Highly accurate long reads are crucial for realizing the potential of biodiversity genomics

BMC Genomics, Journal Year: 2023, Volume and Issue: 24(1)

Published: March 16, 2023

Abstract Background Generating the most contiguous, accurate genome assemblies given available sequencing technologies is a long-standing challenge in science. With rise of long-read sequencing, assembly challenges have shifted from merely increasing contiguity to correctly assembling complex, repetitive regions interest, ideally phased manner. At present, researchers largely choose between two types long read data: longer, but less sequences, or highly accurate, shorter reads (i.e., >Q20 99% accurate). To better understand how these data as well scale mean length and depth) influence outcomes, we compared for caddisfly, Hesperophylax magnus , generated with Oxford Nanopore (ONT) R9.4.1 PacBio HiFi (HiFi) data. Next, expanded this comparison consider sequence on across 6750 plant animal genomes. For broader comparison, used surrogate long-reads broadly could identify when they were GenBank metadata. Results outperformed ONT all metrics tested caddisfly set allowed ~ 20 Kb H-fibroin gene. Across plants animals, that incorporated also more contiguous. plants, average was 501% contiguous (mean contig N50 = 20.5 Mb) than those any other 4.1 Mb). 226% 20.9 versus 9.3 In found limited evidence may offer unique solution overcoming genomic complexity scales size. Conclusions Highly analogous represent key tool maximizing quality wide swath animals. This finding particularly important resources only allow one type be generated. Ultimately, realize promise biodiversity genomics, call greater uptake future studies.

Language: Английский

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Convergent Gene Duplication in Arctic and Antarctic Teleost Fishes

ZOOLOGICAL SCIENCE, Journal Year: 2025, Volume and Issue: 42(1)

Published: Jan. 21, 2025

Teleost fishes have independently colonized polar regions multiple times, facing many physiological and biochemical challenges due to frigid temperatures. Although increased gene copy numbers can contribute adaptive evolution in extreme environments, it remains unclear which categories of genes exhibit associated with colonization. Using 104 species ray-finned fishes, we systematically identified a significant correlation between number colonization after phylogenetic correction. Several encoding extracellular glycoproteins, including zona pellucida (ZP) proteins, increase their Antarctic notothenioid exhibited elevated across fish lineages. Additionally, some reported be highly expressed under cold stress, such as cold-inducible RNA-binding protein (CIRBP), had significantly fishes. Further analysis will provide fundamental basis for understanding the role duplication adaptations.

Language: Английский

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Genome-wide identification and expression profiling of the hemoglobin gene family under hypoxia stress in Sillago sihama

Comparative Biochemistry and Physiology Part D Genomics and Proteomics, Journal Year: 2025, Volume and Issue: unknown, P. 101500 - 101500

Published: March 1, 2025

Language: Английский

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The role of antifreeze genes in the tolerance of cold stress in the Nile tilapia (Oreochromis niloticus)

BMC Genomics, Journal Year: 2023, Volume and Issue: 24(1)

Published: Aug. 23, 2023

Abstract Background Tilapia is one of the most essential farmed fishes in world. It a tropical and subtropical freshwater fish well adapted to warm water but sensitive cold weather. Extreme weather could cause severe stress mass mortalities tilapia. The present study was carried out investigate effects on up-regulation antifreeze protein (AFP) genes Nile tilapia ( Oreochromis niloticus ). Two treatment groups were investigated (5 replicates 15 for each group fibreglass tanks/70 L each): 1) control group; acclimated lab conditions two weeks temperature maintained at 25 °C during whole experimental period with feeding commercial diet (30% crude protein). 2) Cold same as except temperature. Initially, decreased by degree every 12 h. started showing death symptoms when reached 6–8 °C. In this stage tissue (muscle) samples taken from both groups. immune response exposed detected characterized using Differential Display-PCR (DD-PCR). Results results indicated that nine different cold-stressed compared group. These are Integrin-alpha-2 ITGA-2 ), Gap junction gamma-1 protein-like GJC1 WD repeat-containing 59 isoform X2 (WDRP59), NUAK family SNF1-like kinase, G-protein coupled receptor-176 GPR-176 Actin cytoskeleton-regulatory complex pan1-like PAN-1 Whirlin WHRN Suppressor tumorigenicity 7 ST7P ) ATP-binding cassette sub-family A member 1-like ABCA1 gene type-II amplification specific PCR product 600 bp, followed cloning sequencing analysis revealed identified type-II, similarity ranging 70 95%. in-vitro transcribed induced an molecular size 22 kDa. gene, repeat belong lectin (sugar–protein). Conclusions conclusion, under stress, express many defence genes, consisting open reading frame approximately 0.6 kbp.

