1
|
Falk S, Mulley JF. The genome sequence of the variegated flesh fly, Sarcophaga variegata (Scopoli, 1763). Wellcome Open Res 2023; 8:234. [PMID: 38510269 PMCID: PMC10951566 DOI: 10.12688/wellcomeopenres.19483.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/12/2023] [Indexed: 03/22/2024] Open
Abstract
We present a genome assembly from an individual male Sarcophaga variegata (the variegated flesh fly; Arthropoda; Insecta; Diptera; Sarcophagidae). The genome sequence is 718.5 megabases in span. Most of the assembly is scaffolded into 7 chromosomal pseudomolecules including the X and Y sex chromosomes. The mitochondrial genome has also been assembled and is 18.7 kilobases in length. Gene annotation of this assembly on Ensembl identified 16,660 protein coding genes.
Collapse
Affiliation(s)
- Steven Falk
- Independent researcher, Kenilworth, England, UK
| | | | | | | | | | | | | | | |
Collapse
|
2
|
Brekke TD, Papadopulos AST, Julià E, Fornas O, Fu B, Yang F, de la Fuente R, Page J, Baril T, Hayward A, Mulley JF. A new chromosome-assigned Mongolian gerbil genome allows characterization of complete centromeres and a fully heterochromatic chromosome. Mol Biol Evol 2023:7162499. [PMID: 37183864 DOI: 10.1093/molbev/msad115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 04/23/2023] [Accepted: 05/11/2023] [Indexed: 05/16/2023] Open
Abstract
Chromosome-scale genome assemblies based on ultra-long read sequencing technologies are able to illuminate previously intractable aspects of genome biology such as fine-scale centromere structure and large-scale variation in genome features such as heterochromatin, GC content, recombination rate, and gene content. We present here a new chromosome-scale genome of the Mongolian gerbil (Meriones unguiculatus) which includes the complete sequence of all centromeres. Gerbils are thus the one of the first vertebrates to have their centromeres completely sequenced. Gerbil centromeres are composed of four different repeats of length 6pb, 37 bp, 127 bp, or 1747bp which occur in simple alternating arrays and span 1-6Mb. Gerbil genomes have both an extensive set of GC-rich genes and chromosomes strikingly enriched for constitutive heterochromatin. We sought to determine if there was a link between these two phenomena and found that the two heterochromatic chromosomes of the Mongolian gerbil have distinct underpinnings: Chromosome 5 has a large block of intra-arm heterochromatin as the result of a massive expansion of centromeric repeats, while chromosome 13 is comprised of extremely large (>150 kb) repeated sequences. In addition to characterizing centromeres, our results demonstrate the importance of including karyotypic features such as chromosome number and the locations of centromeres in the interpretation of genome sequence data, and highlight novel patterns involved in the evolution of chromosomes.
Collapse
Affiliation(s)
- Thomas D Brekke
- School of Natural Sciences, Bangor University, Bangor, Gwynedd, LL57 2DG, United Kingdom
| | | | - Eva Julià
- Centre for Genomic Regulation (CRG), Barcelona, Spain
| | - Oscar Fornas
- Pompeu Fabra University (UPF), Barcelona, Spain
- Centre for Genomic Regulation (CRG), Barcelona, Spain
| | - Beiyuan Fu
- Cambridge Epigenetix, The Trinity Building, Chesterford Research Park, Cambridge, CB10 1XL, UK
| | | | - Roberto de la Fuente
- Department of Experimental Embryology, Institute of Genetics and Animal Biotechnology of the Polish Academy of Sciences, Jastrzębiec, 05-552 Magdalenka, Poland
| | - Jesus Page
- Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, 28049, Madrid, Spain
| | - Tobias Baril
- University of Exeter, Penryn Campus, Cornwall, TR10 9FE, United Kingdom
| | - Alexander Hayward
- University of Exeter, Penryn Campus, Cornwall, TR10 9FE, United Kingdom
| | - John F Mulley
- School of Natural Sciences, Bangor University, Bangor, Gwynedd, LL57 2DG, United Kingdom
| |
Collapse
|
3
|
Crowley LM, Telfer M, Geiser M, Mulley JF. The genome sequence of Philonthus cognatus (Stephens, 1832) (Coleoptera, Staphylinidae), a rove beetle. Wellcome Open Res 2023; 8:169. [PMID: 37440996 PMCID: PMC10333781 DOI: 10.12688/wellcomeopenres.19336.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/31/2023] [Indexed: 07/15/2023] Open
Abstract
We present a genome assembly from an individual male Philonthus cognatus (a rove beetle; Arthropoda; Insecta; Coleoptera; Staphylinidae). The genome sequence is 1,030.6 megabases in span. Most of the assembly is scaffolded into 12 chromosomal pseudomolecules, including the X and Y sex chromosomes. The mitochondrial genome has also been assembled and is 20.7 kilobases in length. Gene annotation of this assembly on Ensembl identified 29,629 protein coding genes.
