De novogenome sequence assembly of the RNAi-tractable endosymbiosis model systemParamecium bursaria186b reveals factors shaping intron repertoire DOI Creative Commons
Guy Leonard, Benjamin H. Jenkins, Fiona R. Savory

и другие.

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown

Опубликована: Авг. 9, 2024

How two species engage in stable endosymbiosis is a biological quandary. The study of facultative endosymbiotic interactions has emerged as useful approach to understand how functions can arise. ciliate protist Paramecium bursaria hosts green algae the order Chlorellales photo-endosymbiosis. We have recently reported RNAi tool for understanding gene function 186b, CCAP strain 1660/18 [1]. To complement this work, here we report highly complete host genome and trans criptome sequence dataset, using both Illumina PacBio sequencing methods aid analysis enable design experiments. Our analyses demonstrate , like other ciliates such diverse Paramecia possess numerous tiny introns. These data, combined with alternative genetic code common ciliates, makes identification annotation challenging. explore intron evolutionary dynamics further show that splicing leading retention occurs at higher frequency among smaller number longer introns, identifying source selection against data will investigation evolution provide additional exploration functions.

Язык: Английский

OMA orthology in 2024: improved prokaryote coverage, ancestral and extant GO enrichment, a revamped synteny viewer and more in the OMA Ecosystem DOI Creative Commons
Adrian Altenhoff, Alex Warwick Vesztrocy, Charles Bernard

и другие.

Nucleic Acids Research, Год журнала: 2023, Номер 52(D1), С. D513 - D521

Опубликована: Ноя. 14, 2023

In this update paper, we present the latest developments in OMA browser knowledgebase, which aims to provide high-quality orthology inferences and facilitate study of gene families, genomes their evolution. First, discuss addition new species database, particularly an expanded representation prokaryotic species. The now offers Ancestral Genome pages Gene Order viewer, allowing users explore evolutionary history content ancestral genomes. We also introduce a revamped Local Synteny Viewer compare genomic neighborhoods across both extant Hierarchical Orthologous Groups (HOGs) are annotated with Ontology annotations, can easily perform or GO enrichments. Finally, recap tools Ecosystem, including OMAmer for proteome mapping, OMArk quality assessment, OMAMO model organism selection Read2Tree phylogenetic tree construction from reads. These features exciting opportunities analysis comparative genomics. is accessible at https://omabrowser.org.

Язык: Английский

Процитировано

32
Galba: genome annotation with miniprot and AUGUSTUS DOI Creative Commons
Tomáš Brůna, Heng Li, Joseph Guhlin

и другие.

BMC Bioinformatics, Год журнала: 2023, Номер 24(1)

Опубликована: Авг. 31, 2023

The Earth Biogenome Project has rapidly increased the number of available eukaryotic genomes, but most released genomes continue to lack annotation protein-coding genes. In addition, no transcriptome data is for some genomes.

Язык: Английский

Процитировано

31
De novo annotation of the wheat pan-genome reveals complexity and diversity within the hexaploid wheat pan-transcriptome DOI Creative Commons
Benjamen White, Thomas Lux, Rachel Rusholme‐Pilcher

и другие.

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown

Опубликована: Янв. 9, 2024

Abstract Wheat is the most widely cultivated crop in world with over 215 million hectares grown annually. However, to meet demands of a growing global population, breeders face challenge increasing wheat production by approximately 60% within next 40 years. The 10+ Genomes Project recently sequenced and assembled chromosome level genomes nine cultivars develop our understanding genetic diversity selection pan-genome wheat. Here, we provide pan-transcriptome de novo annotation differential expression analysis for these cultivars, across multiple different tissues whole seedlings sampled at dusk/dawn. Analysis annotations facilitated discovery genes absent from Chinese Spring reference, identified specific particular defined core dispensable genomes. Expression revealed conservation between large set homeologous genes, but also widespread changes subgenome homeolog bias cultivars. Co-expression network impact divergence sub-genome cultivar-specific profiles. In case study utilising both newly constructed demonstrate prevalent variation prolamin superfamily immune-reactive proteins pan-cultivars.In summary, this work provides valuable resource wider community reveals gene content patterns

Язык: Английский

Процитировано

8
Chromosome-scale genome assembly reveals how repeat elements shape non-coding RNA landscapes active during newt limb regeneration DOI Creative Commons
Tom Brown, Ketan Mishra, Ahmed Elewa

и другие.

Cell Genomics, Год журнала: 2025, Номер unknown, С. 100761 - 100761

Опубликована: Янв. 1, 2025

Язык: Английский

Процитировано

1
Uncovering gene-family founder events during major evolutionary transitions in animals, plants and fungi using GenEra DOI Creative Commons
Josué Barrera‐Redondo, Jaruwatana Sodai Lotharukpong, Hajk‐Georg Drost

и другие.

