Genome-wide identification of the GDSL-type esterase/lipase protein (GELP) gene family in Ricinus communis and its transcriptional regulation during germination and seedling establishment under different abiotic stresses
GDSL-type esterase/lipase protein (GELP) genes are crucial in the specialized lipid metabolism, in the responses to abiotic stresses, and in the regulation of plant homeostasis. R. communis is an important oilseed crop species that can sustain growth and productivity when exposed to harsh environmen...
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creator | de Almeida, Catherine P. Barbosa, Rhaissa R. Ferraz, Caline G. de Castro, Renato D. Ribeiro, Paulo R. |
description | GDSL-type esterase/lipase protein (GELP) genes are crucial in the specialized lipid metabolism, in the responses to abiotic stresses, and in the regulation of plant homeostasis. R. communis is an important oilseed crop species that can sustain growth and productivity when exposed to harsh environmental conditions. Herein, we raised the question of whether the GELP gene family could be involved in the acquisition of R. communis tolerance to abiotic stresses during seed germination and seedling establishment. Thus, we used bioinformatics and transcriptomics to characterize the R. communis GELP gene family. R. communis genome possesses 96 GELP genes that were characterized by extensive bioinformatics, including phylogenetic analysis, subcellular localization, exon-intron distribution, the analysis of regulatory cis-elements, tandem duplication, and physicochemical properties. Transcriptomics indicated that numerous RcGELP genes are readily responsive to high-temperature and salt stresses and might be potential candidates for genome editing techniques to develop abiotic stress-tolerant crops.
•R. communis GELP gene family was characterized by bioinformatics and transcriptomics.•R. communis genome possesses 96 GELP genes (GDSL-like Lipase/Acylhydrolase domain).•The majority of RcGELP genes are responsive to high-temperature and/or salt stress.•GELP genes are potential candidates to address stress-related agronomic crop issues.•Introduction. |
doi_str_mv | 10.1016/j.plaphy.2024.108939 |
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•R. communis GELP gene family was characterized by bioinformatics and transcriptomics.•R. communis genome possesses 96 GELP genes (GDSL-like Lipase/Acylhydrolase domain).•The majority of RcGELP genes are responsive to high-temperature and/or salt stress.•GELP genes are potential candidates to address stress-related agronomic crop issues.•Introduction.</description><identifier>ISSN: 0981-9428</identifier><identifier>ISSN: 1873-2690</identifier><identifier>EISSN: 1873-2690</identifier><identifier>DOI: 10.1016/j.plaphy.2024.108939</identifier><identifier>PMID: 39029309</identifier><language>eng</language><publisher>France: Elsevier Masson SAS</publisher><subject>Bioinformatics ; carboxylic ester hydrolases ; crops ; Esterases - genetics ; Esterases - metabolism ; family ; GDSL-Type esterase/lipase ; Gene Expression Regulation, Plant ; genes ; Genome, Plant - genetics ; Germination - genetics ; homeostasis ; Lipase - genetics ; Lipase - metabolism ; Lipid metabolism ; Multigene Family ; Oil bodies ; oilseed crops ; Phylogeny ; plant establishment ; Plant Proteins - genetics ; Plant Proteins - metabolism ; Plant-environment interactions ; Ricinus - genetics ; Ricinus - metabolism ; Ricinus communis ; seed germination ; Seedlings - genetics ; Seedlings - growth & development ; Stress, Physiological - genetics ; transcription (genetics) ; transcriptomics</subject><ispartof>Plant physiology and biochemistry, 2024-09, Vol.214, p.108939, Article 108939</ispartof><rights>2024 Elsevier Masson SAS</rights><rights>Copyright © 2024 Elsevier Masson SAS. All rights reserved.</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><cites>FETCH-LOGICAL-c274t-2d6f4965bcbea89129a4a361b6aac9395abcb4df2b47b2408da3e0dd2c3de053</cites><orcidid>0000-0001-9622-5076</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktohtml>$$Uhttps://www.sciencedirect.com/science/article/pii/S0981942824006077$$EHTML$$P50$$Gelsevier$$H</linktohtml><link.rule.ids>314,776,780,3537,27901,27902,65306</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/39029309$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>de Almeida, Catherine P.</creatorcontrib><creatorcontrib>Barbosa, Rhaissa R.</creatorcontrib><creatorcontrib>Ferraz, Caline G.</creatorcontrib><creatorcontrib>de Castro, Renato D.</creatorcontrib><creatorcontrib>Ribeiro, Paulo R.</creatorcontrib><title>Genome-wide identification of the GDSL-type esterase/lipase protein (GELP) gene family in Ricinus communis and its transcriptional regulation during germination and seedling establishment under different abiotic stresses</title><title>Plant physiology and biochemistry</title><addtitle>Plant Physiol Biochem</addtitle><description>GDSL-type esterase/lipase protein (GELP) genes are crucial in the specialized lipid metabolism, in the responses to abiotic stresses, and in the regulation of plant homeostasis. R. communis is an important oilseed crop species that can sustain growth and productivity when exposed to harsh environmental conditions. Herein, we raised the question of whether the GELP gene family could be involved in the acquisition of R. communis tolerance to abiotic stresses during seed germination and seedling establishment. Thus, we used bioinformatics and transcriptomics to characterize the R. communis GELP gene family. R. communis genome possesses 96 GELP genes that were characterized by extensive bioinformatics, including phylogenetic analysis, subcellular localization, exon-intron distribution, the analysis of regulatory cis-elements, tandem duplication, and physicochemical properties. Transcriptomics indicated that numerous RcGELP genes are readily responsive to high-temperature and salt stresses and might be potential candidates for genome editing techniques to develop abiotic stress-tolerant crops.