Collapse
Affiliation(s)
| | | | | | | | - John F. Mulley
- School of Natural Sciences, Bangor University, Bangor, Wales, UK
| | | | | | | | | | | | | |
Collapse
|
4
|
Boyes D, Mulley JF. The genome sequence of the Common Pug, Eupithecia vulgata (Haworth, 1809). Wellcome Open Res 2023; 8:129. [PMID: 38274410 PMCID: PMC10808854 DOI: 10.12688/wellcomeopenres.19246.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/15/2023] [Indexed: 01/27/2024] Open
Abstract
We present a genome assembly from an individual male Eupithecia vulgata (the Common Pug; Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence is 454.7 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the assembled Z sex chromosome. The mitochondrial genome has also been assembled and is 17.1 kilobases in length.
Collapse
Affiliation(s)
- Douglas Boyes
- UK Centre for Ecology & Hydrology, Wallingford, England, UK
| | - John F. Mulley
- School of Natural Sciences, Bangor University, Bangor, Wales, UK
| | | | | | | | | | | | | |
Collapse
|
5
|
Rogerson G, Bock S, Loera Y, Parrott B, Mulley JF. Incubation temperature alters stripe formation and head colouration in American alligator hatchlings and is unaffected by estradiol-induced sex reversal. J Exp Biol 2023; 226:jeb245219. [PMID: 36861779 PMCID: PMC10112970 DOI: 10.1242/jeb.245219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 02/24/2023] [Indexed: 03/03/2023]
Abstract
Considerations of the impact climate change has on reptiles are typically focused on habitat change or loss, range shifts and skewed sex ratios in species with temperature-dependent sex determination. Here, we show that incubation temperature alters stripe number and head colouration of hatchling American alligators (Alligator mississippiensis). Animals incubated at higher temperatures (33.5°C) had, on average, one more stripe than those at lower temperatures (29.5°C), and also had significantly lighter heads. These patterns were not affected by estradiol-induced sex reversal, suggesting independence from hatchling sex. Therefore, increases in nest temperatures as a result of climate change have the potential to alter pigmentation patterning, which may have implications for offspring fitness.
Collapse
Affiliation(s)
- Grace Rogerson
- School of Natural Sciences, Bangor University, Deiniol Road, Bangor, Gwynedd LL57 2UW, UK
| | - Samantha Bock
- Odum School of Ecology, University of Georgia,Athens, GA 30602, USA
- Savannah River Ecology Laboratory, University of Georgia, Aiken, SC 29802, USA
| | - Yeraldi Loera
- Department of Ecology & Evolutionary Biology, Princeton University, Princeton, NJ 08544, USA
| | - Benjamin Parrott
- Odum School of Ecology, University of Georgia,Athens, GA 30602, USA
- Savannah River Ecology Laboratory, University of Georgia, Aiken, SC 29802, USA
| | - John F. Mulley
- School of Natural Sciences, Bangor University, Deiniol Road, Bangor, Gwynedd LL57 2UW, UK
| |
Collapse
|
6
|
Boyes D, Mulley JF. The genome sequence of the Birch Marble, Apotomis betuletana (Haworth, 1811). Wellcome Open Res 2023; 8:66. [PMID: 37082718 PMCID: PMC10111142 DOI: 10.12688/wellcomeopenres.18984.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/03/2023] [Indexed: 02/11/2023] Open
Abstract
We present a genome assembly from an individual male Apotomis betuletana (the Birch Marble; Arthropoda; Insecta; Lepidoptera; Tortricidae). The genome sequence is 684 megabases in span. Most of the assembly is scaffolded into 28 chromosomal pseudomolecules with the Z sex chromosome assembled. The mitochondrial genome has also been assembled and is 15.8 kilobases in length. Gene annotation of this assembly on Ensembl identified 21,717 protein coding genes.
Collapse
Affiliation(s)
- Douglas Boyes
- UK Centre for Ecology and Hydrology, Wallingford, Oxfordshire, UK
| | | | | | | | | | | | - John F. Mulley
- School of Natural Sciences, Bangor University, Bangor, Wales, UK
| | | |
Collapse
|
7
|
Falk S, Mulley JF. The genome sequence of the lesser worm flesh fly, Sarcophaga ( Sarcophaga) subvicina (Baranov, 1937). Wellcome Open Res 2023; 8:65. [PMID: 37600583 PMCID: PMC10435921 DOI: 10.12688/wellcomeopenres.18717.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/15/2022] [Indexed: 08/22/2023] Open
Abstract
We present a genome assembly from an individual male Sarcophaga subvicina (the lesser worm flesh fly; Arthropoda; Insecta; Diptera; Sarcophagidae). The genome sequence is 71 megabases in span. Most of the assembly (95.91%) is scaffolded into six chromosomal pseudomolecules, with the X sex chromosome assembled. The mitochondrial genome has also been assembled and is 16.7 kilobases in length. Gene annotation of this assembly on Ensembl identified 16,793 protein coding genes.
