Next Generation Sequencing-Based Analysis of Repetitive DNA in the Model Dioceous Plant Silene latifolia
Open Access
- 9 November 2011
- journal article
- research article
- Published by Public Library of Science (PLoS) in PLOS ONE
- Vol. 6 (11), e27335
- https://doi.org/10.1371/journal.pone.0027335
Abstract
Silene latifolia is a dioceous plant with well distinguished X and Y chromosomes that is used as a model to study sex determination and sex chromosome evolution in plants. However, efficient utilization of this species has been hampered by the lack of large-scale sequencing resources and detailed analysis of its genome composition, especially with respect to repetitive DNA, which makes up the majority of the genome. We performed low-pass 454 sequencing followed by similarity-based clustering of 454 reads in order to identify and characterize sequences of all major groups of S. latifolia repeats. Illumina sequencing data from male and female genomes were also generated and employed to quantify the genomic proportions of individual repeat families. The majority of identified repeats belonged to LTR-retrotransposons, constituting about 50% of genomic DNA, with Ty3/gypsy elements being more frequent than Ty1/copia. While there were differences between the male and female genome in the abundance of several repeat families, their overall repeat composition was highly similar. Specific localization patterns on sex chromosomes were found for several satellite repeats using in situ hybridization with probes based on k-mer frequency analysis of Illumina sequencing data. This study provides comprehensive information about the sequence composition and abundance of repeats representing over 60% of the S. latifolia genome. The results revealed generally low divergence in repeat composition between the sex chromosomes, which is consistent with their relatively recent origin. In addition, the study generated various data resources that are available for future exploration of the S. latifolia genome.Keywords
This publication has 48 references indexed in Scilit:
- Sequence-specific error profile of Illumina sequencersNucleic Acids Research, 2011
- Genome Size and Transposable Element Content as Determined by High-Throughput Sequencing in Maize and Zea luxuriansGenome Biology and Evolution, 2011
- The Gypsy Database (GyDB) of mobile genetic elements: release 2.0Nucleic Acids Research, 2010
- PatMaN: rapid alignment of short sequences to large databasesBioinformatics, 2008
- The role of chromosomal rearrangements in the evolution of Silene latifolia sex chromosomesMolecular Genetics and Genomics, 2007
- An accumulation of tandem DNA repeats on the Y chromosome in Silene latifolia during early stages of sex chromosome evolutionChromosoma, 2006
- MUSCLE: multiple sequence alignment with high accuracy and high throughputNucleic Acids Research, 2004
- Comparison of DNA Sequences with Protein SequencesGenomics, 1997
- Gapped BLAST and PSI-BLAST: a new generation of protein database search programsNucleic Acids Research, 1997
- A dot-matrix program with dynamic threshold control suited for genomic DNA and protein sequence analysisGene, 1995