Comparison of 15 dinoflagellate genomes reveals extensive sequence and structural divergence in family Symbiodiniaceae and genus Symbiodinium

BMC Biology, Год журнала: 2021, Номер 19(1)

Опубликована: Апрель 13, 2021

Abstract Background Dinoflagellates in the family Symbiodiniaceae are important photosynthetic symbionts cnidarians (such as corals) and other coral reef organisms. Breakdown of coral-dinoflagellate symbiosis due to environmental stress (i.e. bleaching) can lead death potential collapse ecosystems. However, evolution genomes, its implications for coral, is little understood. Genome sequences remain scarce part their large genome sizes (1–5 Gbp) idiosyncratic features. Results Here, we present de novo assemblies seven members genus Symbiodinium , which two free-living, one an opportunistic symbiont, remainder mutualistic symbionts. Integrating available data, compare 15 dinoflagellate genomes revealing high sequence structural divergence. Divergence among some isolates comparable that distinct genera Symbiodiniaceae. We also recovered hundreds gene families specific each lineage, many encode unknown functions. An in-depth comparison between symbiotic tridacnidorum (isolated from a coral) free-living natans reveals greater prevalence transposable elements, genetic duplication, rearrangements, pseudogenisation species. Conclusions Our results underscore impact lifestyle on lineage-specific gene-function innovation, divergence, diversification The divergent features report, putative causes, may apply microbial eukaryotes have undergone phases evolutionary history.

Язык: Английский

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Navigating spaces between conservation research and practice: Are we making progress?

Ecological Solutions and Evidence, Год журнала: 2020, Номер 1(2)

Опубликована: Ноя. 8, 2020

Abstract 1. Despite aspirations for conservation impact, mismatches between research and implementation have limited progress towards this goal. There is, therefore, an urgent need to identify how we can more effectively navigate the spaces practice. 2. In 2014, ran a workshop with researchers practitioners that needed be overcome deliver evidence‐informed action. Five were highlighted: spatial, temporal, priority, communication, institutional. 3. Since thinking around ‘research–implementation gap’ has progressed. The term ‘gap’ been replaced by language dynamic ‘spaces’ action, representing shift in what it takes better align 4. 2019, follow‐up reflecting on shift, whether five identified 2014 still present conservation, had made these during past 5 years. We found while there progress, some way go across all dimensions. 5. Here, report outcomes of 2019 workshop, reflect changed over years, offer 10 recommendations strengthening alignment

Язык: Английский

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Expanding the conservation genomics toolbox: Incorporating structural variants to enhance genomic studies for species of conservation concern

Molecular Ecology, Год журнала: 2021, Номер 30(23), С. 5949 - 5965

Опубликована: Авг. 23, 2021

Structural variants (SVs) are large rearrangements (>50 bp) within the genome that impact gene function and content structure of chromosomes. As a result, SVs significant source functional genomic variation, is, variation at regions underpinning phenotype differences, can have effects on individual population fitness. While there increasing opportunities to investigate in threatened species via single nucleotide polymorphism (SNP) data sets, remain understudied despite their potential influence fitness traits conservation interest. In this future-focused Opinion, we contend characterizing offers genomics community an exciting opportunity complement SNP-based approaches enhance recovery. We also leverage existing literature-predominantly human health, agriculture ecoevolutionary biology-to identify for readily consider how integrating these into toolbox may transform way manage some world's most species.

Язык: Английский

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GenErode: a bioinformatics pipeline to investigate genome erosion in endangered and extinct species

BMC Bioinformatics, Год журнала: 2022, Номер 23(1)

Опубликована: Июнь 13, 2022

Many wild species have suffered drastic population size declines over the past centuries, which led to 'genomic erosion' processes characterized by reduced genetic diversity, increased inbreeding, and accumulation of harmful mutations. Yet, genomic erosion estimates modern-day populations often lack concordance with dwindling sizes conservation status threatened species. One way directly quantify consequences is compare genome-wide data from pre-decline museum samples modern samples. However, doing so requires computational processing analysis tools specifically adapted comparative analyses degraded, ancient or historical, DNA as well personnel trained perform such analyses.Here, we present a highly flexible, scalable, modular pipeline patterns using disparate time periods. The GenErode uses state-of-the-art bioinformatics simultaneously process whole-genome re-sequencing ancient/historical samples, produce comparable several indices. No programming knowledge required run all bioinformatic steps are well-documented, making accessible users different backgrounds. written in Snakemake Python3 Conda Singularity containers achieve reproducibility on high-performance compute clusters. source code freely available GitHub ( https://github.com/NBISweden/GenErode ).GenErode user-friendly reproducible that enables standardization indices temporally sampled whole genome data.

Язык: Английский

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Preadapted to adapt: underpinnings of adaptive plasticity revealed by the downy brome genome

Communications Biology, Год журнала: 2023, Номер 6(1)

Опубликована: Март 27, 2023

Bromus tectorum L. is arguably the most successful invasive weed in world. It has fundamentally altered arid ecosystems of western United States, where it now found on an excess 20 million hectares. Invasion success related to avoidance abiotic stress and human management. Early flowering a heritable trait utilized by B. tectorum, enabling species temporally monopolize limited resources outcompete native plant community. Thus, understanding genetic underpinning time critical for design integrated management strategies. To study traits we assembled chromosome scale reference genome tectorum. assess utility genome, 121 diverse accessions are phenotyped subjected wide association (GWAS). Candidate genes, representing homologs genes that have been previously associated with height or phenology located near QTLs identified. This uses high-resolution GWAS identify reproductive weedy represents considerable step forward mechanisms underlying plasticity one species.