•R. communis GELP gene family was characterized by bioinformatics and transcriptomics.•R. communis genome possesses 96 GELP genes (GDSL-like Lipase/Acylhydrolase domain).•The majority of RcGELP genes are responsive to high-temperature and/or salt stress.•GELP genes are potential candidates to address stress-related agronomic crop issues.•Introduction.</description><subject>Bioinformatics</subject><subject>carboxylic ester hydrolases</subject><subject>crops</subject><subject>Esterases - genetics</subject><subject>Esterases - metabolism</subject><subject>family</subject><subject>GDSL-Type esterase/lipase</subject><subject>Gene Expression Regulation, Plant</subject><subject>genes</subject><subject>Genome, Plant - genetics</subject><subject>Germination - genetics</subject><subject>homeostasis</subject><subject>Lipase - genetics</subject><subject>Lipase - metabolism</subject><subject>Lipid metabolism</subject><subject>Multigene Family</subject><subject>Oil bodies</subject><subject>oilseed crops</subject><subject>Phylogeny</subject><subject>plant establishment</subject><subject>Plant Proteins - genetics</subject><subject>Plant Proteins - metabolism</subject><subject>Plant-environment interactions</subject><subject>Ricinus - genetics</subject><subject>Ricinus - metabolism</subject><subject>Ricinus communis</subject><subject>seed germination</subject><subject>Seedlings - genetics</subject><subject>Seedlings - growth & development</subject><subject>Stress, Physiological - genetics</subject><subject>transcription (genetics)</subject><subject>transcriptomics</subject><issn>0981-9428</issn><issn>1873-2690</issn><issn>1873-2690</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2024</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNqFUsFu1DAQjRCIbgt_gJCP5ZCtY3uz8QUJlbIgrQSC3i3HnuzOynGC7RTtv_IxOErLEQ7WyDNv3hvNvKJ4U9F1Rav65rQenR6P5zWjTORUI7l8VqyqZstLVkv6vFhR2VSlFKy5KC5jPFGakVv-srjgkjLJqVwVv3fghx7KX2iB5OcTdmh0wsGToSPpCGT38ce-TOcRCMQEQUe4cTjmQMYwJEBPrnd3-2_vyAE8kE736M4kZ7-jQT9FYoa-nzxGor0lmCJJQftoAo6zinYkwGFyi6SdAvpDZgo9-iU1d0UA6-ZCnkC3DuOxz5OSyVsIxGLXQZj_usUhoSExBYgR4qviRaddhNeP8aq4_3R3f_u53H_dfbn9sC8N24pUMlt3Qtab1rSgG1kxqYXmddXWWpu81Y3OFWE71optywRtrOZArWWGW6AbflVcL7R5Hz-nPKLqMRpwTnsYpqh4tRGszrTs_1DasIaLfKUMFQvUhCHGAJ0aA_Y6nFVF1ewAdVKLA9TsALU4ILe9fVSY2h7s36ank2fA-wUAeSMPCEFFg-ANWAxgkrID_lvhDw5Iyp8</recordid><startdate>202409</startdate><enddate>202409</enddate><creator>de Almeida, Catherine P.</creator><creator>Barbosa, Rhaissa R.</creator><creator>Ferraz, Caline G.</creator><creator>de Castro, Renato D.</creator><creator>Ribeiro, Paulo R.</creator><general>Elsevier Masson SAS</general><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>7X8</scope><scope>7S9</scope><scope>L.6</scope><orcidid>https://orcid.org/0000-0001-9622-5076</orcidid></search><sort><creationdate>202409</creationdate><title>Genome-wide identification of the GDSL-type esterase/lipase protein (GELP) gene family in Ricinus communis and its transcriptional regulation during germination and seedling establishment under different abiotic stresses</title><author>de Almeida, Catherine P. ; Barbosa, Rhaissa R. ; Ferraz, Caline G. ; de Castro, Renato D. ; Ribeiro, Paulo R.</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c274t-2d6f4965bcbea89129a4a361b6aac9395abcb4df2b47b2408da3e0dd2c3de053</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2024</creationdate><topic>Bioinformatics</topic><topic>carboxylic ester hydrolases</topic><topic>crops</topic><topic>Esterases - genetics</topic><topic>Esterases - metabolism</topic><topic>family</topic><topic>GDSL-Type esterase/lipase</topic><topic>Gene Expression Regulation, Plant</topic><topic>genes</topic><topic>Genome, Plant - genetics</topic><topic>Germination - genetics</topic><topic>homeostasis</topic><topic>Lipase - genetics</topic><topic>Lipase - metabolism</topic><topic>Lipid metabolism</topic><topic>Multigene Family</topic><topic>Oil bodies</topic><topic>oilseed crops</topic><topic>Phylogeny</topic><topic>plant establishment</topic><topic>Plant Proteins - genetics</topic><topic>Plant Proteins - metabolism</topic><topic>Plant-environment interactions</topic><topic>Ricinus - genetics</topic><topic>Ricinus - metabolism</topic><topic>Ricinus communis</topic><topic>seed germination</topic><topic>Seedlings - genetics</topic><topic>Seedlings - growth & development</topic><topic>Stress, Physiological - genetics</topic><topic>transcription (genetics)</topic><topic>transcriptomics</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>de Almeida, Catherine P.