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Article ; Online: Y-Linked Copy Number Polymorphism of Target of Rapamycin Is Associated with Sexual Size Dimorphism in Seed Beetles.

Kaufmann, Philipp / Wiberg, R Axel W / Papachristos, Konstantinos / Scofield, Douglas G / Tellgren-Roth, Christian / Immonen, Elina

Molecular biology and evolution

2023 Volume 40, Issue 8

Abstract: The Y chromosome is theorized to facilitate evolution of sexual dimorphism by accumulating sexually antagonistic loci, but empirical support is scarce. Due to the lack of recombination, Y chromosomes are prone to degenerative processes, which poses a ... ...

Abstract	The Y chromosome is theorized to facilitate evolution of sexual dimorphism by accumulating sexually antagonistic loci, but empirical support is scarce. Due to the lack of recombination, Y chromosomes are prone to degenerative processes, which poses a constraint on their adaptive potential. Yet, in the seed beetle, Callosobruchus maculatus segregating Y linked variation affects male body size and thereby sexual size dimorphism (SSD). Here, we assemble C. maculatus sex chromosome sequences and identify molecular differences associated with Y-linked SSD variation. The assembled Y chromosome is largely euchromatic and contains over 400 genes, many of which are ampliconic with a mixed autosomal and X chromosome ancestry. Functional annotation suggests that the Y chromosome plays important roles in males beyond primary reproductive functions. Crucially, we find that, besides an autosomal copy of the gene target of rapamycin (TOR), males carry an additional TOR copy on the Y chromosome. TOR is a conserved regulator of growth across taxa, and our results suggest that a Y-linked TOR provides a male specific opportunity to alter body size. A comparison of Y haplotypes associated with male size difference uncovers a copy number variation for TOR, where the haplotype associated with decreased male size, and thereby increased sexual dimorphism, has two additional TOR copies. This suggests that sexual conflict over growth has been mitigated by autosome to Y translocation of TOR followed by gene duplications. Our results reveal that despite of suppressed recombination, the Y chromosome can harbor adaptive potential as a male-limited supergene.
MeSH term(s)	Male ; Animals ; DNA Copy Number Variations ; Coleoptera/genetics ; Sex Characteristics ; Y Chromosome ; Seeds
Language	English
Publishing date	2023-07-19
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	998579-7
ISSN	1537-1719 ; 0737-4038
ISSN (online)	1537-1719
ISSN	0737-4038
DOI	10.1093/molbev/msad167
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Article ; Online: Calling Structural Variants with Confidence from Short-Read Data in Wild Bird Populations.

David, Gabriel / Bertolotti, Alicia / Layer, Ryan / Scofield, Douglas / Hayward, Alexander / Baril, Tobias / Burnett, Hamish A / Gudmunds, Erik / Jensen, Henrik / Husby, Arild

Genome biology and evolution

2024 Volume 16, Issue 4

Abstract: ... strategy (e.g. applied by a single curator) can reduce the proportion of putative false positives by up ...

Abstract	Comprehensive characterization of structural variation in natural populations has only become feasible in the last decade. To investigate the population genomic nature of structural variation, reproducible and high-confidence structural variation callsets are first required. We created a population-scale reference of the genome-wide landscape of structural variation across 33 Nordic house sparrows (Passer domesticus). To produce a consensus callset across all samples using short-read data, we compare heuristic-based quality filtering and visual curation (Samplot/PlotCritic and Samplot-ML) approaches. We demonstrate that curation of structural variants is important for reducing putative false positives and that the time invested in this step outweighs the potential costs of analyzing short-read-discovered structural variation data sets that include many potential false positives. We find that even a lenient manual curation strategy (e.g. applied by a single curator) can reduce the proportion of putative false positives by up to 80%, thus enriching the proportion of high-confidence variants. Crucially, in applying a lenient manual curation strategy with a single curator, nearly all (>99%) variants rejected as putative false positives were also classified as such by a more stringent curation strategy using three additional curators. Furthermore, variants rejected by manual curation failed to reflect the expected population structure from SNPs, whereas variants passing curation did. Combining heuristic-based quality filtering with rapid manual curation of structural variants in short-read data can therefore become a time- and cost-effective first step for functional and population genomic studies requiring high-confidence structural variation callsets.
MeSH term(s)	Genomics ; Genome ; Metagenomics ; Polymorphism, Single Nucleotide
Language	English
Publishing date	2024-03-15
Publishing country	England
Document type	Journal Article
ZDB-ID	2495328-3
ISSN	1759-6653 ; 1759-6653
ISSN (online)	1759-6653
ISSN	1759-6653
DOI	10.1093/gbe/evae049
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Article ; Online: A chromosome-level assembly of the seed beetle Callosobruchus maculatus genome with annotation of its repetitive elements.

