Novel and nodulation-regulated microRNAs in soybean roots
<p>Abstract</p> <p>Background</p> <p>Small RNAs regulate a number of developmental processes in plants and animals. However, the role of small RNAs in legume-rhizobial symbiosis is largely unexplored. Symbiosis between legumes (e.g. soybean) and rhizobia bacteria (e.g....
| Main Authors: | , , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2008-04-01
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| Series: | BMC Genomics |
| Online Access: | http://www.biomedcentral.com/1471-2164/9/160 |
| _version_ | 1828412293493293056 |
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| author | Zhu Jian-Kang Barbazuk W Brad Sunkar Ramanjulu Fu Yan Subramanian Senthil Yu Oliver |
| author_facet | Zhu Jian-Kang Barbazuk W Brad Sunkar Ramanjulu Fu Yan Subramanian Senthil Yu Oliver |
| author_sort | Zhu Jian-Kang |
| collection | DOAJ |
| description | <p>Abstract</p> <p>Background</p> <p>Small RNAs regulate a number of developmental processes in plants and animals. However, the role of small RNAs in legume-rhizobial symbiosis is largely unexplored. Symbiosis between legumes (e.g. soybean) and rhizobia bacteria (e.g. <it>Bradyrhizobium japonicum</it>) results in root nodules where the majority of biological nitrogen fixation occurs. We sought to identify microRNAs (miRNAs) regulated during soybean-<it>B. japonicum </it>symbiosis.</p> <p>Results</p> <p>We sequenced ~350000 small RNAs from soybean roots inoculated with <it>B. japonicum </it>and identified conserved miRNAs based on similarity to miRNAs known in other plant species and new miRNAs based on potential hairpin-forming precursors within soybean EST and shotgun genomic sequences. These bioinformatics analyses identified 55 families of miRNAs of which 35 were novel. A subset of these miRNAs were validated by Northern analysis and miRNAs differentially responding to <it>B. japonicum </it>inoculation were identified. We also identified putative target genes of the identified miRNAs and verified <it>in vivo </it>cleavage of a subset of these targets by 5'-RACE analysis. Using conserved miRNAs as internal control, we estimated that our analysis identified ~50% of miRNAs in soybean roots.</p> <p>Conclusion</p> <p>Construction and analysis of a small RNA library led to the identification of 20 conserved and 35 novel miRNA families in soybean. The availability of complete and assembled genome sequence information will enable identification of many other miRNAs. The conserved miRNA loci and novel miRNAs identified in this study enable investigation of the role of miRNAs in rhizobial symbiosis.</p> |
| first_indexed | 2024-12-10T12:46:34Z |
| format | Article |
| id | doaj.art-4ab1cf1bcc1e48c4ae20c38cafd73e60 |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-12-10T12:46:34Z |
| publishDate | 2008-04-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj.art-4ab1cf1bcc1e48c4ae20c38cafd73e602022-12-22T01:48:23ZengBMCBMC Genomics1471-21642008-04-019116010.1186/1471-2164-9-160Novel and nodulation-regulated microRNAs in soybean rootsZhu Jian-KangBarbazuk W BradSunkar RamanjuluFu YanSubramanian SenthilYu Oliver<p>Abstract</p> <p>Background</p> <p>Small RNAs regulate a number of developmental processes in plants and animals. However, the role of small RNAs in legume-rhizobial symbiosis is largely unexplored. Symbiosis between legumes (e.g. soybean) and rhizobia bacteria (e.g. <it>Bradyrhizobium japonicum</it>) results in root nodules where the majority of biological nitrogen fixation occurs. We sought to identify microRNAs (miRNAs) regulated during soybean-<it>B. japonicum </it>symbiosis.</p> <p>Results</p> <p>We sequenced ~350000 small RNAs from soybean roots inoculated with <it>B. japonicum </it>and identified conserved miRNAs based on similarity to miRNAs known in other plant species and new miRNAs based on potential hairpin-forming precursors within soybean EST and shotgun genomic sequences. These bioinformatics analyses identified 55 families of miRNAs of which 35 were novel. A subset of these miRNAs were validated by Northern analysis and miRNAs differentially responding to <it>B. japonicum </it>inoculation were identified. We also identified putative target genes of the identified miRNAs and verified <it>in vivo </it>cleavage of a subset of these targets by 5'-RACE analysis. Using conserved miRNAs as internal control, we estimated that our analysis identified ~50% of miRNAs in soybean roots.</p> <p>Conclusion</p> <p>Construction and analysis of a small RNA library led to the identification of 20 conserved and 35 novel miRNA families in soybean. The availability of complete and assembled genome sequence information will enable identification of many other miRNAs. The conserved miRNA loci and novel miRNAs identified in this study enable investigation of the role of miRNAs in rhizobial symbiosis.</p>http://www.biomedcentral.com/1471-2164/9/160 |
| spellingShingle | Zhu Jian-Kang Barbazuk W Brad Sunkar Ramanjulu Fu Yan Subramanian Senthil Yu Oliver Novel and nodulation-regulated microRNAs in soybean roots BMC Genomics |
| title | Novel and nodulation-regulated microRNAs in soybean roots |
| title_full | Novel and nodulation-regulated microRNAs in soybean roots |
| title_fullStr | Novel and nodulation-regulated microRNAs in soybean roots |
| title_full_unstemmed | Novel and nodulation-regulated microRNAs in soybean roots |
| title_short | Novel and nodulation-regulated microRNAs in soybean roots |
| title_sort | novel and nodulation regulated micrornas in soybean roots |
| url | http://www.biomedcentral.com/1471-2164/9/160 |
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