1
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Ottenburghs J. Avian introgression patterns are consistent with Haldane's Rule. J Hered 2022; 113:363-370. [PMID: 35134952 PMCID: PMC9308041 DOI: 10.1093/jhered/esac005] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Accepted: 01/27/2022] [Indexed: 11/13/2022] Open
Abstract
According to Haldane’s Rule, the heterogametic sex will show the greatest fitness reduction in a hybrid cross. In birds, where sex is determined by a ZW system, female hybrids are expected to experience lower fitness compared to male hybrids. This pattern has indeed been observed in several bird groups, but it is unknown whether the generality of Haldane’s Rule also extends to the molecular level. First, given the lower fitness of female hybrids, we can expect maternally inherited loci (i.e., mitochondrial and W-linked loci) to show lower introgression rates than biparentally inherited loci (i.e., autosomal loci) in females. Second, the faster evolution of Z-linked loci compared to autosomal loci and the hemizygosity of the Z-chromosome in females might speed up the accumulation of incompatible alleles on this sex chromosome, resulting in lower introgression rates for Z-linked loci than for autosomal loci. I tested these expectations by conducting a literature review which focused on studies that directly quantified introgression rates for autosomal, sex-linked, and mitochondrial loci. Although most studies reported introgression rates in line with Haldane’s Rule, it remains important to validate these genetic patterns with estimates of hybrid fitness and supporting field observations to rule out alternative explanations. Genomic data provide exciting opportunities to obtain a more fine-grained picture of introgression rates across the genome, which can consequently be linked to ecological and behavioral observations, potentially leading to novel insights into the genetic mechanisms underpinning Haldane’s Rule.
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Affiliation(s)
- Jente Ottenburghs
- Wildlife Ecology and Conservation, Wageningen University & Research, Wageningen, The Netherlands.,Forest Ecology and Forest Management, Wageningen University & Research, Wageningen, The Netherlands
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2
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Charlesworth D, Graham C, Trivedi U, Gardner J, Bergero R. PromethION sequencing and assembly of the genome of Micropoecilia picta, a fish with a highly Degenerated Y chromosome. Genome Biol Evol 2021; 13:6326803. [PMID: 34297069 PMCID: PMC8449826 DOI: 10.1093/gbe/evab171] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/19/2021] [Indexed: 11/13/2022] Open
Abstract
We here describe sequencing and assembly of both the autosomes and the sex chromosome in M. picta, the closest related species to the guppy, Poecilia reticulata. Poecilia ()Micropoecilia) picta is a close outgroup for studying the guppy, an important organism for studies in evolutionary ecology and in sex chromosome evolution. The guppy XY pair (LG12) has long been studied as a test case for the importance of sexually antagonistic variants in selection for suppressed recombination between Y and X chromosomes. The guppy Y chromosome is not degenerated, but appears to carry functional copies of all genes that are present on its X counterpart. The X chromosomes of M. picta (and its relative M. parae) are homologous to the guppy XY pair, but their Y chromosomes are highly degenerated, and no genes can be identified in the fully Y-linked region. A complete genome sequence of a M. picta male may therefore contribute to understanding how the guppy Y evolved. These fish species' genomes are estimated to be about 750 Mb, with high densities of repetitive sequences, suggesting that long-read sequencing is needed. We evaluated several assembly approaches, and used our results to investigate the extent of Y chromosome degeneration in this species.
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Affiliation(s)
- Deborah Charlesworth
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Charlotte Auerbach Road, EH9 3LF, UK
| | - Chay Graham
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Charlotte Auerbach Road, EH9 3LF, UK.,University of Cambridge, Department of Biochemistry, Sanger Building, 80 Tennis Ct Rd, Cambridge, CB2 1GA, UK
| | - Urmi Trivedi
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Charlotte Auerbach Road, EH9 3LF, UK
| | - Jim Gardner
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Charlotte Auerbach Road, EH9 3LF, UK
| | - Roberta Bergero
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Charlotte Auerbach Road, EH9 3LF, UK
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3
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Naranpanawa DNU, Chandrasekara CHWMRB, Bandaranayake PCG, Bandaranayake AU. Raw transcriptomics data to gene specific SSRs: a validated free bioinformatics workflow for biologists. Sci Rep 2020; 10:18236. [PMID: 33106560 PMCID: PMC7588437 DOI: 10.1038/s41598-020-75270-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2019] [Accepted: 09/21/2020] [Indexed: 02/07/2023] Open
Abstract
Recent advances in next-generation sequencing technologies have paved the path for a considerable amount of sequencing data at a relatively low cost. This has revolutionized the genomics and transcriptomics studies. However, different challenges are now created in handling such data with available bioinformatics platforms both in assembly and downstream analysis performed in order to infer correct biological meaning. Though there are a handful of commercial software and tools for some of the procedures, cost of such tools has made them prohibitive for most research laboratories. While individual open-source or free software tools are available for most of the bioinformatics applications, those components usually operate standalone and are not combined for a user-friendly workflow. Therefore, beginners in bioinformatics might find analysis procedures starting from raw sequence data too complicated and time-consuming with the associated learning-curve. Here, we outline a procedure for de novo transcriptome assembly and Simple Sequence Repeats (SSR) primer design solely based on tools that are available online for free use. For validation of the developed workflow, we used Illumina HiSeq reads of different tissue samples of Santalum album (sandalwood), generated from a previous transcriptomics project. A portion of the designed primers were tested in the lab with relevant samples and all of them successfully amplified the targeted regions. The presented bioinformatics workflow can accurately assemble quality transcriptomes and develop gene specific SSRs. Beginner biologists and researchers in bioinformatics can easily utilize this workflow for research purposes.
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Affiliation(s)
- D N U Naranpanawa
- Agricultural Biotechnology Centre, Faculty of Agriculture, University of Peradeniya, Peradeniya, 20400, Sri Lanka
- Postgraduate Institute of Science, University of Peradeniya, Peradeniya, 20400, Sri Lanka
| | - C H W M R B Chandrasekara
- Agricultural Biotechnology Centre, Faculty of Agriculture, University of Peradeniya, Peradeniya, 20400, Sri Lanka
| | - P C G Bandaranayake
- Agricultural Biotechnology Centre, Faculty of Agriculture, University of Peradeniya, Peradeniya, 20400, Sri Lanka
| | - A U Bandaranayake
- Department of Computer Engineering, Faculty of Engineering, University of Peradeniya, Peradeniya, 20400, Sri Lanka.
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4
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Minias P, Dunn PO, Whittingham LA, Johnson JA, Oyler-McCance SJ. Evaluation of a Chicken 600K SNP genotyping array in non-model species of grouse. Sci Rep 2019; 9:6407. [PMID: 31015535 PMCID: PMC6478925 DOI: 10.1038/s41598-019-42885-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Accepted: 04/11/2019] [Indexed: 12/30/2022] Open
Abstract
The use of single nucleotide polymorphism (SNP) arrays to generate large SNP datasets for comparison purposes have recently become an attractive alternative to other genotyping methods. Although most SNP arrays were originally developed for domestic organisms, they can be effectively applied to wild relatives to obtain large panels of SNPs. In this study, we tested the cross-species application of the Affymetrix 600K Chicken SNP array in five species of North American prairie grouse (Centrocercus and Tympanuchus genera). Two individuals were genotyped per species for a total of ten samples. A high proportion (91%) of the total 580 961 SNPs were genotyped in at least one individual (73–76% SNPs genotyped per species). Principal component analysis with autosomal SNPs separated the two genera, but failed to clearly distinguish species within genera. Gene ontology analysis identified a set of genes related to morphogenesis and development (including genes involved in feather development), which may be primarily responsible for large phenotypic differences between Centrocercus and Tympanuchus grouse. Our study provided evidence for successful cross-species application of the chicken SNP array in grouse which diverged ca. 37 mya from the chicken lineage. As far as we are aware, this is the first reported application of a SNP array in non-passerine birds, and it demonstrates the feasibility of using commercial SNP arrays in research on non-model bird species.
