/13/2019] [Indexed: 11/27/2022]
Abstract
HECT (homologous to the E6AP carboxyl terminus) ubiquitin ligase genes (E3s) are enzymes with diverse functions influencing plant growth, development, and responses to abiotic stresses. However, there is relatively little information available regarding the maize HECT E3 gene family. In the present study, 12 maize HECT E3 genes (ZmUPL1 to ZmUPL12) were identified at the whole-genome level. The phylogenetic relationships, structures, and expression levels of the maize HECT E3 genes were then analyzed. On the basis of the constructed maximum likelihood phylogenetic tree, the HECT E3 genes were divided into six groups. The quantitative real-time polymerase chain reaction assay results revealed that all of the maize ZmUPL genes were expressed in most of the examined tissues and were responsive to three abiotic stresses. Considered together, the study results may provide a useful foundation for future investigations of maize stress-tolerance genes as well as functional analyses of the E3 enzymes in diverse agriculturally important crop species.
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Affiliation(s)
- Yunfeng Li
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou, 510642, China.,College of Agriculture, South China Agricultural University, Guangzhou, 510642, China
| | - Lihong Zhai
- Medical College, Hubei University of Arts and Science, Xiangyang, 441053, China
| | - Jingsheng Fan
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou, 510642, China.,College of Agriculture, South China Agricultural University, Guangzhou, 510642, China
| | - Jiaxin Ren
- Medical College, Hubei University of Arts and Science, Xiangyang, 441053, China
| | - Wenrong Gong
- Medical College, Hubei University of Arts and Science, Xiangyang, 441053, China
| | - Xin Wang
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou, 510642, China.,College of Agriculture, South China Agricultural University, Guangzhou, 510642, China
| | - Jun Huang
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou, 510642, China. .,College of Agriculture, South China Agricultural University, Guangzhou, 510642, China.
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19
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Otto SP. Evolutionary potential for genomic islands of sexual divergence on recombining sex chromosomes. THE NEW PHYTOLOGIST 2019; 224:1241-1251. [PMID: 31361905 DOI: 10.1111/nph.16083] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Accepted: 07/22/2019] [Indexed: 06/10/2023]
Abstract
Differentiated sex chromosomes are thought to develop through the accumulation of polymorphisms at loci subject to opposing selection between males and females, and/or between haploids and diploids. As sex chromosomes differentiate, reduced recombination becomes favored between selected loci and the sex-determining region, strengthening genetic associations between alleles favored in a sex and the corresponding sex chromosome. Here a model is analyzed to explore whether polymorphism at one sexually or ploidally antagonistic locus facilitates the spread of rare alleles at other loci experiencing antagonistic selection, promoting further differentiation of the sex chromosomes. It is found that antagonistic polymorphisms can spread and capture other such loci, building 'genomic islands' of differentiation on sex chromosomes, but the conditions are very restrictive, requiring the loci to be strongly selected, tightly linked and distant from the sex-determining region. Epistatic interactions can facilitate the promotion of polymorphism among selected loci, but only if preferentially favoring heterozygotes. Although these results apply to any taxa, plants provide a fertile ground for testing these and related theories given the recurrent evolutionary transitions to dioecy, which provide multiple opportunities to track the early evolution of sex chromosomes.
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Affiliation(s)
- Sarah P Otto
- Department of Zoology & Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada, V6T 1Z4
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20
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Han L, Li L, Muehlbauer GJ, Fowler JE, Evans MMS. RNA Isolation and Analysis of LncRNAs from Gametophytes of Maize. Methods Mol Biol 2019; 1933:67-86. [PMID: 30945179 DOI: 10.1007/978-1-4939-9045-0_4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The explosion of RNA-Seq data has enabled the identification of expressed genes without relying on gene models with biases toward open reading frames, allowing the identification of many more long noncoding RNAs (lncRNAs) in eukaryotes. Various tissue enrichment strategies and deep sequencing have also enabled the identification of an extensive list of genes expressed in maize gametophytes, tissues that are intractable to both traditional genetic and gene expression analyses. However, the function of very few genes from the lncRNA and gametophyte sets (or from their intersection) has been tested. Methods for isolating and identifying lncRNAs from gametophyte samples of maize are described here. This method is transferable to any maize gametophyte mutant enabling the development of gene networks involving both protein-coding genes and lncRNAs. Additionally, these methods can be adapted to apply to other grass model systems to test for evolutionary conservation of lncRNA expression patterns.
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Affiliation(s)
- Linqian Han
- College of Plant Sciences and Technology, Huazhong Agricultural University, Wuhan, China
| | - Lin Li
- College of Plant Sciences and Technology, Huazhong Agricultural University, Wuhan, China
| | - Gary J Muehlbauer
- Department of Agronomy and Plant Genetics, University of Minnesota, Saint Paul, MN, USA
- Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, MN, USA
| | - John E Fowler
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, USA
| | - Matthew M S Evans
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, USA.
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21
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Wang S, Chen Y. Fine-Tuning the Expression of Duplicate Genes by Translational Regulation in Arabidopsis and Maize. FRONTIERS IN PLANT SCIENCE 2019; 10:534. [PMID: 31156655 PMCID: PMC6530396 DOI: 10.3389/fpls.2019.00534] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Accepted: 04/05/2019] [Indexed: 06/01/2023]
Abstract
Plant genomes are extensively shaped by various types of gene duplication. However, in this active area of investigation, the vast majority of studies focus on the sequence and transcription of duplicate genes, leaving open the question of how translational regulation impacts the expression and evolution of duplicate genes. We explored this issue by analyzing the ribo- and mRNA-seq data sets across six tissue types and stress conditions in Arabidopsis thaliana and maize (Zea mays). We dissected the relative contributions of transcriptional and translational regulation to the divergence in the abundance of ribosome footprint (RF) for different types of duplicate genes. We found that the divergence in RF abundance was largely programmed at the transcription level and that translational regulation plays more of a modulatory role. Intriguingly, translational regulation is characterized by its strong directionality, with the divergence in translational efficiency (TE) globally counteracting the divergence in mRNA abundance, indicating partial buffering of the transcriptional divergence between paralogs by translational regulation. Divergence in TE was associated with several sequence features. The faster-evolving copy in a duplicate pair was more likely to show lower RF abundance, which possibly results from relaxed purifying selection compared with its paralog. A considerable proportion of duplicates displayed differential TE across tissue types and stress conditions, most of which were enriched in photosynthesis, energy production, and translation-related processes. Additionally, we constructed a database TDPDG-DB (http://www.plantdupribo.tk), providing an online platform for data exploration. Overall, our study illustrates the roles of translational regulation in fine-tuning duplicate gene expression in plants.
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Affiliation(s)
- Sishuo Wang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
- Department of Botany, Faculty of Science, The University of British Columbia, Vancouver, BC, Canada
- School of Life Sciences, The Chinese University of Hong Kong, Sha Tin, Hong Kong
| | - Youhua Chen
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
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22
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Washburn JD, Mejia-Guerra MK, Ramstein G, Kremling KA, Valluru R, Buckler ES, Wang H. Evolutionarily informed deep learning methods for predicting relative transcript abundance from DNA sequence. Proc Natl Acad Sci U S A 2019; 116:5542-5549. [PMID: 30842277 PMCID: PMC6431157 DOI: 10.1073/pnas.1814551116] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Deep learning methodologies have revolutionized prediction in many fields and show potential to do the same in molecular biology and genetics. However, applying these methods in their current forms ignores evolutionary dependencies within biological systems and can result in false positives and spurious conclusions. We developed two approaches that account for evolutionary relatedness in machine learning models: (i) gene-family-guided splitting and (ii) ortholog contrasts. The first approach accounts for evolution by constraining model training and testing sets to include different gene families. The second approach uses evolutionarily informed comparisons between orthologous genes to both control for and leverage evolutionary divergence during the training process. The two approaches were explored and validated within the context of mRNA expression level prediction and have the area under the ROC curve (auROC) values ranging from 0.75 to 0.94. Model weight inspections showed biologically interpretable patterns, resulting in the hypothesis that the 3' UTR is more important for fine-tuning mRNA abundance levels while the 5' UTR is more important for large-scale changes.
