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Cheung K, Amos TG, Shine R, DeVore JL, Ducatez S, Edwards RJ, Rollins LA. Whole-mitogenome analysis unveils previously undescribed genetic diversity in cane toads across their invasion trajectory. Ecol Evol 2024; 14:e11115. [PMID: 38435005 PMCID: PMC10909579 DOI: 10.1002/ece3.11115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 02/16/2024] [Accepted: 02/22/2024] [Indexed: 03/05/2024] Open
Abstract
Invasive species offer insights into rapid adaptation to novel environments. The iconic cane toad (Rhinella marina) is an excellent model for studying rapid adaptation during invasion. Previous research using the mitochondrial NADH dehydrogenase 3 (ND3) gene in Hawai'ian and Australian invasive populations found a single haplotype, indicating an extreme genetic bottleneck following introduction. Nuclear genetic diversity also exhibited reductions across the genome in these two populations. Here, we investigated the mitochondrial genomics of cane toads across this invasion trajectory. We created the first reference mitochondrial genome for this species using long-read sequence data. We combined whole-genome resequencing data of 15 toads with published transcriptomic data of 125 individuals to construct nearly complete mitochondrial genomes from the native (French Guiana) and introduced (Hawai'i and Australia) ranges for population genomic analyses. In agreement with previous investigations of these populations, we identified genetic bottlenecks in both Hawai'ian and Australian introduced populations, alongside evidence of population expansion in the invasive ranges. Although mitochondrial genetic diversity in introduced populations was reduced, our results revealed that it had been underestimated: we identified 45 mitochondrial haplotypes in Hawai'ian and Australian samples, none of which were found in the native range. Additionally, we identified two distinct groups of haplotypes from the native range, separated by a minimum of 110 base pairs (0.6%). These findings enhance our understanding of how invasion has shaped the genetic landscape of this species.
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Affiliation(s)
- Kelton Cheung
- Evolution & Ecology Research Centre, School of Biological, Earth & Environmental SciencesUniversity of New South WalesSydneyNew South WalesAustralia
- School of Biotechnology & Biomolecular SciencesUniversity of New South WalesSydneyNew South WalesAustralia
| | - Timothy G. Amos
- School of Biotechnology & Biomolecular SciencesUniversity of New South WalesSydneyNew South WalesAustralia
- Garvan Institute of Medical ResearchSydneyNew South WalesAustralia
| | - Rick Shine
- Department of Biological SciencesMacquarie UniversitySydneyNew South WalesAustralia
| | - Jayna L. DeVore
- Univ. Polynésie FrancaiseUMR 241 EIO (UPF, IRD, IFREMER, ILM) BP 6570 Faa'aTahitiFrench Polynesia
| | - Simon Ducatez
- Institut de Recherche pour le Développement (IRD)UMR 241 EIO (UPF, IRD, IFREMER, ILM) BP 6570 Faa'aTahitiFrench Polynesia
| | - Richard J. Edwards
- School of Biotechnology & Biomolecular SciencesUniversity of New South WalesSydneyNew South WalesAustralia
- Minderoo OceanOmics Centre at UWA, Oceans InstituteThe University of Western AustraliaPerthWestern AustraliaAustralia
| | - Lee Ann Rollins
- Evolution & Ecology Research Centre, School of Biological, Earth & Environmental SciencesUniversity of New South WalesSydneyNew South WalesAustralia
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2
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Chen X, Li J, Yu L, Maule F, Chang L, Gallant JA, Press DJ, Raithatha SA, Hagel JM, Facchini PJ. A cane toad (Rhinella marina) N-methyltransferase converts primary indolethylamines to tertiary psychedelic amines. J Biol Chem 2023; 299:105231. [PMID: 37690691 PMCID: PMC10570959 DOI: 10.1016/j.jbc.2023.105231] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 08/31/2023] [Accepted: 09/03/2023] [Indexed: 09/12/2023] Open
Abstract
Psychedelic indolethylamines have emerged as potential medicines to treat several psychiatric pathologies. Natural sources of these compounds include 'magic mushrooms' (Psilocybe spp.), plants used to prepare ayahuasca, and toads. The skin and parotid glands of certain toads accumulate a variety of specialized metabolites including toxic guanidine alkaloids, lipophilic alkaloids, poisonous steroids, and hallucinogenic indolethylamines such as DMT, 5-methoxy-DMT, and bufotenin. The occurrence of psychedelics has contributed to the ceremonial use of toads, particularly among Mesoamerican peoples. Yet, the biosynthesis of psychedelic alkaloids has not been elucidated. Herein, we report a novel indolethylamine N-methyltransferase (RmNMT) from cane toad (Rhinella marina). The RmNMT sequence was used to identify a related NMT from the common toad, Bufo bufo. Close homologs from various frog species were inactive, suggesting a role for psychedelic indolethylamine biosynthesis in toads. Enzyme kinetic analyses and comparison with functionally similar enzymes showed that recombinant RmNMT was an effective catalyst and not product inhibited. The substrate promiscuity of RmNMT enabled the bioproduction of a variety of substituted indolethylamines at levels sufficient for purification, pharmacological screening, and metabolic stability assays. Since the therapeutic potential of psychedelics has been linked to activity at serotonergic receptors, we evaluated binding of derivatives at 5-HT1A and 5-HT2A receptors. Primary amines exhibited enhanced affinity at the 5-HT1A receptor compared with tertiary amines. With the exception of 6-substituted derivatives, N,N-dimethylation also protected against catabolism by liver microsomes.
