scholarly journals Comparative Phylogenomics, a Stepping Stone for Bird Biodiversity Studies

Diversity ◽  
2019 ◽  
Vol 11 (7) ◽  
pp. 115 ◽  
Author(s):  
Josefin Stiller ◽  
Guojie Zhang
Keyword(s):  
Evolutionary History ◽  
Phylogenetic Signal ◽  
Genomic Data ◽  
Genome Project ◽  
Tree Of Life ◽  
Long Read ◽  
Recent Developments ◽  
Genome Assemblies ◽  
Avian Genomes ◽  
Chromosome Level

Birds are a group with immense availability of genomic resources, and hundreds of forthcoming genomes at the doorstep. We review recent developments in whole genome sequencing, phylogenomics, and comparative genomics of birds. Short read based genome assemblies are common, largely due to efforts of the Bird 10K genome project (B10K). Chromosome-level assemblies are expected to increase due to improved long-read sequencing. The available genomic data has enabled the reconstruction of the bird tree of life with increasing confidence and resolution, but challenges remain in the early splits of Neoaves due to their explosive diversification after the Cretaceous-Paleogene (K-Pg) event. Continued genomic sampling of the bird tree of life will not just better reflect their evolutionary history but also shine new light onto the organization of phylogenetic signal and conflict across the genome. The comparatively simple architecture of avian genomes makes them a powerful system to study the molecular foundation of bird specific traits. Birds are on the verge of becoming an extremely resourceful system to study biodiversity from the nucleotide up.

scholarly journals Macrosynteny analysis between Lentinula edodes and Lentinula novae-zelandiae reveals signals of domestication in Lentinula edodes

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Christopher Alan Smith
Keyword(s):  
Evolutionary History ◽  
Lentinula Edodes ◽  
Reference Genome ◽  
Genomic Change ◽  
Diverse Species ◽  
The World ◽  
Cultivated Mushroom ◽  
Genome Assemblies ◽  
High Degree ◽  
Chromosome Level

AbstractThe basidiomycete fungus Lentinula novae-zelandiae is endemic to New Zealand and is a sister taxon to Lentinula edodes, the second most cultivated mushroom in the world. To explore the biology of this organism, a high-quality chromosome level reference genome of L. novae-zelandiae was produced. Macrosyntenic comparisons between the genome assembly of L. novae-zelandiae, L. edodes and a set of three genome assemblies of diverse species from the Agaricomycota reveal a high degree of macrosyntenic restructuring within L. edodes consistent with signal of domestication. These results show L. edodes has undergone significant genomic change during the course of its evolutionary history, likely a result of its cultivation and domestication over the last 1000 years.

scholarly journals Purge Haplotigs: Synteny Reduction for Third-gen Diploid Genome Assemblies

2018 ◽  
Author(s):  
Michael J Roach ◽  
Simon Schmidt ◽  
Anthony R Borneman
Keyword(s):  
De Novo ◽  
Haplotype Reconstruction ◽  
Minimal Impact ◽  
Variant Discovery ◽  
Rapid Release ◽  
Long Read ◽  
Recent Developments ◽  
Reference Quality ◽  
Downstream Analysis ◽  
Genome Assemblies

AbstractRecent developments in third-gen long read sequencing and diploid-aware assemblers have resulted in the rapid release of numerous reference-quality assemblies for diploid genomes. However, assembling highly heterozygous genomes is still facing a major problem where the two haplotypes for a region are highly polymorphic and the synteny is not recognised during assembly. This causes issues with downstream analysis, for example variant discovery using the haploid assembly, or haplotype reconstruction using the diploid assembly. A new pipeline—Purge Haplotigs—was developed specifically for third-gen assemblies to identify and reassign the duplicate contigs. The pipeline takes a draft haplotype-fused assembly or a diploid assembly, and read alignments to produce an improved assembly. The pipeline was tested on a simulated dataset and on four recent diploid (phased) de novo assemblies from third-generation long-read sequencing. All assemblies after processing with Purge Haplotigs were less duplicated with minimal impact on genome completeness. The software is available at https://bitbucket.org/mroachawri/purge_haplotigs under a permissive MIT licence.