Language: Английский

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Improved assembly of the Pungitius pungitius reference genome

G3 Genes Genomes Genetics, Journal Year: 2024, Volume and Issue: 14(8)

Published: June 11, 2024

Abstract The nine-spined stickleback (Pungitius pungitius) has been increasingly used as a model system in studies of local adaptation and sex chromosome evolution but its current reference genome assembly is far from perfect, lacking distinct chromosomes. We generated an improved the (98.3% BUSCO completeness) with aid linked-read mapping. While new (v8) was similar size earlier version (v7), we were able to assign 4.4 times more contigs linkage groups improve contiguity genome. Moreover, contains ∼22.8 Mb Y-linked scaffold (LG22) consisting mainly previously assigned X-contigs, putative Y-contigs, centromere contigs, highly repetitive elements. male individual showed even mapping depth on LG12 (pseudo X chromosome) LG22 (Y-linked scaffold) segregating sites, suggesting near-pure Y representation v8 assembly. A total 26,803 genes annotated, about 33% found consist high proportion elements (53.10%) suggests it can be difficult assemble complete sequence species’ chromosome. Nevertheless, significant improvement over previous should provide valuable resource for genomic fishes.

Language: Английский

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Long‐read sequencing in ecology and evolution: Understanding how complex genetic and epigenetic variants shape biodiversity