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Affiliation(s)
- Xue Chen
- Discovery Group, Enveric Biosciences Inc, Calgary, Alberta, Canada
| | - Jing Li
- Discovery Group, Enveric Biosciences Inc, Calgary, Alberta, Canada
| | - Lisa Yu
- Discovery Group, Enveric Biosciences Inc, Calgary, Alberta, Canada
| | - Francesca Maule
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
| | - Limei Chang
- Discovery Group, Enveric Biosciences Inc, Calgary, Alberta, Canada
| | | | - David J Press
- Discovery Group, Enveric Biosciences Inc, Calgary, Alberta, Canada
| | | | - Jillian M Hagel
- Discovery Group, Enveric Biosciences Inc, Calgary, Alberta, Canada
| | - Peter J Facchini
- Discovery Group, Enveric Biosciences Inc, Calgary, Alberta, Canada; Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada.
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3
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Yagound B, West AJ, Richardson MF, Gruber J, Reid JG, Whiting MJ, Rollins LA. Captivity induces large and population-dependent brain transcriptomic changes in wild-caught cane toads (Rhinella marina). Mol Ecol 2022; 31:4949-4961. [PMID: 35894800 PMCID: PMC9804778 DOI: 10.1111/mec.16633] [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: 03/18/2022] [Revised: 07/14/2022] [Accepted: 07/25/2022] [Indexed: 01/09/2023]
Abstract
Gene expression levels are key molecular phenotypes at the interplay between genotype and environment. Mounting evidence suggests that short-term changes in environmental conditions, such as those encountered in captivity, can substantially affect gene expression levels. Yet, the exact magnitude of this effect, how general it is, and whether it results in parallel changes across populations are not well understood. Here, we take advantage of the well-studied cane toad, Rhinella marina, to examine the effect of short-term captivity on brain gene expression levels, and determine whether effects of captivity differ between long-colonized and vanguard populations of the cane toad's Australian invasion range. We compared the transcriptomes of wild-caught toads immediately assayed with those from toads captured from the same populations but maintained in captivity for seven months. We found large differences in gene expression levels between captive and wild-caught toads from the same population, with an over-representation of processes related to behaviour and the response to stress. Captivity had a much larger effect on both gene expression levels and gene expression variability in toads from vanguard populations compared to toads from long-colonized areas, potentially indicating an increased plasticity in toads at the leading edge of the invasion. Overall, our findings indicate that short-term captivity can induce large and population-specific transcriptomic changes, which has significant implications for studies comparing phenotypic traits of wild-caught organisms from different populations that have been held in captivity.
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Affiliation(s)
- Boris Yagound
- Evolution & Ecology Research Centre, School of Biological, Earth & Environmental SciencesUniversity of New South WalesSydneyNew South WalesAustralia
| | - Andrea J. West
- Centre for Integrative Ecology, School of Life and Environmental SciencesDeakin UniversityGeelongVictoriaAustralia
| | - Mark F. Richardson
- Centre for Integrative Ecology, School of Life and Environmental SciencesDeakin UniversityGeelongVictoriaAustralia,Deakin Genomics Centre, School of Life and Environmental SciencesDeakin UniversityGeelongVictoriaAustralia
| | - Jodie Gruber
- College of Life and Environmental SciencesUniversity of ExeterPenrynUK,School of Life and Environmental SciencesThe University of SydneySydneyNew South WalesAustralia
| | - Jack G. Reid
- Centre for Integrative Ecology, School of Life and Environmental SciencesDeakin UniversityGeelongVictoriaAustralia
| | - Martin J. Whiting
- Department of Biological SciencesMacquarie UniversitySydneyNew South WalesAustralia
| | - Lee A. Rollins
- Evolution & Ecology Research Centre, School of Biological, Earth & Environmental SciencesUniversity of New South WalesSydneyNew South WalesAustralia,Centre for Integrative Ecology, School of Life and Environmental SciencesDeakin UniversityGeelongVictoriaAustralia
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4
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Firneno TJ, Ramesh B, Maldonado JA, Hernandez-Briones AI, Emery AH, Roelke CE, Fujita MK. Transcriptomic analysis reveals potential candidate pathways and genes involved in toxin biosynthesis in true toads. J Hered 2022; 113:311-324. [PMID: 35325156 DOI: 10.1093/jhered/esac015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 03/21/2022] [Indexed: 11/13/2022] Open
Abstract
Synthesized chemical defenses have broadly evolved across countless taxa and are important in shaping evolutionary and ecological interactions within ecosystems. However, the underlying genomic mechanisms by which these organisms synthesize and utilize their toxins are relatively unknown. Herein, we use comparative transcriptomics to uncover potential toxin synthesizing genes and pathways, as well as interspecific patterns of toxin synthesizing genes across ten species of North American true toads (Bufonidae). Upon assembly and annotation of the ten transcriptomes, we explored patterns of relative gene expression and possible protein-protein interactions across the species to determine what genes and/or pathways may be responsible for toxin synthesis. We also tested our transcriptome dataset for signatures of positive selection to reveal how selection may be acting upon potential toxin producing genes. We assembled high quality transcriptomes of the bufonid parotoid gland, a tissue not often investigated in other bufonid related RNAseq studies. We found several genes involved in metabolic and biosynthetic pathways (e.g. steroid biosynthesis, terpenoid backbone biosynthesis, isoquinoline biosynthesis, glucosinolate biosynthesis) that were functionally enriched and/or relatively expressed across the ten focal species that may be involved in the synthesis of alkaloid and steroid toxins, as well as other small metabolic compounds that cause distastefulness in bufonids. We hope that our study lays a foundation for future studies to explore the genomic underpinnings and specific pathways of toxin synthesis in toads, as well as at the macroevolutionary scale across numerous taxa that produce their own defensive toxins.
