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CRISPR/Cas9-mediated targeted mutagenesis for functional genomics research of crassulacean acid metabolism plants
Abstract Crassulacean acid metabolism (CAM) is an important photosynthetic pathway in diverse lineages of plants featuring high water-use efficiency and drought tolerance. A big challenge facing the CAM research community is to understand the function of the annotated genes in CAM plant genomes. Rec...
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| Published in: | Journal of experimental botany 2019-11, Vol.70 (22), p.6621-6629 |
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| Main Authors: | , , , , , , , , |
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| cited_by | cdi_FETCH-LOGICAL-c435t-3b930d3db304ca1d51a9ac0068d2d7c955254691669c8c6c11168dbd8243be103 |
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| cites | cdi_FETCH-LOGICAL-c435t-3b930d3db304ca1d51a9ac0068d2d7c955254691669c8c6c11168dbd8243be103 |
| container_end_page | 6629 |
| container_issue | 22 |
| container_start_page | 6621 |
| container_title | Journal of experimental botany |
| container_volume | 70 |
| creator | Liu, Degao Chen, Mei Mendoza, Brian Cheng, Hua Hu, Rongbin Li, Linling Trinh, Cong T Tuskan, Gerald A Yang, Xiaohan |
| description | Abstract
Crassulacean acid metabolism (CAM) is an important photosynthetic pathway in diverse lineages of plants featuring high water-use efficiency and drought tolerance. A big challenge facing the CAM research community is to understand the function of the annotated genes in CAM plant genomes. Recently, a new genome editing technology using CRISPR/Cas9 has become a more precise and powerful tool than traditional approaches for functional genomics research in C3 and C4 plants. In this study, we explore the potential of CRISPR/Cas9 to characterize the function of CAM-related genes in the model CAM species Kalanchoë fedtschenkoi. We demonstrate that CRISPR/Cas9 is effective in creating biallelic indel mutagenesis to reveal previously unknown roles of blue light receptor phototropin 2 (KfePHOT2) in the CAM pathway. Knocking out KfePHOT2 reduced stomatal conductance and CO2 fixation in late afternoon and increased stomatal conductance and CO2 fixation during the night, indicating that blue light signaling plays an important role in the CAM pathway. Lastly, we provide a genome-wide guide RNA database targeting 45 183 protein-coding transcripts annotated in the K. fedtschenkoi genome.
Loss-of-function analysis using CRISPR/Cas9-mediated mutagenesis provides new insight into the role of phototropin 2 in crassulacean acid metabolism |
| doi_str_mv | 10.1093/jxb/erz415 |
| format | article |
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Crassulacean acid metabolism (CAM) is an important photosynthetic pathway in diverse lineages of plants featuring high water-use efficiency and drought tolerance. A big challenge facing the CAM research community is to understand the function of the annotated genes in CAM plant genomes. Recently, a new genome editing technology using CRISPR/Cas9 has become a more precise and powerful tool than traditional approaches for functional genomics research in C3 and C4 plants. In this study, we explore the potential of CRISPR/Cas9 to characterize the function of CAM-related genes in the model CAM species Kalanchoë fedtschenkoi. We demonstrate that CRISPR/Cas9 is effective in creating biallelic indel mutagenesis to reveal previously unknown roles of blue light receptor phototropin 2 (KfePHOT2) in the CAM pathway. Knocking out KfePHOT2 reduced stomatal conductance and CO2 fixation in late afternoon and increased stomatal conductance and CO2 fixation during the night, indicating that blue light signaling plays an important role in the CAM pathway. Lastly, we provide a genome-wide guide RNA database targeting 45 183 protein-coding transcripts annotated in the K. fedtschenkoi genome.