Molecular Ecology, Journal Year: 2023, Volume and Issue: 32(6), P. 1229 - 1235

Published: March 1, 2023

Ten years ago, the journal Molecular Ecology published a “road map” paper that reviewed past achievements in discipline of molecular ecology, identified research challenges and charted way forward (Andrew et al., 2013). That was motivated by symposium organized during First Joint Congress on Evolutionary Biology (Ottawa, July 6–10, 2012). In addition, it occurred heels major inflection point ecology life sciences more broadly: development uptake “next”- or “second”-generation sequencing technologies, which deliver short DNA reads (typically shorter than 400 bp) at very high throughput (e.g., several billion per run; Goodwin 2016). As such, Andrew al. (2013) emphasized promise second-generation for diverse subdisciplines such as phylogeography, landscape genomics, adaptation speciation. Representing just technical advancement, predicted to stimulate rapid conceptual breakthroughs field, especially nonmodel species (Stapley 2010; Tautz 2010). illustrated any recent issue journal, these predictions were accurate. While has enabled important discoveries forefront this technology does not come without limitations, most prominent is read length. Indeed, additional validation, standard cannot be used traverse complex regions genome repetitive elements, duplications, inversions other forms structural change (Goodwin 2016; Huddleston 2014). Consequently, have remained relatively unexplored. Ironically, however, they may also particularly understanding ecological evolutionary processes (Wellenreuther 2019), given their mutation rates Hastings 2009), fact can extremely abundant—often surpassing single nucleotide polymorphisms fold, terms total length affected (1000 Genomes Project Consortium 2015; Mérot 2023). The obtain spanning tens thousands kilobases already available 10 ago (Hayden, 2009; Munroe & Harris, 2010), been developed providers, best-known are Pacific Biosciences (hereafter “PacBio”) Oxford Nanopore Technologies “Nanopore”). Also referred third-generation sequencing, approaches initially complement short-read data Laszlo 2014; Despite potential utility long reads, adoption slow, primarily due error reported initial iterations instruments (Glenn, 2011; Ip 2015). Recent brought about two developments. First, dropped considerably, some cases below 1%, approaching characteristic This improvements chemistry, base-calling algorithms methods post-sequencing correction (Logsdon 2020; Rang 2018). Second, assembling stretches from become McCoy Selvaraj 2013; Zheng Collectively, helping biologists tackle highly dynamic genome, largely inaccessible until few ago. Perhaps clearly, consequential role long-read getting job done publication first complete, telomere-to-telomere human (Nurk 2022), decades after our made (International Human Genome Sequencing Consortium, 2001). Special Issue highlights ways ecologists utilizing information explore roles otherwise loci. 19 articles comprise issue, covering range plant, animal, bacteria virus study systems, grouped into six sections, we summarize below. doing so, goal emphasize key findings each study. We highlight, where possible, will need overcome coming years, before realizes its full potential. conclude summarizing underlying thread Issue: genetic epigenetic variation, while traditionally difficult study, make substantial contribution anticipate that, with continued improvement area only continue grow, shaping downstream biodiversity consequences variants. “Epigenetics” refers heritable changes expression achieved means direct modification sequence (Bossdorf 2008). mechanisms known, including methylation, histone modifications small RNAs, evolution focused because characterized increased stability over generations (Verhoeven Among different types methylated nucleotides, 5-methylcytosine (5mC) received attention, dominant methylation pattern eukaryotes (Goll Bestor, 2005). epigenomic studies indicated differential wide-ranging relevance. For example, broad repatterning known follow hybridization genomic background (Rapp Wendel, well, 5mC variants found associated environmental variables phenotypic metabolic traits plant animal 2008; Hu Barrett, 2017; Rapp 2005; Verhoeven To genome-wide profiles population samples, one treat bisulphite prior step converts unmethylated cytosines uracil, rendering vs. identifiable opinion Issue, Nielsen (2023) how revolutionizing studies, using an example bacteriophages, repertoire eukaryotes. authors discuss advantages PacBio offer detection modifications, technologies eliminate treatment enable de novo base modifications. Aside illustrating state-of-the-art acquisition analysis, identify current limitations profiling develop dedicated analytical tools minimize noise neighbouring implement reference libraries signature advances achieved, much better positioned understand relevance ongoing arms race between bacteriophages (Nielsen Repetitive transposable elements source novelty. Well-known routes reshuffling chromosomal segments involve include ectopic recombination nonhomologous end-joining, lead variety outcomes deletions, fusions (González Petrov, 2012; Huang Rieseberg, 2020). contributions included section, benefit investigations repeat karyotype patterns synteny. karyotype, Burley use characterize large (134-Mbp) neo-sex chromosome blue-faced honeyeater. Results demonstrated originated via fusion autosome ancestral Z chromosome, diversity differentiation. Remarkably, same appear fused convergently songbird lineages, potentially facilitated repeats shared chromosomes (Burley synteny, Ferguson sequence, assemble compare genomes three Eucalyptus species. transposon-rich synteny loss small-scale rearrangements. Their thus generally accepted view maintain syntenic genome. Moreover, results showed sizeable fraction rearrangements contained genes, therefore drive species-rich widely distributed genus. Rather representing obstacle assembly, focus Peona (2023), investigated satellite 24 birds. Using linked catalogued monomer sizes ranging 20 bp 4 kb dynamic. abundance did align models evolution. Specifically, similar among deeply diverged