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Affiliation(s)
- Jacob D Washburn
- Institute for Genomic Diversity, Cornell University, Ithaca, NY 14853
| | | | | | - Karl A Kremling
- Institute for Genomic Diversity, Cornell University, Ithaca, NY 14853
| | - Ravi Valluru
- Institute for Genomic Diversity, Cornell University, Ithaca, NY 14853
| | - Edward S Buckler
- Institute for Genomic Diversity, Cornell University, Ithaca, NY 14853;
- Agricultural Research Service, United States Department of Agriculture, Ithaca, NY 14850
| | - Hai Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, 100081 Beijing, China
- Institute for Genomic Diversity, Cornell University, Ithaca, NY 14853
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23
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Gumber HK, McKenna JF, Estrada AL, Tolmie AF, Graumann K, Bass HW. Identification and characterization of genes encoding the nuclear envelope LINC complex in the monocot species Zea mays. J Cell Sci 2019; 132:jcs.221390. [PMID: 30659121 DOI: 10.1242/jcs.221390] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2018] [Accepted: 01/07/2019] [Indexed: 12/18/2022] Open
Abstract
The linker of nucleoskeleton to cytoskeleton (LINC) complex is an essential multi-protein structure spanning the nuclear envelope. It connects the cytoplasm to the nucleoplasm, functions to maintain nuclear shape and architecture and regulates chromosome dynamics during cell division. Knowledge of LINC complex composition and function in the plant kingdom is primarily limited to Arabidopsis, but critically missing from the evolutionarily distant monocots, which include grasses, the most important agronomic crops worldwide. To fill this knowledge gap, we identified and characterized 22 maize genes, including a new grass-specific KASH gene family. By using bioinformatic, biochemical and cell biological approaches, we provide evidence that representative KASH candidates localize to the nuclear periphery and interact with Zea mays (Zm)SUN2 in vivo FRAP experiments using domain deletion constructs verified that this SUN-KASH interaction was dependent on the SUN but not the coiled-coil domain of ZmSUN2. A summary working model is proposed for the entire maize LINC complex encoded by conserved and divergent gene families. These findings expand our knowledge of the plant nuclear envelope in a model grass species, with implications for both basic and applied cellular research.This article has an associated First Person interview with the first author of the paper.
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Affiliation(s)
- Hardeep K Gumber
- Department of Biological Science, Florida State University, Tallahassee, FL 32306-4295, USA
| | - Joseph F McKenna
- Department of Biological and Medical Sciences, Faculty of Health and Life Sciences, Oxford Brookes University, Oxford, OX3 0BP UK
| | - Amado L Estrada
- Department of Biological Science, Florida State University, Tallahassee, FL 32306-4295, USA
| | - Andrea F Tolmie
- Department of Biological and Medical Sciences, Faculty of Health and Life Sciences, Oxford Brookes University, Oxford, OX3 0BP UK
| | - Katja Graumann
- Department of Biological and Medical Sciences, Faculty of Health and Life Sciences, Oxford Brookes University, Oxford, OX3 0BP UK
| | - Hank W Bass
- Department of Biological Science, Florida State University, Tallahassee, FL 32306-4295, USA
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24
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Ha J, Shim S, Lee T, Kang YJ, Hwang WJ, Jeong H, Laosatit K, Lee J, Kim SK, Satyawan D, Lestari P, Yoon MY, Kim MY, Chitikineni A, Tanya P, Somta P, Srinives P, Varshney RK, Lee S. Genome sequence of Jatropha curcas L., a non-edible biodiesel plant, provides a resource to improve seed-related traits. PLANT BIOTECHNOLOGY JOURNAL 2019; 17:517-530. [PMID: 30059608 PMCID: PMC6335072 DOI: 10.1111/pbi.12995] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Accepted: 07/26/2018] [Indexed: 05/02/2023]
Abstract
Jatropha curcas (physic nut), a non-edible oilseed crop, represents one of the most promising alternative energy sources due to its high seed oil content, rapid growth and adaptability to various environments. We report ~339 Mbp draft whole genome sequence of J. curcas var. Chai Nat using both the PacBio and Illumina sequencing platforms. We identified and categorized differentially expressed genes related to biosynthesis of lipid and toxic compound among four stages of seed development. Triacylglycerol (TAG), the major component of seed storage oil, is mainly synthesized by phospholipid:diacylglycerol acyltransferase in Jatropha, and continuous high expression of homologs of oleosin over seed development contributes to accumulation of high level of oil in kernels by preventing the breakdown of TAG. A physical cluster of genes for diterpenoid biosynthetic enzymes, including casbene synthases highly responsible for a toxic compound, phorbol ester, in seed cake, was syntenically highly conserved between Jatropha and castor bean. Transcriptomic analysis of female and male flowers revealed the up-regulation of a dozen family of TFs in female flower. Additionally, we constructed a robust species tree enabling estimation of divergence times among nine Jatropha species and five commercial crops in Malpighiales order. Our results will help researchers and breeders increase energy efficiency of this important oil seed crop by improving yield and oil content, and eliminating toxic compound in seed cake for animal feed.
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Affiliation(s)
- Jungmin Ha
- Department of Plant Science and Research Institute of Agriculture and Life SciencesSeoul National UniversitySeoulKorea
- Plant Genomics and Breeding InstituteSeoul National UniversitySeoulKorea
| | - Sangrea Shim
- Department of Plant Science and Research Institute of Agriculture and Life SciencesSeoul National UniversitySeoulKorea
| | - Taeyoung Lee
- Department of Plant Science and Research Institute of Agriculture and Life SciencesSeoul National UniversitySeoulKorea
| | - Yang J. Kang
- Division of Applied Life Science (BK21 plus program) DepartmentGyeongsang National UniversityPMBBRCJinju‐siKorea
- Division of Life Science DepartmentGyeongsang National UniversityJinju‐siKorea
| | | | - Haneul Jeong
- Department of Plant Science and Research Institute of Agriculture and Life SciencesSeoul National UniversitySeoulKorea
| | - Kularb Laosatit
- Department of AgronomyFaculty of Agriculture at Kamphaeng SaenKasetsart UniversityNakhon PathomThailand
| | - Jayern Lee
- Department of Plant Science and Research Institute of Agriculture and Life SciencesSeoul National UniversitySeoulKorea
| | - Sue K. Kim
- Department of ChemistryCollege of Natural ScienceDankook UniversityCheonanSouth Korea
| | - Dani Satyawan
- Indonesian Center for Agricultural Biotechnology and Genetic Resources Research and Development (ICABIOGRAD‐IAARD)BogorIndonesia
| | - Puji Lestari
- Indonesian Center for Agricultural Biotechnology and Genetic Resources Research and Development (ICABIOGRAD‐IAARD)BogorIndonesia
| | - Min Y. Yoon
- Department of Plant Science and Research Institute of Agriculture and Life SciencesSeoul National UniversitySeoulKorea
| | - Moon Y. Kim
- Department of Plant Science and Research Institute of Agriculture and Life SciencesSeoul National UniversitySeoulKorea
- Plant Genomics and Breeding InstituteSeoul National UniversitySeoulKorea
| | - Annapurna Chitikineni
- Center of Excellence in Genomics & Systems BiologyInternational Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadTelangana StateIndia
| | - Patcharin Tanya
- Department of AgronomyFaculty of Agriculture at Kamphaeng SaenKasetsart UniversityNakhon PathomThailand
| | - Prakit Somta
- Department of AgronomyFaculty of Agriculture at Kamphaeng SaenKasetsart UniversityNakhon PathomThailand
| | - Peerasak Srinives
- Department of AgronomyFaculty of Agriculture at Kamphaeng SaenKasetsart UniversityNakhon PathomThailand
| | - Rajeev K. Varshney
- Center of Excellence in Genomics & Systems BiologyInternational Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadTelangana StateIndia
| | - Suk‐Ha Lee
- Department of Plant Science and Research Institute of Agriculture and Life SciencesSeoul National UniversitySeoulKorea
- Plant Genomics and Breeding InstituteSeoul National UniversitySeoulKorea
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25
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Sigel EM, Schuettpelz E, Pryer KM, Der JP. Overlapping Patterns of Gene Expression Between Gametophyte and Sporophyte Phases in the Fern Polypodium amorphum (Polypodiales). FRONTIERS IN PLANT SCIENCE 2018; 9:1450. [PMID: 30356815 PMCID: PMC6190754 DOI: 10.3389/fpls.2018.01450] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2018] [Accepted: 09/12/2018] [Indexed: 05/16/2023]
Abstract
Ferns are unique among land plants in having sporophyte and gametophyte phases that are both free living and fully independent. Here, we examine patterns of sporophytic and gametophytic gene expression in the fern Polypodium amorphum, a member of the homosporous polypod lineage that comprises 80% of extant fern diversity, to assess how expression of a common genome is partitioned between two morphologically, ecologically, and nutritionally independent phases. Using RNA-sequencing, we generated transcriptome profiles for three replicates of paired samples of sporophyte leaf tissue and whole gametophytes to identify genes with significant differences in expression between the two phases. We found a nearly 90% overlap in the identity and expression levels of the genes expressed in both sporophytes and gametophytes, with less than 3% of genes uniquely expressed in either phase. We compare our results to those from similar studies to establish how phase-specific gene expression varies among major land plant lineages. Notably, despite having greater similarity in the identity of gene families shared between P. amorphum and angiosperms, P. amorphum has phase-specific gene expression profiles that are more like bryophytes and lycophytes than seed plants. Our findings suggest that shared patterns of phase-specific gene expression among seed-free plants likely reflect having relatively large, photosynthetic gametophytes (compared to the gametophytes of seed plants that are highly reduced). Phylogenetic analyses were used to further investigate the evolution of phase-specific expression for the phototropin, terpene synthase, and MADS-box gene families.