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Affiliation(s)
- Thomas J Firneno
- Department of Biology, University of Texas, Arlington, Texas, 76019-0498, USA.,Amphibian and Reptile Diversity Research Center, Department of Biology, University of Texas, Arlington, Texas, 76019-0498, USA
| | - Balan Ramesh
- Department of Biology, University of Texas, Arlington, Texas, 76019-0498, USA
| | - Jose A Maldonado
- Department of Biology, University of Texas, Arlington, Texas, 76019-0498, USA.,Amphibian and Reptile Diversity Research Center, Department of Biology, University of Texas, Arlington, Texas, 76019-0498, USA
| | | | - Alyson H Emery
- Department of Biology, University of Texas, Arlington, Texas, 76019-0498, USA
| | - Corey E Roelke
- Department of Biology, University of Texas, Arlington, Texas, 76019-0498, USA.,Amphibian and Reptile Diversity Research Center, Department of Biology, University of Texas, Arlington, Texas, 76019-0498, USA
| | - Matthew K Fujita
- Department of Biology, University of Texas, Arlington, Texas, 76019-0498, USA.,Amphibian and Reptile Diversity Research Center, Department of Biology, University of Texas, Arlington, Texas, 76019-0498, USA
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5
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Yagound B, West AJ, Richardson MF, Selechnik D, Shine R, Rollins LA. Brain transcriptome analysis reveals gene expression differences associated with dispersal behaviour between range-front and range-core populations of invasive cane toads in Australia. Mol Ecol 2022; 31:1700-1715. [PMID: 35028988 PMCID: PMC9303232 DOI: 10.1111/mec.16347] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 12/19/2021] [Accepted: 01/07/2022] [Indexed: 11/27/2022]
Abstract
Understanding the mechanisms allowing invasive species to adapt to novel environments is a challenge in invasion biology. Many invaders demonstrate rapid evolution of behavioural traits involved in range expansion such as locomotor activity, exploration and risk‐taking. However, the molecular mechanisms that underpin these changes are poorly understood. In 86 years, invasive cane toads (Rhinella marina) in Australia have drastically expanded their geographic range westward from coastal Queensland to Western Australia. During their range expansion, toads have undergone extensive phenotypic changes, particularly in behaviours that enhance the toads’ dispersal ability. Common‐garden experiments have shown that some changes in behavioural traits related to dispersal are heritable. At the molecular level, it is currently unknown whether these changes in dispersal‐related behaviour are underlain by small or large differences in gene expression, nor is known the biological function of genes showing differential expression. Here, we used RNA‐seq to gain a better understanding of the molecular mechanisms underlying dispersal‐related behavioural changes. We compared the brain transcriptomes of toads from the Hawai'ian source population, as well as three distinct populations from across the Australian invasive range. We found markedly different gene expression profiles between the source population and Australian toads. By contrast, toads from across the Australian invasive range had very similar transcriptomic profiles. Yet, key genes with functions putatively related to dispersal behaviour showed differential expression between populations located at each end of the invasive range. These genes could play an important role in the behavioural changes characteristic of range expansion in Australian cane toads.
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Affiliation(s)
- Boris Yagound
- Evolution & Ecology Research Centre, School of Biological, Earth & Environmental Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Andrea J West
- Centre for Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Geelong, VIC, Australia
| | - Mark F Richardson
- Centre for Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Geelong, VIC, Australia.,Deakin Genomics Centre, School of Life and Environmental Sciences, Deakin University, Geelong, VIC, Australia
| | - Daniel Selechnik
- Centre for Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Geelong, VIC, Australia
| | - Richard Shine
- Department of Biological Sciences, Macquarie University, Sydney, NSW, Australia
| | - Lee A Rollins
- Evolution & Ecology Research Centre, School of Biological, Earth & Environmental Sciences, University of New South Wales, Sydney, NSW, Australia.,Centre for Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Geelong, VIC, Australia
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6
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Medina-Ortiz K, López-Alvarez D, Navia F, Hansen T, Fierro L, Castaño S. Identification of Na +/K +-ATPase α/β isoforms in Rhinella marina tissues by RNAseq and a molecular docking approach at the protein level to evaluate α isoform affinities for bufadienolides. Comp Biochem Physiol A Mol Integr Physiol 2021; 254:110906. [PMID: 33476762 DOI: 10.1016/j.cbpa.2021.110906] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 01/12/2021] [Accepted: 01/12/2021] [Indexed: 12/24/2022]
Abstract
Na+/K+-ATPase (NKA) function is inhibited by Bufadienolides (BD), a group of cardiotonic steroids (CTS) primarily produced by anurans of the Bufonidae family, such as Rhinella marina. This study characterized the presence of α and β NKA subunit isoforms in R. marina via RNAseq in four tissues: oocytes, skin, heart, and skeletal muscle. Transcripts encoding three α-like isoforms (α1, α2, α3) and three β-like isoforms (β1, β2, β4) were identified. The amino acid sequence of α1-like isoform shared 99.4% identity with the α1 isoform previously published for R. marina. Sequences for α2, α3, and β4 from R. marina were previously unavailable. The first extracellular loop in the α2-like isoform in R. marina showed similar substitutions to those found in their susceptible homologues in other taxa (L/Q111T and S119T); in contrast, this same loop in α3-like isoform showed similar substitutions (Q111L and G120R) to those reported for toad-eating animals such as snakes, which suggests relatively lower affinity for CTS. Docking results showed that all three α-like isoforms identified in R. marina transcriptomes have low affinity to CTS compared to the susceptible α1 isoform of Sus scrofa (pig), with α1-like isoform being the most resistant. The tissue-specific RNAseq results showed the following expression of NKA α-like and β-like subunit isoforms: Oocytes expressed α1 and β1; skin α1, β1, and low levels of β2; heart α1, α3, and β1; skeletal muscle α1, β4, with low levels of α2, α3, and β1. R. marina could be used as an important model for future structural, functional and pharmacological studies of NKA and its isoforms.
