High-Throughput Sequencing Reveals Diverse Sets of Conserved, Nonconserved, and Species-Specific miRNAs in Jute
MicroRNAs play a pivotal role in regulating a broad range of biological processes, acting by cleaving mRNAs or by translational repression. A group of plant microRNAs are evolutionarily conserved; however, others are expressed in a species-specific manner. Jute is an agroeconomically important fibre...
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| Main Authors: | , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
Wiley
2015-01-01
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| Series: | International Journal of Genomics |
| Online Access: | http://dx.doi.org/10.1155/2015/125048 |
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| _version_ | 1832559002085490688 |
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| author | Md. Tariqul Islam Ahlan Sabah Ferdous Rifat Ara Najnin Suprovath Kumar Sarker Haseena Khan |
| author_facet | Md. Tariqul Islam Ahlan Sabah Ferdous Rifat Ara Najnin Suprovath Kumar Sarker Haseena Khan |
| author_sort | Md. Tariqul Islam |
| collection | DOAJ |
| description | MicroRNAs play a pivotal role in regulating a broad range of biological processes, acting by cleaving mRNAs or by translational repression. A group of plant microRNAs are evolutionarily conserved; however, others are expressed in a species-specific manner. Jute is an agroeconomically important fibre crop; nonetheless, no practical information is available for microRNAs in jute to date. In this study, Illumina sequencing revealed a total of 227 known microRNAs and 17 potential novel microRNA candidates in jute, of which 164 belong to 23 conserved families and the remaining 63 belong to 58 nonconserved families. Among a total of 81 identified microRNA families, 116 potential target genes were predicted for 39 families and 11 targets were predicted for 4 among the 17 identified novel microRNAs. For understanding better the functions of microRNAs, target genes were analyzed by Gene Ontology and their pathways illustrated by KEGG pathway analyses. The presence of microRNAs identified in jute was validated by stem-loop RT-PCR followed by end point PCR and qPCR for randomly selected 20 known and novel microRNAs. This study exhaustively identifies microRNAs and their target genes in jute which will ultimately pave the way for understanding their role in this crop and other crops. |
| format | Article |
| id | doaj-art-60187a9f860745cea0e8bf3209341436 |
| institution | Kabale University |
| issn | 2314-436X 2314-4378 |
| language | English |
| publishDate | 2015-01-01 |
| publisher | Wiley |
| record_format | Article |
| series | International Journal of Genomics |
| spelling | doaj-art-60187a9f860745cea0e8bf32093414362025-02-03T01:31:04ZengWileyInternational Journal of Genomics2314-436X2314-43782015-01-01201510.1155/2015/125048125048High-Throughput Sequencing Reveals Diverse Sets of Conserved, Nonconserved, and Species-Specific miRNAs in JuteMd. Tariqul Islam0Ahlan Sabah Ferdous1Rifat Ara Najnin2Suprovath Kumar Sarker3Haseena Khan4Molecular Biology Laboratory, Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka 1000, BangladeshMolecular Biology Laboratory, Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka 1000, BangladeshMolecular Biology Laboratory, Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka 1000, BangladeshMolecular Biology Laboratory, Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka 1000, BangladeshMolecular Biology Laboratory, Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka 1000, BangladeshMicroRNAs play a pivotal role in regulating a broad range of biological processes, acting by cleaving mRNAs or by translational repression. A group of plant microRNAs are evolutionarily conserved; however, others are expressed in a species-specific manner. Jute is an agroeconomically important fibre crop; nonetheless, no practical information is available for microRNAs in jute to date. In this study, Illumina sequencing revealed a total of 227 known microRNAs and 17 potential novel microRNA candidates in jute, of which 164 belong to 23 conserved families and the remaining 63 belong to 58 nonconserved families. Among a total of 81 identified microRNA families, 116 potential target genes were predicted for 39 families and 11 targets were predicted for 4 among the 17 identified novel microRNAs. For understanding better the functions of microRNAs, target genes were analyzed by Gene Ontology and their pathways illustrated by KEGG pathway analyses. The presence of microRNAs identified in jute was validated by stem-loop RT-PCR followed by end point PCR and qPCR for randomly selected 20 known and novel microRNAs. This study exhaustively identifies microRNAs and their target genes in jute which will ultimately pave the way for understanding their role in this crop and other crops.http://dx.doi.org/10.1155/2015/125048 |
| spellingShingle | Md. Tariqul Islam Ahlan Sabah Ferdous Rifat Ara Najnin Suprovath Kumar Sarker Haseena Khan High-Throughput Sequencing Reveals Diverse Sets of Conserved, Nonconserved, and Species-Specific miRNAs in Jute International Journal of Genomics |
| title | High-Throughput Sequencing Reveals Diverse Sets of Conserved, Nonconserved, and Species-Specific miRNAs in Jute |
| title_full | High-Throughput Sequencing Reveals Diverse Sets of Conserved, Nonconserved, and Species-Specific miRNAs in Jute |
| title_fullStr | High-Throughput Sequencing Reveals Diverse Sets of Conserved, Nonconserved, and Species-Specific miRNAs in Jute |
| title_full_unstemmed | High-Throughput Sequencing Reveals Diverse Sets of Conserved, Nonconserved, and Species-Specific miRNAs in Jute |
| title_short | High-Throughput Sequencing Reveals Diverse Sets of Conserved, Nonconserved, and Species-Specific miRNAs in Jute |
| title_sort | high throughput sequencing reveals diverse sets of conserved nonconserved and species specific mirnas in jute |
| url | http://dx.doi.org/10.1155/2015/125048 |
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