The genome sequence of the stinging nettle, Urtica dioica L. (Urticaceae) DOI Creative Commons
Maarten J. M. Christenhusz, Ilia J. Leitch

Wellcome Open Research, Journal Year: 2025, Volume and Issue: 10, P. 31 - 31

Published: Jan. 28, 2025

We present a genome assembly from specimen of stinging nettle, Urtica dioica (Streptophyta; Magnoliopsida; Rosales; Urticaceae). The sequence has total length 618.00 megabases. Most the is scaffolded into 13 chromosomal pseudomolecules, representing one subgenome tetraploid genome. mitochondrial was submitted as 12 sequences, and single plastid 146.67 kilobases also assembled.

Language: Английский

The European Reference Genome Atlas: piloting a decentralised approach to equitable biodiversity genomics DOI Creative Commons
Ann M. Mc Cartney, Giulio Formenti, Alice Mouton

et al.

npj Biodiversity, Journal Year: 2024, Volume and Issue: 3(1)

Published: Sept. 17, 2024

A genomic database of all Earth's eukaryotic species could contribute to many scientific discoveries; however, only a tiny fraction have information available. In 2018, scientists across the world united under Earth BioGenome Project (EBP), aiming produce high-quality reference genomes containing ~1.5 million recognized species. As European node EBP, Reference Genome Atlas (ERGA) sought implement new decentralised, equitable and inclusive model for producing genomes. For this, ERGA launched Pilot establishing first distributed genome production infrastructure testing it on 98 from 33 countries. Here we outline explore its effectiveness scaling production, whilst considering equity inclusion. The outcomes lessons learned provide solid foundation while offering key learnings other transnational, national resource projects EBP.

Language: Английский

Citations

12
The genome sequence of a cluster fly, Pollenia griseotomentosa (Jacentkovský, 1944) DOI Creative Commons
Olga Sivell,

Ryan Mitchell,

Steven Falk

et al.

Wellcome Open Research, Journal Year: 2025, Volume and Issue: 10, P. 42 - 42

Published: Feb. 3, 2025

We present a genome assembly from an individual Pollenia griseotomentosa (cluster fly; Arthropoda; Insecta; Diptera; Polleniidae). The sequence has total length of 1,046.30 megabases. Most the (99.57%) is scaffolded into 6 chromosomal pseudomolecules, including X sex chromosome. mitochondrial also been assembled and 17.23 kilobases in length.

Language: Английский

Citations

1
The genome sequence of the amphioxus, Branchiostoma lanceolatum (Pallas, 1774) DOI Creative Commons

Patrick Adkins,

John Bishop, Joanna Harley

et al.

Wellcome Open Research, Journal Year: 2025, Volume and Issue: 10, P. 95 - 95

Published: Feb. 24, 2025

We present a genome assembly from specimen of Branchiostoma lanceolatum (Amphioxus; Chordata; Leptocardii; Amphioxiformes; Branchiostomatidae). The contains two haplotypes with total lengths 468.40 megabases and 465.81 megabases, respectively. Most haplotype 1 (99.34%) is scaffolded into 19 chromosomal pseudomolecules. Haplotype 2 scaffold level assembly. mitochondrial has also been assembled 15.14 kilobases in length.

Language: Английский

Citations

1
Genome annotation: From human genetics to biodiversity genomics DOI Creative Commons
Roderic Guigó

Cell Genomics, Journal Year: 2023, Volume and Issue: 3(8), P. 100375 - 100375

Published: Aug. 1, 2023

Within the next decade, genomes of 1.8 million eukaryotic species will be sequenced. Identifying genes in these sequences is essential to understand biology species. This challenging due transcriptional complexity genomes, which encode hundreds thousands transcripts multiple types. Among these, a small set protein-coding mRNAs play disproportionately large role defining phenotypes. Due their sequence conservation, orthology can established, making it possible define universal catalog genes. should substantially contribute uncovering genomic events underlying emergence piece briefly reviews basics gene prediction, discusses challenges finalizing annotation human genome, and proposes strategies for producing annotations across Tree Life. lays groundwork obtaining all genes-the Earth's code life.

Language: Английский

Citations

18
Genome evolution in intracellular parasites: Microsporidia and Apicomplexa DOI Creative Commons
Amjad Khalaf,

Ore Francis,

Mark Blaxter

et al.

Journal of Eukaryotic Microbiology, Journal Year: 2024, Volume and Issue: 71(5)

Published: May 24, 2024

Abstract Microsporidia and Apicomplexa are eukaryotic, single‐celled, intracellular parasites with huge public health economic importance. Typically, these studied separately, emphasizing their uniqueness diversity. In this review, we explore the amount of genomic data that has recently become available for two groups. We compare contrast genome evolution discuss how transitions to life may have shaped it. particular, reduction compaction, expansion ploidy, gene shuffling rearrangements, centromeres telomeres.