recently result promising future Wierzbicki piRNA (PIWI-interacting RNA) clusters Drosophila. These rich crucial defence against elements. resolved four Drosophila species, contiguous assemblies data. developing framework quantitative dynamics clusters, includes establishing loci, show evolve rapidly, mainly insertion deletion old ones. Remaining expanding taxonomic breadth cluster evolution, well extending analyses larger out, both stand implementation ecology. Long-read broadening toolset management populations, enabling reconstruction gap-free, fast pace (Kardos 2021). allows us re-evaluate previous conclusions drawn at-risk populations based data, origin, levels inbreeding structure sets allow new gained regarding long-term demographic histories fitness 2021; Wold examples genome-scale vulnerable threatened instance, Li, Yang, rely Hi-C takin, bovid herbivore currently listed International Union Conservation Nature (IUCN; high-quality chromosome-level assembly used, along resequencing demonstrate declines effective size million uncover evidence runs homozygosity caused inbreeding. another Yan investigate intraspecific divergence hot-spring snake endemic Qinghai–Tibet Plateau near IUCN. infer divergence, reconstruct history find genes under selection local adaptation. By combining able document assess differentiation lineages system. Being thoroughly catalogue critically answering fundamental questions biology, wild likely respond when confronted challenging novel environments Yeaman 2016), whether why adaptive repeatedly makes modules Jones number answer questions. Xie mangroves cope unique environment: interface land sea. combination mangrove closely related inland contrast mangroves, whole duplications preceded colonization habitats, do detect polyploidization. Rather, attribute expansion. Additionally, lack parallelism gene family consistent intertidal environment Evidence repeated functional found, Wang, (2023). relied tropical poplar, obtained reads. Comparisons five poplar provided convergent environments. Hotaling provide exciting fast-tracking Antarctic eelpout, representative Zoarcidae ray-finned fish genome-sequenced. turn allowed haemoglobin antifreeze which, strong candidates cold water adaptation, arranged duplicated tandem arrays (Hotaling species-specific waters Southern Ocean. A series section illustrate architecture functionally traits. Nacif conduct comprehensive investigation sex-determining region Midas cichlid fish. forward-genetics, Bionano optical mapping, narrow down sex determination system ~100-kb Y harbours partial but complete coding gene: duplicate anti-Mullerian receptor 2 (amhr2Y). Because amhr2Y shown act locus teleost fishes (Nacif 2023), represents candidate probably parallelism. At extreme scale duplication, Zhu biennial alpine sustained rounds duplication. system, detail multi-omics dimorphic cleistogamy. Known evolved across plants, cleistogamy manifested production open (available cross-pollination) closed (self-fertilizing) flowers, thought reproductive assurance (Zhu An revealed consists 70% sequences. integrating experiments probed metabolites, metabolites differentiate flowers. trait, least partially attributed duplication events Finally, Cohen genetics pesticide resistance Colorado potato beetle. trio-binning approach haploid considerably improved contiguity, compared existing pest pangenome all population-scale then exposure. abundant, accounting ~30% highlighting adaptive. Such process time, underline designed variants, additionally exploit layers sequencing. second article Shipilina consider illustrate, simulated empirical haplotype technology, selective sweeps. graph reconstruction, addition mutation, take account ancestry recombination. information, computationally numbers could vastly improve resolution polymorphisms, identifying multiple sweeps occur (Shipilina proceeds diverge, isolation gradually develop. Genomic pairs, particular those pairs diverged, represent dissecting speciation barrier loci (Ravinet 2017). Several papers continuum suppression undertake detailed pair whitefish allopatry starting around 60,000 came back contact roughly 12,000 (Mérot combined Dwarf Normal genotype Whitefish repeat-rich, 60% corresponding interspersed repeats. proportion enriched classes bursts generating early even incipient speciation, Wersebe freshwater crustacean Daphnia. present scan pulex–pulicaria separated 150,000 (Wersebe D. pulicaria complemented hybrids, Contrary expectations, windows restricted genic Zhang in-depth variation isolation, so far implemented natural hybrid zone established Lycaeides butterflies 2.4 secondary 14,000 (Zhang Structural genotyped parental individuals validated cline 562 zone. deletions exhibit largest departures neutral pointing gene-rich inversions, facilitating analysis epigenomes, genomes, harnessed interactions. broadly relevant contexts pathogen control biological communities assembled. paper, van Steenbrugge virulence cyst nematodes, destructive pathogens worldwide. nematodes outgroup. families effectors, proteins secreted manipulate physiology virulence. illuminating diversification effector facilitate nematodes. should subsequent matching host genotypes. Handy composition gut bacterial carpenter bee incipiently social. case, ability full-length 16S amplicons classify significantly resolution, reveal interactions would cryptic. distinct microbiome components might structured processes, geographical microbial transmission, investigation. collection providing needed basic applied topics discipline, being groups organisms organization. collectively hard now properly traversed play critical diversification. context, scales exceed individuals. obtaining essential step, gain replicate assemblies, pangenomes Issue. there improvements. explicitly improving computational efficiency methods, long-range efficiently samples. road map next-generation observational abilities, areas position, cusp accelerated progress technology. With toolkits ecologists, increasingly push limits ever sustains surrounds us. like acknowledge who contributed reviewers evaluated manuscripts, editors Emily Warschefsky Ben Sibbett help throughout. Not applicable.