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Affiliation(s)
- Katherine Medina-Ortiz
- Laboratorio de Herpetología y Toxinología, Department of Physiological Sciences, Universidad del Valle, Cali, Colombia.
| | - Diana López-Alvarez
- Laboratorio de Herpetología y Toxinología, Department of Physiological Sciences, Universidad del Valle, Cali, Colombia
| | - Felipe Navia
- Laboratorio de Herpetología y Toxinología, Department of Physiological Sciences, Universidad del Valle, Cali, Colombia
| | - Thomas Hansen
- Laboratorio de Herpetología y Toxinología, Department of Physiological Sciences, Universidad del Valle, Cali, Colombia
| | - Leonardo Fierro
- Laboratorio de Herpetología y Toxinología, Department of Physiological Sciences, Universidad del Valle, Cali, Colombia
| | - Santiago Castaño
- Laboratorio de Herpetología y Toxinología, Department of Physiological Sciences, Universidad del Valle, Cali, Colombia.
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7
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The rise and fall of globins in the amphibia. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2020; 37:100759. [PMID: 33202310 DOI: 10.1016/j.cbd.2020.100759] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2020] [Revised: 10/23/2020] [Accepted: 10/29/2020] [Indexed: 12/28/2022]
Abstract
The globin gene repertoire of gnathostome vertebrates is dictated by differential retention and loss of nine paralogous genes: androglobin, neuroglobin, globin X, cytoglobin, globin Y, myoglobin, globin E, and the α- and β-globins. We report the globin gene repertoire of three orders of modern amphibians: Anura, Caudata, and Gymnophiona. Combining phylogenetic and conserved synteny analysis, we show that myoglobin and globin E were lost only in the Batrachia clade, but retained in Gymnophiona. The major amphibian groups also retained different paralogous copies of globin X. None of the amphibian presented αD-globin gene. Nevertheless, two clades of β-globins are present in all amphibians, indicating that the amphibian ancestor possessed two paralogous proto β-globins. We also show that orthologs of the gene coding for the monomeric hemoglobin found in the heart of Rana catesbeiana are present in Neobatrachia and Pelobatoidea species we analyzed. We suggest that these genes might perform myoglobin- and globin E-related functions. We conclude that the repertoire of globin genes in amphibians is dictated by both retention and loss of the paralogous genes cited above and the rise of a new globin gene through co-option of an α-globin, possibly facilitated by a prior event of transposition.
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8
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Goossens S, Wybouw N, Van Leeuwen T, Bonte D. The physiology of movement. MOVEMENT ECOLOGY 2020; 8:5. [PMID: 32042434 PMCID: PMC7001223 DOI: 10.1186/s40462-020-0192-2] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Accepted: 01/08/2020] [Indexed: 05/05/2023]
Abstract
Movement, from foraging to migration, is known to be under the influence of the environment. The translation of environmental cues to individual movement decision making is determined by an individual's internal state and anticipated to balance costs and benefits. General body condition, metabolic and hormonal physiology mechanistically underpin this internal state. These physiological determinants are tightly, and often genetically linked with each other and hence central to a mechanistic understanding of movement. We here synthesise the available evidence of the physiological drivers and signatures of movement and review (1) how physiological state as measured in its most coarse way by body condition correlates with movement decisions during foraging, migration and dispersal, (2) how hormonal changes underlie changes in these movement strategies and (3) how these can be linked to molecular pathways. We reveale that a high body condition facilitates the efficiency of routine foraging, dispersal and migration. Dispersal decision making is, however, in some cases stimulated by a decreased individual condition. Many of the biotic and abiotic stressors that induce movement initiate a physiological cascade in vertebrates through the production of stress hormones. Movement is therefore associated with hormone levels in vertebrates but also insects, often in interaction with factors related to body or social condition. The underlying molecular and physiological mechanisms are currently studied in few model species, and show -in congruence with our insights on the role of body condition- a central role of energy metabolism during glycolysis, and the coupling with timing processes during migration. Molecular insights into the physiological basis of movement remain, however, highly refractory. We finalise this review with a critical reflection on the importance of these physiological feedbacks for a better mechanistic understanding of movement and its effects on ecological dynamics at all levels of biological organization.
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Affiliation(s)
- Steven Goossens
- Department of Biology, Ghent University, K.L. Ledeganckstraat 35, 9000 Ghent, Belgium
| | - Nicky Wybouw
- Laboratory of Agrozoology, Department of Plants and Crops, Ghent University, Coupure Links 653, 9000 Ghent, Belgium
| | - Thomas Van Leeuwen
- Laboratory of Agrozoology, Department of Plants and Crops, Ghent University, Coupure Links 653, 9000 Ghent, Belgium
| | - Dries Bonte
- Department of Biology, Ghent University, K.L. Ledeganckstraat 35, 9000 Ghent, Belgium
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9
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Selechnik D, Richardson MF, Shine R, DeVore JL, Ducatez S, Rollins LA. Increased Adaptive Variation Despite Reduced Overall Genetic Diversity in a Rapidly Adapting Invader. Front Genet 2019; 10:1221. [PMID: 31850072 PMCID: PMC6901984 DOI: 10.3389/fgene.2019.01221] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Accepted: 11/05/2019] [Indexed: 01/26/2023] Open
Abstract
Invasive species often evolve rapidly following introduction despite genetic bottlenecks that may result from small numbers of founders; however, some invasions may not fit this “genetic paradox”. The invasive cane toad (Rhinella marina) displays high phenotypic variation across its introduced Australian range. Here, we used three genome-wide datasets to characterize their population structure and genetic diversity. We found that toads form three genetic clusters: 1) native range toads, 2) toads from the source population in Hawaii and long-established areas near introduction sites in Australia, and 3) toads from more recently established northern Australian sites. Although we find an overall reduction in genetic diversity following introduction, we do not see this reduction in loci putatively under selection, suggesting that genetic diversity may have been maintained at ecologically relevant traits, or that mutation rates were high enough to maintain adaptive potential. Nonetheless, toads encounter novel environmental challenges in Australia, and the transition between genetic clusters occurs at a point along the invasion transect where temperature rises and rainfall decreases. We identify environmentally associated loci known to be involved in resistance to heat and dehydration. This study highlights that natural selection occurs rapidly and plays a vital role in shaping the structure of invasive populations.