Arnqvist, Göran / Westerberg, Ivar / Galbraith, James / Sayadi, Ahmed / Scofield, Douglas G / Olsen, Remi-André / Immonen, Elina / Bonath, Franziska / Ewels, Philip / Suh, Alexander

G3 (Bethesda, Md.)

2023 Volume 14, Issue 2

Abstract: Callosobruchus maculatus is a major agricultural pest of legume crops worldwide and an established model system in ecology and evolution. Yet, current molecular biological resources for this species are limited. Here, we employ Hi-C sequencing to ... ...

Abstract	Callosobruchus maculatus is a major agricultural pest of legume crops worldwide and an established model system in ecology and evolution. Yet, current molecular biological resources for this species are limited. Here, we employ Hi-C sequencing to generate a greatly improved genome assembly and we annotate its repetitive elements in a dedicated in-depth effort where we manually curate and classify the most abundant unclassified repeat subfamilies. We present a scaffolded chromosome-level assembly, which is 1.01 Gb in total length with 86% being contained within the 9 autosomes and the X chromosome. Repetitive sequences accounted for 70% of the total assembly. DNA transposons covered 18% of the genome, with the most abundant superfamily being Tc1-Mariner (9.75% of the genome). This new chromosome-level genome assembly of C. maculatus will enable future genetic and evolutionary studies not only of this important species but of beetles more generally.
MeSH term(s)	Animals ; Coleoptera/genetics ; Genome ; Repetitive Sequences, Nucleic Acid ; X Chromosome ; DNA Transposable Elements/genetics ; Phylogeny
Chemical Substances	DNA Transposable Elements
Language	English
Publishing date	2023-12-05
Publishing country	England
Document type	Journal Article
ZDB-ID	2629978-1
ISSN	2160-1836 ; 2160-1836
ISSN (online)	2160-1836
ISSN	2160-1836
DOI	10.1093/g3journal/jkad266
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Article ; Online: (with research data) RPASE: Individual-based allele-specific expression detection without prior knowledge of haplotype phase.

Wang, Mi / Uebbing, Severin / Pawitan, Yudi / Scofield, Douglas G

Molecular ecology resources

2018 Volume 18, Issue 6, Page(s) 1247–1262

Abstract: Variation in gene expression is believed to make a significant contribution to phenotypic diversity and divergence. The analysis of allele-specific expression (ASE) can reveal important insights into gene expression regulation. We developed a novel ... ...

Abstract	Variation in gene expression is believed to make a significant contribution to phenotypic diversity and divergence. The analysis of allele-specific expression (ASE) can reveal important insights into gene expression regulation. We developed a novel method called RPASE (Read-backed Phasing-based ASE detection) to test for genes that show ASE. With mapped RNA-seq data from a single individual and a list of SNPs from the same individual as the only input, RPASE is capable of aggregating information across multiple dependent SNPs and producing individual-based gene-level tests for ASE. RPASE performs well in simulations and comparisons. We applied RPASE to multiple bird species and found a potentially rich landscape of ASE.
MeSH term(s)	Alleles ; Animals ; Biological Variation, Population ; Birds ; Gene Expression Profiling/methods ; Polymorphism, Single Nucleotide ; Sequence Analysis, RNA
Language	English
Publishing date	2018-06-20
Publishing country	England
Document type	Journal Article
ZDB-ID	2406833-0
ISSN	1755-0998 ; 1755-098X
ISSN (online)	1755-0998
ISSN	1755-098X
DOI	10.1111/1755-0998.12909
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Article ; Online: Tracking the NGS revolution: managing life science research on shared high-performance computing clusters.

