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

Abstract

The genus Coffea possesses about 100 species, and the most economically important are Coffea canephora and Coffea arabica. The latter is predominantly self-compatible with 2n = 4x = 44, while the others of the genus are diploid with 2n = 2x = 22 and mostly self-incompatible. Studies using molecular markers have been useful to detect differences between genomes in Coffea; however, molecular and cytogenetic studies have produced only limited information on the karyotypes organization. We used DOP-PCR to isolate repetitive elements from genome of Coffea arabica var. typica. The pCa06 clone, containing a fragment of 775 bp length, was characterized by sequencing and used as a probe in chromosomes of C. arabica and six other species: C. canephora, Coffea eugenioides, Coffea kapakata, Coffea liberica var. dewevrei, Coffea racemosa, and Coffea stenophylla. This insert shows similarities with a gag protein of the Ty3-gypsy-like super-family. Dot blot and FISH analyses demonstrated that pCa06 is differentially accumulated between species and chromosomes. Signals appeared scattered and clustered on the chromosomes and were also associated with heterochromatic regions. While the literature shows that there is a high karyotype similarity between Coffea species, our results point out differences in the accumulation and dispersion of this Ty3-gypsy-like retrotransposon during karyotype differentiation of Coffea.

Transcriptional Activity, Chromosomal Distribution and Expression Effects of Transposable Elements in Coffea Genomes

“…Furthermore, C. canephora chromosomes showed preferentially clustered signals, and most C. eugenioides chromosomes showed dispersed signals. These results are in agreement with previous FISH results [30] using another probe containing a fragment homologous to a gag-like element from a Del 1 LTR-retrotransposon isolated from the germplasm of C. arabica var. typica .…”

Allopolyploid origin and genome differentiation of the parasitic speciesCuscuta veatchii(Convolvulaceae) revealed by genomic in situ hybridization

“…Chromosome size variation among closely related species is commonly associated with genome size variation promoted by proliferation/elimination of repetitive sequences, mainly retroelements (Li et al 2017). The extra repetitive sequences may be more concentrated in the proximal region, as in C. nevadensis and other species (e.g., Gaeta et al 2010;Yuyama et al 2012). In addition, the number of rDNA sites in C. nevadensis, with six 5S and 10 35S rDNA sites, was much higher than in C. denticulata, with only one pair of sites for each rDNA family.…”

Genome relationships and LTR-retrotransposon diversity in three cultivated Capsicum L. (Solanaceae) species

“…It is well established in the literature that TEs, especially LTR-RT superfamilies, occupy "specific" chromosomal regions, with the consensus that Copia elements are distributed preferentially along the chromosomes associated with euchromatin, while Gypsy elements are resident in heterochromatin-rich regions (see [7]). In Coffea, Brachiaria, and Secale, for example, Gypsy probes were located in proximal heterochromatin-rich chromosome regions [17,57,58], but in Gossypium species, Gypsy probes were hybridized along chromosomes [59]. However, when the elements are considered according to their phylogenetic positions, i.e., lineages of Copia and Gypsy [5,7,60], it becomes evident that there are many differences in the TE distribution profiles, in both plants (see [10,61]) and animals [62,63].…”