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Affiliation(s)
- Piotr Minias
- Department of Biodiversity Studies and Bioeducation, Faculty of Biology and Environmental Protection, University of Łódź, Banacha 1/3, 90-237, Łódź, Poland.
| | - Peter O Dunn
- Department of Biodiversity Studies and Bioeducation, Faculty of Biology and Environmental Protection, University of Łódź, Banacha 1/3, 90-237, Łódź, Poland.,Behavioral and Molecular Ecology Group, Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin, USA
| | - Linda A Whittingham
- Behavioral and Molecular Ecology Group, Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin, USA
| | - Jeff A Johnson
- Department of Biological Sciences, Institute of Applied Sciences, University of North Texas, Denton, Texas, USA
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5
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Marcionetti A, Rossier V, Roux N, Salis P, Laudet V, Salamin N. Insights into the Genomics of Clownfish Adaptive Radiation: Genetic Basis of the Mutualism with Sea Anemones. Genome Biol Evol 2019; 11:869-882. [PMID: 30830203 PMCID: PMC6430985 DOI: 10.1093/gbe/evz042] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/28/2019] [Indexed: 02/06/2023] Open
Abstract
Clownfishes are an iconic group of coral reef fishes, especially known for their mutualism with sea anemones. This mutualism is particularly interesting as it likely acted as the key innovation that triggered clownfish adaptive radiation. Indeed, after the acquisition of the mutualism, clownfishes diversified into multiple ecological niches linked with host and habitat use. However, despite the importance of this mutualism, the genetic mechanisms allowing clownfishes to interact with sea anemones are still unclear. Here, we used a comparative genomics and molecular evolutionary analyses to investigate the genetic basis of clownfish mutualism with sea anemones. We assembled and annotated the genome of nine clownfish species and one closely related outgroup. Orthologous genes inferred between these species and additional publicly available teleost genomes resulted in almost 16,000 genes that were tested for positively selected substitutions potentially involved in the adaptation of clownfishes to live in sea anemones. We identified 17 genes with a signal of positive selection at the origin of clownfish radiation. Two of them (Versican core protein and Protein O-GlcNAse) show particularly interesting functions associated with N-acetylated sugars, which are known to be involved in sea anemone discharge of toxins. This study provides the first insights into the genetic mechanisms of clownfish mutualism with sea anemones. Indeed, we identified the first candidate genes likely to be associated with clownfish protection form sea anemones, and thus the evolution of their mutualism. Additionally, the genomic resources acquired represent a valuable resource for further investigation of the genomic basis of clownfish adaptive radiation.
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Affiliation(s)
- Anna Marcionetti
- Department of Computational Biology, Génopode, University of Lausanne, Switzerland
| | - Victor Rossier
- Department of Computational Biology, Génopode, University of Lausanne, Switzerland
| | - Natacha Roux
- Observatoire Océanologique de Banyuls-sur-Mer, UMR CNRS 7232 BIOM, Sorbonne University, Banyuls-sur-Mer, France
| | - Pauline Salis
- Observatoire Océanologique de Banyuls-sur-Mer, UMR CNRS 7232 BIOM, Sorbonne University, Banyuls-sur-Mer, France
| | - Vincent Laudet
- Observatoire Océanologique de Banyuls-sur-Mer, UMR CNRS 7232 BIOM, Sorbonne University, Banyuls-sur-Mer, France
| | - Nicolas Salamin
- Department of Computational Biology, Génopode, University of Lausanne, Switzerland
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6
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Kozma R, Rödin-Mörch P, Höglund J. Genomic regions of speciation and adaptation among three species of grouse. Sci Rep 2019; 9:812. [PMID: 30692562 PMCID: PMC6349846 DOI: 10.1038/s41598-018-36880-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Accepted: 11/27/2018] [Indexed: 12/30/2022] Open
Abstract
Understanding the molecular basis of adaption is one of the central goals in evolutionary biology and when investigated across sister species it can provide detailed insight into the mechanisms of speciation. Here, we sequence the genomes of 34 individuals from three closely related grouse species in order to uncover the genomic architecture of speciation and the genes involved in adaptation. We identify 6 regions, containing 7 genes that show lineage specific signs of differential selection across the species. These genes are involved in a variety of cell processes ranging from stress response to neural, gut, olfactory and limb development. Genome wide neutrality test statistics reveal a strong signal of population expansion acting across the genomes. Additionally, we uncover a 3.5 Mb region on chromosome 20 that shows considerably lower levels of differentiation across the three grouse lineages, indicating possible action of uniform selection in this region.
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Affiliation(s)
- Radoslav Kozma
- Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, Uppsala, SE-75236, Sweden
| | - Patrik Rödin-Mörch
- Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, Uppsala, SE-75236, Sweden
| | - Jacob Höglund
- Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, Uppsala, SE-75236, Sweden.
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7
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Kolmogorov M, Armstrong J, Raney BJ, Streeter I, Dunn M, Yang F, Odom D, Flicek P, Keane TM, Thybert D, Paten B, Pham S. Chromosome assembly of large and complex genomes using multiple references. Genome Res 2018; 28:1720-1732. [PMID: 30341161 PMCID: PMC6211643 DOI: 10.1101/gr.236273.118] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Accepted: 09/24/2018] [Indexed: 11/25/2022]
Abstract
Despite the rapid development of sequencing technologies, the assembly of mammalian-scale genomes into complete chromosomes remains one of the most challenging problems in bioinformatics. To help address this difficulty, we developed Ragout 2, a reference-assisted assembly tool that works for large and complex genomes. By taking one or more target assemblies (generated from an NGS assembler) and one or multiple related reference genomes, Ragout 2 infers the evolutionary relationships between the genomes and builds the final assemblies using a genome rearrangement approach. By using Ragout 2, we transformed NGS assemblies of 16 laboratory mouse strains into sets of complete chromosomes, leaving <5% of sequence unlocalized per set. Various benchmarks, including PCR testing and realigning of long Pacific Biosciences (PacBio) reads, suggest only a small number of structural errors in the final assemblies, comparable with direct assembly approaches. We applied Ragout 2 to the Mus caroli and Mus pahari genomes, which exhibit karyotype-scale variations compared with other genomes from the Muridae family. Chromosome painting maps confirmed most large-scale rearrangements that Ragout 2 detected. We applied Ragout 2 to improve draft sequences of three ape genomes that have recently been published. Ragout 2 transformed three sets of contigs (generated using PacBio reads only) into chromosome-scale assemblies with accuracy comparable to chromosome assemblies generated in the original study using BioNano maps, Hi-C, BAC clones, and FISH.
