The birds of Genome10K

O’Brien, Stephen J.; Haussler, David; Ryder, Oliver A.

doi:10.1186/2047-217x-3-32

Cited by 15 publications

(7 citation statements)

References 11 publications

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“…For example, the Earth BioGenome project aims to sequence the genomes of upwards of one million eukaryotic species within the next decade [11]. Regardless of the success of this effort, there are a host of ongoing eukaryotic sequencing projects, including Bat 1 K [12], Bird 10 K (10,000 bird genomes [13]), G10K (10,000 vertebrate genomes [14]), and i5K (5000 arthropod genomes [15]), among others. This suggests that within the next 5 years, most multicellular organisms will have at least one member of their family present in genomic databases, with some groups of multicellular organisms being completely represented at the genus level.…”

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confidence: 99%

Testing the advantages and disadvantages of short- and long- read eukaryotic metagenomics using simulated reads

2020

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Background: The first step in understanding ecological community diversity and dynamics is quantifying community membership. An increasingly common method for doing so is through metagenomics. Because of the rapidly increasing popularity of this approach, a large number of computational tools and pipelines are available for analysing metagenomic data. However, the majority of these tools have been designed and benchmarked using highly accurate short read data (i.e. Illumina), with few studies benchmarking classification accuracy for long error-prone reads (PacBio or Oxford Nanopore). In addition, few tools have been benchmarked for nonmicrobial communities. Results: Here we compare simulated long reads from Oxford Nanopore and Pacific Biosciences (PacBio) with high accuracy Illumina read sets to systematically investigate the effects of sequence length and taxon type on classification accuracy for metagenomic data from both microbial and non-microbial communities. We show that very generally, classification accuracy is far lower for non-microbial communities, even at low taxonomic resolution (e.g. family rather than genus). We then show that for two popular taxonomic classifiers, long reads can significantly increase classification accuracy, and this is most pronounced for non-microbial communities. Conclusions: This work provides insight on the expected accuracy for metagenomic analyses for different taxonomic groups, and establishes the point at which read length becomes more important than error rate for assigning the correct taxon.

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confidence: 99%

Testing the advantages and disadvantages of short- and long- read eukaryotic metagenomics using simulated reads

2020

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“…Not long ago, an ambitious consortium formed with the aim of sequencing 10,000 vertebrate species (Haussler et al 2009) for building an indispensable foundation for future biology studies. In this respect, the bird genomes are part of an even bigger initiative (O'Brien et al 2014), providing a glimpse of what can actually be achieved in the study of evolution and ecology of non-model organisms. Actually, the Avian Genomics papers from December 2014 offer a first example of how true genomic information fosters more applied fields of research, long waiting for large-scale genomic information: conservation genomics (Allendorf et al 2010;Ouborg et al 2010;Piertney 2006;Shafer et al 2015).…”

Section: Discussionmentioning

confidence: 99%

Avian genomics: fledging into the wild!

Kraus

Wink

2015

J Ornithol

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Next generation sequencing (NGS) technologies provide great resources to study bird evolution and avian functional genomics. They also allow for the identification of suitable high-resolution markers for detailed analyses of the phylogeography of a species or the connectivity of migrating birds between breeding and wintering populations. This review discusses the application of DNA markers for the study of systematics and phylogeny, but also population genetics and phylogeography. Emphasis in this review is on the new methodology of NGS and its use to study avian genomics. The recent publication of the first phylogenomic tree of birds based on genome data of 48 bird taxa from 34 orders is presented in more detail.

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“…This 3D photogrammetry pipeline is therefore a step toward a much-needed and more comprehensive method of color analysis based on continuous, whole-organism, full-spectrum color [52]. Combined with large-scale genomic data [53,54] and complete phylogenies for various organismal groups [55,56], color data from 3D digital models will help elucidate links between genotype and phenotype. Considering these links with other extractable phenomic data will open the door to new insights into their ecology, evolution, and functional morphology.…”

Section: Future Directions: Color Analysismentioning

confidence: 99%

A rapid and cost-effective pipeline for digitization of museum specimens with 3D photogrammetry

et al. 2020

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Natural history collections are yielding more information as digitization brings specimen data to researchers, connects specimens across museums, and as new technologies allow for more large-scale data collection. Therefore, a key goal in specimen digitization is developing methods that both increase access and allow for the highest yield of phenomic data. 3D digitization is increasingly popular because it has the potential to meet both aspects of that key goal. However, current methods overlook or do not prioritize some of the most sought-after phenotypic traits, those involving the external appearance of specimens, especially color. Here, we introduce an efficient and cost-effective pipeline for 3D photogrammetry to capture the external appearance of natural history specimens and other museum objects. 3D photogrammetry aligns and compares sets of dozens, hundreds, or even thousands of photos to create 3D models. The hardware setup requires little physical space and around $3,000 in initial investment, while the software pipeline requires $1,400/year for proprietary software subscriptions (with open-source alternatives). The creation of each 3D model takes 1-2 hours/specimen and much of the software pipeline is automated with minimal supervision required, including the onerous step of mesh processing. We showcase the method by creating 3D models for most of the type specimens in the Moore Laboratory of Zoology bird collection and show that digital bill measurements are comparable to handtaken measurements. Color data, while not included as part of this pipeline, is easily extractable from the models and one of the most promising areas of data collection. Future advances can adapt the method for ultraviolet reflectance capture and increased efficiency and model quality. Combined with genomic data, phenomic data from 3D models including photogrammetry will open new doors to understanding organismal evolution.

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The birds of Genome10K

Cited by 15 publications

References 11 publications

Testing the advantages and disadvantages of short- and long- read eukaryotic metagenomics using simulated reads

Testing the advantages and disadvantages of short- and long- read eukaryotic metagenomics using simulated reads

Avian genomics: fledging into the wild!

A rapid and cost-effective pipeline for digitization of museum specimens with 3D photogrammetry

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