Characterization of paralogous protein families in rice
| العنوان: | Characterization of paralogous protein families in rice |
|---|---|
| المؤلفون: | Blake C. Meyers, Amy Egan, Shu Ouyang, Haining Lin, Wei Zhu, Brian J. Haas, C. Robin Buell, Xun Gu, Joana C. Silva, Kan Nobuta |
| المساهمون: | Haas, Brian J. |
| المصدر: | BioMed Central Ltd BMC Plant Biology BMC Plant Biology, Vol 8, Iss 1, p 18 (2008) |
| بيانات النشر: | BioMed Central Ltd, 2007. |
| سنة النشر: | 2007 |
| مصطلحات موضوعية: | 0106 biological sciences, Protein family, Arabidopsis, 2R hypothesis, Plant Science, Genes, Plant, 01 natural sciences, Genome, 03 medical and health sciences, lcsh:Botany, Gene Duplication, Gene duplication, Protein Isoforms, Gene, Phylogeny, Plant Proteins, 030304 developmental biology, Segmental duplication, Expressed Sequence Tags, 2. Zero hunger, Genetics, 0303 health sciences, biology, fungi, food and beverages, Oryza, biology.organism_classification, lcsh:QK1-989, Multigene Family, Functional divergence, Research Article, 010606 plant biology & botany |
| الوصف: | Background: High gene numbers in plant genomes reflect polyploidy and major gene duplication events. Oryza sativa, cultivated rice, is a diploid monocotyledonous species with a ~390 Mb genome that has undergone segmental duplication of a substantial portion of its genome. This, coupled with other genetic events such as tandem duplications, has resulted in a substantial number of its genes, and resulting proteins, occurring in paralogous families. Results: Using a computational pipeline that utilizes Pfam and novel protein domains, we characterized paralogous families in rice and compared these with paralogous families in the model dicotyledonous diploid species, Arabidopsis thaliana. Arabidopsis, which has undergone genome duplication as well, has a substantially smaller genome (~120 Mb) and gene complement compared to rice. Overall, 53% and 68% of the non-transposable element-related rice and Arabidopsis proteins could be classified into paralogous protein families, respectively. Singleton and paralogous family genes differed substantially in their likelihood of encoding a protein of known or putative function; 26% and 66% of singleton genes compared to 73% and 96% of the paralogous family genes encode a known or putative protein in rice and Arabidopsis, respectively. Furthermore, a major skew in the distribution of specific gene function was observed; a total of 17 Gene Ontology categories in both rice and Arabidopsis were statistically significant in their differential distribution between paralogous family and singleton proteins. In contrast to mammalian organisms, we found that duplicated genes in rice and Arabidopsis tend to have more alternative splice forms. Using data from Massively Parallel Signature Sequencing, we show that a significant portion of the duplicated genes in rice show divergent expression although a correlation between sequence divergence and correlation of expression could be seen in very young genes. Conclusion: Collectively, these data suggest that while co-regulation and conserved function are present in some paralogous protein family members, evolutionary pressures have resulted in functional divergence with differential expression patterns. National Science Foundation (U.S.). Plant Genome Research Program (DBI-0321538) National Science Foundation (U.S.) (DBI-0321437) |
| وصف الملف: | application/pdf |
| اللغة: | English |
| URL الوصول: | https://explore.openaire.eu/search/publication?articleId=doi_dedup___::c31113f6e3f73396f011717abf170c87 http://hdl.handle.net/1721.1/58916 |
| حقوق: | OPEN |
| رقم الأكسشن: | edsair.doi.dedup.....c31113f6e3f73396f011717abf170c87 |
| قاعدة البيانات: | OpenAIRE |
| الوصف غير متاح. |