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Affiliation(s)
- Mikhail Kolmogorov
- Department of Computer Science and Engineering, University of California, San Diego, California 92093, USA
| | - Joel Armstrong
- Center for Biomolecular Science and Engineering, University of California, Santa Cruz, California 95064, USA
| | - Brian J Raney
- Center for Biomolecular Science and Engineering, University of California, Santa Cruz, California 95064, USA
| | - Ian Streeter
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton CB10 1SD, United Kingdom
| | - Matthew Dunn
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom
| | - Fengtang Yang
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom
| | - Duncan Odom
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom
- Cancer Research UK Cambridge Institute, University of Cambridge, CB2 0RE Cambridge, United Kingdom
| | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton CB10 1SD, United Kingdom
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom
| | - Thomas M Keane
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton CB10 1SD, United Kingdom
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom
- School of Life Sciences, University of Nottingham, Nottingham NG7 2NR, United Kingdom
| | - David Thybert
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton CB10 1SD, United Kingdom
- Earlham Institute, Norwich Research Park, Norwich NR4 7UG, United Kingdom
| | - Benedict Paten
- Center for Biomolecular Science and Engineering, University of California, Santa Cruz, California 95064, USA
| | - Son Pham
- BioTuring Incorporated, San Diego, California 92121, USA
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8
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Tiley GP, Kimball RT, Braun EL, Burleigh JG. Comparison of the Chinese bamboo partridge and red Junglefowl genome sequences highlights the importance of demography in genome evolution. BMC Genomics 2018; 19:336. [PMID: 29739321 PMCID: PMC5941490 DOI: 10.1186/s12864-018-4711-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Accepted: 04/23/2018] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Recent large-scale whole genome sequencing efforts in birds have elucidated broad patterns of avian phylogeny and genome evolution. However, despite the great interest in economically important phasianids like Gallus gallus (Red Junglefowl, the progenitor of the chicken), we know little about the genomes of closely related species. Gallus gallus is highly sexually dichromatic and polygynous, but its sister genus, Bambusicola, is smaller, sexually monomorphic, and monogamous with biparental care. We sequenced the genome of Bambusicola thoracicus (Chinese Bamboo Partridge) using a single insert library to test hypotheses about genome evolution in galliforms. Selection acting at the phenotypic level could result in more evidence of positive selection in the Gallus genome than in Bambusicola. However, the historical range size of Bambusicola was likely smaller than Gallus, and demographic effects could lead to higher rates of nonsynonymous substitution in Bambusicola than in Gallus. RESULTS We generated a genome assembly suitable for evolutionary analyses. We examined the impact of selection on coding regions by examining shifts in the average nonsynonymous to synonymous rate ratio (dN/dS) and the proportion of sites subject to episodic positive selection. We observed elevated dN/dS in Bambusicola relative to Gallus, which is consistent with our hypothesis that demographic effects may be important drivers of genome evolution in Bambusicola. We also demonstrated that alignment error can greatly inflate estimates of the number of genes that experienced episodic positive selection and heterogeneity in dN/dS. However, overall patterns of molecular evolution were robust to alignment uncertainty. Bambusicola thoracicus has higher estimates of heterozygosity than Gallus gallus, possibly due to migration events over the past 100,000 years. CONCLUSIONS Our results emphasized the importance of demographic processes in generating the patterns of variation between Bambusicola and Gallus. We also demonstrated that genome assemblies generated using a single library can provide valuable insights into avian evolutionary history and found that it is important to account for alignment uncertainty in evolutionary inferences from draft genomes.
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Affiliation(s)
- G P Tiley
- Department of Biology, University of Florida, Gainesville, FL, 32611, USA. .,Department of Biology, Duke University, Durham, NC, 27708, USA.
| | - R T Kimball
- Department of Biology, University of Florida, Gainesville, FL, 32611, USA
| | - E L Braun
- Department of Biology, University of Florida, Gainesville, FL, 32611, USA
| | - J G Burleigh
- Department of Biology, University of Florida, Gainesville, FL, 32611, USA
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9
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Gayk ZG, Le Duc D, Horn J, Lindsay AR. Genomic insights into natural selection in the common loon (Gavia immer): evidence for aquatic adaptation. BMC Evol Biol 2018; 18:64. [PMID: 29703132 PMCID: PMC5921391 DOI: 10.1186/s12862-018-1181-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Accepted: 04/16/2018] [Indexed: 11/12/2022] Open
Abstract
Background The common loon (Gavia immer) is one of five species that comprise the avian order Gaviiformes. Loons are specialized divers, reaching depths up to 60 m while staying submerged for intervals up to three minutes. In this study we used comparative genomics to investigate the genetic basis of the common loon adaptations to its ecological niche. We used Illumina short read DNA sequence data from a female bird to produce a draft assembly of the common loon (Gavia immer) genome. Results We identified 14,169 common loon genes, which based on well-resolved avian genomes, represent approximately 80.7% of common loon genes. Evolutionary analyses between common loon and Adelie penguin (Pygoscelis adeliae), red-throated loon (Gavia stellata), chicken (Gallus gallus), northern fulmar (Fulmarus glacialis), and rock pigeon (Columba livia) show 164 positively selected genes in common and red-throated loons. These genes were enriched for a number of protein classes, including those involved in muscle tissue development, immunoglobulin function, hemoglobin iron binding, G-protein coupled receptors, and ATP metabolism. Conclusions Signatures of positive selection in these areas suggest the genus Gavia may have adapted for underwater diving by modulating their oxidative and metabolic pathways. While more research is required, these adaptations likely result in (1) compensations in oxygen respiration and energetic metabolism, (2) low-light visual acuity, and (3) elevated solute exchange. This work represents the first effort to understand the genomic adaptations of the common loon as well as other Gavia and may have implications for subsequent studies that target particular genes for loon population genetic, ecological or conservation studies. Electronic supplementary material The online version of this article (10.1186/s12862-018-1181-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Zach G Gayk
- Biology Department, Northern Michigan University, 1401 Presque Isle Avenue, Marquette, 49950, Michigan, USA. .,Biology Department, University of Windsor, 401 Sunset Avenue, Windsor, N9B 3P4, Ontario, Canada.
| | - Diana Le Duc
- Institute of Human Genetics, University of Leipzig Hospitals and Clinics, Leipzig, Germany.,Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Jeffrey Horn
- Department of Mathematics and Computer Science, Northern Michigan University, 1401 Presque Isle Avenue, Marquette, 49950, Michigan, USA
| | - Alec R Lindsay
- Biology Department, Northern Michigan University, 1401 Presque Isle Avenue, Marquette, 49950, Michigan, USA
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10
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Lischer HEL, Shimizu KK. Reference-guided de novo assembly approach improves genome reconstruction for related species. BMC Bioinformatics 2017; 18:474. [PMID: 29126390 PMCID: PMC5681816 DOI: 10.1186/s12859-017-1911-6] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Accepted: 11/01/2017] [Indexed: 12/31/2022] Open
Abstract
Background The development of next-generation sequencing has made it possible to sequence whole genomes at a relatively low cost. However, de novo genome assemblies remain challenging due to short read length, missing data, repetitive regions, polymorphisms and sequencing errors. As more and more genomes are sequenced, reference-guided assembly approaches can be used to assist the assembly process. However, previous methods mostly focused on the assembly of other genotypes within the same species. We adapted and extended a reference-guided de novo assembly approach, which enables the usage of a related reference sequence to guide the genome assembly. In order to compare and evaluate de novo and our reference-guided de novo assembly approaches, we used a simulated data set of a repetitive and heterozygotic plant genome. Results The extended reference-guided de novo assembly approach almost always outperforms the corresponding de novo assembly program even when a reference of a different species is used. Similar improvements can be observed in high and low coverage situations. In addition, we show that a single evaluation metric, like the widely used N50 length, is not enough to properly rate assemblies as it not always points to the best assembly evaluated with other criteria. Therefore, we used the summed z-scores of 36 different statistics to evaluate the assemblies. Conclusions The combination of reference mapping and de novo assembly provides a powerful tool to improve genome reconstruction by integrating information of a related genome. Our extension of the reference-guided de novo assembly approach enables the application of this strategy not only within but also between related species. Finally, the evaluation of genome assemblies is often not straight forward, as the truth is not known. Thus one should always use a combination of evaluation metrics, which not only try to assess the continuity but also the accuracy of an assembly. Electronic supplementary material The online version of this article (10.1186/s12859-017-1911-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Heidi E L Lischer
- Department of Evolutionary Biology and Environmental Studies (IEU), University of Zurich, Zurich, Switzerland. .,Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland.
| | - Kentaro K Shimizu
- Department of Evolutionary Biology and Environmental Studies (IEU), University of Zurich, Zurich, Switzerland.,Kihara Institute for Biological Research, Yokohama City University, Yokohama, 244-0813, Japan
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11
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Kang L, George P, Price DK, Sharakhov I, Michalak P. Mapping Genomic Scaffolds to Chromosomes Using Laser Capture Microdissection in Application to Hawaiian Picture-Winged Drosophila. Cytogenet Genome Res 2017; 152:204-212. [PMID: 29130948 DOI: 10.1159/000481790] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/28/2017] [Indexed: 11/19/2022] Open
Abstract
Next-generation sequencing technologies have led to a decreased cost and an increased throughput in genome sequencing. Yet, many genome assemblies based on short sequencing reads have been assembled only to the scaffold level due to the lack of sufficient chromosome mapping information. Traditional ways of mapping scaffolds to chromosomes require a large amount of laboratory work and time to generate genetic and/or physical maps. To address this problem, we conducted a rapid technique which uses laser capture microdissection and enables mapping scaffolds of de novo genome assemblies directly to chromosomes in Hawaiian picture-winged Drosophila. We isolated and sequenced intact chromosome arms from larvae of D. differens. By mapping the reads of each chromosome to the recently assembled scaffolds from 3 Hawaiian picture-winged Drosophila species, at least 67% of the scaffolds were successfully assigned to chromosome arms. Even though the scaffolds are not ordered within a chromosome, the fast-generated chromosome information allows for chromosome-related analyses after genome assembling. We utilize this new information to test the faster-X evolution effect for the first time in these Hawaiian picture-winged Drosophila species.