</creatorcontrib><creatorcontrib>Barbosa, Rhaissa R.</creatorcontrib><creatorcontrib>Ferraz, Caline G.</creatorcontrib><creatorcontrib>de Castro, Renato D.</creatorcontrib><creatorcontrib>Ribeiro, Paulo R.</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>MEDLINE - Academic</collection><collection>AGRICOLA</collection><collection>AGRICOLA - Academic</collection><jtitle>Plant physiology and biochemistry</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>de Almeida, Catherine P.</au><au>Barbosa, Rhaissa R.</au><au>Ferraz, Caline G.</au><au>de Castro, Renato D.</au><au>Ribeiro, Paulo R.</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Genome-wide identification of the GDSL-type esterase/lipase protein (GELP) gene family in Ricinus communis and its transcriptional regulation during germination and seedling establishment under different abiotic stresses</atitle><jtitle>Plant physiology and biochemistry</jtitle><addtitle>Plant Physiol Biochem</addtitle><date>2024-09</date><risdate>2024</risdate><volume>214</volume><spage>108939</spage><pages>108939-</pages><artnum>108939</artnum><issn>0981-9428</issn><issn>1873-2690</issn><eissn>1873-2690</eissn><abstract>GDSL-type esterase/lipase protein (GELP) genes are crucial in the specialized lipid metabolism, in the responses to abiotic stresses, and in the regulation of plant homeostasis. R. communis is an important oilseed crop species that can sustain growth and productivity when exposed to harsh environmental conditions. Herein, we raised the question of whether the GELP gene family could be involved in the acquisition of R. communis tolerance to abiotic stresses during seed germination and seedling establishment. Thus, we used bioinformatics and transcriptomics to characterize the R. communis GELP gene family. R. communis genome possesses 96 GELP genes that were characterized by extensive bioinformatics, including phylogenetic analysis, subcellular localization, exon-intron distribution, the analysis of regulatory cis-elements, tandem duplication, and physicochemical properties. Transcriptomics indicated that numerous RcGELP genes are readily responsive to high-temperature and salt stresses and might be potential candidates for genome editing techniques to develop abiotic stress-tolerant crops.
•R. communis GELP gene family was characterized by bioinformatics and transcriptomics.•R. communis genome possesses 96 GELP genes (GDSL-like Lipase/Acylhydrolase domain).•The majority of RcGELP genes are responsive to high-temperature and/or salt stress.•GELP genes are potential candidates to address stress-related agronomic crop issues.•Introduction.</abstract><cop>France</cop><pub>Elsevier Masson SAS</pub><pmid>39029309</pmid><doi>10.1016/j.plaphy.2024.108939</doi><orcidid>https://orcid.org/0000-0001-9622-5076</orcidid></addata></record> |
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subjects | Bioinformatics carboxylic ester hydrolases crops Esterases - genetics Esterases - metabolism family GDSL-Type esterase/lipase Gene Expression Regulation, Plant genes Genome, Plant - genetics Germination - genetics homeostasis Lipase - genetics Lipase - metabolism Lipid metabolism Multigene Family Oil bodies oilseed crops Phylogeny plant establishment Plant Proteins - genetics Plant Proteins - metabolism Plant-environment interactions Ricinus - genetics Ricinus - metabolism Ricinus communis seed germination Seedlings - genetics Seedlings - growth & development Stress, Physiological - genetics transcription (genetics) transcriptomics |
title | Genome-wide identification of the GDSL-type esterase/lipase protein (GELP) gene family in Ricinus communis and its transcriptional regulation during germination and seedling establishment under different abiotic stresses |
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