The value of new genome references

Abstract

Genomic information has become a ubiquitous and almost essential aspect of biological research. Over the last 10–15 years, the cost of generating sequence data from DNA or RNA samples has dramatically declined and our ability to interpret those data increased just as remarkably. Although it is still possible for biologists to conduct interesting and valuable research on species for which genomic data are not available, the impact of having access to a high quality whole genome reference assembly for a given species is nothing short of transformational. Research on a species for which we have no DNA or RNA sequence data is restricted in fundamental ways. In contrast, even access to an initial draft quality genome (see below for definitions) opens a wide range of opportunities that are simply not available without that reference genome assembly. Although a complete discussion of the impact of genome sequencing and assembly is beyond the scope of this short paper, the goal of this review is to summarize the most common and highest impact contributions that whole genome sequencing and assembly has had on comparative and evolutionary biology.

Signature of adaptive evolution in olfactory receptor genes in Cory’s Shearwater supports molecular basis for smell in procellariiform seabirds

“…genomic complement of OR gene families remains an important but challenging endeavour 34,35 . Multigene families can be reliably studied from high-quality genome references, but the combination of read lengths and the depth of coverage required make these costly and time consuming 36,37 . Conversely, short-read whole genome sequence data, while relatively inexpensive to generate, results in partial gene family sets with missing, truncated and possibly chimeric gene sequences, especially in families composed of genes with high pairwise sequence similarity or highly conserved sequence motifs 38,39 .…”

A hybridde novogenome assembly of the honeybee,Apis mellifera, with chromosome-length scaffolds

“…Due to these various drawbacks, the current state-of-the-art for genome assembly is to use a hybrid approach combining multiple technologies [18][19][20][21]. Several genome assemblies produced in this fashion are of comparable or better quality than finished human and model organisms that have undergone large number of improvements with additional data [1,[22][23][24][25].…”

One fly–one genome: chromosome-scale genome assembly of a single outbred Drosophila melanogaster

“…While short reads can be reassembled into larger contiguous genome segments by identifying overlapping reads, they often fail to generate chromosome length assemblies due to the challenge of assembling repetitive DNA sequences. Consequently, many published genomes are highly fragmented ( 2 ). Fragmented genomes can be valuable for gene-level studies but many genomic analyses such as understanding chromosome-scale evolution, resolving full-length haplotypes, association studies, and quantitative trait locus mapping require high-quality chromosome-scale assemblies.…”

“…Two recent advances in genomic technologies have dramatically raised the quality of genome assemblies ( 4 ). First, third generation long-read sequencing technologies are capable of sequencing entire long repetitive sequences, but they suffer from higher error rates and lower throughput ( 2 ). Second, proximity-ligation sequencing, or Hi-C, produces short-read pairs representing sequences that are close together in three-dimensional space ( 5 ).…”