uu.seUppsala University Publications
Change search
Link to record
Permanent link

Direct link
BETA
Webster, Matthew ThomasORCID iD iconorcid.org/0000-0003-1141-2863
Alternative names
Publications (10 of 60) Show all publications
Wallberg, A., Bunikis, I., Vinnere, O., Mosbech, M.-B., Childers, A. K., Evans, J. D., . . . Webster, M. T. (2019). A hybrid de novo genome assembly of the honeybee, Apis mellifera, with chromosome-length scaffolds. BMC Genomics, 20, Article ID 275.
Open this publication in new window or tab >>A hybrid de novo genome assembly of the honeybee, Apis mellifera, with chromosome-length scaffolds
Show others...
2019 (English)In: BMC Genomics, ISSN 1471-2164, E-ISSN 1471-2164, Vol. 20, article id 275Article in journal (Refereed) Published
Abstract [en]

Background

The ability to generate long sequencing reads and access long-range linkage information is revolutionizing the quality and completeness of genome assemblies. Here we use a hybrid approach that combines data from four genome sequencing and mapping technologies to generate a new genome assembly of the honeybee Apis mellifera. We first generated contigs based on PacBio sequencing libraries, which were then merged with linked-read 10x Chromium data followed by scaffolding using a BioNano optical genome map and a Hi-C chromatin interaction map, complemented by a genetic linkage map.

Results

Each of the assembly steps reduced the number of gaps and incorporated a substantial amount of additional sequence into scaffolds. The new assembly (Amel_HAv3) is significantly more contiguous and complete than the previous one (Amel_4.5), based mainly on Sanger sequencing reads. N50 of contigs is 120-fold higher (5.381 Mbp compared to 0.053 Mbp) and we anchor >98% of the sequence to chromosomes. All of the 16 chromosomes are represented as single scaffolds with an average of three sequence gaps per chromosome. The improvements are largely due to the inclusion of repetitive sequence that was unplaced in previous assemblies. In particular, our assembly is highly contiguous across centromeres and telomeres and includes hundreds of AvaI and AluI repeats associated with these features.

Conclusions

The improved assembly will be of utility for refining gene models, studying genome function, mapping functional genetic variation, identification of structural variants, and comparative genomics.

Place, publisher, year, edition, pages
BMC, 2019
Keywords
Genome assembly, Single-molecule real-time (SMRT) sequencing, Linked-read sequencing, Optical mapping, Hi-C, Telomeres, Centromeres
National Category
Genetics
Identifiers
urn:nbn:se:uu:diva-382559 (URN)10.1186/s12864-019-5642-0 (DOI)000464118800001 ()30961563 (PubMedID)
Funder
Swedish Research Council Formas, 2013-722Swedish Research Council, 2014-5096
Note

Andreas Wallberg and Ignas Bunikis contributed equally to this work.

Available from: 2019-05-03 Created: 2019-05-03 Last updated: 2019-05-03Bibliographically approved
Christmas, M. J., Wallberg, A., Bunikis, I., Olsson, A., Wallerman, O. & Webster, M. T. (2019). Chromosomal inversions associated with environmental adaptation in honeybees. Molecular Ecology, 28(6), 1358-1374
Open this publication in new window or tab >>Chromosomal inversions associated with environmental adaptation in honeybees
Show others...
2019 (English)In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 28, no 6, p. 1358-1374Article in journal (Refereed) Published
Abstract [en]

Chromosomal inversions can facilitate local adaptation in the presence of gene flow by suppressing recombination between well-adapted native haplotypes and poorly adapted migrant haplotypes. East African mountain populations of the honeybee Apis mellifera are highly divergent from neighbouring lowland populations at two extended regions in the genome, despite high similarity in the rest of the genome, suggesting that these genomic regions harbour inversions governing local adaptation. Here, we utilize a new highly contiguous assembly of the honeybee genome to characterize these regions. Using whole-genome sequencing data from 55 highland and lowland bees, we find that the highland haplotypes at both regions are present at high frequencies in three independent highland populations but extremely rare elsewhere. The boundaries of both divergent regions are characterized by regions of high homology with each other positioned in opposite orientations and contain highly repetitive, long inverted repeats with homology to transposable elements. These regions are likely to represent inversion breakpoints that participate in nonallelic homologous recombination. Using long-read data, we confirm that the lowland samples are contiguous across breakpoint regions. We do not find evidence for disruption of functional sequence by these breakpoints, which suggests that the inversions are likely maintained due to their allelic content conferring local adaptation in highland environments. Finally, we identify a third divergent genomic region, which contains highly divergent segregating haplotypes that also may contain inversion variants under selection. The results add to a growing body of evidence indicating the importance of chromosomal inversions in local adaptation.