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Affiliation(s)
- Daniel Selechnik
- School of Life and Environmental Sciences (SOLES), University of Sydney, Sydney, NSW, Australia.,Evolution and Ecology Research Centre, School of Biological, Earth, and Environmental Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Mark F Richardson
- Deakin Genomics Centre, School of Life and Environmental Sciences, Deakin University, Geelong, VIC, Australia.,Centre for Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Geelong, VIC, Australia
| | - Richard Shine
- School of Life and Environmental Sciences (SOLES), University of Sydney, Sydney, NSW, Australia
| | - Jayna L DeVore
- School of Life and Environmental Sciences (SOLES), University of Sydney, Sydney, NSW, Australia
| | - Simon Ducatez
- School of Life and Environmental Sciences (SOLES), University of Sydney, Sydney, NSW, Australia
| | - Lee A Rollins
- Evolution and Ecology Research Centre, School of Biological, Earth, and Environmental Sciences, University of New South Wales, Sydney, NSW, Australia
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10
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do Amaral DF, Guerra V, Motta AGC, de Melo E Silva D, Rocha TL. Ecotoxicity of nanomaterials in amphibians: A critical review. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 686:332-344. [PMID: 31181520 DOI: 10.1016/j.scitotenv.2019.05.487] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2019] [Revised: 05/15/2019] [Accepted: 05/31/2019] [Indexed: 06/09/2023]
Abstract
Nanomaterials (NMs) have been used in a growing number of commercial products, and their rapid expansion could lead to their release into the aquatic environments. However, there is limited knowledge about the impact of NMs in the biota, especially the amphibians. The present study revised the historical use of amphibian species as a model system for nanoecotoxicological studies and summarized the data available in the scientific literature about the genotoxic, mutagenic, histopathological, embryotoxic and reproductive effects of NMs in different groups of amphibians. The interaction, bioaccumulation, mode of action (MoA) and ecotoxicity of NMs on amphibians were also revised. The nanoecotoxicological studies were conducted with 11 amphibian species, being eight species of the order Anura and three species of the order Caudata. Xenopus laevis was the most studied species. The studies were conducted mainly with inorganic NMs (72%) compared to organic ones. The nanoecotoxicity depends on NM behavior and transformation in the environment, as well as the developmental stages of amphibians. The known effects of NMs in amphibians were mainly reported with reactive oxygen species (ROS) production, oxidative stress, and genotoxic effects. Results emphasize the need for further studies testing the ecotoxicity of different NMs, concentrations and exposure periods at environmentally relevant approaches. Furthermore, standard protocols for nanoecotoxicological tests using amphibians are required. Revised data showed that amphibians are suitable organisms to assess the environmental impact of NMs and indicated significant research gaps concerning the ecotoxicity of NMs on freshwater ecosystems and recommendations for future researches.
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Affiliation(s)
- Diogo Ferreira do Amaral
- Laboratory of Mutagenesis, Department of Genetics, Federal University of Goiás, Goiânia, Goiás, Brazil; Laboratory of Environmental Biotechnology and Ecotoxicology, Institute of Tropical Pathology and Public Health, Federal University of Goiás, Goiânia, Goiás, Brazil
| | - Vinicius Guerra
- Laboratory of Herpetology and Animal Behavior, Department of Ecology, Federal University of Goiás, Goiânia, Goiás, Brazil
| | - Andreya Gonçalves Costa Motta
- Laboratory of Mutagenesis, Department of Genetics, Federal University of Goiás, Goiânia, Goiás, Brazil; Laboratory of Environmental Biotechnology and Ecotoxicology, Institute of Tropical Pathology and Public Health, Federal University of Goiás, Goiânia, Goiás, Brazil
| | - Daniela de Melo E Silva
- Laboratory of Mutagenesis, Department of Genetics, Federal University of Goiás, Goiânia, Goiás, Brazil
| | - Thiago Lopes Rocha
- Laboratory of Environmental Biotechnology and Ecotoxicology, Institute of Tropical Pathology and Public Health, Federal University of Goiás, Goiânia, Goiás, Brazil.
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11
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De Novo Assembly and Annotation of the Larval Transcriptome of Two Spadefoot Toads Widely Divergent in Developmental Rate. G3-GENES GENOMES GENETICS 2019; 9:2647-2655. [PMID: 31217263 PMCID: PMC6686947 DOI: 10.1534/g3.119.400389] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Amphibians are highly vulnerable and diverse vertebrates for which we still have modest genomic resources. Amphibian larvae are key components of continental wetlands, where they have strong influences on energy fluxes, nutrient cycling, and community structure. Amphibian larvae are highly sensitive to environmental conditions and can often alter their physiology, behavior and even morphology in response to the local conditions experienced, although we still know relatively little about the transcriptomic changes that enable such plasticity. Here we contribute the larval transcriptomes of two spadefoot toad species with divergent developmental rates and degree of developmental plasticity in response to pond drying.
