The chromosome-level genome of the ctenophore Mnemiopsis leidyi A. Agassiz, 1865 reveals a unique immune gene repertoire

Genome Biology and Evolution, Год журнала: 2025, Номер 17(2)

Опубликована: Янв. 21, 2025

Ctenophora are basal marine metazoans, the sister group of all other animals. Mnemiopsis leidyi is one most successful invasive species worldwide with intense ecological and evolutionary research interest. Here, we generated a chromosome-level genome assembly M. focus on its immune gene repertoire. The was 247.97 Mb, N50 16.84 84.7% completeness. Its karyotype 13 chromosomes. In this that two ctenophores, Bolinopsis microptera Hormiphora californensis, detected high number protein domains related to potential receptors. Among those, proteins containing Toll/interleukin-1 (TIR2) domain, NACHT Scavenger Receptor Cystein-Rich (SRCR) or C-type Lectin domain (CTLD) were abundant presented unique architectures in leidyi. seems lack bona fide Toll-like Receptors, but it does possess repertoire 15 TIR2 domain-containing genes. Besides, NOD-like receptor 38 order verify function those genes, exposed pathogen Vibrio coralliilyticus. differentially expressed identified receptors, including four which upregulated response exposure. To conclude, many common domains, highly conserved across already present Ctenophora. These have large expansions leidyi, findings consistent position group, still might functions immunity host-microbe interaction.

Язык: Английский

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Chromosome-level genome assembly of the spangled emperor, Lethrinus nebulosus (Forsskål 1775)

Scientific Data, Год журнала: 2025, Номер 12(1)

Опубликована: Март 13, 2025

Spangled emperor, Lethrinus nebulosus (Forsskål 1775), is a tropical marine fish of economic and cultural importance throughout the Indo-West Pacific. It one most targeted recreational fishes in Gascoyne Coast Bioregion Western Australia where it serves as an indicator species for fishing. Here, we present highly accurate, near-gapless, chromosome-level, haplotype-phased reference genome assembly L. (Lethrinus (Spangled Emperor) genome, fLetNeb1.1; PRJNA1074345), first high-quality representative family Lethrinidae. The 1.09 Gb was assembled from PacBio HiFi Dovetail Omni-C proximity ligation sequencing data. contig N50 21–24 Mbp BUSCO completeness greater than 99%. A preliminary gene annotation identified 24,583 genes with predicted transcriptome achieving score 99.1% This resource will facilitate genomic studies to inform sustainable management other Lethrinids.

Язык: Английский

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Haplotype‐phased and chromosome‐level genome assembly of Puccinia polysora, a giga‐scale fungal pathogen causing southern corn rust

Molecular Ecology Resources, Год журнала: 2022, Номер 23(3), С. 601 - 620

Опубликована: Ноя. 20, 2022

Rust fungi are characterized by large genomes with high repeat content and have two haploid nuclei in most life stages, which makes achieving high-quality genome assemblies challenging. Here, we described a pipeline using HiFi reads Hi-C data to assemble gigabase-sized fungal pathogen, Puccinia polysora f.sp. zeae, haplotype-phased chromosome-scale. The final assembled is 1.71 Gbp, ~850 Mbp 18 chromosomes each haplotype, being currently one of the giga-scale chromosome level. Transcript-based annotation identified 47,512 genes for dikaryotic similar number haplotype. A level interhaplotype variation was found 10% haplotype-specific BUSCO genes, 5.8 SNPs/kbp, structural accounting 3% size. P. displayed over 85% contents, genome-size expansion copy increasing species-specific orthogroups. Interestingly, these features did not affect overall synteny other species having smaller genomes. Fine-time-point transcriptomics revealed seven clusters coexpressed secreted proteins that conserved between haplotypes. fact candidate effectors interspersed all indicated absence "two-speed genome" evolution polysora. Genome resequencing 79 additional isolates clonal population structure China low geographic differentiation. Nevertheless, minor differentiated from major mutations on including AvrRppC, indicating ongoing virulence evade recognition RppC, resistance gene Chinese corn cultivars. assembly provides valuable genomic resources future studies disease management