Place, publisher, year, edition, pages
WILEY, 2019
Keywords
chromosomal inversion, honeybee, local adaptation, long-read sequencing, nonallelic homologous recombination, structural variation
National Category
Genetics
Identifiers
urn:nbn:se:uu:diva-383207 (URN)10.1111/mec.14944 (DOI)000465219200012 ()30431193 (PubMedID)
Funder
Swedish Research Council Formas, 2013-722Swedish Research Council, 2014-5096
Available from: 2019-05-23 Created: 2019-05-23 Last updated: 2019-08-12Bibliographically approved
Lamichhaney, S., Han, F., Webster, M. T., Grant, B. R., Grant, P. R. & Andersson, L. (2019). Female-biased gene flow between two species of Darwin’s finches.
Open this publication in new window or tab >>Female-biased gene flow between two species of Darwin’s finches
Show others...
2019 (English)In: Article in journal (Refereed) Submitted
Abstract [en]

The mosaic nature of hybrid genomes is well recognized, but little is known of how they are shaped initially by patterns of breeding, selection, recombination and differential incompatibilities. On the small Galápagos island of Daphne Major two species of Darwin’s finches, Geospiza fortis and G. scandens, hybridize rarely and backcross bidirectionally with little or no loss of fitness under conditions of plentiful food. We used whole genome sequences to compare genomes from periods before and after successful interbreeding followed by backcrossing. We inferred extensive introgression from G. fortis to G. scandens on autosomes and mitochondria but not on the Z chromosome. The unique combination of long-term field observations and genomic data shows that the reduction of gene flow for Z-linked loci reflects female-biased gene flow, arising from hybrid male disadvantage in competition for territories and mates, rather than from genetic incompatibilities at Z-linked loci.

Keywords
Darwin's finches, introgression, hybridisation
National Category
Ecology Evolutionary Biology Genetics
Identifiers
urn:nbn:se:uu:diva-396776 (URN)
Available from: 2019-11-09 Created: 2019-11-09 Last updated: 2019-11-09
Kawakami, T., Wallberg, A., Olsson, A., Wintermantel, D., de Miranda, J. R., Allsopp, M., . . . Webster, M. T. (2019). Substantial Heritable Variation in Recombination Rate on Multiple Scales in Honeybees and Bumblebees. Genetics, 212(4), 1101-1119
Open this publication in new window or tab >>Substantial Heritable Variation in Recombination Rate on Multiple Scales in Honeybees and Bumblebees
Show others...
2019 (English)In: Genetics, ISSN 0016-6731, E-ISSN 1943-2631, Vol. 212, no 4, p. 1101-1119Article in journal (Refereed) Published
Abstract [en]

Meiotic recombination shuffles genetic variation and promotes correct segregation of chromosomes. Rates of recombination vary on several scales, both within genomes and between individuals, and this variation is affected by both genetic and environmental factors. Social insects have extremely high rates of recombination, although the evolutionary causes of this are not known. Here, we estimate rates of crossovers and gene conversions in 22 colonies of the honeybee, Apis mellifera, and 9 colonies of the bumblebee, Bombus terrestris, using direct sequencing of 299 haploid drone offspring. We confirm that both species have extremely elevated crossover rates, with higher rates measured in the highly eusocial honeybee than the primitively social bumblebee. There are also significant differences in recombination rate between subspecies of honeybee. There is substantial variation in genome-wide recombination rate between individuals of both A. mellifera and B. terrestris and the distribution of these rates overlap between species. A large proportion of interindividual variation in recombination rate is heritable, which indicates the presence of variation in trans-acting factors that influence recombination genome-wide. We infer that levels of crossover interference are significantly lower in honeybees compared to bumblebees, which may be one mechanism that contributes to higher recombination rates in honeybees. We also find a significant increase in recombination rate with distance from the centromere, mirrored by methylation differences. We detect a strong transmission bias due to GC-biased gene conversion associated with noncrossover gene conversions. Our results shed light on the mechanistic causes of extreme rates of recombination in social insects and the genetic architecture of recombination rate variation.

