Unlocking the genome of perch – From genes to ecology and back again DOI Creative Commons
Anti Vasemägi, Mikhail Ozerov, Kristina Noreikienė

et al.

Ecology Of Freshwater Fish, Journal Year: 2023, Volume and Issue: 32(4), P. 677 - 702

Published: March 16, 2023

Abstract Eurasian perch Perca fluviatilis has been a popular model species for decades in the fields of aquatic ecology, community dynamics, behaviour, physiology and ecotoxicology. Yet, despite extensive research, progress integrating genomic perspective into existing ecological knowledge relatively modest. Meanwhile, emergence high‐throughput sequencing technologies completely changed methods genetic variation assessment conducting biodiversity evolutionary research. During last 5 years, three genome assemblies P. have generated, allowing substantial advancement our understanding interactions between processes at whole‐genome level. We review past progress, current status potential future impact resources tools research focusing on utility recent assemblies. Furthermore, we demonstrate power genome‐wide approaches newly developed outline cases where genomics contributed to new knowledge. explore how availability reference assembly enables efficient application various statistical tools, can provide novel insights resource polymorphism, host–parasite phenotypic changes associated with climate change harvesting‐induced evolution. In summary, call increased integration perch, as well other fish species, which is likely yield linking adaptation plasticity ecosystem functioning environmental change.

Language: Английский

Taking quantitative genomics into the wild DOI Creative Commons
Susan E. Johnston, Nancy Chen, Emily B. Josephs

et al.

Proceedings of the Royal Society B Biological Sciences, Journal Year: 2022, Volume and Issue: 289(1989)

Published: Dec. 21, 2022

We organized this special issue to highlight new work and review recent advances at the cutting edge of 'wild quantitative genomics'. In editorial, we will present some history wild genetic genomic studies, before discussing main themes in papers published highlighting future outlook dynamic field.

Language: Английский

Citations

15
Recent Advances in Genetics and Genomics of Snub-Nosed Monkeys (Rhinopithecus) and Their Implications for Phylogeny, Conservation, and Adaptation DOI Open Access
Weimin Kuang, Dietmar Zinner, Yuan Li

et al.

Genes, Journal Year: 2023, Volume and Issue: 14(5), P. 985 - 985

Published: April 27, 2023

The snub-nosed monkey genus

Language: Английский

Citations

8
The reference genome of an endangered Asteraceae, Deinandra increscens subsp. villosa, endemic to the Central Coast of California DOI Creative Commons
Susan L. McEvoy, Rachel S. Meyer, Kristen E. Hasenstab‐Lehman

et al.

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

Published: June 7, 2024

We present a reference genome for the federally endangered Gaviota tarplant, Deinandra increscens subsp. villosa (Madiinae, Asteraceae), an annual herb endemic to Central California coast. Generating PacBio HiFi, Oxford Nanopore Technologies, and Dovetail Omni-C data, we assembled haploid consensus of 1.67 Gb as 28.7 K scaffolds with scaffold N50 74.9 Mb. annotated repeat content in 74.8% genome. Long terminal repeats (LTRs) covered 44.0% Copia families predominant at 22.9% followed by Gypsy 14.2%. Both elements were common ancestral peaks LTRs, most abundant element was containing nested Copia/Angela sequence similarity, reflecting complex evolutionary history activity. Gene annotation produced 33,257 genes 68,942 transcripts, which 99% functionally annotated. BUSCO scores proteins 96.0% complete 77.6% single copy 18.4% duplicates. Whole duplication synonymous mutation rates tarplant sunflower (Helianthus annuus) shared that correspond last Asteraceae polyploidization event subsequent divergence from ancestor ∼27 MYA. Regions high-density tandem identified, pointing potentially important loci environmental adaptation this species.

Language: Английский

Citations

2
Reviving ghost alleles: Genetically admixed coyotes along the American Gulf Coast are critical for saving the endangered red wolf DOI Creative Commons
Bridgett M. vonHoldt, Joseph W. Hinton, Amy C. Shutt

et al.

Science Advances, Journal Year: 2022, Volume and Issue: 8(26)

Published: June 29, 2022

The last known red wolves were captured in southwestern Louisiana and eastern Texas 1980 to establish a captive breeding population. Before their extirpation, gene flow with coyotes resulted the persistence of endangered wolf genetic variation local coyote populations. We assessed genomic ancestry morphology Louisiana. detected that 38 62% genomes contained acquired past 30 years have an admixture profile similar canids before extirpation wolves. further documented positive correlation between weight. Our findings highlight importance hybrids admixed as reservoir species for innovative conservation efforts. Together, this work presents unprecedented system can leverage enrich recovery program species.

Language: Английский

Citations

10
Unlocking the genome of perch – From genes to ecology and back again DOI Creative Commons
Anti Vasemägi, Mikhail Ozerov, Kristina Noreikienė

et al.

Ecology Of Freshwater Fish, Journal Year: 2023, Volume and Issue: 32(4), P. 677 - 702

Published: March 16, 2023

Abstract Eurasian perch Perca fluviatilis has been a popular model species for decades in the fields of aquatic ecology, community dynamics, behaviour, physiology and ecotoxicology. Yet, despite extensive research, progress integrating genomic perspective into existing ecological knowledge relatively modest. Meanwhile, emergence high‐throughput sequencing technologies completely changed methods genetic variation assessment conducting biodiversity evolutionary research. During last 5 years, three genome assemblies P. have generated, allowing substantial advancement our understanding interactions between processes at whole‐genome level. We review past progress, current status potential future impact resources tools research focusing on utility recent assemblies. Furthermore, we demonstrate power genome‐wide approaches newly developed outline cases where genomics contributed to new knowledge. explore how availability reference assembly enables efficient application various statistical tools, can provide novel insights resource polymorphism, host–parasite phenotypic changes associated with climate change harvesting‐induced evolution. In summary, call increased integration perch, as well other fish species, which is likely yield linking adaptation plasticity ecosystem functioning environmental change.

Language: Английский

Citations

6