Collapse
Affiliation(s)
- Steven Falk
- independent Researcher, Kenilworth, Warwickshire, UK
| | | | | | | | | | | | - John F. Mulley
- School of Natural Sciences, Bangor University, Bangor, Wales, UK
| | | |
Collapse
|
8
|
Boyes D, Mulley JF. The genome sequence of the Riband Wave, Idaea aversata (Linnaeus, 1758). Wellcome Open Res 2023; 8:45. [PMID: 37484483 PMCID: PMC10357074 DOI: 10.12688/wellcomeopenres.18899.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/18/2023] [Indexed: 07/25/2023] Open
Abstract
We present a genome assembly from an individual male Idaea aversata (the Riband Wave; Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence is 437 megabases in span. The whole assembly is scaffolded into 30 chromosomal pseudomolecules, including the assembled Z sex chromosome. The mitochondrial genome has also been assembled and is 17.5 kilobases in length. Gene annotation of this assembly on Ensembl identified 10,165 protein coding genes.
Collapse
Affiliation(s)
- Douglas Boyes
- UK Centre for Ecology and Hydrology, Wallingford, Oxfordshire, UK
| | | | | | | | | | | | - John F. Mulley
- School of Natural Sciences, Bangor University, Bangor, Wales, USA
| | | |
Collapse
|
9
|
Falk S, Mulley JF. The genome of Roselle's flesh fly Sarcophaga ( Helicophagella) rosellei (Böttcher, 1912). Wellcome Open Res 2023; 8:43. [PMID: 37766848 PMCID: PMC10521103 DOI: 10.12688/wellcomeopenres.18874.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/17/2023] [Indexed: 09/29/2023] Open
Abstract
We present a genome assembly from an individual male Sarcophaga rosellei (Roselle's flesh fly; Arthropoda; Insecta; Diptera; Sarcophagidae). The genome sequence is 541 megabases in span. Most of the assembly is scaffolded into six chromosomal pseudomolecules, with the X sex chromosome assembled. The mitochondrial genome has also been assembled and is 19.5 kilobases in length. Gene annotation of this assembly on Ensembl has identified 15,437 protein coding genes.
Collapse
Affiliation(s)
- Steven Falk
- Independent researcher, Kenilworth, Warwickshire, UK
| | | | | | | | | | | | - John F. Mulley
- School of Natural Sciences, Bangor University, Bangor, Wales, UK
| | | |
Collapse
|
10
|
Abstract
We present a genome assembly from an individual male Sarcophaga caerulescens (the bluish flesh fly; Arthropoda; Insecta; Diptera; Sarcophagidae). The genome sequence is 597 megabases in span. Most of the assembly is scaffolded into seven chromosomal pseudomolecules, including the assembled X and Y sex chromosomes. The mitochondrial genome has also been assembled and is 21.1 kilobases in length. Gene annotation of this assembly on Ensembl identified 16,559 protein coding genes.
Collapse
Affiliation(s)
- Steven Falk
- Independent researcher, Kenilworth, Warwickshire,, UK
| | | | | | | | | | | | - John F. Mulley
- School of Natural Sciences, Bangor University, Bangor, Wales, UK
| | | |
Collapse
|
11
|
Mulley JF. Regulation of posterior Hox genes by sex steroids explains vertebral variation in inbred mouse strains. J Anat 2022; 240:735-745. [PMID: 34747015 PMCID: PMC8930804 DOI: 10.1111/joa.13580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 10/08/2021] [Accepted: 10/21/2021] [Indexed: 11/29/2022] Open
Abstract
A series of elegant embryo transfer experiments in the 1950s demonstrated that the uterine environment could alter vertebral patterning in inbred mouse strains. In the intervening decades, attention has tended to focus on the technical achievements involved and neglected the underlying biological question: how can genetically homogenous individuals have a heterogenous number of vertebrae? Here I revisit these experiments and, with the benefit of knowledge of the molecular-level processes of vertebral patterning gained over the intervening decades, suggest a novel hypothesis for homeotic transformation of the last lumbar vertebra to the adjacent sacral type through regulation of Hox genes by sex steroids. Hox genes are involved in both axial patterning and development of male and female reproductive systems and have been shown to be sensitive to sex steroids in vitro and in vivo. Regulation of these genes by sex steroids and resulting alterations to vertebral patterning may hint at a deep evolutionary link between the ribless lumbar region of mammals and the switch from egg-laying to embryo implantation. An appreciation of the impact of sex steroids on Hox genes may explain some puzzling aspects of human disease, and highlights the spine as a neglected target for in utero exposure to endocrine disruptors.
Collapse
|
12
|
Abstract
Recombination increases the local GC-content in genomic regions through GC-biased gene conversion (gBGC). The recent discovery of a large genomic region with extreme GC-content in the fat sand rat Psammomys obesus provides a model to study the effects of gBGC on chromosome evolution. Here, we compare the GC-content and GC-to-AT substitution patterns across protein-coding genes of four gerbil species and two murine rodents (mouse and rat). We find that the known high-GC region is present in all the gerbils, and is characterized by high substitution rates for all mutational categories (AT-to-GC, GC-to-AT, and GC-conservative) both at synonymous and nonsynonymous sites. A higher AT-to-GC than GC-to-AT rate is consistent with the high GC-content. Additionally, we find more than 300 genes outside the known region with outlying values of AT-to-GC synonymous substitution rates in gerbils. Of these, over 30% are organized into at least 17 large clusters observable at the megabase-scale. The unusual GC-skewed substitution pattern suggests the evolution of genomic regions with very high recombination rates in the gerbil lineage, which can lead to a runaway increase in GC-content. Our results imply that rapid evolution of GC-content is possible in mammals, with gerbil species providing a powerful model to study the mechanisms of gBGC.