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Affiliation(s)
- Erin M. Sigel
- Department of Biology, University of Louisiana at Lafayette, Lafayette, LA, United States
| | - Eric Schuettpelz
- Department of Botany, National Museum of Natural History, Smithsonian Institution, Washington, DC, United States
| | | | - Joshua P. Der
- Department of Biological Science, California State University Fullerton, Fullerton, CA, United States
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26
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Shahan R, Zawora C, Wight H, Sittmann J, Wang W, Mount SM, Liu Z. Consensus Coexpression Network Analysis Identifies Key Regulators of Flower and Fruit Development in Wild Strawberry. PLANT PHYSIOLOGY 2018; 178:202-216. [PMID: 29991484 PMCID: PMC6130042 DOI: 10.1104/pp.18.00086] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Accepted: 06/27/2018] [Indexed: 05/19/2023]
Abstract
The diploid strawberry, Fragaria vesca, is a developing model system for the economically important Rosaceae family. Strawberry fleshy fruit develops from the floral receptacle and its ripening is nonclimacteric. The external seed configuration of strawberry fruit facilitates the study of seed-to-fruit cross tissue communication, particularly phytohormone biosynthesis and transport. To investigate strawberry fruit development, we previously generated spatial and temporal transcriptome data profiling F. vesca flower and fruit development pre- and postfertilization. In this study, we combined 46 of our existing RNA-seq libraries to generate coexpression networks using the Weighted Gene Co-Expression Network Analysis package in R. We then applied a post-hoc consensus clustering approach and used bootstrapping to demonstrate consensus clustering's ability to produce robust and reproducible clusters. Further, we experimentally tested hypotheses based on the networks, including increased iron transport from the receptacle to the seed postfertilization and characterized a F. vesca floral mutant and its candidate gene. To increase their utility, the networks are presented in a web interface (www.fv.rosaceaefruits.org) for easy exploration and identification of coexpressed genes. Together, the work reported here illustrates ways to generate robust networks optimized for the mining of large transcriptome data sets, thereby providing a useful resource for hypothesis generation and experimental design in strawberry and related Rosaceae fruit crops.
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Affiliation(s)
- Rachel Shahan
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland 20742
| | - Christopher Zawora
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland 20742
| | - Haley Wight
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland 20742
| | - John Sittmann
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland 20742
| | - Wanpeng Wang
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland 20742
| | - Stephen M Mount
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland 20742
| | - Zhongchi Liu
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland 20742
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27
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RNA-seq Analysis Reveals Gene Expression Profiling of Female Fertile and Sterile Ovules of PinusTabulaeformis Carr. during Free Nuclear Mitosis of the Female Gametophyte. Int J Mol Sci 2018; 19:ijms19082246. [PMID: 30071597 PMCID: PMC6122031 DOI: 10.3390/ijms19082246] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Revised: 07/22/2018] [Accepted: 07/26/2018] [Indexed: 01/08/2023] Open
Abstract
The development of the female gametophyte (FG) is one of the key processes of life cycle alteration between the haploid gametophyte and the diploid sporophytes in plants and it is required for successful seed development after fertilization. It is well demonstrated that free nuclear mitosis (FNM) of FG is crucial for the development of the ovule. However, studies of the molecular mechanism of ovule and FG development focused mainly on angiosperms, such as Arabidopsis thaliana and further investigation of gymnosperms remains to be completed. Here, Illumina sequencing of six transcriptomic libraries obtained from developing and abortive ovules at different stages during free nuclear mitosis of magagametophyte (FNMM) was used to acquire transcriptome data and gene expression profiles of Pinus tabulaeformis. Six cDNA libraries generated a total of 71.0 million high-quality clean reads that aligned with 63,449 unigenes and the comparison between developing and abortive ovules identified 7174 differentially expressed genes (DEGs). From the functional annotation results, DEGs involved in the cell cycle and phytohormone regulation were highlighted to reveal their biological importance in ovule development. Furthermore, validation of DEGs from the phytohormone signal transduction pathway was performed using quantitative real-time PCR analysis, revealing the dynamics of transcriptional networks and potential key components in the regulation of FG development in P. tabulaeformis were identified. These findings provide new insights into the regulatory mechanisms of ovule development in woody gymnosperms.
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28
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Insel PA, Sriram K, Wiley SZ, Wilderman A, Katakia T, McCann T, Yokouchi H, Zhang L, Corriden R, Liu D, Feigin ME, French RP, Lowy AM, Murray F. GPCRomics: GPCR Expression in Cancer Cells and Tumors Identifies New, Potential Biomarkers and Therapeutic Targets. Front Pharmacol 2018; 9:431. [PMID: 29872392 PMCID: PMC5972277 DOI: 10.3389/fphar.2018.00431] [Citation(s) in RCA: 87] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Accepted: 04/12/2018] [Indexed: 12/16/2022] Open
Abstract
G protein-coupled receptors (GPCRs), the largest family of targets for approved drugs, are rarely targeted for cancer treatment, except for certain endocrine and hormone-responsive tumors. Limited knowledge regarding GPCR expression in cancer cells likely has contributed to this lack of use of GPCR-targeted drugs as cancer therapeutics. We thus undertook GPCRomic studies to define the expression of endoGPCRs (which respond to endogenous molecules such as hormones, neurotransmitters and metabolites) in multiple types of cancer cells. Using TaqMan qPCR arrays to quantify the mRNA expression of ∼340 such GPCRs, we found that human chronic lymphocytic leukemia (CLL) cells/stromal cells associated with CLL, breast cancer cell lines, colon cancer cell lines, pancreatic ductal adenocarcinoma (PDAC) cells, cancer associated fibroblasts (CAFs), and PDAC tumors express 50 to >100 GPCRs, including many orphan GPCRs (which lack known physiologic agonists). Limited prior data exist regarding the expression or function of most of the highly expressed GPCRs in these cancer cells and tumors. Independent results from public cancer gene expression databases confirm the expression of such GPCRs. We propose that highly expressed GPCRs in cancer cells (for example, GPRC5A in PDAC and colon cancer cells and GPR68 in PDAC CAFs) may contribute to the malignant phenotype, serve as biomarkers and/or may be novel therapeutic targets for the treatment of cancer.
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Affiliation(s)
- Paul A. Insel
- Department of Pharmacology, University of California, San Diego, San Diego, CA, United States
- Department of Medicine, University of California, San Diego, San Diego, CA, United States
| | - Krishna Sriram
- Department of Pharmacology, University of California, San Diego, San Diego, CA, United States
| | - Shu Z. Wiley
- Department of Pharmacology, University of California, San Diego, San Diego, CA, United States
| | - Andrea Wilderman
- Department of Pharmacology, University of California, San Diego, San Diego, CA, United States
| | - Trishna Katakia
- Department of Pharmacology, University of California, San Diego, San Diego, CA, United States
| | - Thalia McCann
- Department of Pharmacology, University of California, San Diego, San Diego, CA, United States
| | - Hiroshi Yokouchi
- Department of Pharmacology, University of California, San Diego, San Diego, CA, United States
| | - Lingzhi Zhang
- Department of Pharmacology, University of California, San Diego, San Diego, CA, United States
| | - Ross Corriden
- Department of Pharmacology, University of California, San Diego, San Diego, CA, United States
| | - Dongling Liu
- Department of Pharmacology, University of California, San Diego, San Diego, CA, United States
| | - Michael E. Feigin
- Department of Pharmacology and Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, United States
| | - Randall P. French
- Department of Surgery, University of California, San Diego, San Diego, CA, United States
- Moores Cancer Center, University of California, San Diego, San Diego, CA, United States
| | - Andrew M. Lowy
- Department of Surgery, University of California, San Diego, San Diego, CA, United States
- Moores Cancer Center, University of California, San Diego, San Diego, CA, United States
| | - Fiona Murray
- Department of Pharmacology, University of California, San Diego, San Diego, CA, United States
- Department of Medicine, University of California, San Diego, San Diego, CA, United States
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29
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Donaldson ME, Davy CM, Vanderwolf KJ, Willis CKR, Saville BJ, Kyle CJ. Growth medium and incubation temperature alter the Pseudogymnoascus destructans transcriptome: implications in identifying virulence factors. Mycologia 2018; 110:300-315. [PMID: 29737946 DOI: 10.1080/00275514.2018.1438223] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Pseudogymnoascus destructans is the causal agent of bat white-nose syndrome (WNS), which is devastating some North American bat populations. Previous transcriptome studies provided insight regarding the molecular mechanisms involved in WNS; however, it is unclear how different environmental parameters could influence pathogenicity. This information could be useful in developing management strategies to mitigate the negative impacts of P. destructans on bats. We cultured three P. destructans isolates from Atlantic Canada on two growth media (potato dextrose agar and Sabouraud dextrose agar) that differ in their nitrogen source, and at two separate incubation temperatures (4 C and 15 C) that approximate the temperature range of bat hibernacula during the winter and a temperature within its optimal mycelial growth range. We conducted RNA sequencing to determine transcript levels in each sample and performed differential gene expression (DGE) analyses to test the influence of growth medium and incubation temperature on gene expression. We also compared our in vitro results with previous RNA-sequencing data sets generated from P. destructans growing on the wings of a susceptible host, Myotis lucifugus. Our findings point to a critical role for substrate and incubation temperature in influencing the P. destructans transcriptome. DGE analyses suggested that growth medium plays a larger role than temperature in determining P. destructans gene expression and that although the psychrophilic fungus responds to different nitrogen sources, it may have evolved for continued growth at a broad range of low temperatures. Further, our data suggest that down-regulation of the RNA-interference pathway and increased fatty acid metabolism are involved in the P. destructans-bat interaction. Finally, we speculate that to reduce the activation of host defense responses, P. destructans minimizes changes in the expression of genes encoding secreted proteins during bat colonization.