Dahlö, Martin / Scofield, Douglas G / Schaal, Wesley / Spjuth, Ola

GigaScience

2018 Volume 7, Issue 5

Abstract: Background: Next-generation sequencing (NGS) has transformed the life sciences, and many research groups are newly dependent upon computer clusters to store and analyze large datasets. This creates challenges for e-infrastructures accustomed to hosting ... ...

Abstract	Background: Next-generation sequencing (NGS) has transformed the life sciences, and many research groups are newly dependent upon computer clusters to store and analyze large datasets. This creates challenges for e-infrastructures accustomed to hosting computationally mature research in other sciences. Using data gathered from our own clusters at UPPMAX computing center at Uppsala University, Sweden, where core hour usage of ∼800 NGS and ∼200 non-NGS projects is now similar, we compare and contrast the growth, administrative burden, and cluster usage of NGS projects with projects from other sciences. Results: The number of NGS projects has grown rapidly since 2010, with growth driven by entry of new research groups. Storage used by NGS projects has grown more rapidly since 2013 and is now limited by disk capacity. NGS users submit nearly twice as many support tickets per user, and 11 more tools are installed each month for NGS projects than for non-NGS projects. We developed usage and efficiency metrics and show that computing jobs for NGS projects use more RAM than non-NGS projects, are more variable in core usage, and rarely span multiple nodes. NGS jobs use booked resources less efficiently for a variety of reasons. Active monitoring can improve this somewhat. Conclusions: Hosting NGS projects imposes a large administrative burden at UPPMAX due to large numbers of inexperienced users and diverse and rapidly evolving research areas. We provide a set of recommendations for e-infrastructures that host NGS research projects. We provide anonymized versions of our storage, job, and efficiency databases.
MeSH term(s)	Biological Science Disciplines/methods ; Computational Biology/methods ; High-Throughput Nucleotide Sequencing/methods ; Research ; Software
Language	English
Publishing date	2018-04-16
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2708999-X
ISSN	2047-217X ; 2047-217X
ISSN (online)	2047-217X
ISSN	2047-217X
DOI	10.1093/gigascience/giy028
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Article ; Research data: (with research data) Medial pith cells per meter in twigs as a proxy for mitotic growth rate ({Phi}/m) in the apical meristem.

Scofield, Douglas G

American journal of botany

2006 Volume 93, Issue 12, Page(s) 1740–1747

Abstract: The Φ model for plant mating system evolution proposes a causal link between Φ, the number of mitoses that occur within a plant's lifetime from zygote to gamete production, and constraints on the evolution of inbreeding depression and thereby on the ... ...

Abstract	The Φ model for plant mating system evolution proposes a causal link between Φ, the number of mitoses that occur within a plant's lifetime from zygote to gamete production, and constraints on the evolution of inbreeding depression and thereby on the evolution of plant mating systems. Through its use of plant stature, the Φ model emphasizes the important role of morphology in creating developmental and genetic constraints on plant evolution. However, the estimation of Φ itself is likely to be extraordinarily complex. Here I describe a protocol for estimating Φ per meter linear growth by an apical meristem (Φ/m) using medial pith cells from mature internodes of twigs. While such cells are produced by the apical meristem, during internode elongation, these pith cells also undergo further mitoses, and thus their measurement can only approximate a "true" Φ/m via the application of a multiplier (the adjustment ratio) that partially corrects for the occurrence of cell divisions and cell growth beyond the apical meristem. I applied this method to Delonix regia (Caesalpiniaceae) and derived several adjustment ratios from the literature. Because variation in Φ/m can have profound evolutionary implications, I also examined interspecific and intraspecific variation as well as within-individual variation in Φ/m. Conifers apparently have lower Φ/m than do angiosperms, while 20% of the total variance in Φ/m for D. regia was found among individual trees, with the remainder found within trees. Given the large differences in stature between "high-Φ" plants such as trees and "low-Φ" plants such as herbs, these results support the idea that the total per-generation mutation rate for high-Φ plants is likely to be many times higher than that for low-Φ plants.
Language	English
Publishing date	2006-12
Publishing country	United States
Document type	Journal Article
ZDB-ID	2935-x
ISSN	1537-2197 ; 0002-9122 ; 0002-9122
ISSN (online)	1537-2197
ISSN	0002-9122
DOI	10.3732/ajb.93.12.1740
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Article: Bacteria colonising