Language: Английский

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Cold-Driven Hemoglobin Evolution in Antarctic Notothenioid Fishes Prior to Hemoglobin Gene Loss in White-Blooded Icefishes

Molecular Biology and Evolution, Journal Year: 2023, Volume and Issue: 40(11)

Published: Oct. 25, 2023

Expression of multiple hemoglobin isoforms with differing physiochemical properties likely helps species adapt to different environmental and physiological conditions. Antarctic notothenioid fishes inhabit the icy Southern Ocean display fewer isoforms, each less affinity for oxygen than temperate relatives. Reduced multiplicity was proposed result from relaxed selective pressure in cold, thermally stable, highly oxygenated waters. These conditions also permitted survival diversification white-blooded icefishes, only vertebrates living without hemoglobin. To understand evolution during adaptation freezing water, we analyzed genes 36 genome assemblies. Results showed that frigid shaped gene by episodic diversifying selection concomitant cold pervasive notothenioids compared relatives, a continuing Analysis expression adult hematopoietic organs various further revealed switch underlying reduction fish, leading single isoform plunderfishes dragonfishes, sister groups icefishes. The predicted high fish embryos based on transcriptomic data, however, raises questions about molecular bases implications diverse adults. This analysis supports hypothesis last common icefish ancestor vulnerable detrimental mutations affecting ancestral expressed alpha- beta-globin pair, potentially predisposing their subsequent loss.

Language: Английский

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Comparative Evolutionary Genomics in Insects

Methods in molecular biology, Journal Year: 2024, Volume and Issue: unknown, P. 473 - 514

Published: Jan. 1, 2024

Language: Английский

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Editorial 2024

Molecular Ecology, Journal Year: 2023, Volume and Issue: 33(1)