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Affiliation(s)
- Michael E Donaldson
- a Environmental and Life Sciences Graduate Program , Trent University , 2140 East Bank Drive, Peterborough , Ontario , K9L 1Z8, Canada
| | - Christina M Davy
- a Environmental and Life Sciences Graduate Program , Trent University , 2140 East Bank Drive, Peterborough , Ontario , K9L 1Z8, Canada.,b Wildlife Research and Monitoring Section , Ontario Ministry of Natural Resources and Forestry , 2140 East Bank Drive, Peterborough , Ontario , K9L 1Z8, Canada
| | - Karen J Vanderwolf
- c New Brunswick Museum , 277 Douglas Avenue, Saint John , New Brunswick , E2K 1E5, Canada.,d Department of Pathobiological Sciences , University of Wisconsin-Madison , 2015 Linden Drive, Madison , Wisconsin 53706
| | - Craig K R Willis
- e Department of Biology , University of Winnipeg , 515 Portage Avenue, Winnipeg , Manitoba , R3B 2E9, Canada
| | - Barry J Saville
- a Environmental and Life Sciences Graduate Program , Trent University , 2140 East Bank Drive, Peterborough , Ontario , K9L 1Z8, Canada.,f Forensic Science Department , Trent University , 2140 East Bank Drive, Peterborough , Ontario, K9L 1Z8 , Canada
| | - Christopher J Kyle
- a Environmental and Life Sciences Graduate Program , Trent University , 2140 East Bank Drive, Peterborough , Ontario , K9L 1Z8, Canada.,f Forensic Science Department , Trent University , 2140 East Bank Drive, Peterborough , Ontario, K9L 1Z8 , Canada
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30
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Forestan C, Farinati S, Rouster J, Lassagne H, Lauria M, Dal Ferro N, Varotto S. Control of Maize Vegetative and Reproductive Development, Fertility, and rRNAs Silencing by HISTONE DEACETYLASE 108. Genetics 2018; 208:1443-1466. [PMID: 29382649 DOI: 10.1534/genetics.117.300625/-/dc1.1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Accepted: 01/28/2018] [Indexed: 05/28/2023] Open
Abstract
Histone deacetylases (HDACs) catalyze the removal of acetyl groups from acetylated histone tails that consequently interact more closely with DNA, leading to chromatin state refractory to transcription. Zea mays HDA108 belongs to the Rpd3/HDA1 HDAC family and is ubiquitously expressed during development. The newly isolated hda108/hda108 insertional mutant exhibited many developmental defects: significant reduction in plant height, alterations of shoot and leaf development, and alterations of inflorescence patterning and fertility. Western blot analyses and immunolocalization experiments revealed an evident increase in histone acetylation, accompanied by a marked reduction in H3K9 dimethylation, in mutant nuclei. The DNA methylation status, in the CHG sequence context, and the transcript level of ribosomal sequences were also affected in hda108 mutants, while enrichment in H3 and H4 acetylation characterizes both repetitive and nonrepetitive transcriptional up-regulated loci. RNA-Seq of both young leaf and anthers indicated that transcription factor expression is highly affected and that the pollen developmental program is disrupted in hda108 mutants. Crosses between hda108/hda108 and epiregulator mutants did not produce any double mutant progeny indicating possible genetic interactions of HDA108 with distinct epigenetic pathways. Our findings indicate that HDA108 is directly involved in regulation of maize development, fertility, and epigenetic regulation of genome activity.
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Affiliation(s)
- Cristian Forestan
- Department of Agronomy Food Natural Resources, Animals and Environment (DAFNAE) Agripolis, University of Padova, 35020 Legnaro (PD), Italy
| | - Silvia Farinati
- Department of Agronomy Food Natural Resources, Animals and Environment (DAFNAE) Agripolis, University of Padova, 35020 Legnaro (PD), Italy
| | - Jacques Rouster
- GM Trait Cereals, Biogemma, Centre de Research de Chappes, 63720 Chappes, France
| | - Hervé Lassagne
- GM Trait Cereals, Biogemma, Centre de Research de Chappes, 63720 Chappes, France
| | - Massimiliano Lauria
- The Institute of Agricultural Biology and Biotechnology (IBBA), Consiglio Nazionale delle Ricerche (CNR), 20133 Milano, Italy
| | - Nicola Dal Ferro
- Department of Agronomy Food Natural Resources, Animals and Environment (DAFNAE) Agripolis, University of Padova, 35020 Legnaro (PD), Italy
| | - Serena Varotto
- Department of Agronomy Food Natural Resources, Animals and Environment (DAFNAE) Agripolis, University of Padova, 35020 Legnaro (PD), Italy
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31
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Liang Z, Schnable JC. Functional Divergence between Subgenomes and Gene Pairs after Whole Genome Duplications. MOLECULAR PLANT 2018; 11:388-397. [PMID: 29275166 DOI: 10.1016/j.molp.2017.12.010] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2017] [Revised: 11/28/2017] [Accepted: 12/12/2017] [Indexed: 05/20/2023]
Abstract
Gene loss following whole genome duplication (WGD) is often biased, with one subgenome retaining more ancestral genes and the other sustaining more gene deletions. While bias toward the greater expression of gene copies on one subgenome can explain bias in gene loss, this raises the question to what drives differences in gene expression levels between subgenomes. Differences in chromatin modifications and epigenetic markers between subgenomes in several model species are now being identified, providing an explanation for bias in gene expression between subgenomes. WGDs can be classified into duplications with higher, biased gene loss and bias in gene expression between subgenomes versus those with lower, unbiased rates of gene loss and an absence of detectable bias between subgenomes; however, the originally proposed link between these two classes and whether WGD results from an allo- or autopolyploid event is inconsistent with recent data from the allopolyploid Capsella bursa-pastoris. The gene balance hypothesis can explain bias in the functional categories of genes retained following WGD, the difference in gene loss rates between unbiased and biased WGDs, and how plant genomes have avoided being overrun with genes encoding dose-sensitive subunits of multiprotein complexes. Comparisons of gene expression patterns between retained transcription factor pairs in maize suggest the high degree of retention for WGD-derived pairs of transcription factors may instead be explained by the older duplication-degeneration-complementation model.
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Affiliation(s)
- Zhikai Liang
- Plant Science Innovation & Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE 68503, USA
| | - James C Schnable
- Plant Science Innovation & Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE 68503, USA.
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32
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Chastain CJ, Baird LM, Walker MT, Bergman CC, Novbatova GT, Mamani-Quispe CS, Burnell JN. Maize leaf PPDK regulatory protein isoform-2 is specific to bundle sheath chloroplasts and paradoxically lacks a Pi-dependent PPDK activation activity. JOURNAL OF EXPERIMENTAL BOTANY 2018; 69:1171-1181. [PMID: 29281064 PMCID: PMC6019023 DOI: 10.1093/jxb/erx471] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Accepted: 12/04/2017] [Indexed: 05/18/2023]
Abstract
In C4 plants, the pyruvate phosphate dikinase regulatory protein (PDRP) regulates the C4 pathway enzyme pyruvate phosphate dikinase (PPDK) in response to changes in incident light intensity. In maize (Zea mays) leaves, two distinct isoforms of PDRP are expressed, ZmPDRP1 and ZmPDRP2. The properties and C4 function of the ZmPDRP1 isoform are well understood. However, the PDRP2 isoform has only recently been identified and its properties and function(s) in maize leaves are unknown. We therefore initiated an investigation into the maize PDRP2 isoform by performing a side by side comparison of its enzyme properties and cell-specific distribution with PDRP1. In terms of enzyme functionality, PDRP2 was found to possess the same protein kinase-specific activity as PDRP1. However, the PDRP2 isoform was found to lack the phosphotransferase activity of the bifunctional PDRP1 isoform except when PDRP2 in the assays is elevated 5- to 10-fold. A primarily immuno-based approach was used to show that PDRP1 is strictly expressed in mesophyll cells and PDRP2 is strictly expressed in bundle sheath strand cells (BSCs). Additionally, using in situ immunolocalization, we establish a regulatory target for PDRP2 by showing a significant presence of C4 PPDK in BSC chloroplasts. However, a metabolic role for PPDK in this compartment is obscure, assuming PPDK accumulating in this compartment would be irreversibly inactivated each dark cycle by a monofunctional PDRP2.