scholarly journals An improved pig reference genome sequence to enable pig genetics and genomics research

GigaScience ◽  
2020 ◽  
Vol 9 (6) ◽  
Author(s):  
Amanda Warr ◽  
Nabeel Affara ◽  
Bronwen Aken ◽  
Hamid Beiki ◽  
Derek M Bickhart ◽  
...  
Keyword(s):  
Reference Genome ◽  
Genomic Research ◽  
Biomedical Model ◽  
Model Species ◽  
Domestic Pig ◽  
Genomics Research ◽  
Long Read ◽  
Genetics And Genomics ◽  
Genome Assemblies ◽  
Chromosome Level

Abstract Background The domestic pig (Sus scrofa) is important both as a food source and as a biomedical model given its similarity in size, anatomy, physiology, metabolism, pathology, and pharmacology to humans. The draft reference genome (Sscrofa10.2) of a purebred Duroc female pig established using older clone-based sequencing methods was incomplete, and unresolved redundancies, short-range order and orientation errors, and associated misassembled genes limited its utility. Results We present 2 annotated highly contiguous chromosome-level genome assemblies created with more recent long-read technologies and a whole-genome shotgun strategy, 1 for the same Duroc female (Sscrofa11.1) and 1 for an outbred, composite-breed male (USMARCv1.0). Both assemblies are of substantially higher (>90-fold) continuity and accuracy than Sscrofa10.2. Conclusions These highly contiguous assemblies plus annotation of a further 11 short-read assemblies provide an unprecedented view of the genetic make-up of this important agricultural and biomedical model species. We propose that the improved Duroc assembly (Sscrofa11.1) become the reference genome for genomic research in pigs.

scholarly journals Reconstruction of proto-vertebrate, proto-cyclostome and proto-gnathostome genomes provides new insights into early vertebrate evolution

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Yoichiro Nakatani ◽  
Prashant Shingate ◽  
Vydianathan Ravi ◽  
Nisha E. Pillai ◽  
Aravind Prasad ◽  
...  
Keyword(s):  
Evolutionary History ◽  
Gene Loss ◽  
De Novo ◽  
Genome Structure ◽  
Origin And Evolution ◽  
Long Read ◽  
History Of ◽  
And Function ◽  
Genome Assemblies ◽  
Key Questions

AbstractAncient polyploidization events have had a lasting impact on vertebrate genome structure, organization and function. Some key questions regarding the number of ancient polyploidization events and their timing in relation to the cyclostome-gnathostome divergence have remained contentious. Here we generate de novo long-read-based chromosome-scale genome assemblies for the Japanese lamprey and elephant shark. Using these and other representative genomes and developing algorithms for the probabilistic macrosynteny model, we reconstruct high-resolution proto-vertebrate, proto-cyclostome and proto-gnathostome genomes. Our reconstructions resolve key questions regarding the early evolutionary history of vertebrates. First, cyclostomes diverged from the lineage leading to gnathostomes after a shared tetraploidization (1R) but before a gnathostome-specific tetraploidization (2R). Second, the cyclostome lineage experienced an additional hexaploidization. Third, 2R in the gnathostome lineage was an allotetraploidization event, and biased gene loss from one of the subgenomes shaped the gnathostome genome by giving rise to remarkably conserved microchromosomes. Thus, our reconstructions reveal the major evolutionary events and offer new insights into the origin and evolution of vertebrate genomes.

scholarly journals Benchmarking ultra-high molecular weight DNA preservation methods for long-read and long-range sequencing

