Genome-wide screening and evolutionary analysis of ZIP (ZRT–IRT like proteins) family in cowpea (Vigna unguiculata L.)
ZIP is one of the most important gene families associated with zinc transportation in plants. Although ZIP genes have been studied in a variety of plant species, yet remain unexplored in cowpea. VuZIPs family was characterized for physiochemical parameters using phytozome. TBtool and CELLO Life were...
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| Veröffentlicht in: | Genetic resources and crop evolution 2024-03, Vol.71 (3), p.1145-1157 |
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| creator | Ullah, Arif Shah, Zamarud Munir, Iqbal Iqbal, Hamza Ahmad, Muhammad Zulfiqar Sultan, Warda Khan, Afrasyab |
| description | ZIP
is one of the most important gene families associated with zinc transportation in plants. Although
ZIP
genes have been studied in a variety of plant species, yet remain unexplored in cowpea.
VuZIPs
family was characterized for physiochemical parameters using phytozome. TBtool and CELLO Life were used for detecting domain architecture and sub-cellular location, respectively. Phylogenetic, motif and Gene Structure analysis were carried out using MEGA7, MEME and GSDC, respectively. The genes were mapped on the respective chromosome through PhenoGram Plot while SIAS was used for determining level of homology between 2 genes. The nature and selection pressure on homologous duplicated genes was determined through physical distance and Ka/Ks ratio, respectively. PlantCARE was used for uncovering promoter region while heatmap was generated for expression of VuZIP genes. Sixty
ZIP
genes, identified across diverse plant species, were divided into five groups. The duplication (paralogs) and speciation (orthologs) events contributed 29% and 14% respectively, to the extension of
VuZIP
gene family. The
VuZIP
genes were dispersed on eight different chromosomes. Variation was witnessed in motifs and structure of 14
VuZIP
genes associated with five different groups while
VuZIP
belong to the same group exhibited no differences for these parameters. ABRE and LTRE elements exhibited presence in promoter region of nine and four
VuZIP
genes, respectively. Purifying selection was determined as driving force for evolution in duplicated genes.
VuZIP8
and
VuZIP7
exhibited highest expression in leaf and in root, respectively.These results provide valuable information for further functional research of
VuZIPs. |
| doi_str_mv | 10.1007/s10722-023-01682-w |
| format | Article |
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is one of the most important gene families associated with zinc transportation in plants. Although
ZIP
genes have been studied in a variety of plant species, yet remain unexplored in cowpea.
VuZIPs
family was characterized for physiochemical parameters using phytozome. TBtool and CELLO Life were used for detecting domain architecture and sub-cellular location, respectively. Phylogenetic, motif and Gene Structure analysis were carried out using MEGA7, MEME and GSDC, respectively. The genes were mapped on the respective chromosome through PhenoGram Plot while SIAS was used for determining level of homology between 2 genes. The nature and selection pressure on homologous duplicated genes was determined through physical distance and Ka/Ks ratio, respectively. PlantCARE was used for uncovering promoter region while heatmap was generated for expression of VuZIP genes. Sixty
ZIP
genes, identified across diverse plant species, were divided into five groups. The duplication (paralogs) and speciation (orthologs) events contributed 29% and 14% respectively, to the extension of
VuZIP
gene family. The
VuZIP
genes were dispersed on eight different chromosomes. Variation was witnessed in motifs and structure of 14
VuZIP
genes associated with five different groups while
VuZIP
belong to the same group exhibited no differences for these parameters. ABRE and LTRE elements exhibited presence in promoter region of nine and four
VuZIP
genes, respectively. Purifying selection was determined as driving force for evolution in duplicated genes.
