Sequence-Based Analysis of Structural Organization and Composition of the Cultivated Sunflower (Helianthus annuus L.) Genome

Biology

Navdeep Gill²  Matteo Buti¹  Nolan Kane³  Arnaud Bellec⁴  Nicolas Helmstetter⁴  Hélène Berges⁴ 

[1] Applied Rosaceous Genomics Group, Centre for Research and Innovation, Michele all'Adige (TN) P.IVA 020384102, Italy; E-Mail:;Department of Botany and The Biodiversity Research Centre, University of British Columbia, Vancouver V6T 1Z4, BC, Canada; E-Mail:;Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO 80309, USA; E-Mail:;French Plant Genomic Resource Centre, INRA–CNRGV, Chemin de Borde Rouge, CS 52627, 31326 Castanet Tolosan, France; E-Mails:

关键词: sunflower;    genome;    whole genome duplication;    transposable elements;    Class I LTR-retrotransposons;    Class II DNA transposons;    transcriptome;    expressed sequence tags;    expression pattern;   

DOI  :  10.3390/biology3020295

来源: mdpi

【 摘 要 】

Sunflower is an important oilseed crop, as well as a model system for evolutionary studies, but its 3.6 gigabase genome has proven difficult to assemble, in part because of the high repeat content of its genome. Here we report on the sequencing, assembly, and analyses of 96 randomly chosen BACs from sunflower to provide additional information on the repeat content of the sunflower genome, assess how repetitive elements in the sunflower genome are organized relative to genes, and compare the genomic distribution of these repeats to that found in other food crops and model species. We also examine the expression of transposable element-related transcripts in EST databases for sunflower to determine the representation of repeats in the transcriptome and to measure their transcriptional activity. Our data confirm previous reports in suggesting that the sunflower genome is >78% repetitive. Sunflower repeats share very little similarity to other plant repeats such as those of Arabidopsis, rice, maize and wheat; overall 28% of repeats are “novel” to sunflower. The repetitive sequences appear to be randomly distributed within the sequenced BACs. Assuming the 96 BACs are representative of the genome as a whole, then approximately 5.2% of the sunflower genome comprises non TE-related genic sequence, with an average gene density of 18kbp/gene. Expression levels of these transposable elements indicate tissue specificity and differential expression in vegetative and reproductive tissues, suggesting that expressed TEs might contribute to sunflower development. The assembled BACs will also be useful for assessing the quality of several different draft assemblies of the sunflower genome and for annotating the reference sequence.

【 授权许可】

CC BY   
© 2014 by the authors; licensee MDPI, Basel, Switzerland.