Jute (Corchorus sp.) is a commercially important bast fibre-producing crop. Long-awaited industrial demand for improvement of quality of fibre in this crop species is restricted by the lack of knowledge about geneticbasis of economically important characters and their assemblage. Therefore, the present study was aimed at to compare the assemblage of single copy expressed sequence tag loci on nucleolar organizing chromosome of C. capsularis and C. olitorius at the molecular level. The expressed sequence tag loci associated with chromosome 5of C. olitorius were also found to be linked to same chromosome of C. capsularis. However, arrangements of the loci were found to be altered within as well as between the arms of chromosome 5 of Corchorus sp. The present study, for the first time, documented the occurrence of structural alteration at the molecular level between two jute species at least with respect to the chromosome 5. Such cryptic structural alterations resulted from chromosomal rearrangements (intra-chromosomal shift) in either of the species.
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