title: Comparative molecular cytogenetic analyses of a major tandemly repeated DNA family and retrotransposon sequences in cultivated jute Corchorus species (Malvaceae).
abstract: OBJECTIVE
  The cultivated jute species Corchorus olitorius and Corchorus capsularis are important fibre crops. The analysis of repetitive DNA sequences, comprising a major part of plant genomes, has not been carried out in jute but is useful to investigate the long-range organization of chromosomes. The aim of this study was the identification of repetitive DNA sequences to facilitate comparative molecular and cytogenetic studies of two jute cultivars and to develop a fluorescent in situ hybridization (FISH) karyotype for chromosome identification.
  
  
  METHODS
  A plasmid library was generated from C. olitorius and C. capsularis with genomic restriction fragments of 100-500 bp, which was complemented by targeted cloning of satellite DNA by PCR. The diversity of the repetitive DNA families was analysed comparatively. The genomic abundance and chromosomal localization of different repeat classes were investigated by Southern analysis and FISH, respectively. The cytosine methylation of satellite arrays was studied by immunolabelling.
  
  
  RESULTS
  Major satellite repeats and retrotransposons have been identified from C. olitorius and C. capsularis. The satellite family CoSat I forms two undermethylated species-specific subfamilies, while the long terminal repeat (LTR) retrotransposons CoRetro I and CoRetro II show similarity to the Metaviridea of plant retroelements. FISH karyotypes were developed by multicolour FISH using these repetitive DNA sequences in combination with 5S and 18S-5·8S-25S rRNA genes which enable the unequivocal chromosome discrimination in both jute species.
  
  
  CONCLUSIONS
  The analysis of the structure and diversity of the repeated DNA is crucial for genome sequence annotation. The reference karyotypes will be useful for breeding of jute and provide the basis for karyotyping homeologous chromosomes of wild jute species to reveal the genetic and evolutionary relationship between cultivated and wild Corchorus species.
authors.affiliation: Department of Botany, University of Dhaka, Dhaka 1000, Bangladesh.
authors.forename: Rabeya
authors.initials: R
authors.lastname: Begum
authors.forename: Falk
authors.initials: F
authors.lastname: Zakrzewski
authors.forename: Gerhard
authors.initials: G
authors.lastname: Menzel
authors.forename: Beatrice
authors.initials: B
authors.lastname: Weber
authors.forename: Sheikh Shamimul
authors.initials: SS
authors.lastname: Alam
authors.forename: Thomas
authors.initials: T
authors.lastname: Schmidt
mesh_terms: D000595:Amino Acid Sequence; D015139:Blotting, Southern; D003001:Cloning, Molecular; D032381:Corchorus / Q000235:genetics*; D020732:Cytogenetic Analysis; D019175:DNA Methylation; D004276:DNA, Satellite; D017404:In Situ Hybridization, Fluorescence; D007621:Karyotyping; D008969:Molecular Sequence Data; D020161:Physical Chromosome Mapping; D012335:RNA, Ribosomal; D012337:RNA, Ribosomal, 18S; D012340:RNA, Ribosomal, 5.8S; D018626:Retroelements; D020080:Tandem Repeat Sequences
chemical_list: D004276:DNA, Satellite; D012335:RNA, Ribosomal; D012337:RNA, Ribosomal, 18S; D012340:RNA, Ribosomal, 5.8S; D018626:Retroelements; C065039:RNA, ribosomal, 25S
keywords: Corchorus capsularis; Corchorus olitorius; DNA methylation; FISH; immunolabelling; jute; karyotype; physical mapping; satellite DNA