De novo tanscriptome sequencing and functional annotation of differentially expressed genes in large and small seeds of common cocklebur (Xanthium strumarium L.) during seed development
Common cocklebur (Xanthium strumarium L.) is a widespread weed with high medical value and interested for researchers because of deep dormancy in one of its two seeds in one bur. However, lack of genomic data has led to low information about it. Transcriptome large and small seeds were sequenced usi...
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Seed and Plant Certification and Registration Institute
2020-01-01
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| Series: | علوم و فناوری بذر ایران |
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| Online Access: | https://ijsst.areeo.ac.ir/article_121384_1108af34f3db4e4f9be32a1f5d2c8c7d.pdf |
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| author | Iman Nemati Mohammad Sedghi Ghasem Hoseini Salekdeh Reza Tavakkol afshari Mohammadreza Naghavi |
| author_facet | Iman Nemati Mohammad Sedghi Ghasem Hoseini Salekdeh Reza Tavakkol afshari Mohammadreza Naghavi |
| author_sort | Iman Nemati |
| collection | DOAJ |
| description | Common cocklebur (Xanthium strumarium L.) is a widespread weed with high medical value and interested for researchers because of deep dormancy in one of its two seeds in one bur. However, lack of genomic data has led to low information about it. Transcriptome large and small seeds were sequenced using Illumina platform to identify and functional analysis of differentially expressed transcripts in two seeds. Identified sequences in each seeds were compared and differentially expressed genes were functionally annotated. In this research 191192 sequence with a mean of 989.69 bp were detected. Sequence similarity analysis and functional analysis was carried out aginst nr, GO and KEGG databases. Differentially expressed genes had the most similarity with sunflower (83.41 per cent) in terms of top hits. GO analysis led to identify 615 functional annotation distributed in 36 categories. The most abomdant GO in biological process was biosynthesis. Results of our research shows the higher biosynthetic and metabolic processes in large seed of certain bur rather than the small one and also key regulatory role of transcription during seed development. |
| format | Article |
| id | doaj-art-01b600088a424d6c99d4d058d6d88ea4 |
| institution | DOAJ |
| issn | 2322-2646 2588-4638 |
| language | fas |
| publishDate | 2020-01-01 |
| publisher | Seed and Plant Certification and Registration Institute |
| record_format | Article |
| series | علوم و فناوری بذر ایران |
| spelling | doaj-art-01b600088a424d6c99d4d058d6d88ea42025-08-20T03:15:47ZfasSeed and Plant Certification and Registration Instituteعلوم و فناوری بذر ایران2322-26462588-46382020-01-018221122710.22034/ijsst.2019.122712.1220121384De novo tanscriptome sequencing and functional annotation of differentially expressed genes in large and small seeds of common cocklebur (Xanthium strumarium L.) during seed developmentIman Nemati0Mohammad Sedghi1Ghasem Hoseini Salekdeh2Reza Tavakkol afshari3Mohammadreza Naghavi4PhD student, seed science and technology, university of Mohaghegh ArdabiliUniversity of Mohaghegh Ardabili, Faculty of Agriculture and Natural Resources, Department of Agronomy and Plant BreedingAgricultural Biotechnology Institute of IranProfessor/ Dept. of Agrotechnology, Faculty of Agriculture, Ferdowsi University of Mashhad. Iran.Prof./Dept. of Agronomy and Breeding, College of Agriculture and Natural Resources, University of Tehran, Iran.Common cocklebur (Xanthium strumarium L.) is a widespread weed with high medical value and interested for researchers because of deep dormancy in one of its two seeds in one bur. However, lack of genomic data has led to low information about it. Transcriptome large and small seeds were sequenced using Illumina platform to identify and functional analysis of differentially expressed transcripts in two seeds. Identified sequences in each seeds were compared and differentially expressed genes were functionally annotated. In this research 191192 sequence with a mean of 989.69 bp were detected. Sequence similarity analysis and functional analysis was carried out aginst nr, GO and KEGG databases. Differentially expressed genes had the most similarity with sunflower (83.41 per cent) in terms of top hits. GO analysis led to identify 615 functional annotation distributed in 36 categories. The most abomdant GO in biological process was biosynthesis. Results of our research shows the higher biosynthetic and metabolic processes in large seed of certain bur rather than the small one and also key regulatory role of transcription during seed development.https://ijsst.areeo.ac.ir/article_121384_1108af34f3db4e4f9be32a1f5d2c8c7d.pdfcommon cockleburetranscriptomelarge and small seedsdevelopmentsequencing |
| spellingShingle | Iman Nemati Mohammad Sedghi Ghasem Hoseini Salekdeh Reza Tavakkol afshari Mohammadreza Naghavi De novo tanscriptome sequencing and functional annotation of differentially expressed genes in large and small seeds of common cocklebur (Xanthium strumarium L.) during seed development علوم و فناوری بذر ایران common cocklebure transcriptome large and small seeds development sequencing |
| title | De novo tanscriptome sequencing and functional annotation of differentially expressed genes in large and small seeds of common cocklebur (Xanthium strumarium L.) during seed development |
| title_full | De novo tanscriptome sequencing and functional annotation of differentially expressed genes in large and small seeds of common cocklebur (Xanthium strumarium L.) during seed development |
| title_fullStr | De novo tanscriptome sequencing and functional annotation of differentially expressed genes in large and small seeds of common cocklebur (Xanthium strumarium L.) during seed development |
| title_full_unstemmed | De novo tanscriptome sequencing and functional annotation of differentially expressed genes in large and small seeds of common cocklebur (Xanthium strumarium L.) during seed development |
| title_short | De novo tanscriptome sequencing and functional annotation of differentially expressed genes in large and small seeds of common cocklebur (Xanthium strumarium L.) during seed development |
| title_sort | de novo tanscriptome sequencing and functional annotation of differentially expressed genes in large and small seeds of common cocklebur xanthium strumarium l during seed development |
| topic | common cocklebure transcriptome large and small seeds development sequencing |
| url | https://ijsst.areeo.ac.ir/article_121384_1108af34f3db4e4f9be32a1f5d2c8c7d.pdf |
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