Mind the gap; seven reasons to close fragmented genome assemblies

Like other domains of life, research into the biology of filamentous microbes has greatly benefited from the advent of whole-genome sequencing. Next-generation sequencing (NGS) technologies have revolutionized sequencing, making genomic sciences accessible to many academic laboratories including tho...

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Bibliographic Details
Published in:Fungal genetics and biology 2016-05, Vol.90, p.24-30
Main Authors: Thomma, Bart P.H.J., Seidl, Michael F., Shi-Kunne, Xiaoqian, Cook, David E., Bolton, Melvin D., van Kan, Jan A.L., Faino, Luigi
Format: Article
Language:English
Subjects:
Assembly
Chromosome Mapping
DNA Fragmentation
Epigenomics
EPS-2
Evolution, Molecular
Fungal genome
Fungi - genetics
Genome, Fungal
High-Throughput Nucleotide Sequencing - methods
Laboratorium voor Fytopathologie
Laboratorium voor Phytopathologie
Laboratory of Phytopathology
Next-generation sequencing
Repeat
Transposable element
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Summary:Like other domains of life, research into the biology of filamentous microbes has greatly benefited from the advent of whole-genome sequencing. Next-generation sequencing (NGS) technologies have revolutionized sequencing, making genomic sciences accessible to many academic laboratories including those that study non-model organisms. Thus, hundreds of fungal genomes have been sequenced and are publically available today, although these initiatives have typically yielded considerably fragmented genome assemblies that often lack large contiguous genomic regions. Many important genomic features are contained in intergenic DNA that is often missing in current genome assemblies, and recent studies underscore the significance of non-coding regions and repetitive elements for the life style, adaptability and evolution of many organisms. The study of particular types of genetic elements, such as telomeres, centromeres, repetitive elements, effectors, and clusters of co-regulated genes, but also of phenomena such as structural rearrangements, genome compartmentalization and epigenetics, greatly benefits from having a contiguous and high-quality, preferably even complete and gapless, genome assembly. Here we discuss a number of important reasons to produce gapless, finished, genome assemblies to help answer important biological questions.
ISSN:1087-1845
1096-0937
DOI:10.1016/j.fgb.2015.08.010