Standards recommendations for the Earth BioGenome Project

Lawniczak, Mara K. N.; Durbin, Richard; Flicek, Paul; Lindblad‐Toh, Kerstin; Wei, Xiaofeng; Archibald, John M.; Baker, William J.; Belov, Katherine; Blaxter, Mark; Marquès‐Bonet, Tomàs; Childers, Anna K.; Coddington, Jonathan A.; Crandall, Keith A.; Crawford, Andrew J.; Davey, Robert P.; Palma, Federica Di; Haerty, Wilfried; Hall, Neil; Hoff, Katharina J.; Howe, Kerstin; Jarvis, Erich D.; Johnson, Warren E.; Johnson, Rebecca N.; Kersey, Paul J.; Liu, Xin; Lopez, Jose V.; Myers, Eugene W.; Pettersson, Olga Vinnere; Phillippy, Adam M.; Poelchau, Monica F.; Pruitt, Kim D.; Rhie, Arang; Castilla‐Rubio, Juan Carlos; Sahu, Sunil Kumar; Salmon, N; Soltis, Pamela S.; Swarbreck, David; Thibaud‐Nissen, Françoise; Wang, Sibo; Wegrzyn, Jill L.; Zhang, He; Lewin, Harris A.; Richards, Stephen

doi:10.1073/pnas.2115639118

Cited by 64 publications

(58 citation statements)

References 25 publications

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“…Project teams are encouraged to seek funding to facilitate chromosome-length assemblies in the future using HiC ( 48 ) technology. Appropriately collected and stored tissue samples are being archived where possible within Australian museum collections to ensure future assemblies use the same specimen ( 49 ).…”

Section: Threatened Species Initiativementioning

confidence: 99%

“…Sampling requirements for high-quality genomes can be extremely difficult to meet for threatened species, particularly those that are listed as critically endangered ( 49 , 50 ). Many long-read technologies require nonfragmented DNA, which is most easily obtained from tissue samples that are flash-frozen or freshly collected.…”

Section: Threatened Species Initiativementioning

confidence: 99%

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Threatened Species Initiative: Empowering conservation action using genomic resources

Hogg

Ottewell²,

Latch

et al. 2022

Proc. Natl. Acad. Sci. U.S.A.

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Globally, 15,521 animal species are listed as threatened by the International Union for the Conservation of Nature, and of these less than 3% have genomic resources that can inform conservation management. To combat this, global genome initiatives are developing genomic resources, yet production of a reference genome alone does not conserve a species. The reference genome allows us to develop a suite of tools to understand both genome-wide and functional diversity within and between species. Conservation practitioners can use these tools to inform their decision-making. But, at present there is an implementation gap between the release of genome information and the use of genomic data in applied conservation by conservation practitioners. In May 2020, we launched the Threatened Species Initiative and brought a consortium of genome biologists, population biologists, bioinformaticians, population geneticists, and ecologists together with conservation agencies across Australia, including government, zoos, and nongovernment organizations. Our objective is to create a foundation of genomic data to advance our understanding of key Australian threatened species, and ultimately empower conservation practitioners to access and apply genomic data to their decision-making processes through a web-based portal. Currently, we are developing genomic resources for 61 threatened species from a range of taxa, across Australia, with more than 130 collaborators from government, academia, and conservation organizations. Developed in direct consultation with government threatened-species managers and other conservation practitioners, herein we present our framework for meeting their needs and our systematic approach to integrating genomics into threatened species recovery.

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Section: Threatened Species Initiativementioning

confidence: 99%

Section: Threatened Species Initiativementioning

confidence: 99%

Threatened Species Initiative: Empowering conservation action using genomic resources

Hogg

Ottewell²,

Latch

et al. 2022

Proc. Natl. Acad. Sci. U.S.A.

