The swan genome and transcriptome: its not all black and white DOI Open Access
Anjana C. Karawita, Yuanyuan Cheng,

Keng Yih Chew

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2022, Volume and Issue: unknown

Published: May 3, 2022

ABSTRACT The Australian black swan ( Cygnus atratus ) is an iconic species with contrasting plumage to that of the closely related Northern Hemisphere white swans. relative geographic isolation may have resulted in a limited immune repertoire and increased susceptibility infectious disease, notably diseases from which Australia has been largely shielded. Indeed, unlike Mallard ducks mute olor ), extremely sensitive severe highly pathogenic avian influenza (HPAI). Understanding this impaired by absence any available genome transcriptome information. Here, we generate first chromosome-length annotated genomes data, all using long-read based pipelines generated for vertebrate species. We used these transcriptomes, show other wild waterfowl, swans lack expanded gene repertoire, key viral pattern-recognition receptor endothelial cells mount poorly controlled inflammatory response HPAI. also implicate genetic differences SLC45A2 swan. Together, data suggest system such should infection become established its native habitat survival would be significant peril.

Language: Английский

What is a cell type and how to define it? DOI Creative Commons
Hongkui Zeng

Cell, Journal Year: 2022, Volume and Issue: 185(15), P. 2739 - 2755

Published: July 1, 2022

Language: Английский

Citations

278
The Earth BioGenome Project 2020: Starting the clock DOI Creative Commons
Harris A. Lewin, Stephen Richards, E Aiden

et al.

Proceedings of the National Academy of Sciences, Journal Year: 2022, Volume and Issue: 119(4)

Published: Jan. 18, 2022

November 2020 marked 2 y since the launch of Earth BioGenome Project (EBP), which aims to sequence all known eukaryotic species in a 10-y timeframe. Since then, significant progress has been made across aspects EBP roadmap, as outlined 2018 article describing project’s goals, strategies, and challenges (1). The phase ended clock started on reaching EBP’s major milestones. This Special Feature explores many facets EBP, including review progress, description scientific exemplar projects, ethical legal social issues, applications biodiversity genomics. In this Introduction, we summarize current status held virtually October 5 9, 2020, recent updates through February 2021. References nine Perspective articles included are cited guide reader toward deeper understanding goals facing EBP. It is urgent that move forward. year global failure meeting any 20 “Aichi goals” for preservation wildlife ecosystems (2). International Union Conservation Nature now counts more than 35,000 (28%) surveyed plants animals threatened with extinction (3). may lose 50% its by end century if nothing done mitigate anthropogenic factors drive destroy health sustain human existence Degradation aquatic terrestrial continued unabated, soon face possibility massive ecosystem collapse scale. Such would have an enormous impact not only biodiversity, but also political stability, might ultimately affect survival … [↵][1]1To whom correspondence be addressed. Email: lewin{at}ucdavis.edu. [1]: #xref-corresp-1-1

Language: Английский

Citations

239
Evolutionary constraint and innovation across hundreds of placental mammals DOI
Matthew J. Christmas, Irene M. Kaplow, Diane P. Genereux

et al.

Science, Journal Year: 2023, Volume and Issue: 380(6643)

Published: April 27, 2023

Zoonomia is the largest comparative genomics resource for mammals produced to date. By aligning genomes 240 species, we identify bases that, when mutated, are likely affect fitness and alter disease risk. At least 332 million (~10.7%) in human genome unusually conserved across species (evolutionarily constrained) relative neutrally evolving repeats, 4552 ultraconserved elements nearly perfectly conserved. Of 101 significantly constrained single bases, 80% outside protein-coding exons half have no functional annotations Encyclopedia of DNA Elements (ENCODE) resource. Changes genes regulatory associated with exceptional mammalian traits, such as hibernation, that could inform therapeutic development. Earth's vast imperiled biodiversity offers distinctive power identifying genetic variants function organismal phenotypes.

Language: Английский

Citations

137
The swan genome and transcriptome, it is not all black and white DOI Creative Commons
Anjana C. Karawita, Yuanyuan Cheng,

Keng Yih Chew

et al.

Genome biology, Journal Year: 2023, Volume and Issue: 24(1)

Published: Jan. 23, 2023

Abstract Background The Australian black swan ( Cygnus atratus ) is an iconic species with contrasting plumage to that of the closely related northern hemisphere white swans. relative geographic isolation may have resulted in a limited immune repertoire and increased susceptibility infectious diseases, notably diseases from which Australia has been largely shielded. Unlike mallard ducks mute olor ), extremely sensitive highly pathogenic avian influenza. Understanding this impaired by absence any available genome transcriptome information. Results Here, we generate first chromosome-length genomes annotated data, all using long-read based pipelines generated for vertebrate species. We use these transcriptomes show unlike other wild waterfowl, swans lack expanded gene repertoire, key viral pattern-recognition receptor endothelial cells mount poorly controlled inflammatory response also implicate genetic differences SLC45A2 swan. Conclusion Together, data suggest system such should infection become established its native habitat, would be significant peril.