Published: Dec. 25, 2023

Molecular Ecology (MEC) continues to be one of the largest and most influential journals in fields ecology evolution. In 2022, a total 434 citable items were published journal, ranking third out 53 Clarivate's list Evolutionary Biology sixth 171 journals. A similar pattern is seen for citations, where MEC was cited 40,823 times (third fourth Ecology). Additional metrics include journal impact factor (4.9; eighth Biology) EigenFactor (0.030, fifth Biology). The latter metric measures number articles from past five years have been focal year. Google Scholar's h5-index, which h-index over years, offers longer term measure influence. has an h5-index 72, ranks among Lastly, downloads demonstrate wide interest research MEC, reaching close 1.9 million 2021 2022. first evolution require that data supporting results papers archived appropriate public archive (Rieseberg et al., 2010). Over we expanded policy code, programming scripts, software, as well detailed metadata. Earlier this year, members Resources (MER) Editorial Board (along with editors other journals) contributed article Evolution established minimum standards code (Jenkins 2023). While recommendations largely reinforce what are already doing, provides description best practices archiving data, metadata, such analyses given study can fully replicated. We will linking recommendation our author guidelines. also transitioning requiring made available reviewers during peer review. 2020, editorial indicate support Nagoya Protocol principle benefit sharing, educate authors readers about their responsibilities under (Marden 2020). encourages disclose benefits generated by Protocol. This followed encouraged use Biocultural, Traditional Knowledge, Cultural Institution Notices (Liggins 2021). Such intended raise visibility Indigenous communities within systems, encourage collaboration communities, provide platform them develop methodologies permissions biodiversity-related on indigenous land. To continue momentum, 'Indigenous perspectives/methodologies' added area aims scope, perspectives' 'traditional ecological knowledge' keywords MEC/MER websites. Authors now select perspectives methodologies' manuscript subject when submitting article, submitted using new assigned who expertise experience space. Like publishers, Wiley developed policies artificial intelligence (AI) tools ChatGPT large language models (https://authorservices.wiley.com/ethics-guidelines/index.html). Because AIs lack legal standing cannot held accountable or design, does not permit listed articles. However, if AI used development, requires contributions described Methods Acknowledgements. Final decisions whether usage permissible board. case Board, believe represents potentially valuable editing tool improve readability manuscripts, reducing barriers publication researchers, especially those speak English second language. improving spelling, grammar, clarity, ask acknowledge development required policy. 2023, maintained robust social media presence, building upon success previous years. molecology X account (formerly Twitter) boasted following 7400 followers, average more than 49 tweets posted per month. Monthly impressions reached 28,500, slightly less likely due changes landscape year concerns academics these changes. enhance outreach, collaborated team (WileyEcolEvol) strategically broaden audience. monitor community trends explore possibilities better serve molecular community, providing crucial direct source information scientific work MER. conjunction X, continued commitment in-house through Spotlight blog 2023. With 142 posts since 2019, featured interviews highlighted papers, amassing 23,000 visitors 37,000 views. adopted way interviewing tailored questions dynamism promote deeper engagement authors. should help lay broader understand conducted ecologists its implications. It fundamental mission MER hands-on training duties outstanding early career researchers. PhD postdoctoral recognized Harry Smith prize, invited join Junior (JEB). ensure JEB useful experiences members, process implementing three-year stepped programme designed offer exposure range tasks. Our together execute running platforms (Twitter Blog) creating content increasing journal's visibility. addition, second-year gain manuscripts guidance mentor. final tenure, attracting research, organizing special issues review Together, enthusiasm, forms invaluable asset Prize awarded annually 'an scientist significant ecology', selected independent award committee. Dr. Uma Ramakrishnan, Professor at National Centre Biological Sciences, Bangalore, India. Ramakrishnan known her studies tiger mammals, 'poster children' India's natural resources. Her included census estimates combined camera traps genetic surveys, historical inferences museum specimens, demonstrations gene flow impacting genomic variation inbreeding depression. Ramakrishnan's led conservation applications, example evidence Supreme Court ruling wildlife corridors must certain highway expansions. science communication service exemplary, she important role model scientists around world. recognizes paper graduate students scholars no 5 fellowship experience. prize named after FRS, founded served both Chief Managing Editor critical He until 2008, went his early-career scholars. 