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Title: Temporal and spatial transcriptomic and microRNA dynamics of CAM photosynthesis in pineapple

Authors:
 [1]; ORCiD logo [2];  [3];  [3];  [3];  [4];  [5];  [6]; ORCiD logo [6];  [6];  [7]; ORCiD logo [5];  [1]
  1. FAFU and UIUC Joint Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Corps, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou 350002 Fujian China, Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana IL 61801 USA
  2. FAFU and UIUC Joint Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Corps, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou 350002 Fujian China, Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana IL 61801 USA, Donald Danforth Plant Science Center, St. Louis MO USA, Department of Horticulture, Michigan State University, East Lansing MI 48823 USA
  3. FAFU and UIUC Joint Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Corps, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou 350002 Fujian China
  4. Department of Horticulture, Michigan State University, East Lansing MI 48823 USA
  5. Department of Biochemistry and Molecular Biology, MS330, University of Nevada, Reno NV 89557-0330 USA
  6. Donald Danforth Plant Science Center, St. Louis MO USA
  7. Department of Plant Sciences, University of Oxford, South Parks Road Oxford OX1 3RB UK
Publication Date:
Sponsoring Org.:
USDOE
OSTI Identifier:
1375654
Grant/Contract Number:
SC0008834
Resource Type:
Journal Article: Publisher's Accepted Manuscript
Journal Name:
The Plant Journal
Additional Journal Information:
Related Information: CHORUS Timestamp: 2017-10-20 16:25:20; Journal ID: ISSN 0960-7412
Publisher:
Society for Experimental Biology
Country of Publication:
United Kingdom
Language:
English

Citation Formats

Wai, Ching M., VanBuren, Robert, Zhang, Jisen, Huang, Lixian, Miao, Wenjing, Edger, Patrick P., Yim, Won C., Priest, Henry D., Meyers, Blake C., Mockler, Todd, Smith, J. Andrew C., Cushman, John C., and Ming, Ray. Temporal and spatial transcriptomic and microRNA dynamics of CAM photosynthesis in pineapple. United Kingdom: N. p., 2017. Web. doi:10.1111/tpj.13630.
Wai, Ching M., VanBuren, Robert, Zhang, Jisen, Huang, Lixian, Miao, Wenjing, Edger, Patrick P., Yim, Won C., Priest, Henry D., Meyers, Blake C., Mockler, Todd, Smith, J. Andrew C., Cushman, John C., & Ming, Ray. Temporal and spatial transcriptomic and microRNA dynamics of CAM photosynthesis in pineapple. United Kingdom. doi:10.1111/tpj.13630.
Wai, Ching M., VanBuren, Robert, Zhang, Jisen, Huang, Lixian, Miao, Wenjing, Edger, Patrick P., Yim, Won C., Priest, Henry D., Meyers, Blake C., Mockler, Todd, Smith, J. Andrew C., Cushman, John C., and Ming, Ray. 2017. "Temporal and spatial transcriptomic and microRNA dynamics of CAM photosynthesis in pineapple". United Kingdom. doi:10.1111/tpj.13630.
@article{osti_1375654,
title = {Temporal and spatial transcriptomic and microRNA dynamics of CAM photosynthesis in pineapple},
author = {Wai, Ching M. and VanBuren, Robert and Zhang, Jisen and Huang, Lixian and Miao, Wenjing and Edger, Patrick P. and Yim, Won C. and Priest, Henry D. and Meyers, Blake C. and Mockler, Todd and Smith, J. Andrew C. and Cushman, John C. and Ming, Ray},
abstractNote = {},
doi = {10.1111/tpj.13630},
journal = {The Plant Journal},
number = ,
volume = ,
place = {United Kingdom},
year = 2017,
month = 7
}

Journal Article:
Free Publicly Available Full Text
This content will become publicly available on August 21, 2018
Publisher's Accepted Manuscript