Язык: Английский

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Uncovering the history of recombination and population structure in western Canadian stripe rust populations through mating type alleles

BMC Biology, Год журнала: 2023, Номер 21(1)

Опубликована: Окт. 25, 2023

The population structure of crop pathogens such as Puccinia striiformis f. sp. tritici (Pst), the cause wheat stripe rust, is interest to researchers looking understand these on a molecular level well those with an applied focus disease epidemiology. Cereal rusts can reproduce sexually or asexually, and emergence novel lineages has potential serious epidemics one caused by 'Warrior' lineage in Europe. In global context, Pst Canada were not well-characterized origin foreign incursions was known. Additionally, while some mating type genes have been identified published genomes, there no rigorous assessment diversity distribution across species.

Язык: Английский

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Gapless Genome Assembly of Puccinia triticina Provides Insights into Chromosome Evolution in Pucciniales

Microbiology Spectrum, Год журнала: 2023, Номер 11(1)

Опубликована: Янв. 23, 2023

Chromosome evolution drives species evolution, speciation, and adaptive radiation. Accurate genome assembly is crucial to understanding chromosome of species, such as dikaryotic fungi. Rust fungi (Pucciniales) in dikaryons represent the largest group plant pathogens, but evolutionary process radiation Pucciniales remains poorly understood. Here, we report a gapless for wheat leaf rust fungus Puccinia triticina determined using PacBio high-fidelity (HiFi) sequencing. This contains two sets chromosomes, showing that one contig represents chromosome. Comparisons homologous chromosomes between phased haplotypes revealed highly frequent small-scale sequence divergence shapes haplotypic variation. Genome analyses along with other rusts recent transposable element bursts extensive segmental gene duplications synergistically highlight structures. Comparative analysis indicated chromosomal rearrangements may act major contributor rapid Pucciniales. study presents first gapless, provides insights into IMPORTANCE are pathogens. Adaptive predominant feature evolution. plays an important role chromosome-scale required understand We took advantage HiFi sequencing construct triticina. Further structures lineage shaped by combination duplications. comparisons suggested arrangements make remarkable contributions high diversity Our results present shed light on

Язык: Английский

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Austropuccinia psidii uses tetrapolar mating and produces meiotic spores in older infections on Eucalyptus grandis

Fungal Genetics and Biology, Год журнала: 2022, Номер 160, С. 103692 - 103692

Опубликована: Апрель 15, 2022

Язык: Английский

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The chromosome-level genome of the ctenophoreMnemiopsis leidyiA. Agassiz, 1865 reveals a unique immune gene repertoire

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

Опубликована: Янв. 24, 2024

Abstract Ctenophora are basal marine metazoans, the sister group of all other animals. Mnemiopsis leidyi is one most successful invasive species worldwide with intense ecological and evolutionary research interest. Here, we generated a chromosome-level genome assembly M. focus on its immune gene repertoire. The was 247.97 Mb, N50 16.84 84.7% completeness. Its karyotype 13 chromosomes. In this that two ctenophores, Bolinopsis microptera Hormiphora californensis , detected high number protein domains related to potential receptors. Among those, proteins containing Toll/interleukin-1(TIR2) domain, NACHT Scavenger Receptor Cystein-Rich (SRCR) or C-type Lectin domain (CTLD) were abundant presented unique architectures in leidyi. seems lack bona fide Toll like Receptors, but it does possess repertoire 15 TIR2-domain genes. Besides, NOD-like receptor 38 NACHT-domain order verify function those genes, exposed pathogen Vibrio coralliilyticus . differentially expressed identified receptors, including four which upregulated response exposure. To conclude, many common domains, highly conserved across already present Ctenophora. These have large expansions findings consistent position group, still might functions immunity host-microbe interaction.