Collapse
Affiliation(s)
- Rodrigo Pracana
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | | | - John F Mulley
- School of Natural Sciences, Bangor University, Bangor, Gwynedd, United Kingdom
| | | |
Collapse
|
13
|
Zancolli G, Calvete JJ, Cardwell MD, Greene HW, Hayes WK, Hegarty MJ, Herrmann HW, Holycross AT, Lannutti DI, Mulley JF, Sanz L, Travis ZD, Whorley JR, Wüster CE, Wüster W. When one phenotype is not enough: divergent evolutionary trajectories govern venom variation in a widespread rattlesnake species. Proc Biol Sci 2020; 286:20182735. [PMID: 30862287 DOI: 10.1098/rspb.2018.2735] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Understanding the origin and maintenance of phenotypic variation, particularly across a continuous spatial distribution, represents a key challenge in evolutionary biology. For this, animal venoms represent ideal study systems: they are complex, variable, yet easily quantifiable molecular phenotypes with a clear function. Rattlesnakes display tremendous variation in their venom composition, mostly through strongly dichotomous venom strategies, which may even coexist within a single species. Here, through dense, widespread population-level sampling of the Mojave rattlesnake, Crotalus scutulatus, we show that genomic structural variation at multiple loci underlies extreme geographical variation in venom composition, which is maintained despite extensive gene flow. Unexpectedly, neither diet composition nor neutral population structure explain venom variation. Instead, venom divergence is strongly correlated with environmental conditions. Individual toxin genes correlate with distinct environmental factors, suggesting that different selective pressures can act on individual loci independently of their co-expression patterns or genomic proximity. Our results challenge common assumptions about diet composition as the key selective driver of snake venom evolution and emphasize how the interplay between genomic architecture and local-scale spatial heterogeneity in selective pressures may facilitate the retention of adaptive functional polymorphisms across a continuous space.
Collapse
Affiliation(s)
- Giulia Zancolli
- 1 Molecular Ecology and Fisheries Genetics Laboratory, School of Natural Sciences, Bangor University , Bangor LL57 2UW , UK
| | - Juan J Calvete
- 2 Evolutionary and Translational Venomics Laboratory, CSIC , Jaume Roig 11, Valencia 46010 , Spain
| | - Michael D Cardwell
- 3 Department of Biology, San Diego State University , San Diego, CA 92182 , USA
| | - Harry W Greene
- 4 Department of Ecology and Evolutionary Biology, Cornell University , Corson Hall, Ithaca, NY 14853 , USA
| | - William K Hayes
- 5 Department of Earth and Biological Sciences, School of Medicine, Loma Linda University , Loma Linda, CA 92350 , USA
| | - Matthew J Hegarty
- 6 Institute of Biological, Environmental and Rural Sciences, Aberystwyth University , Aberystwyth SY23 3EE , UK
| | - Hans-Werner Herrmann
- 7 Wildlife Conservation and Management, School of Natural Resources and the Environment, University of Arizona , 1064 East Lowell Street (ENR2), Tucson, AZ 85721 , USA
| | - Andrew T Holycross
- 8 Natural History Collections, Arizona State University , 734 W. Alameda Drive, Tempe, AZ 85282 , USA
| | - Dominic I Lannutti
- 9 Department of Biological Sciences, University of Texas at El Paso , 500 W. University, El Paso, TX 79968 , USA
| | - John F Mulley
- 1 Molecular Ecology and Fisheries Genetics Laboratory, School of Natural Sciences, Bangor University , Bangor LL57 2UW , UK
| | - Libia Sanz
- 2 Evolutionary and Translational Venomics Laboratory, CSIC , Jaume Roig 11, Valencia 46010 , Spain
| | - Zachary D Travis
- 5 Department of Earth and Biological Sciences, School of Medicine, Loma Linda University , Loma Linda, CA 92350 , USA
| | - Joshua R Whorley
- 10 Seattle Central College, Science, Technology, Engineering & Mathematics Division , 1701 Broadway Ave. E., Seattle, WA 98122 , USA
| | - Catharine E Wüster
- 1 Molecular Ecology and Fisheries Genetics Laboratory, School of Natural Sciences, Bangor University , Bangor LL57 2UW , UK
| | - Wolfgang Wüster
- 1 Molecular Ecology and Fisheries Genetics Laboratory, School of Natural Sciences, Bangor University , Bangor LL57 2UW , UK
| |
Collapse
|
14
|
Affiliation(s)
- John F. Mulley
- School of Natural SciencesBangor University Deiniol Road Bangor LL57 2UW UK
| |
Collapse
|
15
|
Brekke TD, Supriya S, Denver MG, Thom A, Steele KA, Mulley JF. A high-density genetic map and molecular sex-typing assay for gerbils. Mamm Genome 2019; 30:63-70. [PMID: 30972478 PMCID: PMC6491409 DOI: 10.1007/s00335-019-09799-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Accepted: 03/29/2019] [Indexed: 11/12/2022]
Abstract
We constructed a high-density genetic map for Mongolian gerbils (Meriones unguiculatus). We genotyped 137 F2 individuals with a genotype-by-sequencing (GBS) approach at over 10,000 loci and built the genetic map using a two-step approach. First, we chose the highest-quality set of 485 markers to construct a robust map of 1239 cM with 22 linkage groups as expected from the published karyotype. Second, we added an additional 5449 markers onto the map based on their genotype similarity with the original markers. We used the final marker set to assemble 1140 genomic scaffolds (containing ~ 20% of annotated genes) into a chromosome-level assembly. We used both genetic linkage and relative sequencing coverage in males and females to identify X- and Y-chromosome scaffolds and from these we designed a robust and internally-controlled PCR assay to determine sex. This assay will facilitate early stage sex-typing of embryonic and young gerbils which is difficult using current visual methods. Accession ID: Meriones unguiculatus: 10047.