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Affiliation(s)
- Lin Kang
- Biocomplexity Institute, Virginia Tech, Blacksburg, VA, USA
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12
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Pardal S, Drews A, Alves JA, Ramos JA, Westerdahl H. Characterization of MHC class I in a long distance migratory wader, the Icelandic black-tailed godwit. Immunogenetics 2017; 69:463-478. [PMID: 28534224 PMCID: PMC5486808 DOI: 10.1007/s00251-017-0993-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Accepted: 04/22/2017] [Indexed: 11/29/2022]
Abstract
The major histocompatibility complex (MHC) encodes proteins that are central for antigen presentation and pathogen elimination. MHC class I (MHC-I) genes have attracted a great deal of interest among researchers in ecology and evolution and have been partly characterized in a wide range of bird species. So far, the main focus has been on species within the bird orders Galliformes and Passeriformes, while Charadriiformes remain vastly underrepresented with only two species studied to date. These two Charadriiformes species exhibit striking differences in MHC-I characteristics and MHC-I diversity. We therefore set out to study a third species within Charadriiformes, the Icelandic subspecies of black-tailed godwits (Limosa limosa islandica). This subspecies is normally confined to parasite-poor environments, and we hence expected low MHC diversity. MHC-I was partially characterized first using Sanger sequencing and then using high-throughput sequencing (MiSeq) in 84 individuals. We verified 47 nucleotide alleles in open reading frame with classical MHC-I characteristics, and each individual godwit had two to seven putatively classical MHC alleles. However, in contrast to previous MHC-I data within Charadriiformes, we did not find any evidence of alleles with low sequence diversity, believed to represent non-classical MHC genes. The diversity and divergence of the godwits MHC-I genes to a large extent fell between the previous estimates within Charadriiformes. However, the MHC genes of the migratory godwits had few sites subject to positive selection, and one possible explanation could be a low exposure to pathogens.
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Affiliation(s)
- Sara Pardal
- MARE - Marine and Environmental Sciences Centre, Department of Life Sciences, University of Coimbra, 3000-456, Coimbra, Portugal.
| | - Anna Drews
- MEEL - Molecular Ecology and Evolution Laboratory, Lund University, Ecology building, SE-223 62, Lund, Sweden.
| | - José A Alves
- CESAM - Centre for Environmental and Marine Studies, Department of Biology, University of Aveiro, Campus Universitário de Santiago, 3810-193, Aveiro, Portugal.,South Iceland Research Centre, University of Iceland, Fjolheimer, IS-800, Selfoss, Iceland
| | - Jaime A Ramos
- MARE - Marine and Environmental Sciences Centre, Department of Life Sciences, University of Coimbra, 3000-456, Coimbra, Portugal
| | - Helena Westerdahl
- MEEL - Molecular Ecology and Evolution Laboratory, Lund University, Ecology building, SE-223 62, Lund, Sweden
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13
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Willoughby JR, Ivy JA, Lacy RC, Doyle JM, DeWoody JA. Inbreeding and selection shape genomic diversity in captive populations: Implications for the conservation of endangered species. PLoS One 2017; 12:e0175996. [PMID: 28423000 PMCID: PMC5396937 DOI: 10.1371/journal.pone.0175996] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Accepted: 04/04/2017] [Indexed: 12/01/2022] Open
Abstract
Captive breeding programs are often initiated to prevent species extinction until reintroduction into the wild can occur. However, the evolution of captive populations via inbreeding, drift, and selection can impair fitness, compromising reintroduction programs. To better understand the evolutionary response of species bred in captivity, we used nearly 5500 single nucleotide polymorphisms (SNPs) in populations of white-footed mice (Peromyscus leucopus) to measure the impact of breeding regimes on genomic diversity. We bred mice in captivity for 20 generations using two replicates of three protocols: random mating (RAN), selection for docile behaviors (DOC), and minimizing mean kinship (MK). The MK protocol most effectively retained genomic diversity and reduced the effects of selection. Additionally, genomic diversity was significantly related to fitness, as assessed with pedigrees and SNPs supported with genomic sequence data. Because captive-born individuals are often less fit in wild settings compared to wild-born individuals, captive-estimated fitness correlations likely underestimate the effects in wild populations. Therefore, minimizing inbreeding and selection in captive populations is critical to increasing the probability of releasing fit individuals into the wild.
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Affiliation(s)
- Janna R. Willoughby
- Department of Forestry and Natural Resources, Purdue University, West Lafayette, Indiana, United States of America
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana, United States of America
- * E-mail:
| | - Jamie A. Ivy
- San Diego Zoo Global Collections Department, San Diego, California, United States of America
| | - Robert C. Lacy
- Chicago Zoological Society, Brookfield, Illinois, United States of America
| | - Jacqueline M. Doyle
- Department of Biological Sciences, Towson University, Towson, Maryland, United States of America
| | - J. Andrew DeWoody
- Department of Forestry and Natural Resources, Purdue University, West Lafayette, Indiana, United States of America
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana, United States of America
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14
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Rousselle M, Faivre N, Ballenghien M, Galtier N, Nabholz B. Hemizygosity Enhances Purifying Selection: Lack of Fast-Z Evolution in Two Satyrine Butterflies. Genome Biol Evol 2016; 8:3108-3119. [PMID: 27590089 PMCID: PMC5174731 DOI: 10.1093/gbe/evw214] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The fixation probability of a recessive beneficial mutation is increased on the X or Z chromosome, relative to autosomes, because recessive alleles carried by X or Z are exposed to selection in the heterogametic sex. This leads to an increased dN/dS ratio on sex chromosomes relative to autosomes, a pattern called the “fast-X” or “fast-Z” effect. Besides positive selection, the strength of genetic drift and the efficacy of purifying selection, which affect the rate of molecular evolution, might differ between sex chromosomes and autosomes. Disentangling the complex effects of these distinct forces requires the genome-wide analysis of polymorphism, divergence and gene expression data in a variety of taxa. Here we study the influence of hemizygosity of the Z chromosome in Maniola jurtina and Pyronia tithonus, two species of butterflies (Lepidoptera, Nymphalidae, Satyrinae). Using transcriptome data, we compare the strength of positive and negative selection between Z and autosomes accounting for sex-specific gene expression. We show that M. jurtina and P. tithonus do not experience a faster, but rather a slightly slower evolutionary rate on the Z than on autosomes. Our analysis failed to detect a significant difference in adaptive evolutionary rate between Z and autosomes, but comparison of male-biased, unbiased and female-biased Z-linked genes revealed an increased efficacy of purifying selection against recessive deleterious mutations in female-biased Z-linked genes. This probably contributes to the lack of fast-Z evolution of satyrines. We suggest that the effect of hemizygosity on the fate of recessive deleterious mutations should be taken into account when interpreting patterns of molecular evolution in sex chromosomes vs. autosomes.