Язык: Английский

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Small but mitey: long-read assembly of a streamlined mite genome from contaminated host plant sequencing data

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

Опубликована: Май 20, 2024

Abstract Technological advances have propelled DNA sequencing of non-model organisms, making more accessible and cost effective, which has also increased the availability raw data in public repositories. However, contamination is a significant concern, use reuse requires quality control curation. A reference genome for Australian native rainforest tree Rhodamnia argentea Benth. (malletwood) was assembled from Oxford Nanopore Technologies (ONT) long-reads, 10x Genomics Chromium linked-reads, Hi-C (N50 = 32.3 Mbp BUSCO completeness 98.0%) with 99.0% 347 assembly anchored to 11 chromosomes (2 n 22). The R . will inform conservation efforts Myrtaceae species threatened by global spread fungal disease myrtle rust. We observed further investigation revealed an arthropod source. Here, we demonstrate feasibility assembling high-quality gapless telomere-to-telomere mite using contaminated host plant data. exhibits streamlining 35 (68.6% completeness) on two chromosomes, capped novel TTTGG telomere sequence. Phylogenomic analysis suggests that it previously unsequenced eriophyoid mite. Despite its unknown identity, this complete nuclear provides valuable resource investigate invertebrate reduction. This study emphasises importance checking contamination, especially when working organisms. It enhances our understanding species, including faces substantial challenges, contributing broader biodiversity initiatives. Significance genomes associated mite, data, were first time. generated chromosome-level genomic resources rust impacted pest genomics, streamlining. research underscores growing prevalence experiments organisms while emphasising curation

Язык: Английский

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Parental assigned chromosomes for cultivated cacao provides insights into genetic architecture underlying resistance to vascular streak dieback

The Plant Genome, Год журнала: 2024, Номер 17(4)

Опубликована: Окт. 15, 2024

Diseases of Theobroma cacao L. (Malvaceae) disrupt cocoa bean supply and economically impact growers. Vascular streak dieback (VSD), caused by Ceratobasidium theobromae, is a new encounter disease currently contained to southeast Asia Melanesia. Resistance VSD has been tested with large progeny trials in Sulawesi, Indonesia, Papua New Guinea the identification informative quantitative trait loci (QTLs). Using susceptible tree (clone 26), derived from resistant parental cross, we assembled genome chromosome-level discriminated alleles inherited either or parents. The parentally phased genomes were annotated for all predicted genes then specifically resistance nucleotide-binding site leucine-rich repeat class (NLR). On investigation, determined presence NLR clusters other potential response gene candidates proximity QTLs. We identified structural variants within NLRs parentals. present first diploid, fully scaffolded, resource T. provide insights into genetics underlying susceptibility VSD.

Язык: Английский

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Genomics and resistance assays inform the management of two tree species being devastated by the invasive myrtle rust pathogen

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

Опубликована: Ноя. 2, 2024

Abstract Myrtle rust is a plant disease caused by the invasive fungal pathogen Austropuccinia psidii (G. Winter) Beenken, which has global host list of 480 species. It was detected in Australia 2010 and rapid decline native Myrtaceae species, including rainforest trees Rhodamnia rubescens (Benth.) Miq. (scrub turpentine) Rhodomyrtus psidioides (G.Don) Benth. (native guava). Ex situ collections these species have been established, with goal preserving remaining genetic variation. Analysis reduced representation sequencing (DArTseq; n = 444 for R . 301 ) showed diversity distributed along latitudinal gradient across range each A panel samples ( 27 37 were resequenced at genome scale, revealing large historical e]ective population sizes, little variation among individuals inferred levels deleterious load. In , experimental assays 297) identified that are putatively resistant to myrtle rust. This highlights two important points: there tangible pathways recovery highly susceptible via genetically informed breeding program, critical need act quickly before more standing lost.

Язык: Английский

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