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Title: Light-responsive expression atlas reveals the effects of light quality and intensity in Kalanchoë fedtschenkoi, a plant with crassulacean acid metabolism

Abstract

•Crassulacean acid metabolism (CAM), a specialized mode of photosynthesis, enables plant adaptation to water-limited environments and improves photosynthetic efficiency via a carbon concentrating mechanism. Kalanchoë fedtschenkoi is an obligate CAM model featuring a relatively small genome and easy stable transformation. But the molecular responses of regulation by light quality and intensity in CAM plants is still unknown. •Here we present a genome-wide expression atlas of K. fedtschenkoi plants grown under 12h/12h photoperiod with different light quality (blue, red, far-red, white light) and intensity (0, 150, 250 and 1000 μmol m–2 s–1) based on RNA-Seq performed for mature leaf samples collected at dawn (2-h before the starting of lighting period) and dusk (2-h before the dark period). •An eFP web browser was created for easy access of the gene expression data. Based on the expression atlas, we constructed a light-responsive co-expression network to reveal the potential regulatory relationships in K. fedtschenkoi. Furthermore, CAM-related sub-networks were highlighted to showcase genes relevant to CAM pathway, circadian clock and stomatal movement. •This study provides a novel genomics resource for investigating the molecular mechanism underlying the light regulation of physiology and metabolism in CAM plants.

Authors:
ORCiD logo [1];  [2];  [3];  [4];  [5];  [5];  [4];  [2];  [5];  [6];  [4];  [7];  [8];  [8];  [1];  [1];  [1]; ORCiD logo [1]
+ Show Author Affiliations
  1. Biosciences Division, Oak Ridge National Laboratory, 1 Bethel Valley Rd, Oak Ridge, TN 37831, USA, The Center for Bioenergy Innovation, Oak Ridge National Laboratory, 1 Bethel Valley Rd, Oak Ridge, TN 37831, USA
  2. Biosciences Division, Oak Ridge National Laboratory, 1 Bethel Valley Rd, Oak Ridge, TN 37831, USA
  3. HudsonAlpha Institute for Biotechnology, 601 Genome Way, Huntsville, AL 35801, USA
  4. Department of Biochemistry and Molecular Biology, University of Nevada, 1664 N. Virginia St, Reno, NV 89557, USA
  5. US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
  6. HudsonAlpha Institute for Biotechnology, 601 Genome Way, Huntsville, AL 35801, USA, US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
  7. Biosciences Division, Oak Ridge National Laboratory, 1 Bethel Valley Rd, Oak Ridge, TN 37831, USA, School of Natural and Environmental Science, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
  8. Department of Cell and Systems Biology, Centre for the Analysis of Genome Evolution and Function, University of Toronto, 25 Willcocks St #4038, Toronto, ON M5S 3B2, Canada
Publication Date:
Research Org.:
Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States); Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER)
OSTI Identifier:
1603213
Alternate Identifier(s):
OSTI ID: 1615309; OSTI ID: 1649601
Grant/Contract Number:  
SC0008834; 503025; AC02-05CH11231; AC05-00OR22725
Resource Type:
Published Article
Journal Name:
GigaScience
Additional Journal Information:
Journal Name: GigaScience Journal Volume: 9 Journal Issue: 3; Journal ID: ISSN 2047-217X
Publisher:
BioMed Central
Country of Publication:
United Kingdom
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES