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Affiliation(s)
- Marjolaine Rousselle
- UMR 5554 Institut des Sciences de l'Evolution, CNRS, Université de Montpellier, IRD, EPHE, Place E. Bataillon, Montpellier, France
| | - Nicolas Faivre
- UMR 5554 Institut des Sciences de l'Evolution, CNRS, Université de Montpellier, IRD, EPHE, Place E. Bataillon, Montpellier, France
| | - Marion Ballenghien
- UMR 5554 Institut des Sciences de l'Evolution, CNRS, Université de Montpellier, IRD, EPHE, Place E. Bataillon, Montpellier, France
| | - Nicolas Galtier
- UMR 5554 Institut des Sciences de l'Evolution, CNRS, Université de Montpellier, IRD, EPHE, Place E. Bataillon, Montpellier, France
| | - Benoit Nabholz
- UMR 5554 Institut des Sciences de l'Evolution, CNRS, Université de Montpellier, IRD, EPHE, Place E. Bataillon, Montpellier, France
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15
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Galla SJ, Buckley TR, Elshire R, Hale ML, Knapp M, McCallum J, Moraga R, Santure AW, Wilcox P, Steeves TE. Building strong relationships between conservation genetics and primary industry leads to mutually beneficial genomic advances. Mol Ecol 2016; 25:5267-5281. [PMID: 27641156 DOI: 10.1111/mec.13837] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Revised: 08/23/2016] [Accepted: 08/24/2016] [Indexed: 02/06/2023]
Abstract
Several reviews in the past decade have heralded the benefits of embracing high-throughput sequencing technologies to inform conservation policy and the management of threatened species, but few have offered practical advice on how to expedite the transition from conservation genetics to conservation genomics. Here, we argue that an effective and efficient way to navigate this transition is to capitalize on emerging synergies between conservation genetics and primary industry (e.g., agriculture, fisheries, forestry and horticulture). Here, we demonstrate how building strong relationships between conservation geneticists and primary industry scientists is leading to mutually-beneficial outcomes for both disciplines. Based on our collective experience as collaborative New Zealand-based scientists, we also provide insight for forging these cross-sector relationships.
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Affiliation(s)
- Stephanie J Galla
- School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch, 8140, New Zealand.
| | - Thomas R Buckley
- Landcare Research, Private Bag 92170, Auckland Mail Centre, Auckland, 1142, New Zealand.,School of Biological Sciences, University of Auckland, Auckland, 1010, New Zealand
| | - Rob Elshire
- The Elshire Group, Ltd., 52 Victoria Avenue, Palmerston North, 4410, New Zealand
| | - Marie L Hale
- School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch, 8140, New Zealand
| | - Michael Knapp
- Department of Anatomy, University of Otago, P.O. Box 913, Dunedin, 9054, New Zealand
| | - John McCallum
- Breeding and Genomics, New Zealand Institute for Plant and Food Research, Private Bag 4704, Christchurch, 8140, New Zealand
| | - Roger Moraga
- AgResearch, Ruakura Research Centre, Bisley Road, Private Bag 3115, Hamilton, 3240, New Zealand
| | - Anna W Santure
- School of Biological Sciences, University of Auckland, Auckland, 1010, New Zealand
| | - Phillip Wilcox
- Department of Mathematics and Statistics, University of Otago, P.O. Box 56, 710 Cumberland Street, Dunedin, 9054, New Zealand
| | - Tammy E Steeves
- School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch, 8140, New Zealand
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16
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Delph LF, Demuth JP. Haldane’s Rule: Genetic Bases and Their Empirical Support. J Hered 2016; 107:383-91. [DOI: 10.1093/jhered/esw026] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2016] [Accepted: 04/27/2016] [Indexed: 11/14/2022] Open
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17
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Wright AE, Harrison PW, Zimmer F, Montgomery SH, Pointer MA, Mank JE. Variation in promiscuity and sexual selection drives avian rate of Faster-Z evolution. Mol Ecol 2016; 24:1218-35. [PMID: 25689782 PMCID: PMC4737241 DOI: 10.1111/mec.13113] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2014] [Revised: 02/10/2015] [Accepted: 02/11/2015] [Indexed: 02/02/2023]
Abstract
Higher rates of coding sequence evolution have been observed on the Z chromosome relative to the autosomes across a wide range of species. However, despite a considerable body of theory, we lack empirical evidence explaining variation in the strength of the Faster-Z Effect. To assess the magnitude and drivers of Faster-Z Evolution, we assembled six de novo transcriptomes, spanning 90 million years of avian evolution. Our analysis combines expression, sequence and polymorphism data with measures of sperm competition and promiscuity. In doing so, we present the first empirical evidence demonstrating the positive relationship between Faster-Z Effect and measures of promiscuity, and therefore variance in male mating success. Our results from multiple lines of evidence indicate that selection is less effective on the Z chromosome, particularly in promiscuous species, and that Faster-Z Evolution in birds is due primarily to genetic drift. Our results reveal the power of mating system and sexual selection in shaping broad patterns in genome evolution.
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Affiliation(s)
- Alison E Wright
- Department of Zoology, Edward Grey Institute, University of Oxford, Oxford, OX1 3PS, UK; Department of Genetics, Evolution and Environment, University College London, London, WC1E 6BT, UK
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18
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Kozma R, Melsted P, Magnússon KP, Höglund J. Looking into the past - the reaction of three grouse species to climate change over the last million years using whole genome sequences. Mol Ecol 2016; 25:570-80. [PMID: 26607571 DOI: 10.1111/mec.13496] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2015] [Revised: 11/19/2015] [Accepted: 11/20/2015] [Indexed: 01/08/2023]
Abstract
Tracking past population fluctuations can give insight into current levels of genetic variation present within species. Analysing population dynamics over larger timescales can be aligned to known climatic changes to determine the response of species to varying environments. Here, we applied the Pairwise Sequentially Markovian Coalescent (psmc) model to infer past population dynamics of three widespread grouse species; black grouse, willow grouse and rock ptarmigan. This allowed the tracking of the effective population size (Ne ) of all three species beyond 1 Mya, revealing that (i) early Pleistocene cooling (~2.5 Mya) caused an increase in the willow grouse and rock ptarmigan populations, (ii) the mid-Brunhes event (~430 kya) and following climatic oscillations decreased the Ne of willow grouse and rock ptarmigan, but increased the Ne of black grouse and (iii) all three species reacted differently to the last glacial maximum (LGM) - black grouse increased prior to it, rock ptarmigan experienced a severe bottleneck and willow grouse was maintained at large population size. We postulate that the varying psmc signal throughout the LGM depicts only the local history of the species. Nevertheless, the large population fluctuations in willow grouse and rock ptarmigan indicate that both species are opportunistic breeders while black grouse tracks the climatic changes more slowly and is maintained at lower Ne . Our results highlight the usefulness of the psmc approach in investigating species' reaction to climate change in the deep past, but also that caution should be taken in drawing general conclusions about the recent past.