Place, publisher, year, edition, pages
GENETICS SOCIETY AMERICA, 2019
Keywords
Recombination, honeybee, bumblebee, crossing over, evolution of sociality
National Category
Genetics
Identifiers
urn:nbn:se:uu:diva-393827 (URN)10.1534/genetics.119.302008 (DOI)000482224900009 ()31152071 (PubMedID)
Funder
Swedish Research Council, 2014-6325Swedish Research Council, 2014-5096Swedish Research Council, 2018-03896
Available from: 2019-10-02 Created: 2019-10-02 Last updated: 2019-10-02Bibliographically approved
Montero-Mendieta, S., Tan, K., Christmas, M., Olsson, A., Vila, C., Wallberg, A. & Webster, M. T. (2019). The genomic basis of adaptation to high-altitude habitats in the eastern honey bee (Apis cerana). Molecular Ecology, 28(4), 746-760
Open this publication in new window or tab >>The genomic basis of adaptation to high-altitude habitats in the eastern honey bee (Apis cerana)
Show others...
2019 (English)In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 28, no 4, p. 746-760Article in journal (Refereed) Published
Abstract [en]

The eastern honey bee (Apis cerana) is of central importance for agriculture in Asia. It has adapted to a wide variety of environmental conditions across its native range in southern and eastern Asia, which includes high-altitude regions. eastern honey bees inhabiting mountains differ morphologically from neighbouring lowland populations and may also exhibit differences in physiology and behaviour. We compared the genomes of 60 eastern honey bees collected from high and low altitudes in Yunnan and Gansu provinces, China, to infer their evolutionary history and to identify candidate genes that may underlie adaptation to high altitude. Using a combination of F-ST-based statistics, long-range haplotype tests and population branch statistics, we identified several regions of the genome that appear to have been under positive selection. These candidate regions were strongly enriched for coding sequences and had high haplotype homozygosity and increased divergence specifically in highland bee populations, suggesting they have been subjected to recent selection in high-altitude habitats. Candidate loci in these genomic regions included genes related to reproduction and feeding behaviour in honey bees. Functional investigation of these candidate loci is necessary to fully understand the mechanisms of adaptation to high-altitude habitats in the eastern honey bee.

Place, publisher, year, edition, pages
WILEY, 2019
Keywords
altitude adaptation, genetic differentiation, honeybees, local adaptation, positive selection, selective sweeps
National Category
Genetics
Identifiers
urn:nbn:se:uu:diva-379270 (URN)10.1111/mec.14986 (DOI)000459814500005 ()30576015 (PubMedID)
Funder
Swedish Research Council Formas, 2013-722Swedish Research Council, 2014-5096
Available from: 2019-03-18 Created: 2019-03-18 Last updated: 2019-06-10Bibliographically approved
Henriques, D., Parejo, M., Vignal, A., Wragg, D., Wallberg, A., Webster, M. T. & Pinto, M. A. (2018). Developing reduced SNP assays from whole-genome sequence data to estimate introgression in an organism with complex genetic patterns, the Iberian honeybee (Apis mellifera iberiensis). Evolutionary Applications, 11(8), 1270-1282
Open this publication in new window or tab >>Developing reduced SNP assays from whole-genome sequence data to estimate introgression in an organism with complex genetic patterns, the Iberian honeybee (Apis mellifera iberiensis)
Show others...
2018 (English)In: Evolutionary Applications, ISSN 1752-4571, E-ISSN 1752-4571, Vol. 11, no 8, p. 1270-1282Article in journal (Refereed) Published
Abstract [en]

The most important managed pollinator, the honeybee (Apis mellifera L.), has been subject to a growing number of threats. In western Europe, one such threat is large-scale introductions of commercial strains (C-lineage ancestry), which is leading to introgressive hybridization and even the local extinction of native honeybee populations (M-lineage ancestry). Here, we developed reduced assays of highly informative SNPs from 176 whole genomes to estimate C-lineage introgression in the most diverse and evolutionarily complex subspecies in Europe, the Iberian honeybee (Apis mellifera iberiensis). We started by evaluating the effects of sample size and sampling a geographically restricted area on the number of highly informative SNPs. We demonstrated that a bias in the number of fixed SNPs (F-ST=1) is introduced when the sample size is small (N10) and when sampling only captures a small fraction of a population's genetic diversity. These results underscore the importance of having a representative sample when developing reliable reduced SNP assays for organisms with complex genetic patterns. We used a training data set to design four independent SNP assays selected from pairwise F-ST between the Iberian and C-lineage honeybees. The designed assays, which were validated in holdout and simulated hybrid data sets, proved to be highly accurate and can be readily used for monitoring populations not only in the native range of A.m.iberiensis in Iberia but also in the introduced range in the Balearic islands, Macaronesia and South America, in a time- and cost-effective manner. While our approach used the Iberian honeybee as model system, it has a high value in a wide range of scenarios for the monitoring and conservation of potentially hybridized domestic and wildlife populations.