2021 ◽  
Author(s):  
Hollis A Dahn ◽  
Jacquelyn Mountcastle ◽  
Jennifer Balacco ◽  
Sylke Winkler ◽  
Iliana Bista ◽  
...  
Keyword(s):  
Molecular Weight ◽  
High Molecular Weight ◽  
Long Range ◽  
High Quality ◽  
High Molecular Weight Dna ◽  
Preservation Methods ◽  
Long Read ◽  
Genome Assemblies ◽  
Ultra High Molecular Weight ◽  
Chromosome Level

Studies in vertebrate genomics require sampling from a broad range of tissue types, taxa, and localities. Recent advancements in long-read and long-range genome sequencing have made it possible to produce high-quality chromosome-level genome assemblies for almost any organism. However, adequate tissue preservation for the requisite ultra-high molecular weight DNA (uHMW DNA) remains a major challenge. Here we present a comparative study of preservation methods for field and laboratory tissue sampling, across vertebrate classes and different tissue types. We find that no single method is best for all cases. Instead, the optimal storage and extraction methods vary by taxa, by tissue, and by down-stream application. Therefore, we provide sample preservation guidelines that ensure sufficient DNA integrity and amount required for use with long-read and long-range sequencing technologies across vertebrates. Our best practices generated the uHMW DNA needed for the high-quality reference genomes for Phase 1 of the Vertebrate Genomes Project (VGP), whose ultimate mission is to generate chromosome-level reference genome assemblies of all ~70,000 extant vertebrate species.

scholarly journals Scaffolding of long read assemblies using long range contact information

2016 ◽  
Author(s):  
Jay Ghurye ◽  
Mihai Pop ◽  
Sergey Koren ◽  
Chen-Shan Chin
Keyword(s):  
De Novo ◽  
Chromatin Interaction ◽  
Interaction Data ◽  
Computationally Efficient ◽  
Short Read ◽  
Contact Information ◽  
Genome Wide ◽  
Long Read ◽  
Genome Assemblies ◽  
Chromosome Level

AbstractMotivationLong read technologies have made a revolution in de novo genome assembly by generating contigs of size orders of magnitude more than that of short read assemblies. Although the assembly contiguity has increased, it still does not span a chromosome or an arm of the chromosome, resulting in an unfinished chromosome level assembly. To address this problem, we develop a scalable and computationally efficient scaffolding method that can boost the contiguity of the assembly by a large extent using genome wide chromatin interaction data such as Hi-C. Particularly, we demonstrate an algorithm that uses Hi-C data for longer-range scaffolding of de novo long read genome assemblies.ResultsWe tested our methods on two long read assemblies of different organisms. We compared our method with previously developed method and show that our approach performs better in terms of accuracy of scaffolding.AvailabilityThe software is available for free use and can be downloaded from here: https://github.com/machinegun/[email protected]

scholarly journals An improved pig reference genome sequence to enable pig genetics and genomics research

2019 ◽  
Author(s):  
Amanda Warr ◽  
Nabeel Affara ◽  
Bronwen Aken ◽  
H. Beiki ◽  
Derek M. Bickhart ◽  
...  
Keyword(s):  
Reference Genome ◽  
Genomic Research ◽  
Biomedical Model ◽  
Model Species ◽  
Domestic Pig ◽  
Genomics Research ◽  
Long Read ◽  
Genetics And Genomics ◽  
Genome Assemblies ◽  
Chromosome Level

AbstractThe domestic pig (Sus scrofa) is important both as a food source and as a biomedical model with high anatomical and immunological similarity to humans. The draft reference genome (Sscrofa10.2) of a purebred Duroc female pig established using older clone-based sequencing methods was incomplete and unresolved redundancies, short range order and orientation errors and associated misassembled genes limited its utility. We present two annotated highly contiguous chromosome-level genome assemblies created with more recent long read technologies and a whole genome shotgun strategy, one for the same Duroc female (Sscrofa11.1) and one for an outbred, composite breed male (USMARCv1.0). Both assemblies are of substantially higher (>90-fold) continuity and accuracy than Sscrofa10.2. These highly contiguous assemblies plus annotation of a further 11 short read assemblies provide an unprecedented view of the genetic make-up of this important agricultural and biomedical model species. We propose that the improved Duroc assembly (Sscrofa11.1) become the reference genome for genomic research in pigs.