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Affiliation(s)
- Radoslav Kozma
- Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, Uppsala, SE-75236, Sweden
| | - Páll Melsted
- Faculty of Industrial Engineering, Mechanical Engineering and Computer Science, University of Iceland, Reykjavik, 107, Iceland.,deCODE Genetics/Amgen, Reykjavik, Iceland
| | - Kristinn P Magnússon
- The Icelandic Institute of Natural History, Borgir v. Nordurslod, Akureyri, 600, Iceland.,Department of Natural Resource Sciences, University of Akureyri, Borgir vid Nordurslod, Akureyri, 600, Iceland.,Biomedical Center, University of Iceland, Vatnsmýrarvegur 16, Reykjavik, 101, Iceland
| | - Jacob Höglund
- Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, Uppsala, SE-75236, Sweden
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19
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Heidaritabar M, Calus MPL, Megens HJ, Vereijken A, Groenen MAM, Bastiaansen JWM. Accuracy of genomic prediction using imputed whole-genome sequence data in white layers. J Anim Breed Genet 2016; 133:167-79. [PMID: 26776363 DOI: 10.1111/jbg.12199] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Accepted: 11/26/2015] [Indexed: 01/17/2023]
Abstract
There is an increasing interest in using whole-genome sequence data in genomic selection breeding programmes. Prediction of breeding values is expected to be more accurate when whole-genome sequence is used, because the causal mutations are assumed to be in the data. We performed genomic prediction for the number of eggs in white layers using imputed whole-genome resequence data including ~4.6 million SNPs. The prediction accuracies based on sequence data were compared with the accuracies from the 60 K SNP panel. Predictions were based on genomic best linear unbiased prediction (GBLUP) as well as a Bayesian variable selection model (BayesC). Moreover, the prediction accuracy from using different types of variants (synonymous, non-synonymous and non-coding SNPs) was evaluated. Genomic prediction using the 60 K SNP panel resulted in a prediction accuracy of 0.74 when GBLUP was applied. With sequence data, there was a small increase (~1%) in prediction accuracy over the 60 K genotypes. With both 60 K SNP panel and sequence data, GBLUP slightly outperformed BayesC in predicting the breeding values. Selection of SNPs more likely to affect the phenotype (i.e. non-synonymous SNPs) did not improve the accuracy of genomic prediction. The fact that sequence data were based on imputation from a small number of sequenced animals may have limited the potential to improve the prediction accuracy. A small reference population (n = 1004) and possible exclusion of many causal SNPs during quality control can be other possible reasons for limited benefit of sequence data. We expect, however, that the limited improvement is because the 60 K SNP panel was already sufficiently dense to accurately determine the relationships between animals in our data.
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Affiliation(s)
- M Heidaritabar
- Animal Breeding and Genomics Centre, Wageningen University, Wageningen, the Netherlands
| | - M P L Calus
- Animal Breeding and Genomics Centre, Wageningen UR Livestock Research, Wageningen, the Netherlands
| | - H-J Megens
- Animal Breeding and Genomics Centre, Wageningen University, Wageningen, the Netherlands
| | - A Vereijken
- Hendrix Genetics Research, Technology and Services B.V., Boxmeer, the Netherlands
| | - M A M Groenen
- Animal Breeding and Genomics Centre, Wageningen University, Wageningen, the Netherlands
| | - J W M Bastiaansen
- Animal Breeding and Genomics Centre, Wageningen University, Wageningen, the Netherlands
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20
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Successful Recovery of Nuclear Protein-Coding Genes from Small Insects in Museums Using Illumina Sequencing. PLoS One 2015; 10:e0143929. [PMID: 26716693 PMCID: PMC4696846 DOI: 10.1371/journal.pone.0143929] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Accepted: 10/12/2015] [Indexed: 01/30/2023] Open
Abstract
In this paper we explore high-throughput Illumina sequencing of nuclear protein-coding, ribosomal, and mitochondrial genes in small, dried insects stored in natural history collections. We sequenced one tenebrionid beetle and 12 carabid beetles ranging in size from 3.7 to 9.7 mm in length that have been stored in various museums for 4 to 84 years. Although we chose a number of old, small specimens for which we expected low sequence recovery, we successfully recovered at least some low-copy nuclear protein-coding genes from all specimens. For example, in one 56-year-old beetle, 4.4 mm in length, our de novo assembly recovered about 63% of approximately 41,900 nucleotides in a target suite of 67 nuclear protein-coding gene fragments, and 70% using a reference-based assembly. Even in the least successfully sequenced carabid specimen, reference-based assembly yielded fragments that were at least 50% of the target length for 34 of 67 nuclear protein-coding gene fragments. Exploration of alternative references for reference-based assembly revealed few signs of bias created by the reference. For all specimens we recovered almost complete copies of ribosomal and mitochondrial genes. We verified the general accuracy of the sequences through comparisons with sequences obtained from PCR and Sanger sequencing, including of conspecific, fresh specimens, and through phylogenetic analysis that tested the placement of sequences in predicted regions. A few possible inaccuracies in the sequences were detected, but these rarely affected the phylogenetic placement of the samples. Although our sample sizes are low, an exploratory regression study suggests that the dominant factor in predicting success at recovering nuclear protein-coding genes is a high number of Illumina reads, with success at PCR of COI and killing by immersion in ethanol being secondary factors; in analyses of only high-read samples, the primary significant explanatory variable was body length, with small beetles being more successfully sequenced.
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21
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Oyler-McCance SJ, Cornman RS, Jones KL, Fike JA. Z chromosome divergence, polymorphism and relative effective population size in a genus of lekking birds. Heredity (Edinb) 2015; 115:452-9. [PMID: 26014526 PMCID: PMC4611240 DOI: 10.1038/hdy.2015.46] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2014] [Revised: 03/13/2015] [Accepted: 04/07/2015] [Indexed: 01/29/2023] Open
Abstract
Sex chromosomes contribute disproportionately to species boundaries as they diverge faster than autosomes and often have reduced diversity. Their hemizygous nature contributes to faster divergence and reduced diversity, as do some types of selection. In birds, other factors (mating system and bottlenecks) can further decrease the effective population size of Z-linked loci and accelerate divergence (Fast-Z). We assessed Z-linked divergence and effective population sizes for two polygynous sage-grouse species and compared them to estimates from birds with various mating systems. We found lower diversity and higher FST for Z-linked loci than for autosomes, as expected. The π(Z)/π(A) ratio was 0.38 in Centrocercus minimus, 0.48 in Centrocercus urophasianus and 0.59 in a diverged, parapatric population of C. urophasianus, a broad range given the mating system among these groups is presumably equivalent. The full data set had unequal males and females across groups, so we compared an equally balanced reduced set of C. minimus and individuals pooled from both C. urophasianus subgroups recovering similar estimates: 0.54 for C. urophasianus and 0.38 for C. minimus. We provide further evidence that N(eZ)/N(eA) in birds is often lower than expected under random mating or monogamy. The lower ratio in C. minimus could be a consequence of stronger selection or drift acting on Z loci during speciation, as this species differs strongly from C. urophasianus in sexually selected characters with minimal mitochondrial divergence. As C. minimus also exhibited lower genomic diversity, it is possible that a more severe demographic history may contribute to its lower ratio.
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Affiliation(s)
- S J Oyler-McCance
- U.S. Geological Survey, Fort Collins Science Center, Fort Collins, CO, USA
| | - R S Cornman
- U.S. Geological Survey, Leetown Science Center, Kearneysville, WV, USA
| | - K L Jones
- Department of Biochemistry and Molecular Genetics, University of Colorado, School of Medicine, Aurora, CO, USA
| | - J A Fike
- U.S. Geological Survey, Fort Collins Science Center, Fort Collins, CO, USA
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22
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Dunn CW, Ryan JF. The evolution of animal genomes. Curr Opin Genet Dev 2015; 35:25-32. [PMID: 26363125 DOI: 10.1016/j.gde.2015.08.006] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2015] [Revised: 08/18/2015] [Accepted: 08/20/2015] [Indexed: 11/18/2022]
Abstract
Genome sequences are now available for hundreds of species sampled across the animal phylogeny, bringing key features of animal genome evolution into sharper focus. The field of animal evolutionary genomics has focused on identifying and classifying the diversity genomic features, reconstructing the history of evolutionary changes in animal genomes, and testing hypotheses about the evolutionary relationships of animals. The grand challenges moving forward are to connect evolutionary changes in genomes with particular evolutionary changes in phenotypes, and to determine which changes are driven by selection. This will require far greater genome sampling both across and within species, extensive phenotype data, a well resolved animal phylogeny, and advances in comparative methods.
