Returning to more finished genomes

Multiplexed Non-barcoded Long-Read Sequencing and Assembling Genomes of Bacillus Strains in Error-Free Simulations

The generation of genomic data from microorganisms has revolutionized our abilities to understand their biology, but it is still challenging to obtain complete genome sequences of microbes in an automated high-throughput and cost-effective manner. While the advent of second-generation sequencing technologies provided significantly higher throughput, their shorter lengths and more pronounced sequence-context bias led to a shift towards resequencing applications. Recently, single molecule real-time (SMRT) DNA sequencing has been used to generate sequencing reads that are much longer than other sequencing platforms, facilitating de novo genome assembly and genome finishing. Here we introduced a novel multiplex strategy to make full use of the capacity and characteristics of SMRT sequencing in microbe genome assembly. We used error-free simulations to evaluate the practicability of assembling SMRT genomic sequencing data from multiple microbes into finished genomes once at a time. Then we compared the influence of two key factors, including sequencing coverage and read length, on multiplex assembling. Our results showed that long-read genomic sequencing inherently provided the ability to assemble genomic sequencing data from multiple microbes into finished genomes due to its long length. This approach might be helpful for the various groups of microbial genome projects or metagenomics research.

Chromosome-scale assemblies reveal the structural evolution of African cichlid genomes

BACKGROUND

African cichlid fishes are well known for their rapid radiations and are a model system for studying evolutionary processes. Here we compare multiple, high-quality, chromosome-scale genome assemblies to elucidate the genetic mechanisms underlying cichlid diversification and study how genome structure evolves in rapidly radiating lineages.

RESULTS

We re-anchored our recent assembly of the Nile tilapia (Oreochromis niloticus) genome using a new high-density genetic map. We also developed a new de novo genome assembly of the Lake Malawi cichlid, Metriaclima zebra, using high-coverage Pacific Biosciences sequencing, and anchored contigs to linkage groups (LGs) using 4 different genetic maps. These new anchored assemblies allow the first chromosome-scale comparisons of African cichlid genomes. Large intra-chromosomal structural differences (∼2-28 megabase pairs) among species are common, while inter-chromosomal differences are rare (<10 megabase pairs total). Placement of the centromeres within the chromosome-scale assemblies identifies large structural differences that explain many of the karyotype differences among species. Structural differences are also associated with unique patterns of recombination on sex chromosomes. Structural differences on LG9, LG11, and LG20 are associated with reduced recombination, indicative of inversions between the rock- and sand-dwelling clades of Lake Malawi cichlids. M. zebra has a larger number of recent transposable element insertions compared with O. niloticus, suggesting that several transposable element families have a higher rate of insertion in the haplochromine cichlid lineage.

CONCLUSION

This study identifies novel structural variation among East African cichlid genomes and provides a new set of genomic resources to support research on the mechanisms driving cichlid adaptation and speciation.

Towards precision medicine

There is great potential for genome sequencing to enhance patient care through improved diagnostic sensitivity and more precise therapeutic targeting. To maximize this potential, genomics strategies that have been developed for genetic discovery - including DNA-sequencing technologies and analysis algorithms - need to be adapted to fit clinical needs. This will require the optimization of alignment algorithms, attention to quality-coverage metrics, tailored solutions for paralogous or low-complexity areas of the genome, and the adoption of consensus standards for variant calling and interpretation. Global sharing of this more accurate genotypic and phenotypic data will accelerate the determination of causality for novel genes or variants. Thus, a deeper understanding of disease will be realized that will allow its targeting with much greater therapeutic precision.