Loss-of-function analysis using CRISPR/Cas9-mediated mutagenesis provides new insight into the role of phototropin 2 in crassulacean acid metabolism</description><identifier>ISSN: 0022-0957</identifier><identifier>EISSN: 1460-2431</identifier><identifier>DOI: 10.1093/jxb/erz415</identifier><identifier>PMID: 31562521</identifier><language>eng</language><publisher>UK: Oxford University Press</publisher><subject>Base Sequence ; BASIC BIOLOGICAL SCIENCES ; Carboxylic Acids - metabolism ; crassulacean acid metabolism ; CRISPR-Cas Systems - genetics ; CRISPR/Cas9 ; Databases, Genetic ; functional genomics ; genome-editing ; Genomics ; Mutagenesis - genetics ; Mutation - genetics ; phototropin 2 ; Plants - genetics ; Research Papers ; RNA, Guide, CRISPR-Cas Systems - genetics</subject><ispartof>Journal of experimental botany, 2019-11, Vol.70 (22), p.6621-6629</ispartof><rights>The Author(s) 2019. Published by Oxford University Press on behalf of the Society for Experimental Biology. 2019</rights><rights>The Author(s) 2019. Published by Oxford University Press on behalf of the Society for Experimental Biology.</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c435t-3b930d3db304ca1d51a9ac0068d2d7c955254691669c8c6c11168dbd8243be103</citedby><cites>FETCH-LOGICAL-c435t-3b930d3db304ca1d51a9ac0068d2d7c955254691669c8c6c11168dbd8243be103</cites><orcidid>0000-0001-5207-4210</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><link.rule.ids>230,314,780,784,885,27924,27925</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/31562521$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink><backlink>$$Uhttps://www.osti.gov/servlets/purl/1569393$$D View this record in Osti.gov$$Hfree_for_read</backlink></links><search><contributor>Hultine, Kevin</contributor><creatorcontrib>Liu, Degao</creatorcontrib><creatorcontrib>Chen, Mei</creatorcontrib><creatorcontrib>Mendoza, Brian</creatorcontrib><creatorcontrib>Cheng, Hua</creatorcontrib><creatorcontrib>Hu, Rongbin</creatorcontrib><creatorcontrib>Li, Linling</creatorcontrib><creatorcontrib>Trinh, Cong T</creatorcontrib><creatorcontrib>Tuskan, Gerald A</creatorcontrib><creatorcontrib>Yang, Xiaohan</creatorcontrib><creatorcontrib>Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States)</creatorcontrib><title>CRISPR/Cas9-mediated targeted mutagenesis for functional genomics research of crassulacean acid metabolism plants</title><title>Journal of experimental botany</title><addtitle>J Exp Bot</addtitle><description>Abstract
Crassulacean acid metabolism (CAM) is an important photosynthetic pathway in diverse lineages of plants featuring high water-use efficiency and drought tolerance. A big challenge facing the CAM research community is to understand the function of the annotated genes in CAM plant genomes. Recently, a new genome editing technology using CRISPR/Cas9 has become a more precise and powerful tool than traditional approaches for functional genomics research in C3 and C4 plants. In this study, we explore the potential of CRISPR/Cas9 to characterize the function of CAM-related genes in the model CAM species Kalanchoë fedtschenkoi. We demonstrate that CRISPR/Cas9 is effective in creating biallelic indel mutagenesis to reveal previously unknown roles of blue light receptor phototropin 2 (KfePHOT2) in the CAM pathway. Knocking out KfePHOT2 reduced stomatal conductance and CO2 fixation in late afternoon and increased stomatal conductance and CO2 fixation during the night, indicating that blue light signaling plays an important role in the CAM pathway. Lastly, we provide a genome-wide guide RNA database targeting 45 183 protein-coding transcripts annotated in the K. fedtschenkoi genome.
Loss-of-function analysis using CRISPR/Cas9-mediated mutagenesis provides new insight into the role of phototropin 2 in crassulacean acid metabolism</description><subject>Base Sequence</subject><subject>BASIC BIOLOGICAL SCIENCES</subject><subject>Carboxylic Acids - metabolism</subject><subject>crassulacean acid metabolism</subject><subject>CRISPR-Cas Systems - genetics</subject><subject>CRISPR/Cas9</subject><subject>Databases, Genetic</subject><subject>functional genomics</subject><subject>genome-editing</subject><subject>Genomics</subject><subject>Mutagenesis - genetics</subject><subject>Mutation - genetics</subject><subject>phototropin 2</subject><subject>Plants - genetics</subject><subject>Research Papers</subject><subject>RNA, Guide, CRISPR-Cas Systems - genetics</subject><issn>0022-0957</issn><issn>1460-2431</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2019</creationdate><recordtype>article</recordtype><sourceid>TOX</sourceid><recordid>eNp9kVFrFDEQx4NY7Fl98QNIEPoibC_ZbNLNiyBHtYWCUtvnMDubvUvZTc4kK62fvjmuLfbFp4TMj9_M5E_IB85OONNieXvXLW3823D5iix4o1hVN4K_JgvG6rpiWp4ekrcp3TLGJJPyDTkUXKpa1nxBfq-uLn79vFquIOlqsr2DbHuaIa7t7jLNGdbW2-QSHUKkw-wxu-BhpOU5TA4TjTZZiLihYaAYIaV5BLTgKaArBpuhC6NLE92O4HN6Rw4GGJN9_3gekZtvZ9er8-ryx_eL1dfLChshcyU6LVgv-k6wBoH3koMGZEy1fd2fopaylo3SXCmNLSrknJdS17dl985yJo7Il713O3dlMbQ-RxjNNroJ4r0J4MzLincbsw5_jGpbUStRBJ_2gpCyMwldtrjB4L3FbMoHaqF30Oc9hDGkFO3w3IAzs0vHlHTMPp0Cf_x3pGf0KY4CHD-2nLf_Ez0Ae56a1A</recordid><startdate>20191129</startdate><enddate>20191129</enddate><creator>Liu, Degao</creator><creator>Chen, Mei</creator><creator>Mendoza, Brian</creator><creator>Cheng, Hua</creator><creator>Hu, Rongbin</creator><creator>Li, Linling</creator><creator>Trinh, Cong