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Affiliation(s)
- Casey W Dunn
- Department of Ecology and Evolutionary Biology, Brown University, 80 Waterman St., Providence, RI 02906, USA.
| | - Joseph F Ryan
- Whitney Laboratory for Marine Bioscience, University of Florida, 9505 Ocean Shore Blvd., St Augustine, FL 32080, USA; Department of Biology, University of Florida, Gainesville, FL 32611, USA
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23
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Hoen DR, Hickey G, Bourque G, Casacuberta J, Cordaux R, Feschotte C, Fiston-Lavier AS, Hua-Van A, Hubley R, Kapusta A, Lerat E, Maumus F, Pollock DD, Quesneville H, Smit A, Wheeler TJ, Bureau TE, Blanchette M. A call for benchmarking transposable element annotation methods. Mob DNA 2015; 6:13. [PMID: 26244060 PMCID: PMC4524446 DOI: 10.1186/s13100-015-0044-6] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Accepted: 07/22/2015] [Indexed: 12/31/2022] Open
Abstract
DNA derived from transposable elements (TEs) constitutes large parts of the genomes of complex eukaryotes, with major impacts not only on genomic research but also on how organisms evolve and function. Although a variety of methods and tools have been developed to detect and annotate TEs, there are as yet no standard benchmarks-that is, no standard way to measure or compare their accuracy. This lack of accuracy assessment calls into question conclusions from a wide range of research that depends explicitly or implicitly on TE annotation. In the absence of standard benchmarks, toolmakers are impeded in improving their tools, annotators cannot properly assess which tools might best suit their needs, and downstream researchers cannot judge how accuracy limitations might impact their studies. We therefore propose that the TE research community create and adopt standard TE annotation benchmarks, and we call for other researchers to join the authors in making this long-overdue effort a success.
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Affiliation(s)
- Douglas R Hoen
- School of Computer Science, McGill University, McConnell Engineering Bldg., Rm. 318, 3480 Rue University, Montréal, Québec H3A 0E9 Canada ; Department of Biology, McGill University, Stewart Biology Bldg., 1205 Ave. du Docteur-Penfield, Montréal, Québec H3A 1B1 Canada
| | - Glenn Hickey
- School of Computer Science, McGill University, McConnell Engineering Bldg., Rm. 318, 3480 Rue University, Montréal, Québec H3A 0E9 Canada ; McGill Centre for Bioinformatics, McGill University, Montréal, Québec Canada
| | - Guillaume Bourque
- Department of Human Genetics, McGill University, Montréal, Québec Canada ; McGill University and Génome Québec Innovation Center, Montréal, Québec Canada
| | - Josep Casacuberta
- Centre for Research in Agricultural Genomics CSIC-IRTA-UAB-UB, 08193 Barcelona, Spain
| | - Richard Cordaux
- Université de Poitiers, UMR CNRS 7267 Ecologie et Biologie des Interactions, Equipe Ecologie Evolution Symbiose, 5 Rue Albert Turpin, 86073 Poitiers Cedex 9, France
| | - Cédric Feschotte
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT 84112 USA
| | - Anna-Sophie Fiston-Lavier
- Institut des Sciences de l'Evolution de Montpellier (ISE-M), Equipe Evolution, Vecteurs, Adaptation et Symbiose, UMR5554 CNRS-Université Montpellier, Montpellier, 34090 cedex 05 France
| | - Aurélie Hua-Van
- Laboratoire Evolution, Génomes, Comportement Ecologie, CNRS-Université Paris-Sud (UMR 9191)-IRD (UMR 247)-Université Paris-Saclay, F-91198 Gif-sur-Yvette, France
| | - Robert Hubley
- Institute for Systems Biology, 401 Terry Ave. N, Seattle, WA 98109 USA
| | - Aurélie Kapusta
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT 84112 USA
| | - Emmanuelle Lerat
- Laboratoire Biometrie et Biologie Evolutive, Universite Claude Bernard-Lyon 1, UMR-CNRS 5558-Bat. Mendel, 43 bd du 11 novembre 1918, 69622 Villeurbanne cedex, France
| | - Florian Maumus
- INRA, UR1164 URGI-Research Unit in Genomics-Info, INRA de Versailles-Grignon, Route de Saint-Cyr, Versailles, 78026 France
| | - David D Pollock
- University of Colorado School of Medicine, Aurora, CO 80045 USA
| | - Hadi Quesneville
- INRA, UR1164 URGI-Research Unit in Genomics-Info, INRA de Versailles-Grignon, Route de Saint-Cyr, Versailles, 78026 France
| | - Arian Smit
- Institute for Systems Biology, 401 Terry Ave. N, Seattle, WA 98109 USA
| | - Travis J Wheeler
- Department of Computer Science, University of Montana, Missoula, MT 59812 USA
| | - Thomas E Bureau
- Department of Biology, McGill University, Stewart Biology Bldg., 1205 Ave. du Docteur-Penfield, Montréal, Québec H3A 1B1 Canada
| | - Mathieu Blanchette
- School of Computer Science, McGill University, McConnell Engineering Bldg., Rm. 318, 3480 Rue University, Montréal, Québec H3A 0E9 Canada ; McGill Centre for Bioinformatics, McGill University, Montréal, Québec Canada
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Schmid M, Smith J, Burt DW, Aken BL, Antin PB, Archibald AL, Ashwell C, Blackshear PJ, Boschiero C, Brown CT, Burgess SC, Cheng HH, Chow W, Coble DJ, Cooksey A, Crooijmans RPMA, Damas J, Davis RVN, de Koning DJ, Delany ME, Derrien T, Desta TT, Dunn IC, Dunn M, Ellegren H, Eöry L, Erb I, Farré M, Fasold M, Fleming D, Flicek P, Fowler KE, Frésard L, Froman DP, Garceau V, Gardner PP, Gheyas AA, Griffin DK, Groenen MAM, Haaf T, Hanotte O, Hart A, Häsler J, Hedges SB, Hertel J, Howe K, Hubbard A, Hume DA, Kaiser P, Kedra D, Kemp SJ, Klopp C, Kniel KE, Kuo R, Lagarrigue S, Lamont SJ, Larkin DM, Lawal RA, Markland SM, McCarthy F, McCormack HA, McPherson MC, Motegi A, Muljo SA, Münsterberg A, Nag R, Nanda I, Neuberger M, Nitsche A, Notredame C, Noyes H, O'Connor R, O'Hare EA, Oler AJ, Ommeh SC, Pais H, Persia M, Pitel F, Preeyanon L, Prieto Barja P, Pritchett EM, Rhoads DD, Robinson CM, Romanov MN, Rothschild M, Roux PF, Schmidt CJ, Schneider AS, Schwartz MG, Searle SM, Skinner MA, Smith CA, Stadler PF, Steeves TE, Steinlein C, Sun L, Takata M, Ulitsky I, Wang Q, Wang Y, Warren WC, Wood JMD, Wragg D, Zhou H. Third Report on Chicken Genes and Chromosomes 2015. Cytogenet Genome Res 2015; 145:78-179. [PMID: 26282327 PMCID: PMC5120589 DOI: 10.1159/000430927] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Affiliation(s)
- Michael Schmid
- Department of Human Genetics, University of Würzburg, Würzburg, Germany
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Miller JM, Moore SS, Stothard P, Liao X, Coltman DW. Harnessing cross-species alignment to discover SNPs and generate a draft genome sequence of a bighorn sheep (Ovis canadensis). BMC Genomics 2015; 16:397. [PMID: 25990117 PMCID: PMC4438629 DOI: 10.1186/s12864-015-1618-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2015] [Accepted: 05/05/2015] [Indexed: 02/08/2023] Open
Abstract
Background Whole genome sequences (WGS) have proliferated as sequencing technology continues to improve and costs decline. While many WGS of model or domestic organisms have been produced, a growing number of non-model species are also being sequenced. In the absence of a reference, construction of a genome sequence necessitates de novo assembly which may be beyond the ability of many labs due to the large volumes of raw sequence data and extensive bioinformatics required. In contrast, the presence of a reference WGS allows for alignment which is more tractable than assembly. Recent work has highlighted that the reference need not come from the same species, potentially enabling a wide array of species WGS to be constructed using cross-species alignment. Here we report on the creation a draft WGS from a single bighorn sheep (Ovis canadensis) using alignment to the closely related domestic sheep (Ovis aries). Results Two sequencing libraries on SOLiD platforms yielded over 865 million reads, and combined alignment to the domestic sheep reference resulted in a nearly complete sequence (95% coverage of the reference) at an average of 12x read depth (104 SD). From this we discovered over 15 million variants and annotated them relative to the domestic sheep reference. We then conducted an enrichment analysis of those SNPs showing fixed differences between the reference and sequenced individual and found significant differences in a number of gene ontology (GO) terms, including those associated with reproduction, muscle properties, and bone deposition. Conclusion Our results demonstrate that cross-species alignment enables the creation of novel WGS for non-model organisms. The bighorn sheep WGS will provide a resource for future resequencing studies or comparative genomics. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1618-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Joshua M Miller
- Department of Biological Science, University of Alberta, Edmonton, Alberta, Canada.
| | - Stephen S Moore
- Centre for Animal Science, Queensland Alliance for Agriculture & Food Innovation, University of Queensland, St Lucia, QLD, Australia. .,Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, Canada.
| | - Paul Stothard
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, Canada.
| | - Xiaoping Liao
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China.
| | - David W Coltman
- Department of Biological Science, University of Alberta, Edmonton, Alberta, Canada.
