How complete are "complete" genome assemblies?: An avian perspective

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Peona, ValentinaUppsala universitet,Evolutionsbiologi,Alexander Suh Lab (author)

How complete are "complete" genome assemblies? : An avian perspective

Article/chapterEnglish2018

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2018-08-16
John Wiley & Sons,2018
electronicrdacarrier

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LIBRIS-ID:oai:DiVA.org:uu-358682
https://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-358682URI
https://doi.org/10.1111/1755-0998.12933DOI

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Language:English
Summary in:English

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Subject category:art swepub-publicationtype

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The genomics revolution has led to the sequencing of a large variety of non-model organisms often referred to as 'whole' or 'complete' genome assemblies. But how complete are these, really? Here we use birds as an example for non-model 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 ~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. Finally, we emphasize the importance of knowing the location, size, and potential content of assembly gaps when making population genetic inferences about adjacent genomic regions.

Subject headings and genre

NATURVETENSKAP Biologi Evolutionsbiologi hsv//swe
NATURAL SCIENCES Biological Sciences Evolutionary Biology hsv//eng
birds
genomics
hybrid assembly
long reads
multiplatform sequencing
repeats

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Weissensteiner, MatthiasUppsala universitet,Evolutionsbiologi,Ludwig-Maximilian University of Munich(Swepub:uu)matwe340 (author)
Suh, AlexanderUppsala universitet,Evolutionsbiologi(Swepub:uu)alesu519 (author)
Uppsala universitetEvolutionsbiologi (creator_code:org_t)

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In:Molecular Ecology Resources: John Wiley & Sons18:6, s. 1188-11951755-098X1755-0998

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NATURAL SCIENCES: NATURAL SCIENCES; and Biological Scien ...; and Evolutionary Bio ...

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