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Affiliation(s)
- Chris J Chastain
- Department of Biosciences, Minnesota State University-Moorhead, USA
- Correspondence:
| | - Lisa M Baird
- Department of Biology, University of San Diego, San Diego, CA, USA
| | | | | | | | | | - Jim N Burnell
- Department of Molecular and Cell Biology, James Cook University, Australia
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33
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Control of Maize Vegetative and Reproductive Development, Fertility, and rRNAs Silencing by HISTONE DEACETYLASE 108. Genetics 2018; 208:1443-1466. [PMID: 29382649 PMCID: PMC5887141 DOI: 10.1534/genetics.117.300625] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Accepted: 01/28/2018] [Indexed: 12/27/2022] Open
Abstract
Histone deacetylases (HDACs) catalyze the removal of acetyl groups from acetylated histone tails that consequently interact more closely with DNA, leading to chromatin state refractory to transcription. Zea mays HDA108 belongs to the Rpd3/HDA1 HDAC family and is ubiquitously expressed during development. The newly isolated hda108/hda108 insertional mutant exhibited many developmental defects: significant reduction in plant height, alterations of shoot and leaf development, and alterations of inflorescence patterning and fertility. Western blot analyses and immunolocalization experiments revealed an evident increase in histone acetylation, accompanied by a marked reduction in H3K9 dimethylation, in mutant nuclei. The DNA methylation status, in the CHG sequence context, and the transcript level of ribosomal sequences were also affected in hda108 mutants, while enrichment in H3 and H4 acetylation characterizes both repetitive and nonrepetitive transcriptional up-regulated loci. RNA-Seq of both young leaf and anthers indicated that transcription factor expression is highly affected and that the pollen developmental program is disrupted in hda108 mutants. Crosses between hda108/hda108 and epiregulator mutants did not produce any double mutant progeny indicating possible genetic interactions of HDA108 with distinct epigenetic pathways. Our findings indicate that HDA108 is directly involved in regulation of maize development, fertility, and epigenetic regulation of genome activity.
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34
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Jia H, Sun W, Li M, Zhang Z. Integrated Analysis of Protein Abundance, Transcript Level, and Tissue Diversity To Reveal Developmental Regulation of Maize. J Proteome Res 2018; 17:822-833. [DOI: 10.1021/acs.jproteome.7b00586] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Haitao Jia
- National Key Laboratory of
Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, P. R. China
| | - Wei Sun
- National Key Laboratory of
Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, P. R. China
| | - Manfei Li
- National Key Laboratory of
Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, P. R. China
| | - Zuxin Zhang
- National Key Laboratory of
Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, P. R. China
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35
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Forestan C, Farinati S, Aiese Cigliano R, Lunardon A, Sanseverino W, Varotto S. Maize RNA PolIV affects the expression of genes with nearby TE insertions and has a genome-wide repressive impact on transcription. BMC PLANT BIOLOGY 2017; 17:161. [PMID: 29025411 PMCID: PMC5639751 DOI: 10.1186/s12870-017-1108-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Accepted: 10/04/2017] [Indexed: 05/09/2023]
Abstract
BACKGROUND RNA-directed DNA methylation (RdDM) is a plant-specific epigenetic process that relies on the RNA polymerase IV (Pol IV) for the production of 24 nucleotide small interfering RNAs (siRNA) that guide the cytosine methylation and silencing of genes and transposons. Zea mays RPD1/RMR6 gene encodes the largest subunit of Pol IV and is required for normal plant development, paramutation, transcriptional repression of certain transposable elements (TEs) and transcriptional regulation of specific alleles. RESULTS In this study we applied a total RNA-Seq approach to compare the B73 and rpd1/rmr6 leaf transcriptomes. Although previous studies indicated that loss of siRNAs production in RdDM mutants provokes a strong loss of CHH DNA methylation but not massive gene or TEs transcriptional activation in both Arabidopsis and maize, our total RNA-Seq analysis of rpd1/rmr6 transcriptome reveals that loss of Pol IV activity causes a global increase in the transcribed fraction of the maize genome. Our results point to the genes with nearby TE insertions as being the most strongly affected by Pol IV-mediated gene silencing. TEs modulation of nearby gene expression is linked to alternative methylation profiles on gene flanking regions, and these profiles are strictly dependent on specific characteristics of the TE member inserted. Although Pol IV is essential for the biogenesis of siRNAs, the genes with associated siRNA loci are less affected by the pol IV mutation. CONCLUSIONS This deep and integrated analysis of gene expression, TEs distribution, smallRNA targeting and DNA methylation levels, reveals that loss of Pol IV activity globally affects genome regulation, pointing at TEs as modulator of nearby gene expression and indicating the existence of multiple level epigenetic silencing mechanisms. Our results also suggest a predominant role of the Pol IV-mediated RdDM pathway in genome dominance regulation, and subgenome stability and evolution in maize.
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Affiliation(s)
- Cristian Forestan
- Department of Agronomy, Food, Natural resources, Animals and Environment, University of Padova, Viale dell’Università 16, 35020 Legnaro, PD Italy
| | - Silvia Farinati
- Department of Agronomy, Food, Natural resources, Animals and Environment, University of Padova, Viale dell’Università 16, 35020 Legnaro, PD Italy
| | | | - Alice Lunardon
- Department of Agronomy, Food, Natural resources, Animals and Environment, University of Padova, Viale dell’Università 16, 35020 Legnaro, PD Italy
- Present Address: Department of Biology and Huck Institutes of the Life Sciences, Penn State University, University Park, Pennsylvania, PA 16802 USA
| | | | - Serena Varotto
- Department of Agronomy, Food, Natural resources, Animals and Environment, University of Padova, Viale dell’Università 16, 35020 Legnaro, PD Italy
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Chen J, Strieder N, Krohn NG, Cyprys P, Sprunck S, Engelmann JC, Dresselhaus T. Zygotic Genome Activation Occurs Shortly after Fertilization in Maize. THE PLANT CELL 2017; 29:2106-2125. [PMID: 28814645 PMCID: PMC5635985 DOI: 10.1105/tpc.17.00099] [Citation(s) in RCA: 95] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Revised: 07/19/2017] [Accepted: 08/15/2017] [Indexed: 05/18/2023]
Abstract
The formation of a zygote via the fusion of an egg and sperm cell and its subsequent asymmetric division herald the start of the plant's life cycle. Zygotic genome activation (ZGA) is thought to occur gradually, with the initial steps of zygote and embryo development being primarily maternally controlled, and subsequent steps being governed by the zygotic genome. Here, using maize (Zea mays) as a model plant system, we determined the timing of zygote development and generated RNA-seq transcriptome profiles of gametes, zygotes, and apical and basal daughter cells. ZGA occurs shortly after fertilization and involves ∼10% of the genome being activated in a highly dynamic pattern. In particular, genes encoding transcriptional regulators of various families are activated shortly after fertilization. Further analyses suggested that chromatin assembly is strongly modified after fertilization, that the egg cell is primed to activate the translational machinery, and that hormones likely play a minor role in the initial steps of early embryo development in maize. Our findings provide important insights into gamete and zygote activity in plants, and our RNA-seq transcriptome profiles represent a comprehensive, unique RNA-seq data set that can be used by the research community.
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Affiliation(s)
- Junyi Chen
- Cell Biology and Plant Biochemistry, Biochemie-Zentrum Regensburg, University of Regensburg, 93053 Regensburg, Germany
| | - Nicholas Strieder
- Institute of Functional Genomics, University of Regensburg, 93053 Regensburg, Germany
| | - Nadia G Krohn
- Cell Biology and Plant Biochemistry, Biochemie-Zentrum Regensburg, University of Regensburg, 93053 Regensburg, Germany
| | - Philipp Cyprys
- Cell Biology and Plant Biochemistry, Biochemie-Zentrum Regensburg, University of Regensburg, 93053 Regensburg, Germany
| | - Stefanie Sprunck
- Cell Biology and Plant Biochemistry, Biochemie-Zentrum Regensburg, University of Regensburg, 93053 Regensburg, Germany
| | - Julia C Engelmann
- Institute of Functional Genomics, University of Regensburg, 93053 Regensburg, Germany
| | - Thomas Dresselhaus
- Cell Biology and Plant Biochemistry, Biochemie-Zentrum Regensburg, University of Regensburg, 93053 Regensburg, Germany
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Conze LL, Berlin S, Le Bail A, Kost B. Transcriptome profiling of tobacco (Nicotiana tabacum) pollen and pollen tubes. BMC Genomics 2017; 18:581. [PMID: 28784084 PMCID: PMC5545845 DOI: 10.1186/s12864-017-3972-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Accepted: 07/31/2017] [Indexed: 01/20/2023] Open
Abstract
BACKGROUND Pollen tube growth is essential for plant reproduction and represents a widely employed model to investigate polarized cell expansion, a process important for plant morphogenesis and development. Cellular and regulatory mechanisms underlying pollen tube elongation are under intense investigation, which stands to greatly benefit from a comprehensive understanding of global gene expression profiles in pollen and pollen tubes. Here, RNA sequencing technology was applied to de novo assemble a Nicotiana tabacum male gametophytic transcriptome and to compare transcriptome profiles at two different stages of gametophyte development: mature pollen grains (MPG) and pollen tubes grown for six hours in vitro (PT6). RESULTS De novo assembly of data obtained by 454 sequencing of a normalized cDNA library representing tobacco pollen and pollen tube mRNA (pooled mRNA isolated from mature pollen grains [MPG] and from pollen tubes grown in vitro for 3 [PT3] or 6 [PT6] hours) resulted in the identification of 78,364 unigenes. Among these unigenes, which mapped to 24,933 entries in the Sol Genomics Network (SGN) N. tabacum unigene database, 24,672 were predicted to represent full length cDNAs. In addition, quantitative analyses of data obtained by Illumina sequencing of two separate non-normalized MPG and PT6 cDNA libraries showed that 8979 unigenes were differentially expressed (differentially expressed unigenes: DEGs) between these two developmental stages at a FDR q-value of <0.0001. Interestingly, whereas most of these DEGs were downregulated in PT6, the minor fraction of DEGs upregulated in PT6 was enriched for GO (gene ontology) functions in pollen tube growth or fertilization. CONCLUSIONS A major output of our study is the development of two different high-quality databases representing the tobacco male gametophytic transcriptome and containing encompassing information about global changes in gene expression after pollen germination. Quantitative analyses of these databases 1) indicated that roughly 30% of all tobacco genes are expressed in the male gametophyte, and 2) support previous observations suggesting a global reduction of transcription after pollen germination. Interestingly, a small number of genes, many of which predicted to function in pollen tube growth or fertilization, were found to be upregulated in elongating pollen tubes despite globally reduced transcription.
