Abstract
Centromeric regions of plants are generally composed of large array of satellites from a specific lineage of Gypsy LTR-retrotransposons, called Centromeric Retrotransposons. Repeated sequences interact with a specific H3 histone, playing a crucial function on kinetochore formation. To study the structure and composition of centromeric regions in the genus Coffea, we annotated and classified Centromeric Retrotransposons sequences from the allotetraploid C. arabica genome and its two diploid ancestors: Coffea canephora and C. eugenioides. Ten distinct CRC (Centromeric Retrotransposons in Coffea) families were found. The sequence mapping and FISH experiments of CRC Reverse Transcriptase domains in C. canephora, C. eugenioides, and C. arabica clearly indicate a strong and specific targeting mainly onto proximal chromosome regions, which can be associated also with heterochromatin. PacBio genome sequence analyses of putative centromeric regions on C. arabica and C. canephora chromosomes showed an exceptional density of one family of CRC elements, and the complete absence of satellite arrays, contrasting with usual structure of plant centromeres. Altogether, our data suggest a specific centromere organization in Coffea, contrasting with other plant genomes.
Highlights
LTR-retrotransposons pertain to the Class I of Transposable Elements (TEs), they move via the synthesis of an intermediate RNA using “copy and paste” mechanisms (Wicker et al, 2007)
Despite numerous centromeric retrotransposons elements identified in monocot and dicot species (Neumann et al, 2011), their diversity and classification into types, as well as their respective contribution to the structure of centromeric regions is poorly known for most higher plant groups
We identified 10 groups of Centromeric Retrotransposons of Coffea (CRC) in the genomes of C. arabica, an allotetraploid species and its two diploid parents, C. canephora and C. eugenioides
Summary
LTR-retrotransposons pertain to the Class I of Transposable Elements (TEs), they move via the synthesis of an intermediate RNA using “copy and paste” mechanisms (Wicker et al, 2007). Due to their mobility, LTR-retrotransposons are the most abundant TEs (Grandbastien, 2015). Copia is sub-classified into Tork, Retrofit, Oryco, SIRE, and Bianca, while Gypsy is sub-classified into TAT, Athila, Galadriel, Reina, Del, and CRM (Llorens et al, 2009, 2011), based on Reverse-Transcriptase (RT) domain phylogenetic analyses. Gypsy lineages are grouped into different branches according to the presence of a chromodomain; grouping together Galadriel, Reina, Del, and CRM lineages into the Chromovirus branch
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