How Next-Generation Sequencing Has Aided Our Understanding of the Sequence Composition and Origin of B Chromosomes
Open Access
- 25 October 2017
- Vol. 8 (11), 294
- https://doi.org/10.3390/genes8110294
Abstract
Accessory, supernumerary, or—most simply—B chromosomes, are found in many eukaryotic karyotypes. These small chromosomes do not follow the usual pattern of segregation, but rather are transmitted in a higher than expected frequency. As increasingly being demonstrated by next-generation sequencing (NGS), their structure comprises fragments of standard (A) chromosomes, although in some plant species, their sequence also includes contributions from organellar genomes. Transcriptomic analyses of various animal and plant species have revealed that, contrary to what used to be the common belief, some of the B chromosome DNA is protein-encoding. This review summarizes the progress in understanding B chromosome biology enabled by the application of next-generation sequencing technology and state-of-the-art bioinformatics. In particular, a contrast is drawn between a direct sequencing approach and a strategy based on a comparative genomics as alternative routes that can be taken towards the identification of B chromosome sequences.Funding Information
- Deutsche Forschungsgemeinschaft (HO 1779/26-1, SCHO 1420/2-1)
This publication has 78 references indexed in Scilit:
- Formation and Expression of Pseudogenes on the B Chromosome of RyeTHE PLANT CELL ONLINE, 2013
- Selfish supernumerary chromosome reveals its origin as a mosaic of host genome and organellar sequencesProceedings of the National Academy of Sciences of the United States of America, 2012
- Fast gapped-read alignment with Bowtie 2Nature Methods, 2012
- Unlocking the Barley Genome by Chromosomal and Comparative GenomicsTHE PLANT CELL ONLINE, 2011
- A fast, lock-free approach for efficient parallel counting of occurrences of k-mersBioinformatics, 2011
- Graph-based clustering and characterization of repetitive sequences in next-generation sequencing dataBMC Bioinformatics, 2010
- The Sequence Alignment/Map format and SAMtoolsBioinformatics, 2009
- Fast and accurate short read alignment with Burrows–Wheeler transformBioinformatics, 2009
- Coupling amplified DNA from flow-sorted chromosomes to high-density SNP mapping in barleyBMC Genomics, 2008
- The proto-oncogene C-KIT maps to canid B-chromosomesChromosome Research, 2005