Language: Английский

Citations

15
Sensitive clustering of protein sequences at tree-of-life scale using DIAMOND DeepClust DOI Creative Commons
Benjamin Buchfink, Haim Ashkenazy, Klaus Reuter

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2023, Volume and Issue: unknown

Published: Jan. 25, 2023

Abstract The biosphere genomics era is transforming life science research, but existing methods struggle to efficiently reduce the vast dimensionality of protein universe. We present DIAMOND DeepClust, an ultra-fast cascaded clustering method optimized cluster 19 billion sequences currently defining biosphere. As a result, we detect 1.7 clusters which 32% hold more than one sequence. This means that 544 million represent 94% all known proteins, illustrating across tree can significantly accelerate comparative studies in Earth BioGenome era.

Language: Английский

Citations

15
Environmental DNA and biodiversity patterns: a call for a community phylogenetics approach DOI Creative Commons
José Alexandre Felizola Diniz‐Filho, Luís Maurício Bini, Cíntia Pelegrineti Targueta

et al.

Perspectives in Ecology and Conservation, Journal Year: 2024, Volume and Issue: 22(1), P. 15 - 23

Published: Jan. 1, 2024

Environmental DNA (eDNA) metabarcoding is a relatively new technology allowing effective non-invasive analyses and monitoring of biodiversity patterns. Studies on eDNA focus using sequence data to delimit basic units (i.e., such as Molecular Operational Taxonomic Units – MOTUS or Amplicon Sequence Variation ASVs), after this definition standard analytical approaches from community ecology are applied. However, there more information inherent it now straightforward use general in which based directly phylogenies genetic distances between MOTUs ASVs, rather than discrete without any accounting for hierarchical structure, providing continuum understanding Here we briefly review the concepts methods incorporate phylogenetic patterns into analyses, illustrating some main issues with eukaryote diversity along Araguaia River Basin. Hopefully perspective stimulates researchers obtaining perform their under phylogenetics framework instead (or addition to) approach.

Language: Английский

Citations

4
Evolutionary feedback from the environment shapes mechanisms that generate genome variation DOI
Lynn Helena Caporale

The Journal of Physiology, Journal Year: 2024, Volume and Issue: 602(11), P. 2601 - 2614

Published: Jan. 9, 2024

Abstract Darwin recognized that ‘a grand and almost untrodden field of inquiry will be opened, on the causes laws variation.’ However, because Modern Synthesis assumes intrinsic probability any individual mutation is unrelated to mutation's potential adaptive value, attention has been focused selection rather than generation variation. Yet many examples illustrate term ‘random’ mutation, as widely understood, inaccurate. The probabilities distinct classes variation are neither evenly distributed across a genome nor invariant over time, their value. Because acts upon variation, multiple biochemical mechanisms can have evolved increase relative mutations. In effect, heritable in feedback loop with selection, such those tend generate variants survive recurring challenges environment would captured by this survival thus inherited accumulated within lineages genomes. Moreover, affected wide range processes, regulated. Biochemical sense stress, from lack nutrients DNA damage, specific A deeper understanding evolution involves of, environmental influences upon, generated gametes, other words generations. These concepts profound implications for types questions should asked, omics databases become more comprehensive, detection methods sensitive, computation experimental analyses even high throughput capable revealing gametes. also evolutionary theory, which, reflection it argued, predicts generating mutations, words, ability evolve itself evolves. image

Language: Английский

Citations

3
PacBio Hi-Fi genome assembly of the Iberian dolphin freshwater mussel Unio delphinus Spengler, 1793 DOI Creative Commons
André Gomes‐dos‐Santos, Manuel Lopes‐Lima, André M. Machado

et al.

Scientific Data, Journal Year: 2023, Volume and Issue: 10(1)

Published: June 1, 2023

Abstract Mussels of order Unionida are a group strictly freshwater bivalves with nearly 1,000 described species widely dispersed across world ecosystems. They highly threatened showing the highest record extinction events within faunal taxa. Conservation is particularly concerning in occurring Mediterranean biodiversity hotspot that exposed to multiple anthropogenic threats, possibly acting synergy. That case dolphin mussel Unio delphinus Spengler, 1793, endemic western Iberian Peninsula recently strong population declines. To date, only four genome assemblies available for and one European species. We present first assembly . used PacBio HiFi generate contiguous assembly. The 2.5 Gb long, possessing 1254 contigs contig N50 length 10 Mbp. This most date an essential resource investigating species’ biology evolutionary history ultimately will help support conservation strategies.

Language: Английский

Citations

9
Earth Biogenome Project: present status and future plans DOI
P. K. Gupta

Trends in Genetics, Journal Year: 2022, Volume and Issue: 38(8), P. 811 - 820

Published: May 19, 2022

Language: Английский

Citations

14
Grand challenges in arachnid genetics and biomaterials DOI Creative Commons
Sean J. Blamires

Frontiers in Arachnid Science, Journal Year: 2024, Volume and Issue: 3

Published: Jan. 15, 2024

SPECIALTY GRAND CHALLENGE article Front. Arachn. Sci., 15 January 2024Sec. Arachnid Genetics and Biomaterials Volume 3 - 2024 | https://doi.org/10.3389/frchs.2024.1356170

Language: Английский

Citations

2