Place, publisher, year, edition, pages
WILEY, 2018
Keywords
Apis mellifera iberiensis, fixation index, informative SNPs, reduced SNP assays
National Category
Evolutionary Biology Genetics
Identifiers
urn:nbn:se:uu:diva-362481 (URN)10.1111/eva.12623 (DOI)000442210300007 ()30151039 (PubMedID)
Available from: 2018-10-10 Created: 2018-10-10 Last updated: 2018-10-10Bibliographically approved
Makino, T., Rubin, C.-J., Carneiro, M., Axelsson, E., Andersson, L. & Webster, M. T. (2018). Elevated proportions of deleterious genetic variation in domestic animals and plants. Genome Biology and Evolution, 10(1), 276-290
Open this publication in new window or tab >>Elevated proportions of deleterious genetic variation in domestic animals and plants
Show others...
2018 (English)In: Genome Biology and Evolution, ISSN 1759-6653, E-ISSN 1759-6653, Vol. 10, no 1, p. 276-290Article in journal (Refereed) Published
Abstract [en]

A fraction of genetic variants segregating in any population are deleterious, which negatively impacts individual fitness. The domestication of animals and plants is associated with population bottlenecks and artificial selection, which are predicted to increase the proportion of deleterious variants. However, the extent to which this is a general feature of domestic species is unclear. Here we examine the effects of domestication on the prevalence of deleterious variation using pooled whole-genome resequencing data from five domestic animal species (dog, pig, rabbit, chicken and silkworm) and two domestic plant species (rice and soybean) compared to their wild ancestors. We find significantly reduced genetic variation and increased proportion of nonsynonymous amino acid changes in all but one of the domestic species. These differences are observable across a range of allele frequencies, both common and rare. We find proportionally more SNPs in highly conserved elements in domestic species and a tendency for domestic species to harbour a higher proportion of changes classified as damaging. Our findings most likely reflect an increased incidence of deleterious variants in domestic species, which is most likely attributable to population bottlenecks that lead to a reduction in the efficacy of selection. An exception to this pattern is displayed by European domestic pigs, which do not show traces of a strong population bottleneck and probably continued to exchange genes with wild boar populations after domestication. The results presented here indicate that an elevated proportion of deleterious variants is a common, but not ubiquitous, feature of domestic species.

Place, publisher, year, edition, pages
Oxford University Press, 2018
Keywords
artificial selection, domestication, effective population size, mutational load, natural selection, population bottleneck
National Category
Evolutionary Biology Biochemistry and Molecular Biology
Identifiers
urn:nbn:se:uu:diva-339437 (URN)10.1093/gbe/evy004 (DOI)000424893500020 ()29325102 (PubMedID)
Available from: 2018-01-18 Created: 2018-01-18 Last updated: 2018-04-10Bibliographically approved
Lamichhaney, S., Han, F., Webster, M. T., Andersson, L., Grant, B. R. & Grant, P. R. (2018). Rapid hybrid speciation in Darwin's finches.. Science, 359(6372), 224-228
Open this publication in new window or tab >>Rapid hybrid speciation in Darwin's finches.
Show others...
2018 (English)In: Science, ISSN 0036-8075, E-ISSN 1095-9203, Vol. 359, no 6372, p. 224-228Article in journal (Refereed) Published
Abstract [en]

Homoploid hybrid speciation in animals has been inferred frequently from patterns of variation, but few examples have withstood critical scrutiny. Here we report a directly documented example, from its origin to reproductive isolation. An immigrant Darwin's finch to Daphne Major in the Galápagos archipelago initiated a new genetic lineage by breeding with a resident finch (Geospiza fortis). Genome sequencing of the immigrant identified it as a G. conirostris male that originated on Española >100 kilometers from Daphne Major. From the second generation onward, the lineage bred endogamously and, despite intense inbreeding, was ecologically successful and showed transgressive segregation of bill morphology. This example shows that reproductive isolation, which typically develops over hundreds of generations, can be established in only three.