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Hormozdiari F, Eskin E. Memory efficient assembly of human genome. J Bioinform Comput Biol 2015; 13:1550008. [PMID: 25603998 DOI: 10.1142/s0219720015500080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The ability to detect the genetic variations between two individuals is an essential component for genetic studies. In these studies, obtaining the genome sequence of both individuals is the first step toward variation detection problem. The emergence of high-throughput sequencing (HTS) technology has made DNA sequencing practical, and is widely used by diagnosticians to increase their knowledge about the casual factor in genetic related diseases. As HTS advances, more data are generated every day than the amount that scientists can process. Genome assembly is one of the existing methods to tackle the variation detection problem. The de Bruijn graph formulation of the assembly problem is widely used in the field. Furthermore, it is the only method which can assemble any genome in linear time. However, it requires an enormous amount of memory in order to assemble any mammalian size genome. The high demands of sequencing more individuals and the urge to assemble them are the driving forces for a memory efficient assembler. In this work, we propose a novel method which builds the de Bruijn graph while consuming lower memory. Moreover, our proposed method can reduce the memory usage by 37% compared to the existing methods. In addition, we used a real data set (chromosome 17 of A/J strain) to illustrate the performance of our method.
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Affiliation(s)
- Farhad Hormozdiari
- Department of Computer Science, University of California Los Angeles, Los Angeles, CA 90095, USA
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Abstract
The Genome 10K Project was established in 2009 by a consortium of biologists and genome scientists determined to facilitate the sequencing and analysis of the complete genomes of 10,000 vertebrate species. Since then the number of selected and initiated species has risen from ∼26 to 277 sequenced or ongoing with funding, an approximately tenfold increase in five years. Here we summarize the advances and commitments that have occurred by mid-2014 and outline the achievements and present challenges of reaching the 10,000-species goal. We summarize the status of known vertebrate genome projects, recommend standards for pronouncing a genome as sequenced or completed, and provide our present and future vision of the landscape of Genome 10K. The endeavor is ambitious, bold, expensive, and uncertain, but together the Genome 10K Consortium of Scientists and the worldwide genomics community are moving toward their goal of delivering to the coming generation the gift of genome empowerment for many vertebrate species.
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Affiliation(s)
- Klaus-Peter Koepfli
- Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, 199034 St. Petersburg, Russian Federation;
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28
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Differential introgression and effective size of marker type influence phylogenetic inference of a recently divergent avian group (Phasianidae: Tympanuchus). Mol Phylogenet Evol 2014; 84:1-13. [PMID: 25554526 DOI: 10.1016/j.ympev.2014.12.012] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2014] [Revised: 12/12/2014] [Accepted: 12/18/2014] [Indexed: 11/20/2022]
Abstract
Life history strategies can influence the effective population size (Ne) of loci differently based on their mode of inheritance. Recognizing how this may affect the rate of lineage sorting among marker types is important for studies focused on resolving phylogenetic relationships among recently divergent taxa. In this study, we use gene tree, coalescent-based species tree, and isolation-with-migration analyses to explore the differences between marker types (autosomal, Z-linked, and mitochondrial) in resolving phylogenetic relationships among North American prairie grouse (Tympanuchus). We found that Z-linked loci were more likely to identify monophyletic relationships among prairie grouse species compared to autosomal and mtDNA loci in both species and gene tree analyses, with species tree analyses outperforming gene trees. These results were further supported with isolation-with-migration analyses, where Z-linked loci largely followed a strict isolation model while autosomal loci were more likely to fit a model with gene flow between species following population divergence. While accounting for differences in inheritance pattern (or Ne) for marker type, results suggest that additional factors, such as strong sexual selection and sex-biased introgression (i.e., male-biased postzygotic hybrid behavioral isolation or "unsexy son"), may further explain the decreased diversity levels and increased rate of lineage sorting observed with the Z-linked loci relative to autosomal and mtDNA loci. In fact, to our knowledge no hybrid male prairie grouse have been observed breeding in the wild, yet hybrid females along with backcross females are known to produce viable offspring. Overall, this study highlights that more work is needed to determine how complex models of gene flow (i.e., sex biased introgression) and differences in the effective size among marker types based on differing life history strategies influence divergence date estimation and species delimitation.
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McMahon BJ, Teeling EC, Höglund J. How and why should we implement genomics into conservation? Evol Appl 2014; 7:999-1007. [PMID: 25553063 PMCID: PMC4231591 DOI: 10.1111/eva.12193] [Citation(s) in RCA: 111] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2014] [Accepted: 06/19/2014] [Indexed: 12/14/2022] Open
Abstract
Conservation genetics has provided important information into the dynamics of endangered populations. The rapid development of genomic methods has posed an important question, namely where do genetics and genomics sit in relation to their application in the conservation of species? Although genetics can answer a number of relevant questions related to conservation, the argument for the application of genomics is not yet fully exploited. Here, we explore the transition and rationale for the move from genetic to genomic research in conservation biology and the utility of such research. We explore the idea of a 'conservation prior' and how this can be determined by genomic data and used in the management of populations. We depict three different conservation scenarios and describe how genomic data can drive management action in each situation. We conclude that the most effective applications of genomics will be to inform stakeholders with the aim of avoiding 'emergency room conservation'.
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Affiliation(s)
- Barry J McMahon
- UCD School of Agriculture & Food Science, University College DublinBelfield, Dublin 4, Ireland
| | - Emma C Teeling
- UCD School of Biology & Environmental Science, University College DublinBelfield, Dublin 4, Ireland
| | - Jacob Höglund
- Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala UniversityUppsala, Sweden
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Ekblom R, Wolf JBW. A field guide to whole-genome sequencing, assembly and annotation. Evol Appl 2014; 7:1026-42. [PMID: 25553065 PMCID: PMC4231593 DOI: 10.1111/eva.12178] [Citation(s) in RCA: 188] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2014] [Accepted: 05/20/2014] [Indexed: 12/12/2022] Open
Abstract
Genome sequencing projects were long confined to biomedical model organisms and required the concerted effort of large consortia. Rapid progress in high-throughput sequencing technology and the simultaneous development of bioinformatic tools have democratized the field. It is now within reach for individual research groups in the eco-evolutionary and conservation community to generate de novo draft genome sequences for any organism of choice. Because of the cost and considerable effort involved in such an endeavour, the important first step is to thoroughly consider whether a genome sequence is necessary for addressing the biological question at hand. Once this decision is taken, a genome project requires careful planning with respect to the organism involved and the intended quality of the genome draft. Here, we briefly review the state of the art within this field and provide a step-by-step introduction to the workflow involved in genome sequencing, assembly and annotation with particular reference to large and complex genomes. This tutorial is targeted at scientists with a background in conservation genetics, but more generally, provides useful practical guidance for researchers engaging in whole-genome sequencing projects.
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Affiliation(s)
- Robert Ekblom
- Department of Evolutionary Biology, Uppsala University Uppsala, Sweden
| | - Jochen B W Wolf
- Department of Evolutionary Biology, Uppsala University Uppsala, Sweden
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