scholarly journals Comparison of long read methods for sequencing and assembly of a plant genome

2020 ◽  
Author(s):  
Valentine Murigneux ◽  
Subash Kumar Rai ◽  
Agnelo Furtado ◽  
Timothy J.C. Bruxner ◽  
Wei Tian ◽  
...  
Keyword(s):  
De Novo ◽  
Cost Effective ◽  
Genome Project ◽  
Plant Genome ◽  
Sequencing Data ◽  
Sequencing Technologies ◽  
Oxford Nanopore ◽  
Long Read ◽  
The Cost ◽  
Genome Assemblies

AbstractSequencing technologies have advanced to the point where it is possible to generate high accuracy, haplotype resolved, chromosome scale assemblies. Several long read sequencing technologies are available on the market and a growing number of algorithms have been developed over the last years to assemble the reads generated by those technologies. When starting a new genome project, it is therefore challenging to select the most cost-effective sequencing technology as well as the most appropriate software for assembly and polishing. For this reason, it is important to benchmark different approaches applied to the same sample. Here, we report a comparison of three long read sequencing technologies applied to the de novo assembly of a plant genome, Macadamia jansenii. We have generated sequencing data using Pacific Biosciences (Sequel I), Oxford Nanopore Technologies (PromethION) and BGI (single-tube Long Fragment Read) technologies for the same sample. Several assemblers were benchmarked in the assembly of PacBio and Nanopore reads. Results obtained from combining long read technologies or short read and long read technologies are also presented. The assemblies were compared for contiguity, accuracy and completeness as well as sequencing costs and DNA material requirements. Overall, the three long read technologies produced highly contiguous and complete genome assemblies of Macadamia jansenii. At the time of sequencing, the cost associated with each method was significantly different but continuous improvements in technologies have resulted in greater accuracy, increased throughput and reduced costs. We propose updating this comparison regularly with reports on significant iterations of the sequencing technologies.

Disentangling the role of shared ancestry and the environment on leaf stable isotopes

2019 ◽  
Author(s):  
Marko J. Spasojevic ◽  
Sören Weber1
Keyword(s):  
Stable Isotopes ◽  
Environmental Conditions ◽  
Evolutionary History ◽  
Environmental Control ◽  
Phylogenetic Signal ◽  
Individual Species ◽  
Habitat Types ◽  
Δ13c And Δ15n ◽  
Environmental Controls ◽  
Shared Ancestry

Stable carbon (C) and nitrogen (N) isotopes in plants are important indicators of plant water use efficiency and N acquisition strategies. While often regarded as being under environmental control, there is growing evidence that evolutionary history may also shape variation in stable isotope ratios (δ13C and δ15N) among plant species. Here we examined patterns of foliar δ13C and δ15N in alpine tundra for 59 species in 20 plant families. To assess the importance of environmental controls and evolutionary history, we examined if average δ13C and δ15N predictably differed among habitat types, if individual species exhibited intraspecific trait variation (ITV) in δ13C and δ15N, and if there were a significant phylogenetic signal in δ13C and δ15N. We found that variation among habitat types in both δ13C and δ15N mirrored well-known patterns of water and nitrogen limitation. Conversely, we also found that 40% of species exhibited no ITV in δ13C and 35% of species exhibited no ITV in δ15N, suggesting that some species are under stronger evolutionary control. However, we only found a modest signal of phylogenetic conservatism in δ13C and no phylogenetic signal in δ15N suggesting that shared ancestry is a weaker driver of tundra wide variation in stable isotopes. Together, our results suggest that both evolutionary history and local environmental conditions play a role in determining variation in δ13C and δ15N and that considering both factors can help with interpreting isotope patterns in nature and with predicting which species may be able to respond to rapidly changing environmental conditions.

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