Identification, evolution and alternative splicing profile analysis of the splicing factor 30 (SPF30) in plant species
In eukaryotes, one pre-mRNA can generate multiple mRNA transcripts by alternative splicing (AS), which expands transcriptome and proteome diversity. Splicing factor 30 (SPF30), also known as survival motor neuron domain containing protein 1 (SMNDC1), is a spliceosomal protein that plays an essential...
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| Veröffentlicht in: | Planta 2019-06, Vol.249 (6), p.1997-2014 |
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| container_issue | 6 |
| container_start_page | 1997 |
| container_title | Planta |
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| creator | Zhang, Di Yang, Jing-Fang Gao, Bei Liu, Tie-Yuan Hao, Ge-Fei Yang, Guang-Fu Fu, Li-Jun Chen, Mo-Xian Zhang, Jianhua |
| description | In eukaryotes, one pre-mRNA can generate multiple mRNA transcripts by alternative splicing (AS), which expands transcriptome and proteome diversity. Splicing factor 30 (SPF30), also known as survival motor neuron domain containing protein 1 (SMNDC1), is a spliceosomal protein that plays an essential role in spliceosomal assembly. Although SPF30 genes have been well characterised in human and yeast, little is known about their homologues in plants. Here, we report the genomewide identification and phylogenetic analysis of SPF30 genes in the plant kingdom. In total, 82 SPF30 genes were found in 64 plant species from algae to land plants. Alternative transcripts were found in many SPF30 genes and splicing profile analysis revealed that the second intron in SPF30 genome is frequently associated with AS events and contributed to the birth of novel exons in a few SPF30 members. In addition, different conserved sequences were observed at these putative splice sites among moss, monocots and dicots, respectively. Our findings will facilitate further functional characterization of plant SPF30 genes as putative splicing factors. |
| doi_str_mv | 10.1007/s00425-019-03146-x |
| format | Article |
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Splicing factor 30 (SPF30), also known as survival motor neuron domain containing protein 1 (SMNDC1), is a spliceosomal protein that plays an essential role in spliceosomal assembly. Although SPF30 genes have been well characterised in human and yeast, little is known about their homologues in plants. Here, we report the genomewide identification and phylogenetic analysis of SPF30 genes in the plant kingdom. In total, 82 SPF30 genes were found in 64 plant species from algae to land plants. Alternative transcripts were found in many SPF30 genes and splicing profile analysis revealed that the second intron in SPF30 genome is frequently associated with AS events and contributed to the birth of novel exons in a few SPF30 members. In addition, different conserved sequences were observed at these putative splice sites among moss, monocots and dicots, respectively. Our findings will facilitate further functional characterization of plant SPF30 genes as putative splicing factors.</description><identifier>ISSN: 0032-0935</identifier><identifier>EISSN: 1432-2048</identifier><identifier>DOI: 10.1007/s00425-019-03146-x</identifier><identifier>PMID: 30904945</identifier><language>eng</language><publisher>Berlin/Heidelberg: Springer Science + Business Media</publisher><subject>Agriculture ; Algae ; Alternative splicing ; Alternative Splicing - genetics ; Biological Evolution ; Biomedical and Life Sciences ; Conserved Sequence ; Ecology ; Eukaryotes ; Exons ; Exons - genetics ; Flowers & plants ; Forestry ; Gene expression ; Genes ; Genomes ; Homology ; Introns - genetics ; Life Sciences ; ORIGINAL ARTICLE ; Phylogenetics ; Phylogeny ; Plant Proteins - genetics ; Plant Proteins - metabolism ; Plant Sciences ; Plant species ; Plants - genetics ; Proteins ; Proteomes ; RNA Precursors - genetics ; RNA Splicing Factors - genetics ; RNA Splicing Factors - metabolism ; RNA, Messenger - genetics ; RNA, Plant - genetics ; Spliceosomes - genetics ; Spliceosomes - metabolism ; Splicing ; Splicing factors ; Yeast ; Yeasts</subject><ispartof>Planta, 2019-06, Vol.249 (6), p.1997-2014</ispartof><rights>Springer-Verlag GmbH Germany, part of Springer Nature 2019</rights><rights>Planta is a copyright of Springer, (2019). All Rights Reserved.</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c397t-495bf53430bb654cb0508fb2a07a8f61a10ceba01fc88b732a7b5e813d9976383</citedby><cites>FETCH-LOGICAL-c397t-495bf53430bb654cb0508fb2a07a8f61a10ceba01fc88b732a7b5e813d9976383</cites><orcidid>0000-0003-3942-5797</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.jstor.org/stable/pdf/48702110$$EPDF$$P50$$Gjstor$$H</linktopdf><linktohtml>$$Uhttps://www.jstor.org/stable/48702110$$EHTML$$P50$$Gjstor$$H</linktohtml><link.rule.ids>314,776,780,799,27903,27904,41467,42536,51297,57995,58228</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/30904945$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Zhang, Di</creatorcontrib><creatorcontrib>Yang, Jing-Fang</creatorcontrib><creatorcontrib>Gao, Bei</creatorcontrib><creatorcontrib>Liu, Tie-Yuan</creatorcontrib><creatorcontrib>Hao, Ge-Fei</creatorcontrib><creatorcontrib>Yang, Guang-Fu</creatorcontrib><creatorcontrib>Fu, Li-Jun</creatorcontrib><creatorcontrib>Chen, Mo-Xian</creatorcontrib><creatorcontrib>Zhang, Jianhua</creatorcontrib><title>Identification, evolution