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  • Pineapple (Ananas comosus (L.) Merr.) is the most economically valuable crop possessing crassulacean acid metabolism (CAM), a photosynthetic carbon assimilation pathway with high water-use efficiency, and the second most important tropical fruit. We sequenced the genomes of pineapple varieties F153 and MD2 and a wild pineapple relative, Ananas bracteatus accession CB5. The pineapple genome has one fewer ancient whole-genome duplication event than sequenced grass genomes and a conserved karyotype with seven chromosomes from before the ρ duplication event. The pineapple lineage has transitioned from C 3 photosynthesis to CAM, with CAM-related genes exhibiting a diel expression pattern in photosynthetic tissues.more » CAM pathway genes were enriched with cis-regulatory elements associated with the regulation of circadian clock genes, providing the first cis-regulatory link between CAM and circadian clock regulation. Lastly, we found pineapple CAM photosynthesis evolved by the reconfiguration of pathways in C 3 plants, through the regulatory neofunctionalization of preexisting genes and not through the acquisition of neofunctionalized genes via whole-genome or tandem gene duplication.« less
  • Pineapple ( Ananas comosus (L.) Merr.) is the most economically valuable crop possessing crassulacean acid metabolism (CAM), a photosynthetic carbon assimilation pathway with high water-use efficiency, and the second most important tropical fruit. We sequenced the genomes of pineapple varieties F153 and MD2 and a wild pineapple relative, Ananas bracteatus accession CB5. The pineapple genome has one fewer ancient whole-genome duplication event than sequenced grass genomes and a conserved karyotype with seven chromosomes from before the ρ duplication event. The pineapple lineage has transitioned from C 3 photosynthesis to CAM, with CAM-related genes exhibiting a diel expression pattern in photosyntheticmore » tissues. CAM pathway genes were enriched with cis-regulatory elements associated with the regulation of circadian clock genes, providing the first cis-regulatory link between CAM and circadian clock regulation. Pineapple CAM photosynthesis evolved by the reconfiguration of pathways in C 3 plants, through the regulatory neofunctionalization of preexisting genes and not through the acquisition of neofunctionalized genes via whole-genome or tandem gene duplication.« less
  • Cited by 5
  • Desulfovibrio vulgaris was cultivated in a defined mediumand biomass was sampled over time for approximately 70 h to characterizethe shifts in gene expression as cells transitioned from exponential tostationary phase during electron donor depletion. In addition to temporaltranscriptomics; total protein, carbohydrate, lactate, acetate, andsulfate levels were measured. The microarray data were analyzed forstatistically significant expression changes, hierarchical clusteranalysis, and promoter element prediction, and were validated viaquantitative PCR. As the cells transitioned from exponential tostationary-phase a majority of the down-expressed genes were involved intranslation and transcription, and this trend continued in the remainingtime points. Intracellular trafficking and secretion, ion transport, andcoenzymemore » metabolism showed a general increase in relative expression asthe cells entered stationary phase. As expected, DNA replicationmachinery was down expressed, and genes involved in DNA repair increasedin expression during stationary-phase. Genes involved in amino acidacquisition, carbohydrate metabolism, energy production, and cellenvelope biogenesis did not exhibit uniform transcriptional responses.Interestingly, most phage-related genes were up-expressed at the onset ofstationary-phase. This result suggested that nutrient depletion mayimpact community dynamics and DNA transfer mechanisms of sulfate-reducingbacteria via phage cycle. The putative feoAB system (in addition to otherpresumptive iron metabolism genes) was significantly up-expressed, andsuggested the possible importance of Fe2+ acquisition undermetal-reducing conditions. A large subset of carbohydrate-related geneshad altered gene expression, and the total cellular carbohydrate levelsdeclined during the growth phase transition. Interestingly, the D.vulgaris genome does not contain a putative rpoS gene, a common attributeof the d-Proteobacteria genomes sequenced to date, and other putative rpogenes did not have significantly altered transcription profiles. Ourresults indicated that in addition to expected changes (e.g., energyconversion, protein turnover, translation, transcription, and DNAreplication/repair) genes related to phage, stress response, carbohydrateflux, outer envelop, and iron homeostasis played important roles as D.vulgaris cells experienced electron donor depletion.« less
  • Desulfovibrio vulgaris was cultivated in a defined medium, and biomass was sampled for approximately 70 h to characterize the shifts in gene expression as cells transitioned from the exponential to the stationary phase during electron donor depletion. In addition to temporal transcriptomics, total protein, carbohydrate, lactate, acetate, and sulfate levels were measured. The microarray data were examined for statistically significant expression changes, hierarchical cluster analysis, and promoter element prediction and were validated by quantitative PCR. As the cells transitioned from the exponential phase to the stationary phase, a majority of the down-expressed genes were involved in translation and transcription, andmore » this trend continued at the remaining times. There were general increases in relative expression for intracellular trafficking and secretion, ion transport, and coenzyme metabolism as the cells entered the stationary phase. As expected, the DNA replication machinery was down-expressed, and the expression of genes involved in DNA repair increased during the stationary phase. Genes involved in amino acid acquisition, carbohydrate metabolism, energy production, and cell envelope biogenesis did not exhibit uniform transcriptional responses. Interestingly, most phage-related genes were up-expressed at the onset of the stationary phase. This result suggested that nutrient depletion may affect community dynamics and DNA transfer mechanisms of sulfate-reducing bacteria via the phage cycle. The putative feoAB system (in addition to other presumptive iron metabolism genes) was significantly up-expressed, and this suggested the possible importance of Fe{sup 2+} acquisition under metal-reducing conditions. The expression of a large subset of carbohydrate-related genes was altered, and the total cellular carbohydrate levels declined during the growth phase transition. Interestingly, the D. vulgaris genome does not contain a putative rpoS gene, a common attribute of the {delta}-Proteobacteria genomes sequenced to date, and the transcription profiles of other putative rpo genes were not significantly altered. Our results indicated that in addition to expected changes (e.g., energy conversion, protein turnover, translation, transcription, and DNA replication and repair), genes related to phage, stress response, carbohydrate flux, the outer envelope, and iron homeostasis played important roles as D. vulgaris cells experienced electron donor depletion.« less