Abstract
BackgroundSugar beet (Beta vulgaris) is an important crop of temperate climate zones, which provides nearly 30 % of the world’s annual sugar needs. From the total genome size of 758 Mb, only 567 Mb were incorporated in the recently published genome sequence, due to the fact that regions with high repetitive DNA contents (e.g. satellite DNAs) are only partially included. Therefore, to fill these gaps and to gain information about the repeat composition of centromeres and heterochromatic regions, we performed chromatin immunoprecipitation followed by sequencing (ChIP-Seq) using antibodies against the centromere-specific histone H3 variant of sugar beet (CenH3) and the heterochromatic mark of dimethylated lysine 9 of histone H3 (H3K9me2).ResultsChIP-Seq analysis revealed that active centromeres containing CenH3 consist of the satellite pBV and the Ty3-gypsy retrotransposon Beetle7, while heterochromatin marked by H3K9me2 exhibits heterogeneity in repeat composition. H3K9me2 was mainly associated with the satellite family pEV, the Ty1-copia retrotransposon family Cotzilla and the DNA transposon superfamily of the En/Spm type. In members of the section Beta within the genus Beta, immunostaining using the CenH3 antibody was successful, indicating that orthologous CenH3 proteins are present in closely related species within this section.ConclusionsThe identification of repetitive genome portions by ChIP-Seq experiments complemented the sugar beet reference sequence by providing insights into the repeat composition of poorly characterized CenH3-chromatin and H3K9me2-heterochromatin. Therefore, our work provides the basis for future research and application concerning the sugar beet centromere and repeat-rich heterochromatic regions characterized by the presence of H3K9me2.Electronic supplementary materialThe online version of this article (doi:10.1186/s12870-016-0805-5) contains supplementary material, which is available to authorized users.
Highlights
Sugar beet (Beta vulgaris) is an important crop of temperate climate zones, which provides nearly 30 % of the world’s annual sugar needs
Sugar beet highly repetitive sequences are largely amplified in heterochromatic regions and centromeric chromatin but are only fragmentary included in the genome sequence
The repeat composition of sugar beet heterochromatin and centromeric chromatin was annotated and characterized using ChIP-Seq and subsequent sequence clustering approaches via RepeatExplorer: Centromeric chromatin is hallmarked by the sugar beet centromere-specific histone H3 variant of sugar beet (CenH3), which binds to pBV satellites and to elements of the Ty3-gypsy retrotransposon family Beetle7
Summary
Sugar beet (Beta vulgaris) is an important crop of temperate climate zones, which provides nearly 30 % of the world’s annual sugar needs. From the total genome size of 758 Mb, only 567 Mb were incorporated in the recently published genome sequence, due to the fact that regions with high repetitive DNA contents (e.g. satellite DNAs) are only partially included To fill these gaps and to gain information about the repeat composition of centromeres and heterochromatic regions, we performed chromatin immunoprecipitation followed by sequencing (ChIP-Seq) using antibodies against the centromere-specific histone H3 variant of sugar beet (CenH3) and the heterochromatic mark of dimethylated lysine 9 of histone H3 (H3K9me). Vulgaris (hereinafter referred to as sugar beet) is an important crop of the temperate climate zones It possesses 2n = 18 chromosomes, an estimated genome size of 758 megabases (Mb) [1] and a repeat content of 63 % [2]. For plants it is known that CenH3 is preferentially associated with satellite DNA often intermingled with Ty3-gypsy retrotransposon elements [28,29,30]
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Free) 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a call