VuZIP8
and
VuZIP7
exhibited highest expression in leaf and in root, respectively.These results provide valuable information for further functional research of
VuZIPs.</description><identifier>ISSN: 0925-9864</identifier><identifier>EISSN: 1573-5109</identifier><identifier>DOI: 10.1007/s10722-023-01682-w</identifier><language>eng</language><publisher>Dordrecht: Springer Netherlands</publisher><subject>Agriculture ; Biomedical and Life Sciences ; Cellular structure ; Chromosomes ; Cowpeas ; domain ; Evolutionary genetics ; family ; Flowers & plants ; Gene duplication ; Gene expression ; Gene families ; Genes ; Genomes ; Homology ; leaves ; Life Sciences ; Parameters ; Phylogeny ; Physiochemistry ; Plant Genetics and Genomics ; Plant Physiology ; Plant Sciences ; Plant species ; Plant Systematics/Taxonomy/Biogeography ; Plants (botany) ; promoter regions ; Research Article ; selection pressure ; Speciation ; species ; Structural analysis ; transportation ; Vigna unguiculata ; zinc</subject><ispartof>Genetic resources and crop evolution, 2024-03, Vol.71 (3), p.1145-1157</ispartof><rights>The Author(s), under exclusive licence to Springer Nature B.V. 2023. Springer Nature or its licensor (e.g. a society or other partner) holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law.</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c352t-e020e3b6119cf16b2fc48f1b73c72258a5a93636e874e2cca259ab5d2b17606e3</citedby><cites>FETCH-LOGICAL-c352t-e020e3b6119cf16b2fc48f1b73c72258a5a93636e874e2cca259ab5d2b17606e3</cites><orcidid>0000-0001-6217-264X</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://link.springer.com/content/pdf/10.1007/s10722-023-01682-w$$EPDF$$P50$$Gspringer$$H</linktopdf><linktohtml>$$Uhttps://link.springer.com/10.1007/s10722-023-01682-w$$EHTML$$P50$$Gspringer$$H</linktohtml><link.rule.ids>314,776,780,27901,27902,41464,42533,51294</link.rule.ids></links><search><creatorcontrib>Ullah, Arif</creatorcontrib><creatorcontrib>Shah, Zamarud</creatorcontrib><creatorcontrib>Munir, Iqbal</creatorcontrib><creatorcontrib>Iqbal, Hamza</creatorcontrib><creatorcontrib>Ahmad, Muhammad Zulfiqar</creatorcontrib><creatorcontrib>Sultan, Warda</creatorcontrib><creatorcontrib>Khan, Afrasyab</creatorcontrib><title>Genome-wide screening and evolutionary analysis of ZIP (ZRT–IRT like proteins) family in cowpea (Vigna unguiculata L.)</title><title>Genetic resources and crop evolution</title><addtitle>Genet Resour Crop Evol</addtitle><description>ZIP
is one of the most important gene families associated with zinc transportation in plants. Although
ZIP
genes have been studied in a variety of plant species, yet remain unexplored in cowpea.
VuZIPs
family was characterized for physiochemical parameters using phytozome. TBtool and CELLO Life were used for detecting domain architecture and sub-cellular location, respectively. Phylogenetic, motif and Gene Structure analysis were carried out using MEGA7, MEME and GSDC, respectively. The genes were mapped on the respective chromosome through PhenoGram Plot while SIAS was used for determining level of homology between 2 genes. The nature and selection pressure on homologous duplicated genes was determined through physical distance and Ka/Ks ratio, respectively. PlantCARE was used for uncovering promoter region while heatmap was generated for expression of VuZIP genes. Sixty
ZIP
genes, identified across diverse plant species, were divided into five groups. The duplication (paralogs) and speciation (orthologs) events contributed 29% and 14% respectively, to the extension of
VuZIP
gene family. The
VuZIP
genes were dispersed on eight different chromosomes. Variation was witnessed in motifs and structure of 14
VuZIP
genes associated with five different groups while
VuZIP
belong to the same group exhibited no differences for these parameters. ABRE and LTRE elements exhibited presence in promoter region of nine and four
VuZIP
genes, respectively. Purifying selection was determined as driving force for evolution in duplicated genes.