Collapse
Affiliation(s)
- Thomas D Brekke
- School of Natural Sciences, Bangor University, Bangor, Gwynedd, LL57 2DG, UK
| | - Sushmita Supriya
- School of Natural Sciences, Bangor University, Bangor, Gwynedd, LL57 2DG, UK
| | - Megan G Denver
- School of Natural Sciences, Bangor University, Bangor, Gwynedd, LL57 2DG, UK
| | - Angharad Thom
- School of Natural Sciences, Bangor University, Bangor, Gwynedd, LL57 2DG, UK
| | - Katherine A Steele
- School of Natural Sciences, Bangor University, Bangor, Gwynedd, LL57 2DG, UK
| | - John F Mulley
- School of Natural Sciences, Bangor University, Bangor, Gwynedd, LL57 2DG, UK.
| |
Collapse
|
16
|
Abstract
Nonmodel rodents are widely used as subjects for both basic and applied biological research, but the genetic diversity of the study individuals is rarely quantified. University-housed colonies tend to be small and subject to founder effects and genetic drift; so they may be highly inbred or show substantial genetic divergence from other colonies, even those derived from the same source. Disregard for the levels of genetic diversity in an animal colony may result in a failure to replicate results if a different colony is used to repeat an experiment, as different colonies may have fixed alternative variants. Here we use high throughput sequencing to demonstrate genetic divergence in three isolated colonies of Mongolian gerbil (Meriones unguiculatus) even though they were all established recently from the same source. We also show that genetic diversity in allegedly "outbred" colonies of nonmodel rodents (gerbils, hamsters, house mice, deer mice, and rats) varies considerably from nearly no segregating diversity to very high levels of polymorphism. We conclude that genetic divergence in isolated colonies may play an important role in the "replication crisis." In a more positive light, divergent rodent colonies represent an opportunity to leverage genetically distinct individuals in genetic crossing experiments. In sum, awareness of the genetic diversity of an animal colony is paramount as it allows researchers to properly replicate experiments and also to capitalize on other genetically distinct individuals to explore the genetic basis of a trait.
Collapse
Affiliation(s)
- Thomas D Brekke
- School of Biological Sciences, Bangor University, LL57 2DG, United Kingdom
| | - Katherine A Steele
- School of Environment, Natural Resources and Geography, Bangor University, LL57 2DG, United Kingdom
| | - John F Mulley
- School of Biological Sciences, Bangor University, LL57 2DG, United Kingdom
| |
Collapse
|
17
|
Braasch I, Gehrke AR, Smith JJ, Kawasaki K, Manousaki T, Pasquier J, Amores A, Desvignes T, Batzel P, Catchen J, Berlin AM, Campbell MS, Barrell D, Martin KJ, Mulley JF, Ravi V, Lee AP, Nakamura T, Chalopin D, Fan S, Wcisel D, Cañestro C, Sydes J, Beaudry FEG, Sun Y, Hertel J, Beam MJ, Fasold M, Ishiyama M, Johnson J, Kehr S, Lara M, Letaw JH, Litman GW, Litman RT, Mikami M, Ota T, Saha NR, Williams L, Stadler PF, Wang H, Taylor JS, Fontenot Q, Ferrara A, Searle SMJ, Aken B, Yandell M, Schneider I, Yoder JA, Volff JN, Meyer A, Amemiya CT, Venkatesh B, Holland PWH, Guiguen Y, Bobe J, Shubin NH, Di Palma F, Alfo¨ldi J, Lindblad-Toh K, Postlethwait JH. Erratum: Corrigendum: The spotted gar genome illuminates vertebrate evolution and facilitates human-teleost comparisons. Nat Genet 2016; 48:700. [DOI: 10.1038/ng0616-700c] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
|
18
|
Hargreaves AD, Mulley JF. Assessing the utility of the Oxford Nanopore MinION for snake venom gland cDNA sequencing. PeerJ 2015; 3:e1441. [PMID: 26623194 PMCID: PMC4662598 DOI: 10.7717/peerj.1441] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2015] [Accepted: 11/04/2015] [Indexed: 12/29/2022] Open
Abstract
Portable DNA sequencers such as the Oxford Nanopore MinION device have the potential to be truly disruptive technologies, facilitating new approaches and analyses and, in some cases, taking sequencing out of the lab and into the field. However, the capabilities of these technologies are still being revealed. Here we show that single-molecule cDNA sequencing using the MinION accurately characterises venom toxin-encoding genes in the painted saw-scaled viper, Echis coloratus. We find the raw sequencing error rate to be around 12%, improved to 0–2% with hybrid error correction and 3% with de novo error correction. Our corrected data provides full coding sequences and 5′ and 3′ UTRs for 29 of 33 candidate venom toxins detected, far superior to Illumina data (13/40 complete) and Sanger-based ESTs (15/29). We suggest that, should the current pace of improvement continue, the MinION will become the default approach for cDNA sequencing in a variety of species.