Burdon, Rosalie C F / Junker, Robert R / Scofield, Douglas G / Parachnowitsch, Amy L

Chemoecology

2018 Volume 28, Issue 1, Page(s) 11–19

Abstract: Bacteria on floral tissue can have negative effects by consuming resources and affecting nectar quality, which subsequently could reduce pollinator visitation and plant fitness. Plants however can employ chemical defences to reduce bacteria density. In ... ...

Abstract	Bacteria on floral tissue can have negative effects by consuming resources and affecting nectar quality, which subsequently could reduce pollinator visitation and plant fitness. Plants however can employ chemical defences to reduce bacteria density. In North American, bee-pollinated
Language	English
Publishing date	2018-03-01
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	1458504-2
ISSN	1423-0445 ; 0937-7409
ISSN (online)	1423-0445
ISSN	0937-7409
DOI	10.1007/s00049-018-0252-x
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Article ; Online: LTR Retrotransposons Show Low Levels of Unequal Recombination and High Rates of Intraelement Gene Conversion in Large Plant Genomes.

Cossu, Rosa Maria / Casola, Claudio / Giacomello, Stefania / Vidalis, Amaryllis / Scofield, Douglas G / Zuccolo, Andrea

Genome biology and evolution

2018 Volume 9, Issue 12, Page(s) 3449–3462

Abstract: The accumulation and removal of transposable elements (TEs) is a major driver of genome size evolution in eukaryotes. In plants, long terminal repeat (LTR) retrotransposons (LTR-RTs) represent the majority of TEs and form most of the nuclear DNA in large ...

Abstract	The accumulation and removal of transposable elements (TEs) is a major driver of genome size evolution in eukaryotes. In plants, long terminal repeat (LTR) retrotransposons (LTR-RTs) represent the majority of TEs and form most of the nuclear DNA in large genomes. Unequal recombination (UR) between LTRs leads to removal of intervening sequence and formation of solo-LTRs. UR is a major mechanism of LTR-RT removal in many angiosperms, but our understanding of LTR-RT-associated recombination within the large, LTR-RT-rich genomes of conifers is quite limited. We employ a novel read-based methodology to estimate the relative rates of LTR-RT-associated UR within the genomes of four conifer and seven angiosperm species. We found the lowest rates of UR in the largest genomes studied, conifers and the angiosperm maize. Recombination may also resolve as gene conversion, which does not remove sequence, so we analyzed LTR-RT-associated gene conversion events (GCEs) in Norway spruce and six angiosperms. Opposite the trend for UR, we found the highest rates of GCEs in Norway spruce and maize. Unlike previous work in angiosperms, we found no evidence that rates of UR correlate with retroelement structural features in the conifers, suggesting that another process is suppressing UR in these species. Recent results from diverse eukaryotes indicate that heterochromatin affects the resolution of recombination, by favoring gene conversion over crossing-over, similar to our observation of opposed rates of UR and GCEs. Control of LTR-RT proliferation via formation of heterochromatin would be a likely step toward large genomes in eukaryotes carrying high LTR-RT content.
MeSH term(s)	Computational Biology ; Evolution, Molecular ; Gene Conversion ; Genome Size ; Magnoliopsida/genetics ; Picea/genetics ; Recombination, Genetic ; Retroelements ; Terminal Repeat Sequences ; Zea mays/genetics
Chemical Substances	Retroelements
Language	English
Publishing date	2018-01-15
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	1759-6653
ISSN (online)	1759-6653
DOI	10.1093/gbe/evx260
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Article ; Online: Natural Selection and Recombination Rate Variation Shape Nucleotide Polymorphism Across the Genomes of Three Related Populus Species.

Wang, Jing / Street, Nathaniel R / Scofield, Douglas G / Ingvarsson, Pär K

Genetics

2016 Volume 202, Issue 3, Page(s) 1185–1200

Abstract: A central aim of evolutionary genomics is to identify the relative roles that various evolutionary forces have played in generating and shaping genetic variation within and among species. Here we use whole-genome resequencing data to characterize and ... ...