Language: Английский

Citations

8
Remarkably High Repeat Content in the Genomes of Sparrows: The Importance of Genome Assembly Completeness for Transposable Element Discovery DOI Creative Commons
Phred M. Benham, Carla Cicero, Merly Escalona

et al.

Genome Biology and Evolution, Journal Year: 2024, Volume and Issue: 16(4)

Published: April 1, 2024

Abstract Transposable elements (TE) play critical roles in shaping genome evolution. Highly repetitive TE sequences are also a major source of assembly gaps making it difficult to fully understand the impact these on host genomes. The increased capacity long-read sequencing technologies span highly regions promises provide new insights into patterns activity across diverse taxa. Here we report generation contiguous reference genomes using PacBio and Omni-C for three species Passerellidae sparrow. We compared assemblies chromosome-level sparrow nine other generated variety short- technologies. All based were longer (range: 1.12 1.41 Gb) than short-read (0.91 1.08 length was strongly correlated with amount repeat content. Repeat content Bell's (31.2% genome) highest level ever reported within order Passeriformes, which comprises over half avian diversity. levels (79.2% 93.7%) found W chromosome relative genome. Finally, show that proliferation different classes varied even among similar These support dynamic model expansion contraction clade where TEs once thought be fairly depauperate static. Our work highlights how resolution difficult-to-assemble transform our understanding

Language: Английский

Citations

6
Toward genome assemblies for all marine vertebrates: current landscape and challenges DOI Creative Commons
Emma de Jong, Lara Parata, Philipp E. Bayer

et al.

GigaScience, Journal Year: 2024, Volume and Issue: 13

Published: Jan. 1, 2024

Marine vertebrate biodiversity is fundamental to ocean ecosystem health but threatened by climate change, overharvesting, and habitat degradation. High-quality reference genomes are valuable foundational scientific resources that can inform conservation efforts. Consequently, global consortia striving produce for representatives of all life. Here, we summarize the current landscape available marine genomes, including their phylogenetic diversity geographic hotspots production. We discuss key logistical technical challenges remain be overcome if realize vision a comprehensive genome library vertebrates.

Language: Английский

Citations

4
The European Reference Genome Atlas: piloting a decentralised approach to equitable biodiversity genomics DOI Creative Commons
Ann M. Mc Cartney, Giulio Formenti, Alice Mouton

et al.

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

Published: Sept. 28, 2023

A global genome database of all Earth's species diversity could be a treasure trove scientific discoveries. However, regardless the major advances in sequencing technologies, only tiny fraction have genomic information available. To contribute to more complete planetary database, scientists and institutions across world united under Earth BioGenome Project (EBP), which plans sequence assemble high-quality reference genomes for ~1.5 million recognized eukaryotic through stepwise phased approach. As initiative transitions into Phase II, where 150,000 are sequenced just four years, worldwide participation project will fundamental success. European node EBP, Reference Genome Atlas (ERGA) seeks implement new decentralised, accessible, equitable inclusive model producing genomes, inform EBP as it scales. embark on this mission, ERGA launched Pilot establish network Europe develop test first infrastructure its kind coordinated distributed production 98 from sample providers 34 countries. Here we outline process challenges faced during development pilot resources, explore effectiveness approach terms production, considering also equity inclusion. The outcomes lessons learned provide solid foundation while offering key learnings other transnational national resource projects.

Language: Английский

Citations

11
The genome sequence of a sawfly, Abia candens Konow, 1887 DOI Creative Commons
Andrew A. Cunningham,

A. J. Halstead

Wellcome Open Research, Journal Year: 2025, Volume and Issue: 10, P. 2 - 2

Published: Jan. 10, 2025

We present a genome assembly from an individual male specimen of Abia candens (sawfly; Arthropoda; Insecta; Hymenoptera; Cimbicidae). The sequence has total length 261.00 megabases. Most the (82.7%) is scaffolded into 16 chromosomal pseudomolecules. mitochondrial also been assembled and 19.72 kilobases in length.

Language: Английский

Citations

0
The genome sequence of the liver fluke Opisthorchis viverrini (Poirier, 1886) Stiles & Hassall, 1896 DOI Creative Commons

Arporn Wangwiwatsin,

Siriyakorn Kulwong,

Chitsakul Phuyao

et al.

Wellcome Open Research, Journal Year: 2025, Volume and Issue: 10, P. 1 - 1

Published: Jan. 10, 2025

We present a genome assembly from specimen of Opisthorchis viverrini (liver fluke; Platyhelminthes; Trematoda; Opisthorchiida; Opisthorchiidae). The sequence has total length 627.20 megabases. Most the (97.89%) is scaffolded into 6 chromosomal pseudomolecules. mitochondrial also been assembled and 18.04 kilobases in length.

Language: Английский

Citations

0