Collapse
Affiliation(s)
- Adam D Hargreaves
- Department of Zoology, University of Oxford , Oxford , United Kingdom
| | - John F Mulley
- School of Biological Sciences, Bangor University , Bangor , United Kingdom
| |
Collapse
|
19
|
Mulley JF. Developmental biology teaching - the importance of a practical approach. F1000Res 2015; 4:126. [PMID: 26167273 PMCID: PMC4482206 DOI: 10.12688/f1000research.6559.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 05/22/2015] [Indexed: 11/20/2022] Open
Abstract
The huge growth in knowledge in many areas of biological sciences over the past few decades has created a major dilemma for those of us in higher education, for not only must we adequately and efficiently convey these new facts and concepts to our students, we must also ensure that they understand and appreciate them. The field of developmental biology has witnessed such a massive growth in knowledge since the mid-1980s, driven mainly by advances in cell and molecular biology, and the development of new imaging techniques and tools. Ensuring that students fully appreciate the four-dimensional nature of embryonic development and morphogenesis is a particular issue, and one that I argue can only be properly learned via direct exposure to embryos via laboratory practicals.
Collapse
Affiliation(s)
- John F Mulley
- School of Biological Sciences, Bangor University, Bangor, Wales, LL57 2UW, UK
| |
Collapse
|
20
|
Hargreaves AD, Swain MT, Hegarty MJ, Logan DW, Mulley JF. Restriction and recruitment-gene duplication and the origin and evolution of snake venom toxins. Genome Biol Evol 2015; 6:2088-95. [PMID: 25079342 PMCID: PMC4231632 DOI: 10.1093/gbe/evu166] [Citation(s) in RCA: 102] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Snake venom has been hypothesized to have originated and diversified through a process that involves duplication of genes encoding body proteins with subsequent recruitment of the copy to the venom gland, where natural selection acts to develop or increase toxicity. However, gene duplication is known to be a rare event in vertebrate genomes, and the recruitment of duplicated genes to a novel expression domain (neofunctionalization) is an even rarer process that requires the evolution of novel combinations of transcription factor binding sites in upstream regulatory regions. Therefore, although this hypothesis concerning the evolution of snake venom is very unlikely and should be regarded with caution, it is nonetheless often assumed to be established fact, hindering research into the true origins of snake venom toxins. To critically evaluate this hypothesis, we have generated transcriptomic data for body tissues and salivary and venom glands from five species of venomous and nonvenomous reptiles. Our comparative transcriptomic analysis of these data reveals that snake venom does not evolve through the hypothesized process of duplication and recruitment of genes encoding body proteins. Indeed, our results show that many proposed venom toxins are in fact expressed in a wide variety of body tissues, including the salivary gland of nonvenomous reptiles and that these genes have therefore been restricted to the venom gland following duplication, not recruited. Thus, snake venom evolves through the duplication and subfunctionalization of genes encoding existing salivary proteins. These results highlight the danger of the elegant and intuitive “just-so story” in evolutionary biology.
Collapse
Affiliation(s)
| | - Martin T Swain
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, United Kingdom
| | - Matthew J Hegarty
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, United Kingdom
| | - Darren W Logan
- Wellcome Trust Sanger Institute, Hinxton, United Kingdom
| | - John F Mulley
- School of Biological Sciences, Bangor University, United Kingdom
| |
Collapse
|
21
|
Hargreaves AD, Swain MT, Logan DW, Mulley JF. Testing the Toxicofera: comparative transcriptomics casts doubt on the single, early evolution of the reptile venom system. Toxicon 2014; 92:140-56. [PMID: 25449103 DOI: 10.1016/j.toxicon.2014.10.004] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2014] [Accepted: 10/01/2014] [Indexed: 12/01/2022]
Abstract
The identification of apparently conserved gene complements in the venom and salivary glands of a diverse set of reptiles led to the development of the Toxicofera hypothesis - the single, early evolution of the venom system in reptiles. However, this hypothesis is based largely on relatively small scale EST-based studies of only venom or salivary glands and toxic effects have been assigned to only some putative Toxicoferan toxins in some species. We set out to examine the distribution of these proposed venom toxin transcripts in order to investigate to what extent conservation of gene complements may reflect a bias in previous sampling efforts. Our quantitative transcriptomic analyses of venom and salivary glands and other body tissues in five species of reptile, together with the use of available RNA-Seq datasets for additional species, shows that the majority of genes used to support the establishment and expansion of the Toxicofera are in fact expressed in multiple body tissues and most likely represent general maintenance or "housekeeping" genes. The apparent conservation of gene complements across the Toxicofera therefore reflects an artefact of incomplete tissue sampling. We therefore conclude that venom has evolved multiple times in reptiles.
