期刊
MOLECULAR ECOLOGY RESOURCES
卷 18, 期 6, 页码 1188-1195出版社
WILEY
DOI: 10.1111/1755-0998.12933
关键词
birds; genomics; hybrid assembly; long reads; multiplatform sequencing; repeats
资金
- SciLifeLab Swedish Biodiversity Program [2015-R14]
- Swedish Science Foundation [2016-05139]
- Swedish Research Council [2016-05139] Funding Source: Swedish Research Council
- Vinnova [2016-05139] Funding Source: Vinnova
The genomics revolution has led to the sequencing of a large variety of nonmodel organisms often referred to as whole or complete genome assemblies. But how complete are these, really? Here, we use birds as an example for nonmodel vertebrates and find that, although suitable in principle for genomic studies, the current standard of short-read assemblies misses a significant proportion of the expected genome size (7% to 42%; mean 20 +/- 9%). In particular, regions with strongly deviating nucleotide composition (e.g., guanine-cytosine-[GC]-rich) and regions highly enriched in repetitive DNA (e.g., transposable elements and satellite DNA) are usually underrepresented in assemblies. However, long-read sequencing technologies successfully characterize many of these underrepresented GC-rich or repeat-rich regions in several bird genomes. For instance, only similar to 2% of the expected total base pairs are missing in the last chicken reference (galGal5). These assemblies still contain thousands of gaps (i.e., fragmented sequences) because some chromosomal structures (e.g., centromeres) likely contain arrays of repetitive DNA that are too long to bridge with currently available technologies. We discuss how to minimize the number of assembly gaps by combining the latest available technologies with complementary strengths. At last, we emphasize the importance of knowing the location, size and potential content of assembly gaps when making population genetic inferences about adjacent genomic regions.
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