Identification and characterization of jute LTR retrotransposons

Ahmed, Salim; Shafiuddin,; Azam, Muhammad; Islam, Md Shahidul; Ghosh, Ajit; Khan, Haseena

doi:10.4161/mge.1.1.16433

Cited by 8 publications

(2 citation statements)

References 49 publications

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“…Despite its great agronomic importance, research on jute at the molecular level is insignificant [ 43 ]. Genome sequence of jute is not available in the public database.…”

Section: Introductionmentioning

confidence: 99%

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High-Throughput Sequencing Reveals Diverse Sets of Conserved, Nonconserved, and Species-Specific miRNAs in Jute

Islam

Ferdous

Najnin

et al. 2015

International Journal of Genomics

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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.

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“…Despite its great agronomic importance, research on jute at the molecular level is insignificant [ 43 ]. Genome sequence of jute is not available in the public database.…”

Section: Introductionmentioning

confidence: 99%

“…Genome sequence of jute is not available in the public database. So far only 1,210 sequences are found in the GenBank [ 43 ] with no deposits of any miRNA sequences in miRBase database. Within this context, the current study has employed the deep sequencing strategy in an attempt to effectively identify conserved and novel jute miRNAs.…”

Section: Introductionmentioning

confidence: 99%