and alternative splicing profile analysis of the splicing factor 30 (SPF30) in plant species</title><title>Planta</title><addtitle>Planta</addtitle><addtitle>Planta</addtitle><description>In eukaryotes, one pre-mRNA can generate multiple mRNA transcripts by alternative splicing (AS), which expands transcriptome and proteome diversity. Splicing factor 30 (SPF30), also known as survival motor neuron domain containing protein 1 (SMNDC1), is a spliceosomal protein that plays an essential role in spliceosomal assembly. Although SPF30 genes have been well characterised in human and yeast, little is known about their homologues in plants. Here, we report the genomewide identification and phylogenetic analysis of SPF30 genes in the plant kingdom. In total, 82 SPF30 genes were found in 64 plant species from algae to land plants. Alternative transcripts were found in many SPF30 genes and splicing profile analysis revealed that the second intron in SPF30 genome is frequently associated with AS events and contributed to the birth of novel exons in a few SPF30 members. In addition, different conserved sequences were observed at these putative splice sites among moss, monocots and dicots, respectively. Our findings will facilitate further functional characterization of plant SPF30 genes as putative splicing factors.</description><subject>Agriculture</subject><subject>Algae</subject><subject>Alternative splicing</subject><subject>Alternative Splicing - genetics</subject><subject>Biological Evolution</subject><subject>Biomedical and Life Sciences</subject><subject>Conserved Sequence</subject><subject>Ecology</subject><subject>Eukaryotes</subject><subject>Exons</subject><subject>Exons - genetics</subject><subject>Flowers & plants</subject><subject>Forestry</subject><subject>Gene expression</subject><subject>Genes</subject><subject>Genomes</subject><subject>Homology</subject><subject>Introns - genetics</subject><subject>Life Sciences</subject><subject>ORIGINAL ARTICLE</subject><subject>Phylogenetics</subject><subject>Phylogeny</subject><subject>Plant Proteins - genetics</subject><subject>Plant Proteins - metabolism</subject><subject>Plant Sciences</subject><subject>Plant species</subject><subject>Plants - 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Academic</collection><jtitle>Planta</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Zhang, Di</au><au>Yang, Jing-Fang</au><au>Gao, Bei</au><au>Liu, Tie-Yuan</au><au>Hao, Ge-Fei</au><au>Yang, Guang-Fu</au><au>Fu, Li-Jun</au><au>Chen, Mo-Xian</au><au>Zhang, Jianhua</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Identification, evolution and alternative splicing profile analysis of the splicing factor 30 (SPF30) in plant species</atitle><jtitle>Planta</jtitle><stitle>Planta</stitle><addtitle>Planta</addtitle><date>2019-06-01</date><risdate>2019</risdate><volume>249</volume><issue>6</issue><spage>1997</spage><epage>2014</epage><pages>1997-2014</pages><issn>0032-0935</issn><eissn>1432-2048</eissn><abstract>In eukaryotes, one pre-mRNA can generate multiple mRNA transcripts by alternative splicing (AS), which expands transcriptome and proteome diversity. Splicing factor 30 (SPF30), also known as survival motor neuron domain containing protein 1 (SMNDC1), is a spliceosomal protein that plays an essential role in spliceosomal assembly. Although SPF30 genes have been well characterised in human and yeast, little is known about their homologues in plants. Here, we report the genomewide identification and phylogenetic analysis of SPF30 genes in the plant kingdom. In total, 82 SPF30 genes were found in 64 plant species from algae to land plants. Alternative transcripts were found in many SPF30 genes and splicing profile analysis revealed that the second intron in SPF30 genome is frequently associated with AS events and contributed to the birth of novel exons in a few SPF30 members. In addition, different conserved sequences were observed at these putative splice sites among moss, monocots and dicots, respectively. Our findings will facilitate further functional characterization of plant SPF30 genes as putative splicing factors.</abstract><cop>Berlin/Heidelberg</cop><pub>Springer Science + Business Media</pub><pmid>30904945</pmid><doi>10.1007/s00425-019-03146-x</doi><tpages>18</tpages><orcidid>https://orcid.org/0000-0003-3942-5797</orcidid></addata></record> |
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| source | Jstor Complete Legacy; MEDLINE; Springer Nature - Complete Springer Journals |
| subjects | Agriculture Algae Alternative splicing Alternative Splicing - genetics Biological Evolution Biomedical and Life Sciences Conserved Sequence Ecology Eukaryotes Exons Exons - genetics Flowers & plants Forestry Gene expression Genes Genomes Homology Introns - genetics Life Sciences ORIGINAL ARTICLE Phylogenetics Phylogeny Plant Proteins - genetics Plant Proteins - metabolism Plant Sciences Plant species Plants - genetics Proteins Proteomes RNA Precursors - genetics RNA Splicing Factors - genetics RNA Splicing Factors - metabolism RNA, Messenger - genetics RNA, Plant - genetics Spliceosomes - genetics Spliceosomes - metabolism Splicing Splicing factors Yeast Yeasts |
| title | Identification, evolution and alternative splicing profile analysis of the splicing factor 30 (SPF30) in plant species |
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