Abstract	A central aim of evolutionary genomics is to identify the relative roles that various evolutionary forces have played in generating and shaping genetic variation within and among species. Here we use whole-genome resequencing data to characterize and compare genome-wide patterns of nucleotide polymorphism, site frequency spectrum, and population-scaled recombination rates in three species of Populus: Populus tremula, P. tremuloides, and P. trichocarpa. We find that P. tremuloides has the highest level of genome-wide variation, skewed allele frequencies, and population-scaled recombination rates, whereas P. trichocarpa harbors the lowest. Our findings highlight multiple lines of evidence suggesting that natural selection, due to both purifying and positive selection, has widely shaped patterns of nucleotide polymorphism at linked neutral sites in all three species. Differences in effective population sizes and rates of recombination largely explain the disparate magnitudes and signatures of linked selection that we observe among species. The present work provides the first phylogenetic comparative study on a genome-wide scale in forest trees. This information will also improve our ability to understand how various evolutionary forces have interacted to influence genome evolution among related species.
MeSH term(s)	Amino Acid Substitution ; DNA, Plant/genetics ; Evolution, Molecular ; Gene Frequency ; Genetic Fitness ; Genetics, Population ; Genome, Plant ; Genotype ; Linkage Disequilibrium ; Phylogeny ; Polymorphism, Single Nucleotide ; Populus/classification ; Populus/genetics ; Recombination, Genetic ; Selection, Genetic ; Sequence Analysis, DNA
Chemical Substances	DNA, Plant
Language	English
Publishing date	2016-03
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2167-2
ISSN	1943-2631 ; 0016-6731
ISSN (online)	1943-2631
ISSN	0016-6731
DOI	10.1534/genetics.115.183152
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Article ; Online: Variation in Linked Selection and Recombination Drive Genomic Divergence during Allopatric Speciation of European and American Aspens.

Wang, Jing / Street, Nathaniel R / Scofield, Douglas G / Ingvarsson, Pär K

Molecular biology and evolution

2016 Volume 33, Issue 7, Page(s) 1754–1767

Abstract: Despite the global economic and ecological importance of forest trees, the genomic basis of differential adaptation and speciation in tree species is still poorly understood. Populus tremula and Populus tremuloides are two of the most widespread tree ... ...

Abstract	Despite the global economic and ecological importance of forest trees, the genomic basis of differential adaptation and speciation in tree species is still poorly understood. Populus tremula and Populus tremuloides are two of the most widespread tree species in the Northern Hemisphere. Using whole-genome re-sequencing data of 24 P. tremula and 22 P. tremuloides individuals, we find that the two species diverged ∼2.2-3.1 million years ago, coinciding with the severing of the Bering land bridge and the onset of dramatic climatic oscillations during the Pleistocene. Both species have experienced substantial population expansions following long-term declines after species divergence. We detect widespread and heterogeneous genomic differentiation between species, and in accordance with the expectation of allopatric speciation, coalescent simulations suggest that neutral evolutionary processes can account for most of the observed patterns of genetic differentiation. However, there is an excess of regions exhibiting extreme differentiation relative to those expected under demographic simulations, which is indicative of the action of natural selection. Overall genetic differentiation is negatively associated with recombination rate in both species, providing strong support for a role of linked selection in generating the heterogeneous genomic landscape of differentiation between species. Finally, we identify a number of candidate regions and genes that may have been subject to positive and/or balancing selection during the speciation process.
MeSH term(s)	DNA, Plant/genetics ; Europe ; Gene Flow ; Genetic Speciation ; Genetic Variation ; Genetics, Population ; Genome, Plant ; Linkage Disequilibrium ; North America ; Phylogeny ; Populus/genetics ; Recombination, Genetic ; Selection, Genetic ; Sequence Analysis, DNA
Chemical Substances	DNA, Plant
Language	English
Publishing date	2016-07
Publishing country	United States
Document type	Journal Article
ZDB-ID	998579-7
ISSN	1537-1719 ; 0737-4038
ISSN (online)	1537-1719
ISSN	0737-4038
DOI	10.1093/molbev/msw051
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