Collapse
Affiliation(s)
- Adam D Hargreaves
- School of Biological Sciences, Bangor University, Brambell Building, Deiniol Road, Bangor, Gwynedd LL57 2UW, United Kingdom.
| | - Martin T Swain
- Institute of Biological, Environmental & Rural Sciences, Aberystwyth University, Penglais, Aberystwyth, Ceredigion SY23 3DA, United Kingdom.
| | - Darren W Logan
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1HH, United Kingdom.
| | - John F Mulley
- School of Biological Sciences, Bangor University, Brambell Building, Deiniol Road, Bangor, Gwynedd LL57 2UW, United Kingdom.
| |
Collapse
|
22
|
Mulley JF, Hargreaves AD, Hegarty MJ, Heller RS, Swain MT. Transcriptomic analysis of the lesser spotted catshark (Scyliorhinus canicula) pancreas, liver and brain reveals molecular level conservation of vertebrate pancreas function. BMC Genomics 2014; 15:1074. [PMID: 25480530 PMCID: PMC4362833 DOI: 10.1186/1471-2164-15-1074] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2014] [Accepted: 11/27/2014] [Indexed: 12/20/2022] Open
Abstract
Background Understanding the evolution of the vertebrate pancreas is key to understanding its functions. The chondrichthyes (cartilaginous fish such as sharks and rays) have often been suggested to possess the most ancient example of a distinct pancreas with both hormonal (endocrine) and digestive (exocrine) roles. The lack of genetic, genomic and transcriptomic data for cartilaginous fish has hindered a more thorough understanding of the molecular-level functions of the chondrichthyan pancreas, particularly with respect to their “unusual” energy metabolism (where ketone bodies and amino acids are the main oxidative fuel source) and their paradoxical ability to both maintain stable blood glucose levels and tolerate extensive periods of hypoglycemia. In order to shed light on some of these processes, we carried out the first large-scale comparative transcriptomic survey of multiple cartilaginous fish tissues: the pancreas, brain and liver of the lesser spotted catshark, Scyliorhinus canicula. Results We generated a mutli-tissue assembly comprising 86,006 contigs, of which 44,794 were assigned to a particular tissue or combination of tissues based on mapping of sequencing reads. We have characterised transcripts encoding genes involved in insulin regulation, glucose sensing, transcriptional regulation, signaling and digestion, as well as many peptide hormone precursors and their receptors for the first time. Comparisons to mammalian pancreas transcriptomes reveals that mechanisms of glucose sensing and insulin regulation used to establish and maintain a stable internal environment are conserved across jawed vertebrates and likely pre-date the vertebrate radiation. Conservation of pancreatic hormones and genes encoding digestive proteins support the single, early evolution of a distinct pancreatic gland with endocrine and exocrine functions in jawed vertebrates. In addition, we demonstrate that chondrichthyes lack pancreatic polypeptide (PP) and that reports of PP in the literature are likely due cross-reaction with PYY and/or NPY in the pancreas. A three hormone islet organ is therefore the ancestral jawed vertebrate condition, later elaborated upon only in the tetrapod lineage. Conclusions The cartilaginous fish are a great untapped resource for the reconstruction of patterns and processes of vertebrate evolution and new approaches such as those described in this paper will greatly facilitate their incorporation into the rank of “model organism”. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-1074) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- John F Mulley
- School of Biological Sciences, Bangor University, Brambell Building, Deiniol Road, Bangor, Gwynedd LL57 2UW, United Kingdom.
| | | | | | | | | |
Collapse
|
23
|
Mulley JF, Holland PW. Genomic organisation of the seven ParaHox genes of coelacanths. J Exp Zool (Mol Dev Evol ) 2014; 322:352-8. [PMID: 23775937 PMCID: PMC4471637 DOI: 10.1002/jez.b.22513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/27/2013] [Revised: 04/25/2013] [Accepted: 04/25/2013] [Indexed: 11/30/2022]
Abstract
Human and mouse genomes contain six ParaHox genes implicated in gut and neural patterning. In coelacanths and cartilaginous fish, an additional ParaHox gene exists—Pdx2—that dates back to the genome duplications in early vertebrate evolution. Here we examine the genomic arrangement and flanking genes of all ParaHox genes in coelacanths, to determine the full complement of these genes. We find that coelacanths have seven ParaHox genes in total, in four chromosomal locations, revealing that five gene losses occurred soon after vertebrate genome duplication. Comparison of intergenic sequences reveals that some Pdx1 regulatory regions associated with development of pancreatic islets are older than tetrapods, that Pdx1 and Pdx2 share few if any conserved non-coding elements, and that there is very high sequence conservation between coelacanth species.