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12
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Rogers RL, Zhou L, Chu C, Márquez R, Corl A, Linderoth T, Freeborn L, MacManes MD, Xiong Z, Zheng J, Guo C, Xun X, Kronforst MR, Summers K, Wu Y, Yang H, Richards-Zawacki CL, Zhang G, Nielsen R. Genomic Takeover by Transposable Elements in the Strawberry Poison Frog. Mol Biol Evol 2019; 35:2913-2927. [PMID: 30517748 PMCID: PMC6278860 DOI: 10.1093/molbev/msy185] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
We sequenced the genome of the strawberry poison frog, Oophaga pumilio, at a depth of 127.5× using variable insert size libraries. The total genome size is estimated to be 6.76 Gb, of which 4.76 Gb are from high copy number repetitive elements with low differentiation across copies. These repeats encompass DNA transposons, RNA transposons, and LTR retrotransposons, including at least 0.4 and 1.0 Gb of Mariner/Tc1 and Gypsy elements, respectively. Expression data indicate high levels of gypsy and Mariner/Tc1 expression in ova of O. pumilio compared with Xenopus laevis. We further observe phylogenetic evidence for horizontal transfer (HT) of Mariner elements, possibly between fish and frogs. The elements affected by HT are present in high copy number and are highly expressed, suggesting ongoing proliferation after HT. Our results suggest that the large amphibian genome sizes, at least partially, can be explained by a process of repeated invasion of new transposable elements that are not yet suppressed in the germline. We also find changes in the spliceosome that we hypothesize are related to permissiveness of O. pumilio to increases in intron length due to transposon proliferation. Finally, we identify the complement of ion channels in the first genomic sequenced poison frog and discuss its relation to the evolution of autoresistance to toxins sequestered in the skin.
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Affiliation(s)
- Rebekah L Rogers
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, NC
| | - Long Zhou
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,China National Genebank, BGI-Shenzhen, Shenzhen, Guangdong, China
| | - Chong Chu
- Harvard Medical School, Harvard University, Cambridge, MA
| | - Roberto Márquez
- Department of Ecology and Evolution, University of Chicago, Chicago, IL
| | - Ammon Corl
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA
| | - Tyler Linderoth
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA
| | - Layla Freeborn
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA
| | - Matthew D MacManes
- Department of Molecular Cellular and Biomedical Sciences, University of New Hampshire, Durham, NH.,Hubbard Center for Genomic Studies, University of New Hampshire, Durham, NH
| | - Zijun Xiong
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Jiao Zheng
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Chunxue Guo
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Xu Xun
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | | | - Kyle Summers
- Department of Biology, Eastern Carolina University, Greenville, NC
| | - Yufeng Wu
- Department of Computer Science, University of Connecticut, Storrs, CT
| | - Huanming Yang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,James D. Watson Institute of Genome Sciences, Hangzhou, China
| | | | - Guojie Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,China National Genebank, BGI-Shenzhen, Shenzhen, Guangdong, China.,Department of Biology, Centre for Social Evolution, Universitetsparken 15, University of Copenhagen, Copenhagen, Denmark
| | - Rasmus Nielsen
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA
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13
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Selechnik D, Richardson MF, Shine R, Brown GP, Rollins LA. Immune and environment-driven gene expression during invasion: An eco-immunological application of RNA-Seq. Ecol Evol 2019; 9:6708-6721. [PMID: 31236254 PMCID: PMC6580278 DOI: 10.1002/ece3.5249] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Revised: 04/19/2019] [Accepted: 04/23/2019] [Indexed: 12/18/2022] Open
Abstract
Host-pathogen associations change rapidly during a biological invasion and are predicted to impose strong selection on immune function. It has been proposed that the invader may experience an abrupt reduction in pathogen-mediated selection ("enemy release"), thereby favoring decreased investment into "costly" immune responses. Across plants and animals, there is mixed support for this prediction. Pathogens are not the only form of selection imposed on invaders; differences in abiotic environmental conditions between native and introduced ranges are also expected to drive rapid evolution. Here, we use RNA-Seq to assess the expression patterns of immune and environmentally associated genes in the cane toad (Rhinella marina) across its invasive Australian range. Transcripts encoding mediators of costly immune responses (inflammation, cytotoxicity) showed a curvilinear relationship with invasion history, with highest expression in toads from oldest and newest colonized areas. This pattern is surprising given theoretical expectations of density dynamics in invasive species and may be because density influences both intraspecific competition and parasite transmission, generating conflicting effects on the strength of immune responses. Alternatively, this expression pattern may be the result of other evolutionary forces, such as spatial sorting and genetic drift, working simultaneously with natural selection. Our findings do not support predictions about immune function based on the enemy release hypothesis and suggest instead that the effects of enemy release are difficult to isolate in wild populations, especially in the absence of information regarding parasite and pathogen infection. Additionally, expression patterns of genes underlying putatively environmentally associated traits are consistent with previous genetic studies, providing further support that Australian cane toads have adapted to novel abiotic challenges.