Citation Formats

Zhang, Jin, Hu, Rongbin, Sreedasyam, Avinash, Garcia, Travis M., Lipzen, Anna, Wang, Mei, Yerramsetty, Pradeep, Liu, Degao, Ng, Vivian, Schmutz, Jeremy, Cushman, John C., Borland, Anne M., Pasha, Asher, Provart, Nicholas J., Chen, Jin-Gui, Muchero, Wellington, Tuskan, Gerald A., and Yang, Xiaohan. Light-responsive expression atlas reveals the effects of light quality and intensity in Kalanchoë fedtschenkoi, a plant with crassulacean acid metabolism. United Kingdom: N. p., 2020. Web. doi:10.1093/gigascience/giaa018.
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Zhang, Jin, Hu, Rongbin, Sreedasyam, Avinash, Garcia, Travis M., Lipzen, Anna, Wang, Mei, Yerramsetty, Pradeep, Liu, Degao, Ng, Vivian, Schmutz, Jeremy, Cushman, John C., Borland, Anne M., Pasha, Asher, Provart, Nicholas J., Chen, Jin-Gui, Muchero, Wellington, Tuskan, Gerald A., & Yang, Xiaohan. Light-responsive expression atlas reveals the effects of light quality and intensity in Kalanchoë fedtschenkoi, a plant with crassulacean acid metabolism. United Kingdom. https://doi.org/10.1093/gigascience/giaa018
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Zhang, Jin, Hu, Rongbin, Sreedasyam, Avinash, Garcia, Travis M., Lipzen, Anna, Wang, Mei, Yerramsetty, Pradeep, Liu, Degao, Ng, Vivian, Schmutz, Jeremy, Cushman, John C., Borland, Anne M., Pasha, Asher, Provart, Nicholas J., Chen, Jin-Gui, Muchero, Wellington, Tuskan, Gerald A., and Yang, Xiaohan. Thu . "Light-responsive expression atlas reveals the effects of light quality and intensity in Kalanchoë fedtschenkoi, a plant with crassulacean acid metabolism". United Kingdom. https://doi.org/10.1093/gigascience/giaa018.
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@article{osti_1603213,
title = {Light-responsive expression atlas reveals the effects of light quality and intensity in Kalanchoë fedtschenkoi, a plant with crassulacean acid metabolism},
author = {Zhang, Jin and Hu, Rongbin and Sreedasyam, Avinash and Garcia, Travis M. and Lipzen, Anna and Wang, Mei and Yerramsetty, Pradeep and Liu, Degao and Ng, Vivian and Schmutz, Jeremy and Cushman, John C. and Borland, Anne M. and Pasha, Asher and Provart, Nicholas J. and Chen, Jin-Gui and Muchero, Wellington and Tuskan, Gerald A. and Yang, Xiaohan},
abstractNote = {•Crassulacean acid metabolism (CAM), a specialized mode of photosynthesis, enables plant adaptation to water-limited environments and improves photosynthetic efficiency via a carbon concentrating mechanism. Kalanchoë fedtschenkoi is an obligate CAM model featuring a relatively small genome and easy stable transformation. But the molecular responses of regulation by light quality and intensity in CAM plants is still unknown. •Here we present a genome-wide expression atlas of K. fedtschenkoi plants grown under 12h/12h photoperiod with different light quality (blue, red, far-red, white light) and intensity (0, 150, 250 and 1000 μmol m–2 s–1) based on RNA-Seq performed for mature leaf samples collected at dawn (2-h before the starting of lighting period) and dusk (2-h before the dark period). •An eFP web browser was created for easy access of the gene expression data. Based on the expression atlas, we constructed a light-responsive co-expression network to reveal the potential regulatory relationships in K. fedtschenkoi. Furthermore, CAM-related sub-networks were highlighted to showcase genes relevant to CAM pathway, circadian clock and stomatal movement. •This study provides a novel genomics resource for investigating the molecular mechanism underlying the light regulation of physiology and metabolism in CAM plants.},
doi = {10.1093/gigascience/giaa018},
journal = {GigaScience},
number = 3,
volume = 9,
place = {United Kingdom},
year = {Thu Mar 05 00:00:00 EST 2020},
month = {Thu Mar 05 00:00:00 EST 2020}
}
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Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record
https://doi.org/10.1093/gigascience/giaa018
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Cited by: 7 works
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Figures / Tables:

Figure 1 Figure 1: Kalanchoë light-responsive eFP browser. (a)View of the eFP browser including the RNA-Seq dataset described in this study. Expression values in the samples are indicated by a color gradient, where yellow indicates low expression and red indicates high expression. The legend describing the color gradient and expression valuesmore » is shown in the bottom left corner. CCA1 gene Kaladp0496s0018 is used as an example. The leaf samples were collected at dawn (i.e., 2 h before the light period) and dusk (i.e., 2 h before the dark period) under control condition (white light) and various light quality conditions (blue, red, and far-red light) and light intensity conditions (dark growth, low light intensity, and high light intensity). TPM: transcripts per million. (b) Kalanchoë genes CCA1 (Kaladp0496s0018) and HY5 (Kaladp0060s0460) displayed in a comparative view of the expression level extracted from the eFP browser. The legend describing the color gradient and log2 ratio is shown in the bottom left corner.« less
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