Occurrence and chromosome distribution of retroelements and NUPT sequences in Copaifera langsdorffii Desf. (Caesalpinioideae)

Abstract

Copaifera langsdorffii possesses 2n = 24 large meta- and submetacentric chromosomes (5.97-2.60 microm) in comparison with other Caesalpinioideae trees. Chromosome banding revealed an abundance of GC-rich blocks with a few differences in the size and location of bands between different populations. Polymerase chain reaction and digestion with restriction enzyme RsaI were carried out in order to isolate repetitive DNAs, yielding three fragments of different size: (1) cp-rDNA-like, 109 bp (pCl03 clone); (2) Ty1-copia-like retroelement, 185 bp (pCl23 clone); and (3) Ty3-gypsy-like retroelement, 269 bp (pCl08 clone). The first clone produced unmistakable hybridization signals at subterminal and intercalary positions, coinciding with or adjacent to most of the GC-rich bands. The second clone (pCl23 clone) showed dispersed signals distributed throughout several chromosomes, while the pCl08 clone exhibited hybridization signals scattered and organized in blocks in all chromosomes of the complement. Fluorescent in situ hybridization and chromosome banding results allowed the detection of translocation events and unequal crossing-over involving 45S rDNA regions (pairs 7, 8, and 11). However, the most intriguing result was the insertion and subsequent overamplification of a cp-rDNA-like fragment and its distribution over the chromosomes of C. langsdorffii. Additionally, the results suggest that this segment behaves like satellite DNA. These different chromosome markers produced by cytomolecular techniques show that samples from different locations, although isolated, retain more karyotypic similarities than differences.

Polyploidy, B chromosomes, and heterochromatin characterization of Mimosa caesalpiniifolia Benth. (Fabaceae-Mimosoideae)

“…These different patterns reinforce the necessity to get data from a large number of species to better understand the heterochromatin pattern in the whole family. Combining the CMA/DAPI banding and FISH techniques, it seems that M. caesalpiniifolia has two groups of GC-rich bands: terminal CMA ++ bands (pair 12) associated to the NORs and interstitial The coincidence of physical location of the CMA + marks and 45S rDNA sites here observed has already been reported in plants (Sousa et al 2009;Brasileiro-Vidal et al 2009;Dantas and Guerra 2010;Nardy et al 2010;Gaeta et al 2010;Silva et al 2010). Variation in the amount of heterochromatin has been reported as a useful character in karyosystematic and phylogenetic studies (Schwarzacher et al 1980;Grif 2000).…”

“…The same pattern was also observed for other species of the family such as Crotalaria juncea (Mondin et al 2007), some species of Arachis (Silva et al 2010), and Copaifera langsdorfii (Gaeta et al 2010). However, within the same family, a different pattern of AT-rich heterochromatic blocks was reported for the Erythrina (Nardy et al 2010), Senna, and Chamaecrista (Souza and Benko-Iseppon 2004).…”

“…Regarding NOR polymorphisms observed on chromosome 12 of M. caesalpiniifolia, the different sizes could be due to unequal crossing over or deletions in 45S rDNA regions, as observed by Gaeta et al (2010) in C. langsdorfii (Fabaceae). This hypothesis can also explain the different sizes of secondary constrictions observed by CMA banding, Ag-NOR banding, and FISH.…”

FISH using a gag-like fragment probe reveals a common Ty3-gypsy-like retrotransposon in genome of Coffea species

“…FISH with the 45S rDNA probe did not show signals co-localized with pCa06 signals, except to C. racemosa . In relation to DAPI + bands we did observe co-location especially in C. arabica The strategy of isolating transposable elements using PCR with degenerate primers has been widely used to amplify conserved fragments of Ty1-copia-like or Ty3-gypsy-like retrotransposons in many plant species (Belyayev et al 2005;Fregonezi et al 2007;Gaeta et al 2010). The DOP-PCR procedure has been used to amplify different repetitive DNAs from entire genomes.…”

Legume phylogeny and classification in the 21st century: Progress, prospects and lessons for other species–rich clades

“…Although this eliminates problems of paralogy within the plastid genome, the continual incorporation of organellar sequences into the nucleus (e.g., Gaeta & al., 2010) suggests caution in assuming orthology (Arthofer & al., 2011). Absence of historical recombination is one of the most useful phylogenetic properties of the plastid genome, because in theory it means that every nucleotide should track the same historical signal and can thus be combined to produce a single robust phylogeny.…”