VuZIP8
and
VuZIP7
exhibited highest expression in leaf and in root, respectively.These results provide valuable information for further functional research of
VuZIPs.</description><subject>Agriculture</subject><subject>Biomedical and Life Sciences</subject><subject>Cellular structure</subject><subject>Chromosomes</subject><subject>Cowpeas</subject><subject>domain</subject><subject>Evolutionary genetics</subject><subject>family</subject><subject>Flowers & plants</subject><subject>Gene duplication</subject><subject>Gene expression</subject><subject>Gene families</subject><subject>Genes</subject><subject>Genomes</subject><subject>Homology</subject><subject>leaves</subject><subject>Life Sciences</subject><subject>Parameters</subject><subject>Phylogeny</subject><subject>Physiochemistry</subject><subject>Plant Genetics and Genomics</subject><subject>Plant Physiology</subject><subject>Plant Sciences</subject><subject>Plant species</subject><subject>Plant Systematics/Taxonomy/Biogeography</subject><subject>Plants (botany)</subject><subject>promoter regions</subject><subject>Research Article</subject><subject>selection pressure</subject><subject>Speciation</subject><subject>species</subject><subject>Structural analysis</subject><subject>transportation</subject><subject>Vigna unguiculata</subject><subject>zinc</subject><issn>0925-9864</issn><issn>1573-5109</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2024</creationdate><recordtype>article</recordtype><recordid>eNp9kcFqGzEQhkVJoE7aF-hJ0ItzUDqSLO3qWEKaGAwNwckhF6GVZ43SteSsduv41nfoG_ZJqtaFQA85DQzf_zPz_4R84HDOAapPmUMlBAMhGXBdC7Z7QyZcVZIpDuaITMAIxUytZ2_JSc6PAGAqXU_I8xXGtEG2Cyuk2feIMcQ1dXFF8XvqxiGk6Pp9Wbhun0OmqaUP8xs6fbhd_vrxc367pF34hnTbpwFDzGe0dZvQ7WmI1KfdFh2d3od1dHSM6zH4sXODo4vzs3fkuHVdxvf_5im5-3K5vLhmi69X84vPC-alEgNDEICy0Zwb33LdiNbP6pY3lfTlYVU75YzUUmNdzVB474QyrlEr0fBKg0Z5SqYH33Lh04h5sJuQPXadi5jGbCVXUoMpKRX043_oYxr78ni2wgheixlIVShxoHyfcu6xtds-bEpGloP9U4Y9lGFLGfZvGXZXRPIgygWOa-xfrF9R_QYFcY07</recordid><startdate>20240301</startdate><enddate>20240301</enddate><creator>Ullah, Arif</creator><creator>Shah, Zamarud</creator><creator>Munir, Iqbal</creator><creator>Iqbal, Hamza</creator><creator>Ahmad, Muhammad Zulfiqar</creator><creator>Sultan, Warda</creator><creator>Khan, Afrasyab</creator><general>Springer Netherlands</general><general>Springer Nature B.V</general><scope>AAYXX</scope><scope>CITATION</scope><scope>7S9</scope><scope>L.6</scope><orcidid>https://orcid.org/0000-0001-6217-264X</orcidid></search><sort><creationdate>20240301</creationdate><title>Genome-wide screening and evolutionary analysis of ZIP (ZRT–IRT like proteins) family in cowpea (Vigna unguiculata L.)</title><author>Ullah, Arif ; Shah, Zamarud ; Munir, Iqbal ; Iqbal, Hamza ; Ahmad, Muhammad Zulfiqar ; Sultan, Warda ; Khan, Afrasyab</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c352t-e020e3b6119cf16b2fc48f1b73c72258a5a93636e874e2cca259ab5d2b17606e3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2024</creationdate><topic>Agriculture</topic><topic>Biomedical and Life Sciences</topic><topic>Cellular structure</topic><topic>Chromosomes</topic><topic>Cowpeas</topic><topic>domain</topic><topic>Evolutionary genetics</topic><topic>family</topic><topic>Flowers & plants</topic><topic>Gene duplication</topic><topic>Gene expression</topic><topic>Gene families</topic><topic>Genes</topic><topic>Genomes</topic><topic>Homology</topic><topic>leaves</topic><topic>Life Sciences</topic><topic>Parameters</topic><topic>Phylogeny</topic><topic>Physiochemistry</topic><topic>Plant Genetics and Genomics</topic><topic>Plant Physiology</topic><topic>Plant Sciences</topic><topic>Plant species</topic><topic>Plant Systematics/Taxonomy/Biogeography</topic><topic>Plants (botany)</topic><topic>promoter regions</topic><topic>Research Article</topic><topic>selection pressure</topic><topic>Speciation</topic><topic>species</topic><topic>Structural analysis</topic><topic>transportation</topic><topic>Vigna