2023 Antonino Malacrinò 'Host species identity shapes diversity structure insect microbiota' (Malacrinò, 2022). His work, 'Invited Reviews Syntheses' presents leveraging powerful open insights into field microbiome research. committee, up excellent Alexander Blumenfeld colleagues titled, 'Consistent signatures urban adaptation native, invader ant Tapinoma sessile paper', runner-up Prize. al. (2022) genetic, behavioural, chemical populations sessile. They documented multiple transitions organization response urbanization, restricted between populations, adding growing human-altered habitats profoundly influence species. saw loss two distinguished longest-serving editors, Robert (Bob) Wayne Louis Bernatchez. Both joined 1997 became senior 1999. Bob helped Aims Scope authored sentence, 'Molecular publishes utilize techniques address consequential ecology, evolution, behaviour, conservation', primary guide decisions. When passed away December he editor (26 years!). addition regular 15 (2004–2018), recruiting dozen reviews topics covered full disciplinary microbes plants animals population genetics interactions environmental genomics. (119!) any author. recognition many 2016 lieu society ecologists, intellectual home community. includes (see above), focuses Resources, News Views perspectives, issues, reviews, opinion so forth. Ecologist (http://www.molecularecologist.com/), covers news reported venues beyond Ecology, eye interests people necessarily experts field. Please let us know you would like contribute perspective, review, opinion, organize issue. annual highlight advances (below). Every impactful chosen board perspectives. Among these, few standout From Cover pieces. nine pieces showcase how applications analytical advanced understanding novel across organizational scales, time. Three Gaertner (2023), Shi Bucholz examine adaptation, flow, speciation biological scales—from cellular levels. Understanding evolutionary forces shape architecture underpinning adaptive elucidating evolve changing environments. concept, (2023) analyse genome-wide broadcast-spawning nest-spawning riverine fish species, expected differ levels flow. find that, general, higher associated tighter clustering alleles, protects recombination. perspective piece, Schaal explain 'provides empirical foundational theoretical simulation studies' helps reveal complex nature evolves different organisms. How level? question investigating differentiation 'housekeeping functions' closely related hares. fibroblasts obtained wild hares regulation differences mountain brown hares, interfertile but ecologically distinct. show expression patterns hare affect processes including cell growth, respiration, metabolism, clear impacts cellular-level functions. Moreover, Palsson Steele note accompanying 'This suggests immortalized utility divergence metabolic traits basis organismal physiology'. Several hypotheses proposed relationships abundance diversity. test three hypotheses, conducting extensive surveys sequencing freshwater mussel southeastern USA. more-individuals hypothesis, posits areas exhibit greater richness, relationship abundance. they do positive correlations within-species Petersen Wares conclude 'their among-species variability … pushing forward frontier community-wide assessment applications'. biology long captivated dynamics coevolutionary relationships, Epstein Hague Leclaire nuanced comprehensive processes. well-studied legume-rhizobia symbiosis, GWAS approaches evaluate selection plant microbial genomes. suggested symbiotic may involve fitness conflicts partners characterized balancing symbiosis genes, little hypothesis. Instead, show, legume rhizobial partners, involved primarily stabilizing selection. As Carlson Frederickson write indicates 'that there ongoing conflict legumes rhizobia host symbiont genomes'. Antagonistic lead coevolution, often arms race organisms involved. cases coevolution cascading effects trophic fascinating system toxic Pacific newts predators, garter snakes, geographic mosaic escalation, increase newt toxicity matched increased toxin resistance retention snakes. Using combination experimental observational identify clines snakes hotspots bright coloration, serving aposematic signal own predators. Thompson notes paired 'the ripple throughout networks interacting species'. Whether host-microbiome classified remains topic some debate. Nevertheless, recent revealing far-reaching microbiome, extend health reproductive outcomes. microbiome's black-legged kittiwake, seabird specific compositions portions female bird's body (neck flank feathers, choanae, outer bill, cloaca) success, same result male birds. Turjeman correlative fitness—a deserves additional study. Research documenting Anthropocene shaping biodiversity increasingly focusing implications future affected ecosystems inhabit. Beichman Crossley Kocher approach vastly systems angles, demonstrating anthropogenic activity context-specific. declines California sea otter nearly hunted extinction 18th–19th centuries. Kreiner Booker 'combine spatiotemporal set simulations only quantify demographic change exploitation, consequences collapse persistence'. decline forward-in-time modelling could negative recovery populations. buffered historically low effective prior fur trade. human activities, trade, had obvious diversity, others apparent. ways land change, specifically agriculture, aquatic Utilizing existing 700 croplands degraded sharpest observed 1950s. contrast, rebounds converted uses, even urbanization. Atmore Buss highlights power publicly answer regarding current biospheric emergency'. Theories disease prevalence importance Anthropocene, difficult because life histories pathogens. 