T</creator><creator>Tuskan, Gerald A</creator><creator>Yang, Xiaohan</creator><general>Oxford University Press</general><scope>TOX</scope><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>OIOZB</scope><scope>OTOTI</scope><scope>5PM</scope><orcidid>https://orcid.org/0000-0001-5207-4210</orcidid></search><sort><creationdate>20191129</creationdate><title>CRISPR/Cas9-mediated targeted mutagenesis for functional genomics research of crassulacean acid metabolism plants</title><author>Liu, Degao ; Chen, Mei ; Mendoza, Brian ; Cheng, Hua ; Hu, Rongbin ; Li, Linling ; Trinh, Cong T ; Tuskan, Gerald A ; Yang, Xiaohan</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c435t-3b930d3db304ca1d51a9ac0068d2d7c955254691669c8c6c11168dbd8243be103</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2019</creationdate><topic>Base Sequence</topic><topic>BASIC BIOLOGICAL SCIENCES</topic><topic>Carboxylic Acids - metabolism</topic><topic>crassulacean acid metabolism</topic><topic>CRISPR-Cas Systems - genetics</topic><topic>CRISPR/Cas9</topic><topic>Databases, Genetic</topic><topic>functional genomics</topic><topic>genome-editing</topic><topic>Genomics</topic><topic>Mutagenesis - genetics</topic><topic>Mutation - genetics</topic><topic>phototropin 2</topic><topic>Plants - genetics</topic><topic>Research Papers</topic><topic>RNA, Guide, CRISPR-Cas Systems - genetics</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Liu, Degao</creatorcontrib><creatorcontrib>Chen, Mei</creatorcontrib><creatorcontrib>Mendoza, Brian</creatorcontrib><creatorcontrib>Cheng, Hua</creatorcontrib><creatorcontrib>Hu, Rongbin</creatorcontrib><creatorcontrib>Li, Linling</creatorcontrib><creatorcontrib>Trinh, Cong T</creatorcontrib><creatorcontrib>Tuskan, Gerald A</creatorcontrib><creatorcontrib>Yang, Xiaohan</creatorcontrib><creatorcontrib>Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States)</creatorcontrib><collection>OUP_牛津大学出版社OA刊</collection><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>OSTI.GOV - Hybrid</collection><collection>OSTI.GOV</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>Journal of experimental botany</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Liu, Degao</au><au>Chen, Mei</au><au>Mendoza, Brian</au><au>Cheng, Hua</au><au>Hu, Rongbin</au><au>Li, Linling</au><au>Trinh, Cong T</au><au>Tuskan, Gerald A</au><au>Yang, Xiaohan</au><au>Hultine, Kevin</au><aucorp>Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States)</aucorp><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>CRISPR/Cas9-mediated targeted mutagenesis for functional genomics research of crassulacean acid metabolism plants</atitle><jtitle>Journal of experimental botany</jtitle><addtitle>J Exp Bot</addtitle><date>2019-11-29</date><risdate>2019</risdate><volume>70</volume><issue>22</issue><spage>6621</spage><epage>6629</epage><pages>6621-6629</pages><issn>0022-0957</issn><eissn>1460-2431</eissn><abstract>Abstract
Crassulacean acid metabolism (CAM) is an important photosynthetic pathway in diverse lineages of plants featuring high water-use efficiency and drought tolerance. A big challenge facing the CAM research community is to understand the function of the annotated genes in CAM plant genomes. Recently, a new genome editing technology using CRISPR/Cas9 has become a more precise and powerful tool than traditional approaches for functional genomics research in C3 and C4 plants. In this study, we explore the potential of CRISPR/Cas9 to characterize the function of CAM-related genes in the model CAM species Kalanchoë fedtschenkoi. We demonstrate that CRISPR/Cas9 is effective in creating biallelic indel mutagenesis to reveal previously unknown roles of blue light receptor phototropin 2 (KfePHOT2) in the CAM pathway. Knocking out KfePHOT2 reduced stomatal conductance and CO2 fixation in late afternoon and increased stomatal conductance and CO2 fixation during the night, indicating that blue light signaling plays an important role in the CAM pathway. Lastly, we provide a genome-wide guide RNA database targeting 45 183 protein-coding transcripts annotated in the K. fedtschenkoi genome.
Loss-of-function analysis using CRISPR/Cas9-mediated mutagenesis provides new insight into the role of phototropin 2 in crassulacean acid metabolism</abstract><cop>UK</cop><pub>Oxford University Press</pub><pmid>31562521</pmid><doi>10.1093/jxb/erz415</doi><tpages>9</tpages><orcidid>https://orcid.org/0000-0001-5207-4210</orcidid><oa>free_for_read</oa></addata></record> |
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| ispartof | Journal of experimental botany, 2019-11, Vol.70 (22), p.6621-6629 |
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| language | eng |
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| source | Oxford Journals Online |
| subjects | Base Sequence BASIC BIOLOGICAL SCIENCES Carboxylic Acids - metabolism crassulacean acid metabolism CRISPR-Cas Systems - genetics CRISPR/Cas9 Databases, Genetic functional genomics genome-editing Genomics Mutagenesis - genetics Mutation - genetics phototropin 2 Plants - genetics Research Papers RNA, Guide, CRISPR-Cas Systems - genetics |
| title | CRISPR/Cas9-mediated targeted mutagenesis for functional genomics research of crassulacean acid metabolism plants |
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