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Affiliation(s)
- Daniel Selechnik
- School of Life and Environmental Sciences (SOLES)University of SydneySydneyNew South WalesAustralia
| | - Mark F. Richardson
- Deakin Genomics Centre, School of Life and Environmental SciencesDeakin UniversityGeelongVictoriaAustralia
- Centre for Integrative Ecology, School of Life and Environmental SciencesDeakin UniversityGeelongVictoriaAustralia
| | - Richard Shine
- School of Life and Environmental Sciences (SOLES)University of SydneySydneyNew South WalesAustralia
| | - Gregory P. Brown
- School of Life and Environmental Sciences (SOLES)University of SydneySydneyNew South WalesAustralia
| | - Lee Ann Rollins
- Centre for Integrative Ecology, School of Life and Environmental SciencesDeakin UniversityGeelongVictoriaAustralia
- Evolution & Ecology Research Centre, School of Biological, Earth and Environmental SciencesUNSW SydneySydneyNew South WalesAustralia
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14
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RNA Sequencing of Peripheral Blood Revealed that the Neurotropic TRK Receptor Signaling Pathway Shows Apparent Correlation in Recovery Following Spinal Cord Injury at Small Cohort. J Mol Neurosci 2019; 68:221-233. [PMID: 30993646 DOI: 10.1007/s12031-019-01273-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Accepted: 01/29/2019] [Indexed: 12/14/2022]
Abstract
Spinal cord injury (SCI) can be lethal; however, the precise mechanisms underlying healing are unclear, limiting the development of effective therapies. In this study, the molecular mechanisms involved in SCI were investigated. Clinical peripheral blood samples from normal individuals and patients with incomplete SCI (ISCI) and complete SCI (CSCI) were analyzed by RNA-Seq. The expression levels of EPHA4, CDK16, BAD, MAP2 Normal 2, EGR, and RHOB differed significantly between the SCI group and normal individuals, and these results were verified by q-PCR. A gene ontology (GO) enrichment analysis showed that differentially expressed genes were mostly enriched for the neurotrophin TRK receptor signaling pathway. We verified the expression of neurotrophic factors and found that they were all expressed most highly in the SCI group. The results of this study demonstrate that neurotrophic factors are highly expressed after SCI and the neurotrophin TRK receptor signaling pathway may be involved in the initiation of nerve system regeneration.
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15
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Richardson MF, Sequeira F, Selechnik D, Carneiro M, Vallinoto M, Reid JG, West AJ, Crossland MR, Shine R, Rollins LA. Improving amphibian genomic resources: a multitissue reference transcriptome of an iconic invader. Gigascience 2018; 7:1-7. [PMID: 29186423 PMCID: PMC5765561 DOI: 10.1093/gigascience/gix114] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Accepted: 11/16/2017] [Indexed: 01/23/2023] Open
Abstract
Background Cane toads (Rhinella marina) are an iconic invasive species introduced to 4 continents and well utilized for studies of rapid evolution in introduced environments. Despite the long introduction history of this species, its profound ecological impacts, and its utility for demonstrating evolutionary principles, genetic information is sparse. Here we produce a de novo transcriptome spanning multiple tissues and life stages to enable investigation of the genetic basis of previously identified rapid phenotypic change over the introduced range. Findings Using approximately 1.9 billion reads from developing tadpoles and 6 adult tissue-specific cDNA libraries, as well as a transcriptome assembly pipeline encompassing 100 separate de novo assemblies, we constructed 62 202 transcripts, of which we functionally annotated ∼50%. Our transcriptome assembly exhibits 90% full-length completeness of the Benchmarking Universal Single-Copy Orthologs data set. Robust assembly metrics and comparisons with several available anuran transcriptomes and genomes indicate that our cane toad assembly is one of the most complete anuran genomic resources available. Conclusions This comprehensive anuran transcriptome will provide a valuable resource for investigation of genes under selection during invasion in cane toads, but will also greatly expand our general knowledge of anuran genomes, which are underrepresented in the literature. The data set is publically available in NCBI and GigaDB to serve as a resource for other researchers.
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Affiliation(s)
- Mark F Richardson
- Deakin University, Bioinformatics Core Research Group, 75 Pigdons Road, Locked Bag 20000, Geelong, VIC 3220, Australia.,Deakin University, School of Life and Environmental Sciences, Centre for Integrative Ecology (Waurn Ponds Campus), 75 Pigdons Road, Locked Bag 20000, Geelong, VIC 3220, Australia
| | - Fernando Sequeira
- CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Campus Agrário de Vairão, Universidade do Porto, 4485-661, Vairão, Portugal
| | - Daniel Selechnik
- School of Life and Environmental Sciences, The University of Sydney, NSW 2006, Australia
| | - Miguel Carneiro
- CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Campus Agrário de Vairão, Universidade do Porto, 4485-661, Vairão, Portugal.,Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n., 4169-007 Porto, Portugal
| | - Marcelo Vallinoto
- Laboratório de Evolução (LEVO), Instituto de Estudos Costeiros (IECOS), Universidade Federal do Pará, Campus de Bragança, Pará, Brasil
| | - Jack G Reid
- Deakin University, School of Life and Environmental Sciences, Centre for Integrative Ecology (Waurn Ponds Campus), 75 Pigdons Road, Locked Bag 20000, Geelong, VIC 3220, Australia
| | - Andrea J West
- Deakin University, School of Life and Environmental Sciences, Centre for Integrative Ecology (Waurn Ponds Campus), 75 Pigdons Road, Locked Bag 20000, Geelong, VIC 3220, Australia
| | - Michael R Crossland
- School of Life and Environmental Sciences, The University of Sydney, NSW 2006, Australia
| | - Richard Shine
- School of Life and Environmental Sciences, The University of Sydney, NSW 2006, Australia
| | - Lee A Rollins
- Deakin University, School of Life and Environmental Sciences, Centre for Integrative Ecology (Waurn Ponds Campus), 75 Pigdons Road, Locked Bag 20000, Geelong, VIC 3220, Australia
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16
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Edwards RJ, Tuipulotu DE, Amos TG, O'Meally D, Richardson MF, Russell TL, Vallinoto M, Carneiro M, Ferrand N, Wilkins MR, Sequeira F, Rollins LA, Holmes EC, Shine R, White PA. Draft genome assembly of the invasive cane toad, Rhinella marina. Gigascience 2018; 7:5096832. [PMID: 30101298 PMCID: PMC6145236 DOI: 10.1093/gigascience/giy095] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Accepted: 07/22/2018] [Indexed: 12/28/2022] Open
Abstract
Background The cane toad (Rhinella marina formerly Bufo marinus) is a species native to Central and South America that has spread across many regions of the globe. Cane toads are known for their rapid adaptation and deleterious impacts on native fauna in invaded regions. However, despite an iconic status, there are major gaps in our understanding of cane toad genetics. The availability of a genome would help to close these gaps and accelerate cane toad research. Findings We report a draft genome assembly for R. marina, the first of its kind for the Bufonidae family. We used a combination of long-read Pacific Biosciences RS II and short-read Illumina HiSeq X sequencing to generate 359.5 Gb of raw sequence data. The final hybrid assembly of 31,392 scaffolds was 2.55 Gb in length with a scaffold N50 of 168 kb. BUSCO analysis revealed that the assembly included full length or partial fragments of 90.6% of tetrapod universal single-copy orthologs (n = 3950), illustrating that the gene-containing regions have been well assembled. Annotation predicted 25,846 protein coding genes with similarity to known proteins in Swiss-Prot. Repeat sequences were estimated to account for 63.9% of the assembly. Conclusions The R. marina draft genome assembly will be an invaluable resource that can be used to further probe the biology of this invasive species. Future analysis of the genome will provide insights into cane toad evolution and enrich our understanding of their interplay with the ecosystem at large.