unguiculata</topic><topic>zinc</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Ullah, Arif</creatorcontrib><creatorcontrib>Shah, Zamarud</creatorcontrib><creatorcontrib>Munir, Iqbal</creatorcontrib><creatorcontrib>Iqbal, Hamza</creatorcontrib><creatorcontrib>Ahmad, Muhammad Zulfiqar</creatorcontrib><creatorcontrib>Sultan, Warda</creatorcontrib><creatorcontrib>Khan, Afrasyab</creatorcontrib><collection>CrossRef</collection><collection>AGRICOLA</collection><collection>AGRICOLA - Academic</collection><jtitle>Genetic resources and crop evolution</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Ullah, Arif</au><au>Shah, Zamarud</au><au>Munir, Iqbal</au><au>Iqbal, Hamza</au><au>Ahmad, Muhammad Zulfiqar</au><au>Sultan, Warda</au><au>Khan, Afrasyab</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Genome-wide screening and evolutionary analysis of ZIP (ZRT–IRT like proteins) family in cowpea (Vigna unguiculata L.)</atitle><jtitle>Genetic resources and crop evolution</jtitle><stitle>Genet Resour Crop Evol</stitle><date>2024-03-01</date><risdate>2024</risdate><volume>71</volume><issue>3</issue><spage>1145</spage><epage>1157</epage><pages>1145-1157</pages><issn>0925-9864</issn><eissn>1573-5109</eissn><abstract>ZIP
is one of the most important gene families associated with zinc transportation in plants. Although
ZIP
genes have been studied in a variety of plant species, yet remain unexplored in cowpea.
VuZIPs
family was characterized for physiochemical parameters using phytozome. TBtool and CELLO Life were used for detecting domain architecture and sub-cellular location, respectively. Phylogenetic, motif and Gene Structure analysis were carried out using MEGA7, MEME and GSDC, respectively. The genes were mapped on the respective chromosome through PhenoGram Plot while SIAS was used for determining level of homology between 2 genes. The nature and selection pressure on homologous duplicated genes was determined through physical distance and Ka/Ks ratio, respectively. PlantCARE was used for uncovering promoter region while heatmap was generated for expression of VuZIP genes. Sixty
ZIP
genes, identified across diverse plant species, were divided into five groups. The duplication (paralogs) and speciation (orthologs) events contributed 29% and 14% respectively, to the extension of
VuZIP
gene family. The
VuZIP
genes were dispersed on eight different chromosomes. Variation was witnessed in motifs and structure of 14
VuZIP
genes associated with five different groups while
VuZIP
belong to the same group exhibited no differences for these parameters. ABRE and LTRE elements exhibited presence in promoter region of nine and four
VuZIP
genes, respectively. Purifying selection was determined as driving force for evolution in duplicated genes.
VuZIP8
and
VuZIP7
exhibited highest expression in leaf and in root, respectively.These results provide valuable information for further functional research of
VuZIPs.</abstract><cop>Dordrecht</cop><pub>Springer Netherlands</pub><doi>10.1007/s10722-023-01682-w</doi><tpages>13</tpages><orcidid>https://orcid.org/0000-0001-6217-264X</orcidid></addata></record> |
| fulltext | fulltext |
| identifier | ISSN: 0925-9864 |
| ispartof | Genetic resources and crop evolution, 2024-03, Vol.71 (3), p.1145-1157 |
| issn | 0925-9864 1573-5109 |
| language | eng |
| recordid | cdi_proquest_journals_2921824035 |
| source | SpringerLink Journals |
| subjects | Agriculture Biomedical and Life Sciences Cellular structure Chromosomes Cowpeas domain Evolutionary genetics family Flowers & plants Gene duplication Gene expression Gene families Genes Genomes Homology leaves Life Sciences Parameters Phylogeny Physiochemistry Plant Genetics and Genomics Plant Physiology Plant Sciences Plant species Plant Systematics/Taxonomy/Biogeography Plants (botany) promoter regions Research Article selection pressure Speciation species Structural analysis transportation Vigna unguiculata zinc |
| title | Genome-wide screening and evolutionary analysis of ZIP (ZRT–IRT like proteins) family in cowpea (Vigna unguiculata L.) |
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