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 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.
Laboratory of Phytopathology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands. Electronic address: bart.thomma@wur.nl.
Bart P H J
BPHJ
Thomma
Laboratory of Phytopathology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands.
Michael F
MF
Seidl
Laboratory of Phytopathology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands.
Xiaoqian
X
Shi-Kunne
Laboratory of Phytopathology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands.
David E
DE
Cook
United States Department of Agriculture, Agricultural Research Service, Northern Crop Science Laboratory, Fargo, ND 58102-2765, USA.
Melvin D
MD
Bolton
Laboratory of Phytopathology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands.
Jan A L
JAL
van Kan
Laboratory of Phytopathology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands.
Luigi
L
Faino
D002874:Chromosome Mapping; D053938:DNA Fragmentation; D057890:Epigenomics; D019143:Evolution, Molecular; D005658:Fungi / Q000235:genetics*; D016681:Genome, Fungal; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods
Assembly; Fungal genome; Next-generation sequencing; Repeat; Transposable element