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Affiliation(s)
- Richard J Edwards
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Daniel Enosi Tuipulotu
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Timothy G Amos
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Denis O'Meally
- Sydney School of Veterinary Science, Faculty of Science, University of Sydney, Camperdown, NSW, 2052, Australia
| | - Mark F Richardson
- School of Life and Environmental Sciences, Centre for Integrative Ecology, Deakin University, Geelong, VIC, 3216, Australia.,Bioinformatics Core Research Group, Deakin University, Geelong, VIC, 3216, Australia
| | - Tonia L Russell
- Ramaciotti Centre for Genomics, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Marcelo Vallinoto
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vairão, Portugal.,Laboratório de Evolução, Instituto de Estudos Costeiros (IECOS), Universidade Federal do Pará, Bragança, Pará, Brazil
| | - Miguel Carneiro
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vairão, Portugal
| | - Nuno Ferrand
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vairão, Portugal.,Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal.,Department of Zoology, Faculty of Sciences, University of Johannesburg, Auckland Park, South Africa
| | - Marc R Wilkins
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, 2052, Australia.,Ramaciotti Centre for Genomics, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Fernando Sequeira
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vairão, Portugal
| | - Lee A Rollins
- School of Life and Environmental Sciences, Centre for Integrative Ecology, Deakin University, Geelong, VIC, 3216, Australia.,Evolution and Ecology Research Centre, School of Biological Earth and Environmental Sciences, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Edward C Holmes
- Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences and Sydney Medical School, University of Sydney, Sydney, NSW, 2006, Australia
| | - Richard Shine
- School of Life and Environmental Sciences, Faculty of Science, University of Sydney, Camperdown, NSW, 2006, Australia
| | - Peter A White
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, 2052, Australia
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17
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Quinn TP, Crowley TM, Richardson MF. Benchmarking differential expression analysis tools for RNA-Seq: normalization-based vs. log-ratio transformation-based methods. BMC Bioinformatics 2018; 19:274. [PMID: 30021534 PMCID: PMC6052553 DOI: 10.1186/s12859-018-2261-8] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Accepted: 06/25/2018] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Count data generated by next-generation sequencing assays do not measure absolute transcript abundances. Instead, the data are constrained to an arbitrary "library size" by the sequencing depth of the assay, and typically must be normalized prior to statistical analysis. The constrained nature of these data means one could alternatively use a log-ratio transformation in lieu of normalization, as often done when testing for differential abundance (DA) of operational taxonomic units (OTUs) in 16S rRNA data. Therefore, we benchmark how well the ALDEx2 package, a transformation-based DA tool, detects differential expression in high-throughput RNA-sequencing data (RNA-Seq), compared to conventional RNA-Seq methods such as edgeR and DESeq2. RESULTS To evaluate the performance of log-ratio transformation-based tools, we apply the ALDEx2 package to two simulated, and two real, RNA-Seq data sets. One of the latter was previously used to benchmark dozens of conventional RNA-Seq differential expression methods, enabling us to directly compare transformation-based approaches. We show that ALDEx2, widely used in meta-genomics research, identifies differentially expressed genes (and transcripts) from RNA-Seq data with high precision and, given sufficient sample sizes, high recall too (regardless of the alignment and quantification procedure used). Although we show that the choice in log-ratio transformation can affect performance, ALDEx2 has high precision (i.e., few false positives) across all transformations. Finally, we present a novel, iterative log-ratio transformation (now implemented in ALDEx2) that further improves performance in simulations. CONCLUSIONS Our results suggest that log-ratio transformation-based methods can work to measure differential expression from RNA-Seq data, provided that certain assumptions are met. Moreover, these methods have very high precision (i.e., few false positives) in simulations and perform well on real data too. With previously demonstrated applicability to 16S rRNA data, ALDEx2 can thus serve as a single tool for data from multiple sequencing modalities.
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Affiliation(s)
- Thomas P. Quinn
- Centre for Molecular and Medical Research, School of Medicine, Deakin University, Geelong, 3220 Australia
- Bioinformatics Core Research Group, Deakin University, Geelong, 3220 Australia
| | - Tamsyn M. Crowley
- Centre for Molecular and Medical Research, School of Medicine, Deakin University, Geelong, 3220 Australia
- Bioinformatics Core Research Group, Deakin University, Geelong, 3220 Australia
- Poultry Hub Australia, University of New England, Armidale, 2351 Australia
| | - Mark F. Richardson
- Bioinformatics Core Research Group, Deakin University, Geelong, 3220 Australia
- Centre for Integrative Ecology, School of Life and Environmental Science, Deakin University, Geelong, 3220 Australia
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