Genome biology, Год журнала: 2023, Номер 24(1)

Опубликована: Март 24, 2023

Abstract We present GenEra ( https://github.com/josuebarrera/GenEra ), a DIAMOND-fueled gene-family founder inference framework that addresses previously raised limitations and biases in genomic phylostratigraphy, such as homology detection failure. also reduces computational time from several months to few days for any genome of interest. analyze the emergence taxonomically restricted gene families during major evolutionary transitions plants, animals, fungi. Our results indicate impact failure on inferred patterns is lineage-dependent, suggesting plants are more prone evolve novelty through new genes compared animals

Язык: Английский

Процитировано

21
Accurate microRNA annotation of animal genomes using trained covariance models of curated microRNA complements in MirMachine DOI Creative Commons
Sinan U. Umu, Vanessa Molin Paynter,

Håvard Trondsen

и другие.

Cell Genomics, Год журнала: 2023, Номер 3(8), С. 100348 - 100348

Опубликована: Июнь 25, 2023

The annotation of microRNAs depends on the availability transcriptomics data and expert knowledge. This has led to a gap between novel genomes high-quality microRNA complements. Using >16,000 from manually curated gene database MirGeneDB, we generated trained covariance models for all conserved families. These are available in our tool MirMachine, which annotates within genomes. We successfully applied MirMachine range animal species, including those with large genome duplications extinct where small RNA sequencing is hard achieve. further describe score expected that can be used assess completeness assemblies. closes long-persisting field by facilitating automated pipelines deeper studies into evolution regulation, even organisms.

Язык: Английский

Процитировано

18
Reconstructing the last common ancestor of all eukaryotes DOI Creative Commons
Thomas A. Richards, Laura Eme, John M. Archibald

и другие.

PLoS Biology, Год журнала: 2024, Номер 22(11), С. e3002917 - e3002917

Опубликована: Ноя. 25, 2024

Understanding the origin of eukaryotic cells is one most difficult problems in all biology. A key challenge relevant to question eukaryogenesis reconstructing gene repertoire last common ancestor (LECA). As data sets grow, sketching an accurate genomics-informed picture early cellular complexity requires provision analytical resources and a commitment sharing. Here, we summarise progress towards understanding biology LECA outline community approach inferring its wider repertoire. Once assembled, robust set will be useful tool for evaluating alternative hypotheses about eukaryotes evolution traits descendant lineages, with relevance diverse fields such as cell biology, microbial ecology, biotechnology, agriculture, medicine. In this Consensus View, put forth status quo agreed path forward reconstruct LECA's content.

Язык: Английский

Процитировано

5
PSAURON: a tool for assessing protein annotation across a broad range of species DOI Creative Commons
Markus J. Sommer, Aleksey V. Zimin, Steven L. Salzberg

и другие.

NAR Genomics and Bioinformatics, Год журнала: 2025, Номер 7(1)

Опубликована: Янв. 7, 2025

Abstract Evaluating the accuracy of protein-coding sequences in genome annotations is a challenging problem for which there no broadly applicable solution. In this manuscript, we introduce PSAURON (Protein Sequence Assessment Using Reference ORF Network), novel software tool developed to help assess quality gene annotations. Utilizing machine learning model trained on diverse dataset from over 1000 plant and animal genomes, assigns score coding DNA or protein sequence that reflects likelihood genuine region. scores can be used genome-wide annotation assessment as well rapid identification potentially spurious annotated proteins. Validation against established benchmarks demonstrates PSAURON’s effectiveness correlation with recognized measures quality, highlighting its potential use widely method evaluate precision annotation. open source freely available at https://github.com/salzberg-lab/PSAURON.

Язык: Английский

Процитировано

0
The Monochoria genome provides insights into the molecular mechanisms underlying floral heteranthery DOI
Jingshan Yang, Jinming Chen, Xiangyan He

и другие.

Journal of genetics and genomics/Journal of Genetics and Genomics, Год журнала: 2025, Номер unknown

Опубликована: Фев. 1, 2025

Язык: Английский

Процитировано

0
Beyond venomous fangs: Uloboridae spiders have lost their venom but not their toxicity DOI

Xiaojing Peng,

Ludwig Dersch,

Josephine Dresler

и другие.

Research Square (Research Square), Год журнала: 2025, Номер unknown

Опубликована: Апрель 10, 2025

Abstract Background Venom, one of nature’s most potent secretions, has played a crucial role in the evolutionary success many animal groups, including spiders. However, Uloboridae spiders appear to lack venom and capture their prey, unlike venomous spiders, by extensive silk-wrapping regurgitation digestive fluids onto entire prey package. A prevailing hypothesis posits that toxins may have been reallocated from alternative like silk or fluids. Yet, whether uloborids retained mechanisms underlying immobilisation remain unresolved. Here, we employed multi-disciplinary approach assess absence glands Uluborus plumipes, toxin gene expression toxicity proteins.Results Our findings confirm U. plumipes lacks apparatus, while neurotoxin-like transcripts were highly expressed system. Midgut extract had comparable levels Parasteatoda tepidariorum. no inhibitory effects on sodium nor potassium channels observed, indicating different toxic mechanism.Conclusions These support lost apparatus retaining toxin-like genes. The fluids, trait conserved across likely compensate for venom, ensuring effective digestion.

Язык: Английский

Процитировано

0