Collapse
Affiliation(s)
- John F. Mulley
- School of Biological SciencesBangor UniversityBangorGwynedd, United Kingdom
| | | |
Collapse
|
24
|
Abstract
The Pdx1 or Ipf1 gene encodes an important homeodomain-containing protein with key roles in pancreas development and function. Mutations in human PDX1 are implicated in developmental defects and disease of the pancreas. Extensive research, including genome sequencing, has indicated that Pdx1 is the only member of its gene family in mammals, birds, amphibians, and ray-finned fish, and with the exception of teleost fish, this gene forms part of the ParaHox gene cluster along with Gsx1 and Cdx2. The ParaHox cluster, however, is a remnant of a 4-fold genome duplication; the three other ParaHox paralogues lack a Pdx-like gene in all vertebrate genomes examined to date. We have used bacterial artificial chromosome cloning and synteny analysis to show that the ancestor of living jawed vertebrates in fact had more ParaHox genes, including two Pdx genes (Pdx1 and Pdx2). Surprisingly, the two Pdx genes have been retained in parallel in two quite distantly related lineages, the cartilaginous fish (sharks, skates, and chimeras) and the Indonesian coelacanth, Latimeria menadoensis. The Pdx2 gene has been lost independently in ray-finned fish and in tetrapods.
Collapse
Affiliation(s)
- John F Mulley
- Department of Zoology, University of Oxford, Oxford, United Kingdom.
| | | |
Collapse
|
25
|
Abstract
Background The chondrichthyan or cartilaginous fish (chimeras, sharks, skates and rays) occupy an important phylogenetic position as the sister group to all other jawed vertebrates and as an early lineage to diverge from the vertebrate lineage following two whole genome duplication events in vertebrate evolution. There have been few comparative genomic analyses incorporating data from chondrichthyan fish and none comparing genomic information from within the group. We have sequenced the complete Hoxa cluster of the Little Skate (Leucoraja erinacea) and compared to the published Hoxa cluster of the Horn Shark (Heterodontus francisci) and to available data from the Elephant Shark (Callorhinchus milii) genome project. Results A BAC clone containing the full Little Skate Hoxa cluster was fully sequenced and assembled. Analyses of coding sequences and conserved non-coding elements reveal a strikingly high level of conservation across the cartilaginous fish, with twenty ultraconserved elements (100%,100 bp) found between Skate and Horn Shark, compared to three between human and marsupials. We have also identified novel potential non-coding RNAs in the Skate BAC clone, some of which are conserved to other species. Conclusion We find that the Little Skate Hoxa cluster is remarkably similar to the previously published Horn Shark Hoxa cluster with respect to sequence identity, gene size and intergenic distance despite over 180 million years of separation between the two lineages. We suggest that the genomes of cartilaginous fish are more highly conserved than those of tetrapods or teleost fish and so are more likely to have retained ancestral non-coding elements. While useful for isolating homologous DNA, this complicates bioinformatic approaches to identify chondrichthyan-specific non-coding DNA elements
Collapse
Affiliation(s)
- John F Mulley
- Department of Zoology, University of Oxford, South Parks Road, Oxford, OX13PS UK.
| | | | | |
Collapse
|
26
|
Martin KJ, Mulley JF, Holland PW. 15-P045 The hox gene complement of a basal teleost, Pantodon bucholzi (Osteoglossomorpha). Mech Dev 2009. [DOI: 10.1016/j.mod.2009.06.689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
|
27
|
Abstract
Abstract The ParaHox genes comprise three Hox-related homeobox gene families, found throughout the animals. They were first discovered in the invertebrate chordate amphioxus, where they are tightly clustered. In this paper we carry out a comparative review of ParaHox gene cluster organization among the deuterostomes, and discuss how the recently published hagfish ParaHox clusters fit into current theories about the evolution of this group of genes.
Collapse
Affiliation(s)
- Rebecca F Furlong
- Department of Zoology, Oxford University, South Parks Road, Oxford OX13PS, UK.
| | | |
Collapse
|
28
|
Abstract
Several families of homeobox genes are arranged in genomic clusters in metazoan genomes, including the Hox, ParaHox, NK, Rhox, and Iroquois gene clusters. The selective pressures responsible for maintenance of these gene clusters are poorly understood. The ParaHox gene cluster is evolutionarily conserved between amphioxus and human but is fragmented in teleost fishes. We show that two basal ray-finned fish, Polypterus and Amia, each possess an intact ParaHox cluster; this implies that the selective pressure maintaining clustering was lost after whole-genome duplication in teleosts. Cluster breakup is because of gene loss, not transposition or inversion, and the total number of ParaHox genes is the same in teleosts, human, mouse, and frog. We propose that this homeobox gene cluster is held together in chordates by the existence of interdigitated control regions that could be separated after locus duplication in the teleost fish.
Collapse
Affiliation(s)
- John F Mulley
- *Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS, United Kingdom; and
| | - Chi-Hua Chiu
- Rutgers University, Department of Genetics, Life Sciences Building, Piscataway, NJ 08854
| | - Peter W H Holland
- *Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS, United Kingdom; and
| |
Collapse
|