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Affiliation(s)
- Lei Liu Conze
- Department of Plant Biology, Swedish University of Agricultural Sciences, Uppsala BioCenter, Linnean Centre for Plant Biology, Uppsala, Sweden
| | - Sofia Berlin
- Department of Plant Biology, Swedish University of Agricultural Sciences, Uppsala BioCenter, Linnean Centre for Plant Biology, Uppsala, Sweden
| | - Aude Le Bail
- Cell Biology Division, Department of Biology, Friedrich Alexander University, Erlangen/Nuremberg, Germany
| | - Benedikt Kost
- Cell Biology Division, Department of Biology, Friedrich Alexander University, Erlangen/Nuremberg, Germany
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38
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Lai X, Behera S, Liang Z, Lu Y, Deogun JS, Schnable JC. STAG-CNS: An Order-Aware Conserved Noncoding Sequences Discovery Tool for Arbitrary Numbers of Species. MOLECULAR PLANT 2017; 10:990-999. [PMID: 28602693 DOI: 10.1016/j.molp.2017.05.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Revised: 05/24/2017] [Accepted: 05/30/2017] [Indexed: 06/07/2023]
Abstract
One method for identifying noncoding regulatory regions of a genome is to quantify rates of divergence between related species, as functional sequence will generally diverge more slowly. Most approaches to identifying these conserved noncoding sequences (CNSs) based on alignment have had relatively large minimum sequence lengths (≥15 bp) compared with the average length of known transcription factor binding sites. To circumvent this constraint, STAG-CNS that can simultaneously integrate the data from the promoters of conserved orthologous genes in three or more species was developed. Using the data from up to six grass species made it possible to identify conserved sequences as short as 9 bp with false discovery rate ≤0.05. These CNSs exhibit greater overlap with open chromatin regions identified using DNase I hypersensitivity assays, and are enriched in the promoters of genes involved in transcriptional regulation. STAG-CNS was further employed to characterize loss of conserved noncoding sequences associated with retained duplicate genes from the ancient maize polyploidy. Genes with fewer retained CNSs show lower overall expression, although this bias is more apparent in samples of complex organ systems containing many cell types, suggesting that CNS loss may correspond to a reduced number of expression contexts rather than lower expression levels across the entire ancestral expression domain.
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Affiliation(s)
- Xianjun Lai
- Department of Agronomy and Horticulture, Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE 68588, USA; Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Sairam Behera
- Department of Computer Science and Engineering, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
| | - Zhikai Liang
- Department of Agronomy and Horticulture, Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
| | - Yanli Lu
- Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Jitender S Deogun
- Department of Computer Science and Engineering, University of Nebraska-Lincoln, Lincoln, NE 68588, USA.
| | - James C Schnable
- Department of Agronomy and Horticulture, Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE 68588, USA.
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Donaldson ME, Ostrowski LA, Goulet KM, Saville BJ. Transcriptome analysis of smut fungi reveals widespread intergenic transcription and conserved antisense transcript expression. BMC Genomics 2017; 18:340. [PMID: 28464849 PMCID: PMC5414199 DOI: 10.1186/s12864-017-3720-8] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Accepted: 04/25/2017] [Indexed: 12/12/2022] Open
Abstract
Background Biotrophic fungal plant pathogens cause billions of dollars in losses to North American crops annually. The model for functional investigation of these fungi is Ustilago maydis. Its 20.5 Mb annotated genome sequence has been an excellent resource for investigating biotrophic plant pathogenesis. Expressed-sequence tag libraries and microarray hybridizations have provided insight regarding the type of transcripts produced by U. maydis but these analyses were not comprehensive and there were insufficient data for transcriptome comparison to other smut fungi. To improve transcriptome annotation and enable comparative analyses, comprehensive strand-specific RNA-seq was performed on cell-types of three related smut species: U. maydis (common smut of corn), Ustilago hordei (covered smut of barley), and Sporisorium reilianum (head smut of corn). Results In total, >1 billion paired-end sequence reads were obtained from haploid cell, dikaryon and teliospore RNA of U. maydis, haploid cell RNA of U. hordei, and haploid and dikaryon cell RNA of S. reilianum. The sequences were assembled into transfrags using Trinity, and updated gene models were created using PASA and categorized with Cufflinks Cuffcompare. Representative genes that were predicted for the first time with these RNA-seq analyses and genes with novel annotation features were independently assessed by reverse transcriptase PCR. The analyses indicate hundreds more predicted proteins, relative to the previous genome annotation, could be produced by U. maydis from altered transcript forms, and that the number of non-coding RNAs produced, including transcribed intergenic sequences and natural antisense transcripts, approximately equals the number of mRNAs. This high representation of non-coding RNAs appears to be a conserved feature of the smut fungi regardless of whether they have RNA interference machinery. Approximately 50% of the identified NATs were conserved among the smut fungi. Conclusions Overall, these analyses revealed: 1) smut genomes encode a number of transcriptional units that is twice the number of annotated protein-coding genes, 2) a small number of intergenic transcripts may encode proteins with characteristics of fungal effectors, 3) the vast majority of intergenic and antisense transcripts do not contain ORFs, 4) a large proportion of the identified antisense transcripts were detected at orthologous loci among the smut fungi, and 5) there is an enrichment of functional categories among orthologous loci that suggests antisense RNAs could have a genome-wide, non-RNAi-mediated, influence on gene expression in smut fungi. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3720-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Michael E Donaldson
- Environmental and Life Sciences Graduate Program, Trent University, Peterborough, K9L 0G2, ON, Canada
| | - Lauren A Ostrowski
- Environmental and Life Sciences Graduate Program, Trent University, Peterborough, K9L 0G2, ON, Canada.,Present Address: Department of Laboratory Medicine and Pathobiology, Faculty of Medicine, University of Toronto, Toronto, M5S 1A8, ON, Canada
| | - Kristi M Goulet
- Environmental and Life Sciences Graduate Program, Trent University, Peterborough, K9L 0G2, ON, Canada
| | - Barry J Saville
- Environmental and Life Sciences Graduate Program, Trent University, Peterborough, K9L 0G2, ON, Canada. .,Forensic Science Program, Trent University, Peterborough, K9L 0G2, ON, Canada.
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40
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Wang G, Köhler C. Epigenetic processes in flowering plant reproduction. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:797-807. [PMID: 28062591 DOI: 10.1093/jxb/erw486] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Seeds provide up to 70% of the energy intake of the human population, emphasizing the relevance of understanding the genetic and epigenetic mechanisms controlling seed formation. In flowering plants, seeds are the product of a double fertilization event, leading to the formation of the embryo and the endosperm surrounded by maternal tissues. Analogous to mammals, plants undergo extensive epigenetic reprogramming during both gamete formation and early seed development, a process that is supposed to be required to enforce silencing of transposable elements and thus to maintain genome stability. Global changes of DNA methylation, histone modifications, and small RNAs are closely associated with epigenome programming during plant reproduction. Here, we review current knowledge on chromatin changes occurring during sporogenesis and gametogenesis, as well as early seed development in major flowering plant models.
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Affiliation(s)
- Guifeng Wang
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala, Sweden
- Shanghai Key Laboratory of Bio-Energy Crops, School of Life Sciences, Shanghai University, Shanghai 200444, China
| | - Claudia Köhler
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala, Sweden
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Huang S, Liu Z, Li C, Yao R, Li D, Hou L, Li X, Liu W, Feng H. Transcriptome Analysis of a Female-sterile Mutant ( fsm) in Chinese Cabbage ( Brassica campestris ssp. pekinensis). FRONTIERS IN PLANT SCIENCE 2017; 8:546. [PMID: 28443127 PMCID: PMC5385380 DOI: 10.3389/fpls.2017.00546] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Accepted: 03/27/2017] [Indexed: 05/03/2023]
Abstract
Female-sterile mutants are ideal materials for studying pistil development in plants. Here, we identified a female-sterile mutant fsm in Chinese cabbage. This mutant, which exhibited stable inheritance, was derived from Chinese cabbage DH line 'FT' using a combination of isolated microspore culture and ethyl methanesulfonate mutagenesis. Compared with the wild-type line 'FT,' the fsm plants exhibited pistil abortion, and floral organs were also relatively smaller. Genetic analysis indicated that the phenotype of fsm is controlled by a single recessive nuclear gene. Morphological observations revealed that the presence of abnormal ovules in fsm likely influenced normal fertilization process, ultimately leading to female sterility. Comparative transcriptome analysis on the flower buds of 'FT' and fsm using RNA-Seq revealed a total of 1,872 differentially expressed genes (DEGs). Of these, a number of genes involved in pistil development were identified, such as PRETTY FEW SEEDS 2 (PFS2), temperature-induced lipocalin (TIL), AGAMOUS-LIKE (AGL), and HECATE (HEC). Furthermore, GO and KEGG pathway enrichment analyses of the DEGs suggested that a variety of biological processes and metabolic pathways are significantly enriched during pistil development. In addition, the expression patterns of 16 DEGs, including four pistil development-related genes and 12 floral organ development-related genes, were analyzed using qRT-PCR. A total of 31,272 single nucleotide polymorphisms were specifically detected in fsm. These results contribute to shed light on the regulatory mechanisms underlying pistil development in Chinese cabbage.