Язык: Английский

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Restoring faith in conservation action: Maintaining wild genetic diversity through the Tasmanian devil insurance program

iScience, Год журнала: 2022, Номер 25(7), С. 104474 - 104474

Опубликована: Май 26, 2022

Conservation breeding programs aim to maintain 90% wild genetic diversity, but rarely assess functional diversity. Here, we compare both genome-wide and diversity (in over 500 genes) of Tasmanian devils (Sarcophilus harrisii) within the insurance metapopulation across species' range (64,519 km2). Populations have declined by 80% since 1996 due a contagious cancer, devil facial tumor disease (DFTD). However, predicted local extinctions not occurred. Recent suggestions selection for "resistance" alleles in precipitated concerns that population may be unsuitable translocations. Using 830 samples collected at 31 locations between 2012 2021, 553 devils, show is representative current Allele frequencies DFTD-associated loci were substantially different captive devils. Methods presented here are valuable others investigating evolutionary potential threatened species, particularly ones under significant selective pressures.

Язык: Английский

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Population genomics of a predatory mammal reveals patterns of decline and impacts of exposure to toxic toads

Molecular Ecology, Год журнала: 2022, Номер 31(21), С. 5468 - 5486

Опубликована: Сен. 3, 2022

Mammal declines across northern Australia are one of the major biodiversity loss events occurring globally. There has been no regional assessment implications these species for genomic diversity. To address this, we conducted a species-wide diversity in quoll (Dasyurus hallucatus), an Endangered marsupial carnivore. We used next generation sequencing methods to genotype 10,191 single nucleotide polymorphisms (SNPs) 352 individuals from 3220-km length continent, investigating patterns population structure and diversity, identifying loci showing signals putative selection. found strong heterogeneity distribution characterized by (i) biogeographical barriers driving hierarchical through long-term isolation, (ii) severe reductions resulting declines, exacerbated spread introduced toxic cane toads (Rhinella marina). These results warn large ongoing associated adaptive capacity as mammals decline Australia. Encouragingly, populations established on toad-free islands translocations appear have maintained most initial after 16 years. By mapping within among populations, context can provide conservation managers with data critical informed decision-making. This includes identification that candidates genetic management, importance remnant island insurance/translocated characterization evolutionarily significant units.

Язык: Английский

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Genomic richness enables worldwide invasive success

Research Square (Research Square), Год журнала: 2024, Номер unknown

Опубликована: Фев. 28, 2024

Abstract Biological invasions are a major threat to biodiversity. Therefore, monitoring genomic features of invasive species is crucial understand their population structure and adaptive processes. However, resources scarce, compromising the study success. Here, we present reference genome Styela plicata , one most widespread marine species, combined with data 24 individuals from 6 populations distributed worldwide. We characterized large inversions in four chromosomes, accounting for ~ 15% size. These polymorphic through species’ distribution area, enriched genes enhancing fitness estuary harbor environments. Nonetheless, mask detection S. structure. When these structural variants removed, successfully identify main oceanographic barriers accurately characterize differentiation between within ocean basins. Several located chromosome 3 showcased as drivers biogeographic regions. Moreover, recover three mitogenomic clades, involving rearrangements leading cyto-nuclear coevolution likely involved mitochondrion during cell division. Our results suggest that contribute structuring adaptation processes, potentially success when colonizing new habitats.

Язык: Английский

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The first Antechinus reference genome provides a resource for investigating the genetic basis of semelparity and age-related neuropathologies

Gigabyte, Год журнала: 2020, Номер 2020, С. 1 - 22

Опубликована: Ноя. 5, 2020

Antechinus are a genus of mouse-like marsupials that exhibit rare reproductive strategy known as semelparity and also naturally develop age-related neuropathologies similar to those in humans. We provide the first annotated antechinus reference genome for brown (Antechinus stuartii). The is 3.3 Gb size with scaffold N50 73Mb 93.3% complete mammalian BUSCOs. Using bioinformatic methods we assign scaffolds chromosomes identify 0.78 Mb Y-chromosome scaffolds. Comparative genomics revealed interesting expansions NMRK2 gene protocadherin gamma family, which have previously been associated aging dementias respectively. Transcriptome data displayed expression common Alzheimer’s related genes brain highlight potential utilising future disease model. valuable genomic resources provided herein will enable research explore genetic basis processes antechinus.

Язык: Английский

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The Genome Assembly and Annotation of the Apollo Butterfly Parnassius apollo, a Flagship Species for Conservation Biology

Genome Biology and Evolution, Год журнала: 2021, Номер 13(8)

Опубликована: Июнь 9, 2021

Conservation genomics has made dramatic improvements over the past decade, leveraging power of genomes to infer diverse parameters central conservation management questions. However, much this effort focused upon vertebrate species, despite insects providing similar flagship status with added benefit smaller genomes, shorter generation times and extensive historical collections in museums. Here we present genome Apollo butterfly (Parnassius apollo, Papilionidae), an iconic endangered butterfly, which like many species genus, needs genomic attention yet lacks a genome. Using 68.7 Gb long-read data (N50 = 15.2 kb) assembled 1.4 for making largest sequenced Lepidopteran date. The assembly was highly contiguous 7.1 Mb) complete (97% BUSCOs were single-copy complete) consisted 1,707 contigs. RNAseq Arthropoda proteins, annotated 28.3K genes. Alignment closest-related chromosome-level assembly, Papilio bianor, reveals conserved chromosomal organization, albeit size is expanded due primarily increase repetitive element content. alignment superscaffolding places P. apollo 31 scaffolds, together our functional annotation, provides essential resource advancing insect conservation.

Язык: Английский

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