National Category
Evolutionary Biology
Identifiers
urn:nbn:se:uu:diva-340986 (URN)10.1126/science.aao4593 (DOI)000419816600048 ()29170277 (PubMedID)
Funder
Knut and Alice Wallenberg FoundationSwedish Research CouncilScience for Life Laboratory - a national resource center for high-throughput molecular bioscience
Available from: 2018-02-05 Created: 2018-02-05 Last updated: 2018-02-14Bibliographically approved
Henriques, D., Wallberg, A., Chavez-Galarza, J., Johnston, J. S., Webster, M. T. & Alice Pinto, M. (2018). Whole genome SNP-associated signatures of local adaptation in honeybees of the Iberian Peninsula. Scientific Reports, 8, Article ID 11145.
Open this publication in new window or tab >>Whole genome SNP-associated signatures of local adaptation in honeybees of the Iberian Peninsula
Show others...
2018 (English)In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 8, article id 11145Article in journal (Refereed) Published
Abstract [en]

The availability of powerful high-throughput genomic tools, combined with genome scans, has helped identifying genes and genetic changes responsible for environmental adaptation in many organisms, including the honeybee. Here, we resequenced 87 whole genomes of the honeybee native to Iberia and used conceptually different selection methods (Sam beta ada, LFMM, PCAdapt, iHs) together with in sillico protein modelling to search for selection footprints along environmental gradients. We found 670 outlier SNPs, most of which associated with precipitation, longitude and latitude. Over 88.7% SNPs laid outside exons and there was a significant enrichment in regions adjacent to exons and UTRs. Enrichment was also detected in exonic regions. Furthermore, in silico protein modelling suggests that several non-synonymous SNPs are likely direct targets of selection, as they lead to amino acid replacements in functionally important sites of proteins. We identified genomic signatures of local adaptation in 140 genes, many of which are putatively implicated in fitness-related functions such as reproduction, immunity, olfaction, lipid biosynthesis and circadian clock. Our genome scan suggests that local adaptation in the Iberian honeybee involves variations in regions that might alter patterns of gene expression and in protein-coding genes, which are promising candidates to underpin adaptive change in the honeybee.

Place, publisher, year, edition, pages
NATURE PUBLISHING GROUP, 2018
National Category
Genetics
Identifiers
urn:nbn:se:uu:diva-361681 (URN)10.1038/s41598-018-29469-5 (DOI)000439550200017 ()30042407 (PubMedID)
Available from: 2018-10-05 Created: 2018-10-05 Last updated: 2018-10-05Bibliographically approved
Montero-Mendieta, S., Grabherr, M., Lantz, H., De la Riva, I., Leonard, J. A., Webster, M. T. & Vila, C. (2017). A practical guide to build de-novo assemblies for single tissues of non-model organisms: the example of a Neotropical frog. PeerJ, 5, Article ID e3702.
Open this publication in new window or tab >>A practical guide to build de-novo assemblies for single tissues of non-model organisms: the example of a Neotropical frog
Show others...
2017 (English)In: PeerJ, ISSN 2167-8359, E-ISSN 2167-8359, Vol. 5, article id e3702Article in journal (Refereed) Published
Abstract [en]

Whole genome sequencing (WGS) is a very valuable resource to understand the evolutionary history of poorly known species. However, in organisms with large genomes, as most amphibians, WGS is still excessively challenging and transcriptome sequencing (RNA-seq) represents a cost-effective tool to explore genome-wide variability. Non-model organisms do not usually have a reference genome and the transcriptome must be assembled de-novo. Weused RNA-seq to obtain the transcriptomic profile for Oreobates cruralis, a poorly known South American direct-developing frog. In total, 550,871 transcripts were assembled, corresponding to 422,999 putative genes. Of those, we identified 23,500, 37,349, 38,120 and 45,885 genes present in the Pfam, EggNOG, KEGG and GO databases, respectively. Interestingly, our results suggested that genes related to immune system and defense mechanisms are abundant in the transcriptome of O. cruralis. We also present a pipeline to assist with pre-processing, assembling, evaluating and functionally annotating a de-novo transcriptome from RNA-seq data of non-model organisms. Our pipeline guides the inexperienced user in an intuitive way through all the necessary steps to build de-novo transcriptome assemblies using readily available software and is freely available at: https://github. com/biomendi/TRANSCRIPTOMEASSEMBLY- PIPELINE/wiki.

Place, publisher, year, edition, pages
PEERJ INC, 2017
Keywords
Genomics, Transcriptomics, RNA-seq, Frog transcriptome, Trinity, Gene ontology, Protein domain identification, Clusters of Orthologous Groups, Kyoto encyclopedia of genes and genomes
National Category
Biological Sciences
Identifiers
urn:nbn:se:uu:diva-336834 (URN)10.7717/peerj.3702 (DOI)000411957600001 ()28879061 (PubMedID)
Available from: 2017-12-18 Created: 2017-12-18 Last updated: 2017-12-18Bibliographically approved
Organisations
Identifiers
ORCID iD: ORCID iD iconorcid.org/0000-0003-1141-2863

Search in DiVA

Show all publications