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Yang L, Wu Y, Yu M, Mao B, Zhao B, Wang J. Genome-wide transcriptome analysis of female-sterile rice ovule shed light on its abortive mechanism. PLANTA 2016; 244:1011-1028. [PMID: 27357232 DOI: 10.1007/s00425-016-2563-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Accepted: 06/23/2016] [Indexed: 05/03/2023]
Abstract
The comprehensive transcriptome analysis of rice female-sterile line and wild-type line ovule provides an important clue for exploring the regulatory network of the formation of rice fertile female gametophyte. Ovules are the female reproductive tissues of rice (Oryza sativa L.) and play a major role in sexual reproduction. To investigate the potential mechanism of rice female gametophyte fertility, we used RNA sequencing, combined with genetic subtraction, to compare the transcriptome of the ovules of a high-frequency female-sterile line (fsv1) and a rice wild-type line (Gui 99) during ovule development. Ovules were harvested at three developmental stages: ovule containing megaspore mother cell in meiosis process (stage 1), ovule containing functional megaspore in mitosis process (stage 2), and ovule containing mature female gametophyte (stage 3). Six cDNA libraries generated a total of 42.2 million high-quality clean reads that aligned with 30,204 genes. The comparison between the fsv1 and Gui 99 ovules identified a large number of differentially expressed genes (DEGs), i.e., 45, 495, and 932 DEGs at the three ovule developmental stages, respectively. From the comparison of the two rice lines, Gene Ontology, Kyoto Encyclopedia of Genes and Genomes, and MapMan analyses indicated that a large number of DEGs associated with starch and sucrose metabolism, plant hormone signal transduction, protein modification and degradation, oxidative phosphorylation, and receptor kinase. These DEGs might play roles in ovule development and fertile female gametophyte formation. Many transcription factor genes and epigenetic-related genes also exhibit different expression patterns and significantly different expression levels in two rice lines during ovule development, which might provide important information regarding the abortive mechanism of the female gametophyte in rice.
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Affiliation(s)
- Liyu Yang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Ya Wu
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Meiling Yu
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Bigang Mao
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha, 410125, China
| | - Bingran Zhao
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha, 410125, China.
| | - Jianbo Wang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China.
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Forestan C, Aiese Cigliano R, Farinati S, Lunardon A, Sanseverino W, Varotto S. Stress-induced and epigenetic-mediated maize transcriptome regulation study by means of transcriptome reannotation and differential expression analysis. Sci Rep 2016; 6:30446. [PMID: 27461139 PMCID: PMC4962059 DOI: 10.1038/srep30446] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Accepted: 06/27/2016] [Indexed: 12/25/2022] Open
Abstract
Plant's response and adaptation to abiotic stresses involve sophisticated genetic and epigenetic regulatory systems. To obtain a global view of molecular response to osmotic stresses, including the non-coding portion of genome, we conducted a total leaf transcriptome analysis on maize plants subjected to prolonged drought and salt stresses. Stress application to both B73 wild type and the epiregulator mutant rpd1-1/rmr6 allowed dissection of the epigenetic component of stress response. Coupling total RNA-Seq and transcriptome re-assembly we annotated thousands of new maize transcripts, together with 13,387 lncRNAs that may play critical roles in regulating gene expression. Differential expression analysis revealed hundreds of genes modulated by long-term stress application, including also many lncRNAs and transposons specifically induced by stresses. The amplitude and dynamic of the stress-modulated gene sets are very different between B73 and rpd1-1/rmr6 mutant plants, as result of stress-like effect on genome regulation caused by the mutation itself, which activates many stress-related genes even in control condition. The analyzed extensive set of total RNA-Seq data, together with the improvement of the transcriptome and the identification of the non-coding portion of the transcriptome give a revealing insight into the genetic and epigenetic mechanism responsible for maize molecular response to abiotic stresses.
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Affiliation(s)
- Cristian Forestan
- Department of Agronomy, Animals, Food, Natural Resources and Environment, University of Padova, Viale dell’Università 16, 35020 Legnaro (PD)-Italy
| | | | - Silvia Farinati
- Department of Agronomy, Animals, Food, Natural Resources and Environment, University of Padova, Viale dell’Università 16, 35020 Legnaro (PD)-Italy
| | - Alice Lunardon
- Department of Biology and Huck Institutes of the Life Sciences, Penn State University, University Park, PA 16802 USA
| | | | - Serena Varotto
- Department of Agronomy, Animals, Food, Natural Resources and Environment, University of Padova, Viale dell’Università 16, 35020 Legnaro (PD)-Italy
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Liang Z, Schnable JC. RNA-Seq Based Analysis of Population Structure within the Maize Inbred B73. PLoS One 2016; 11:e0157942. [PMID: 27348435 PMCID: PMC4922647 DOI: 10.1371/journal.pone.0157942] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Accepted: 06/07/2016] [Indexed: 12/23/2022] Open
Abstract
Recent reports have shown than many identically named genetic lines used in research around the world actually contain large amounts of uncharacterized genetic variation as a result of cross contamination of stocks, unintentional crossing, residual heterozygosity within original stocks, or de novo mutation. 27 public, large scale, RNA-seq datasets from 20 independent research groups around the world were used to assess variation within the maize (Zea mays ssp. mays) inbred B73, a four decade old variety which served as the reference genotype for the original maize genome sequencing project and is widely used in genetic, genomic, and phenotypic research. Several clearly distinct clades were identified among putatively B73 samples. A number of these clades were defined by the presence of clearly defined genomic blocks containing a haplotype which did not match the published B73 reference genome. The overall proportion of the maize genotype where multiple distinct haplotypes were observed across different research groups was approximately 2.3%. In some cases the relationship among B73 samples generated by different research groups recapitulated mentor/mentee relationships within the maize genetics community.
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Affiliation(s)
- Zhikai Liang
- Center for Plant Science Innovation & Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, United States of America
| | - James C. Schnable
- Center for Plant Science Innovation & Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, United States of America
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45
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Characterizing and annotating the genome using RNA-seq data. SCIENCE CHINA-LIFE SCIENCES 2016; 60:116-125. [PMID: 27294835 DOI: 10.1007/s11427-015-0349-4] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Accepted: 12/16/2015] [Indexed: 10/21/2022]
Abstract
Bioinformatics methods for various RNA-seq data analyses are in fast evolution with the improvement of sequencing technologies. However, many challenges still exist in how to efficiently process the RNA-seq data to obtain accurate and comprehensive results. Here we reviewed the strategies for improving diverse transcriptomic studies and the annotation of genetic variants based on RNA-seq data. Mapping RNA-seq reads to the genome and transcriptome represent two distinct methods for quantifying the expression of genes/transcripts. Besides the known genes annotated in current databases, many novel genes/transcripts (especially those long noncoding RNAs) still can be identified on the reference genome using RNA-seq. Moreover, owing to the incompleteness of current reference genomes, some novel genes are missing from them. Genome- guided and de novo transcriptome reconstruction are two effective and complementary strategies for identifying those novel genes/transcripts on or beyond the reference genome. In addition, integrating the genes of distinct databases to conduct transcriptomics and genetics studies can improve the results of corresponding analyses.
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46
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Ambrosino L, Bostan H, Ruggieri V, Chiusano ML. Bioinformatics resources for pollen. PLANT REPRODUCTION 2016; 29:133-147. [PMID: 27271281 DOI: 10.1007/s00497-016-0284-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Accepted: 05/19/2016] [Indexed: 06/06/2023]
Abstract
Bioinformatics for Pollen. Pollen plays a key role in crop production, and its development is the most delicate phase in reproduction. Different metabolic pathways are involved in pollen development, and changes in the level of some metabolites, as well as responses to stress, are correlated with the reduction in pollen viability, leading consequently to a decrease in the fruit production. However, studies on pollen may be hard because gamete development and fertilization are complex processes that occur during a short window of time. The rise of the so-called -omics sciences provided key strategies to promote molecular research in pollen tissues, starting from model organisms and moving to increasing number of species. An integrated multi-level approach based on investigations from genomics, transcriptomics, proteomics and metabolomics appears now feasible to clarify key molecular processes in pollen development and viability. To this aim, bioinformatics has a fundamental role for data production and analysis, contributing varied and ad hoc methodologies, endowed with different sensitivity and specificity, necessary for extracting added-value information from the large amount of molecular data achievable. Bioinformatics is also essential for data management, organization, distribution and integration in suitable resources. This is necessary to catch the biological features of the pollen tissues and to design effective approaches to identifying structural or functional properties, enabling the modeling of the major involved processes in normal or in stress conditions. In this review, we provide an overview of the available bioinformatics resources for pollen, ranging from raw data collections to complete databases or platforms, when available, which include data and/or results from -omics efforts on the male gametophyte. Perspectives in the fields will also be described.