Self Cite

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“…In terms of sequence accuracy and read length, both approaches have their advantages, but at the moment, PacBio HiFi sequencing represents an optimal compromise ensuring >99.9% accuracy for reads up to 25 kb [ 2 ]. Consequently, PacBio HiFi data are included in the current best-practice genome assembly guidelines of different genome sequencing consortia, from extensive ones such as Earth BioGenome Project [ 3 ] to more specialized ones, such as the Ag100Pest Initiative, which aims to generate reference genome assemblies for agricultural pest arthropods [ 4 ].…”

Section: Introductionmentioning

confidence: 99%

Reference-Guided De Novo Genome Assembly of the Flour Beetle Tribolium freemani

Volarić

Despot-Slade

Veseljak

et al. 2022

IJMS

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The flour beetle Tribolium freemani is a sibling species of the model organism and important pest Tribolium castaneum. The two species are so closely related that they can produce hybrid progeny, but the genetic basis of their differences has not been revealed. In this work, we sequenced the T. freemani genome by applying PacBio HiFi technology. Using the well-assembled T. castaneum genome as a reference, we assembled 262 Mb of the T. freemani genomic sequence and anchored it in 10 linkage groups corresponding to nine autosomes and sex chromosome X. The assembly showed 99.8% completeness of conserved insect genes, indicating a high-quality reference genome. Comparison with the T. castaneum assembly revealed that the main differences in genomic sequence between the two sibling species come from repetitive DNA, including interspersed and tandem repeats. In this work, we also provided the complete assembled mitochondrial genome of T. freemani. Although the genome assembly needs to be ameliorated in tandemly repeated regions, the first version of the T. freemani reference genome and the complete mitogenome presented here represent useful resources for comparative evolutionary studies of related species and for further basic and applied research on different biological aspects of economically important pests.

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“…Overall, the ilHelZeax1.1 assembly exceeds the minimum reference standard of 6.C.Q40 (>1.0 Mb contig and >10.0 Mb scaffold N50) set for eukaryotic species by the Earth BioGenome Project (Lewin et al 2018) and meets the qualifications for chromosome level (7.C.Q50; Lawniczak et al 2022). Assessing the assembly relative to short-reads, k-mer spectra indicated a moderate degree of heterozygosity in the primary pseudo-haploid assembly, shown by a histogram peak (x = 90) corresponding to both haplotypes that is much greater compared to that for single-copy k-mers (x = 45; fig.…”

Section: Resultsmentioning

confidence: 94%

A chromosome-scale genome assembly of aBacillus thuringiensisCry1Ac insecticidal protein resistant strain ofHelicoverpa zea

Stahlke

Chang

Tembrock

et al. 2022

Preprint

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Helicoverpa zea (Lepidoptera: Noctuidae) is an insect pest of major cultivated crops in North and South America. The species has adapted to different host plants and developed resistance to several insecticidal agents, including Bacillus thuringiensis (Bt) insecticidal proteins in transgenic cotton and maize. H. zea populations persist year-round in tropical and subtropical regions, but seasonal migrations into temperate zones increase the geographic range of associated crop damage. To better understand the genetic basis of these physiological and ecological characteristics, we generated a high-quality chromosome-level assembly for a single H. zea male from Bt resistant strain, HzStark_Cry1AcR. Hi-C data were used to scaffold an initial 375.2 Mb contig assembly into 30 autosomes and the Z sex chromosome (scaffold N50 = 12.8 Mb and L50 = 14). The scaffolded assembly was error-corrected with a novel pipeline, polishCLR. The mitochondrial genome was assembled through an improved pipeline and annotated. Assessment of this genome assembly indicated 98.8% of the Lepidopteran Benchmark Universal Single-Copy Ortholog set were complete (98.5% as complete single-copy). Repetitive elements comprised approximately 29.5% of the assembly with the plurality (11.2%) classified as retroelements. This chromosome-scale reference assembly for H. zea, ilHelZeax1.1, will facilitate future research to evaluate and enhance sustainable crop production practices.

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Standards recommendations for the Earth BioGenome Project

Cited by 64 publications

References 25 publications

Threatened Species Initiative: Empowering conservation action using genomic resources

Threatened Species Initiative: Empowering conservation action using genomic resources

Reference-Guided De Novo Genome Assembly of the Flour Beetle Tribolium freemani

A chromosome-scale genome assembly of aBacillus thuringiensisCry1Ac insecticidal protein resistant strain ofHelicoverpa zea

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