'dilution effect' theory, wherein pathogens controlled presence inefficient vectors ecosystem. combine DNA metabarcoding innovative tropical parasite Leishmania, mammalian reservoirs, sand fly vectors. decrease infection flies mammal high, dilution effect, density sandflies, leading overall effect infected vectors, which, Levi Massey point indicator Leishmania transmission risk'. Opinion present ideas viewpoints relevant ecology. These opinions speculative controversial discussion debate discipline. six Pegg describe efforts forecast risk cross-species transmission, received attention COVID-19 pandemic. make sugars, glycans, coat surface macromolecules accuracy assessment. another broadly paper, Čapková Frydrychová argues key assumptions telomere aging hold considered taxa, discrepancies resolved context strategies. Two focused utilized reversal days phylogeography genomics, report nuclear genome only. noted Blair unfortunate oversight organellar identification, addressing dispersal mechanisms limits. Blanchet put framework—based phylogenetically conserved candidate genes functional traits—for eco-evolutionary scales. longstanding questions. One maintenance history loci Arnqvist Rowe hypothesize frequency-dependent responsible polymorphism major epistatic piece tackles confusion inconsistent terms parallel convergent Cerca relation ancestral condition, taking place condition arising conditions. being done emerging entitled 'Ecological Inferences Long-Read Sequencing'. Dan Bock, Jianquan Liu, Polina Novikova, Loren Rieseberg editorial, compilation 19 'highlights utilizing long-read roles repetitive otherwise loci' (Bock issue diverse plants, animals, bacteria, viruses, share common themes: profiling epigenetic modifications (Nielsen 2023), novelty (Burley 2023; Ferguson Peona Wierzbicki genomics (Li, Yang, Yan (Cohen Hotaling Li, Wang, Nacif Shipilina Xie Zhu hybridization (Mérot Wersebe Zhang (Handy van Steenbrugge works variation, while traditionally study, substantial contribution speciation' Special Issue, Human-Associated Microbes, edited Tatiana Giraud, Jeanne Ropars, Eva Stukenbrock, Katherine Ryan Amato, Ricardo Rodriguez de la Vega. 21 focus various types domesticates, pathogens, host-associated microbiota, metagenomics, laboratory experiments. whole, main subjects: domesticated microorganisms thriving environments (Harrouard Silva von Gastrow fungal (Ali Louet Rogério Saubin Stalder Wang Zewdie metagenomics microbiomes (Bischofberger & Hall, Corsi Mac Alpine Moeller, Pedro Peimbert Alcaraz, Tessandier Yuan crops (Gao Richard Collectively Issue 'underline huge environment emergence spread provided mutualistic fungi bacteria' (Giraud Finally, Insights Ecological Processes via Community Metabarcoding 'papers high-throughput (HTS) classic particularly (amplicon) datasets complementary -omics and/or models/theory infer ecosystem processes' (Gillespie impressive collection 44 topics: assembly (Andujar 2022; Arjona Emerson Govender Guerrieri Ip, Chang, Oh, Kiemel Li Macheriotou Menéndez-Serra Nappi Noguerales Overcast Pino Van der Loos 2022), interaction (Ando Bell Dürrbaum Encinas-Viso Ficetola Taberlet, Graham Tun, Lowe Lu Lue Pitteloud Srivathsan Tommasi cross-scale (Brinker Câmara dos Reis Hu Kivistik Manthey Merges Michel Molina Navine Pereira Perez-Lamarque Morlon, Rolshausen invasive species/homogenization (Andrés Hampel Kennedy Rosemary Gillespie, Holly Bik, Michael Hickerson, Henrik Krehenwinkel, Isaac Overcast, Andrew Rominger writes taken together, gained approaches, dynamics' hope discussion, exceptional journal. wish thank readers, authors, reviewers, your support, welcome suggestions individuals reviewing contains reviewed 1 October 2022 30 September Aanen, Duur Abad-Recio, Ion Abbott, Jessica Abreu, Clare Adams, Nicole Rachelle Affenzeller, Matthias Afiq-Rosli, Lutfi Aguilar, Andres Aguillon, Stepfanie Aguirre, Windsor Ahi, Ehsan Pashay Ahrens, Collin Aivelo, Tuomas Akita, Tetsuya Albach, Dirk Alberoni, Daniele Aldred, Nick Allen, Natalie Allio, Rémi Almer, Jasmin Alonso, Conchita Alverson, Amos, William Amsler, Charles An, Shiheng Anastasiad

Language: Английский

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Genomic architecture and sex chromosome systems of commercially important fish species in Asia – Current status, knowledge gaps and future prospects

Reviews in Aquaculture, Journal Year: 2024, Volume and Issue: 16(4), P. 1918 - 1946

Published: June 8, 2024

Abstract Aquaculture is one of the fastest growing agro‐food industries in world and Asia dominates world's fish production (70% total) with a high potential to ensure global food security. The leading aquaculture species show sexual dimorphism for traits such as growth, age at maturity etc. which sex outperforms other, increasing need controlling sex‐ratio farming system. Despite huge contribution Asian production, facing lot challenges, example, maintaining genetic purity balancing culture Many these difficulties arise due lack deep understanding genetics, or duplicated genome cultured species, unavailability high‐quality reference genomes information on determination mechanisms (crucial monosex establishing appropriate breeding programme). This review has described existing knowledge architecture four commercially important groups (carps, tilapias, catfishes snakeheads). We also have outlined possible strategies identifying sex‐determining gene/s using modern sequencing computational technologies. Finally, we highlighted challenges future prospects aquaculture. anticipate that developments technologies will help address biological complexities exist commercial be value growth industry Asia.

Language: Английский

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