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Affiliation(s)
- Luca Ambrosino
- Department of Agricultural Sciences, University of Naples "Federico II", via Università 100, Portici (NA), 80055, Italy
| | - Hamed Bostan
- Department of Agricultural Sciences, University of Naples "Federico II", via Università 100, Portici (NA), 80055, Italy
| | - Valentino Ruggieri
- Department of Agricultural Sciences, University of Naples "Federico II", via Università 100, Portici (NA), 80055, Italy
| | - Maria Luisa Chiusano
- Department of Agricultural Sciences, University of Naples "Federico II", via Università 100, Portici (NA), 80055, Italy.
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Lora J, Hormaza JI, Herrero M. The Diversity of the Pollen Tube Pathway in Plants: Toward an Increasing Control by the Sporophyte. FRONTIERS IN PLANT SCIENCE 2016; 7:107. [PMID: 26904071 PMCID: PMC4746263 DOI: 10.3389/fpls.2016.00107] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2015] [Accepted: 01/20/2016] [Indexed: 05/06/2023]
Abstract
Plants, unlike animals, alternate multicellular diploid, and haploid generations in their life cycle. While this is widespread all along the plant kingdom, the size and autonomy of the diploid sporophyte and the haploid gametophyte generations vary along evolution. Vascular plants show an evolutionary trend toward a reduction of the gametophyte, reflected both in size and lifespan, together with an increasing dependence from the sporophyte. This has resulted in an overlooking of the importance of the gametophytic phase in the evolution of higher plants. This reliance on the sporophyte is most notorious along the pollen tube journey, where the male gametophytes have to travel a long way inside the sporophyte to reach the female gametophyte. Along evolution, there is a change in the scenery of the pollen tube pathway that favors pollen competition and selection. This trend, toward apparently making complicated what could be simple, appears to be related to an increasing control of the sporophyte over the gametophyte with implications for understanding plant evolution.
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Affiliation(s)
- Jorge Lora
- Department of Subtropical Fruit Crops, Instituto de Hortofruticultura Subtropical y Mediterránea La Mayora – University of Málaga – Consejo Superior de Investigaciones CientíficasMálaga, Spain
| | - José I. Hormaza
- Department of Subtropical Fruit Crops, Instituto de Hortofruticultura Subtropical y Mediterránea La Mayora – University of Málaga – Consejo Superior de Investigaciones CientíficasMálaga, Spain
| | - María Herrero
- Department of Pomology, Estación Experimental Aula Dei, Consejo Superior de Investigaciones CientíficasZaragoza, Spain
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48
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Freeling M, Scanlon MJ, Fowler JE. Fractionation and subfunctionalization following genome duplications: mechanisms that drive gene content and their consequences. Curr Opin Genet Dev 2015; 35:110-8. [PMID: 26657818 DOI: 10.1016/j.gde.2015.11.002] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2015] [Revised: 11/09/2015] [Accepted: 11/09/2015] [Indexed: 12/11/2022]
Abstract
A gene's duplication relaxes selection. Loss of duplicate, low-function DNA (fractionation) sometimes follows, mostly by deletion in plants, but mostly via the pseudogene pathway in fish and other clades with smaller population sizes. Subfunctionalization--the founding term of the Xfunctionalization lexicon--while not the general cause of differences in duplicate gene retention, becomes primary as the number of a gene's cis-regulatory sites increases. Balanced gene drive explains retention for the average gene. Both maintenance-of-balance and subfunctionalization drive gene content nonrandomly, and currently fall outside of our accepted Theory of Evolution. The 'typical' mutation encountered by a gene duplicate is not a neutral loss-of-function; dominant mutations (Muller's lexicon; these are not neutral) abound, and confound X functionalization terms like 'neofunctionalization'. Confusion of words may cause confusion of thought. As with many plants, fish tetraploidies provide a higher throughput surrogate-genetic method to infer function from human and other vertebrate ENCODE-like regulatory sites.
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Affiliation(s)
- Michael Freeling
- Department of Plant and Microbial Biology, Univ. California, Berkeley, CA 94720, United States.
| | - Michael J Scanlon
- Section of Plant Biology, Cornell University, Ithaca, NY 14853, United States
| | - John E Fowler
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, United States
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49
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Uebler S, Márton ML, Dresselhaus T. Classification of EA1-box proteins and new insights into their role during reproduction in grasses. PLANT REPRODUCTION 2015; 28:183-197. [PMID: 26498589 DOI: 10.1007/s00497-015-0269-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2015] [Accepted: 10/15/2015] [Indexed: 06/05/2023]
Abstract
EA1-box protein classification. Success in reproduction and vegetative development in flowering plants strongly depends on precise cell-to-cell signaling events mediated by secreted peptides.A small peptide family named as EA1-like (EAL) has been first described 10 years ago and includes EA1 involved in pollen tubes attraction by the female gametophyte and EAL1-regulating germ cell identity in maize. EALs consist of an N-terminal endoplasmic reticulum-targeting motif, the highly conserved EA1-box and a short C-terminal alanine-rich domain. Whereas EAL peptides are exclusively found in the Gramineae, the EA1-box is widely distributed throughout the plant kingdom. Based on in silico analysis and subcellular localization studies, we report here a new classification of EA1-box proteins in flowering plants. They can be distinguished into three protein classes: the already defined EAL proteins, the EAG (EA1-box glycine-rich) proteins and the EAC (EA1-box containing)proteins. While fusion proteins of EAL and EAC classes locate to the secretory pathway, EAGs are cytoplasmic and locate also to the nucleus. Moreover, we further show that the third EAL protein of Zea mays, EAL2, appears to be also involved in processes related to late embryogenic development as its peptide level increases after formation of leaf primordia. Immunohistochemical studies indicate its presence in the scutellar parenchyma and around the vasculature, where it is secreted to the extracellular space. In conclusion, the members of the maize EAL family possess very diverse functions during reproduction and it will now be exciting to elucidate the functions of EAGs and EACs in plants.
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Harkess A, Mercati F, Shan HY, Sunseri F, Falavigna A, Leebens-Mack J. Sex-biased gene expression in dioecious garden asparagus (Asparagus officinalis). THE NEW PHYTOLOGIST 2015; 207:883-92. [PMID: 25817071 DOI: 10.1111/nph.13389] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2014] [Accepted: 02/07/2015] [Indexed: 05/21/2023]
Abstract
Sex chromosomes have evolved independently in phylogenetically diverse flowering plant lineages. The genes governing sex determination in dioecious species remain unknown, but theory predicts that the linkage of genes influencing male and female function will spur the origin and early evolution of sex chromosomes. For example, in an XY system, the origin of an active Y may be spurred by the linkage of female suppressing and male promoting genes. Garden asparagus (Asparagus officinalis) serves as a model for plant sex chromosome evolution, given that it has recently evolved an XX/XY sex chromosome system. In order to elucidate the molecular basis of gender differences and sex determination, we used RNA-sequencing (RNA-Seq) to identify differentially expressed genes between female (XX), male (XY) and supermale (YY) individuals. We identified 570 differentially expressed genes, and showed that significantly more genes exhibited male-biased than female-biased expression in garden asparagus. In the context of anther development, we identified genes involved in pollen microspore and tapetum development that were specifically expressed in males and supermales. Comparative analysis of genes in the Arabidopsis thaliana, Zea mays and Oryza sativa anther development pathways shows that anther sterility in females probably occurs through interruption of tapetum development before microspore meiosis.
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Affiliation(s)
- Alex Harkess
- Department of Plant Biology, University of Georgia, Athens, GA, 30602, USA
| | - Francesco Mercati
- Dipartimento di AGRARIA, Università Mediterranea di Reggio Calabria, Salita Melissari, 89124, Reggio Calabria (RC), Italy
- CNR - National Research Council of Italy, Institute of Biosciences and Bioresources, Corso Calatafimi 414, 90129, Palermo, Italy
| | - Hong-Yan Shan
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, 20 Nanxincu, Xiangshan, Beijing, 100093, China
| | - Francesco Sunseri
- Dipartimento di AGRARIA, Università Mediterranea di Reggio Calabria, Salita Melissari, 89124, Reggio Calabria (RC), Italy
| | - Agostino Falavigna
- Consiglio per la Ricerca e la Sperimentazione in Agricoltura - Research Unit for Vegetable Crops, Montanaso Lombardo, 26836, Lodi, Italy
| | - Jim Leebens-Mack
- Department of Plant Biology, University of Georgia, Athens, GA, 30602, USA
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