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Sun S, Kanzaki N, Dayi M, Maeda Y, Yoshida A, Tanaka R, Kikuchi T. The compact genome of Caenorhabditis niphades n. sp., isolated from a wood-boring weevil, Niphades variegatus. BMC Genomics 2022; 23:765. [PMID: 36418933 PMCID: PMC9682657 DOI: 10.1186/s12864-022-09011-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2022] [Accepted: 11/14/2022] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND The first metazoan genome sequenced, that of Caenorhabditis elegans, has motivated animal genome evolution studies. To date > 50 species from the genus Caenorhabditis have been sequenced, allowing research on genome variation. RESULTS In the present study, we describe a new gonochoristic species, Caenorhabditis niphades n. sp., previously referred as C. sp. 36, isolated from adult weevils (Niphades variegatus), with whom they appear to be tightly associated during its life cycle. Along with a species description, we sequenced the genome of C. niphades n. sp. and produced a chromosome-level assembly. A genome comparison highlighted that C. niphades n. sp. has the smallest genome (59 Mbp) so far sequenced in the Elegans supergroup, despite being closely related to a species with an exceptionally large genome, C. japonica. CONCLUSIONS The compact genome of C. niphades n. sp. can serve as a key resource for comparative evolutionary studies of genome and gene number expansions in Caenorhabditis species.
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Affiliation(s)
- Simo Sun
- grid.26999.3d0000 0001 2151 536XDepartment of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, 277-8562 Japan ,grid.410849.00000 0001 0657 3887Department of Infectious Diseases, Faculty of Medicine, University of Miyazaki, 5200 Kihara, Miyazaki, 889-1692 Japan
| | - Natsumi Kanzaki
- grid.417935.d0000 0000 9150 188XKansai Research Center, Forestry and Forest Products Research Institute, 68 Nagaikyutaroh, Momoyama, Fushimi, Kyoto, 612-0855 Japan
| | - Mehmet Dayi
- grid.26999.3d0000 0001 2151 536XDepartment of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, 277-8562 Japan ,grid.412121.50000 0001 1710 3792Forestry Vocational School, Duzce University, 81620 Duzce, Türkiye
| | - Yasunobu Maeda
- grid.26999.3d0000 0001 2151 536XDepartment of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, 277-8562 Japan ,grid.410849.00000 0001 0657 3887Department of Infectious Diseases, Faculty of Medicine, University of Miyazaki, 5200 Kihara, Miyazaki, 889-1692 Japan
| | - Akemi Yoshida
- grid.410849.00000 0001 0657 3887Genomics and Bioenvironmental Science, Frontier Science Research Center, University of Miyazaki, Miyazaki, 889-1692 Japan
| | - Ryusei Tanaka
- grid.410849.00000 0001 0657 3887Department of Infectious Diseases, Faculty of Medicine, University of Miyazaki, 5200 Kihara, Miyazaki, 889-1692 Japan
| | - Taisei Kikuchi
- grid.26999.3d0000 0001 2151 536XDepartment of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, 277-8562 Japan ,grid.410849.00000 0001 0657 3887Department of Infectious Diseases, Faculty of Medicine, University of Miyazaki, 5200 Kihara, Miyazaki, 889-1692 Japan
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HODDA M. Phylum Nematoda: trends in species descriptions, the documentation of diversity, systematics, and the species concept. Zootaxa 2022; 5114:290-317. [DOI: 10.11646/zootaxa.5114.1.2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Indexed: 11/04/2022]
Abstract
This paper summarizes the trends in nematode species description and systematics emerging from a comparison of the latest comprehensive classification and census of Phylum Nematoda (Hodda 2022a, b) with earlier classifications (listed in Hodda 2007). It also offers some general observations on trends in nematode systematics emerging from the review of the voluminous literature used to produce the classification. The trends in nematodes can be compared with developments in the systematics of other organisms to shed light on many of the general issues confronting systematists now and into the future.
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3
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Dayi M, Kanzaki N, Sun S, Ide T, Tanaka R, Masuya H, Okabe K, Kajimura H, Kikuchi T. Additional description and genome analyses of Caenorhabditis auriculariae representing the basal lineage of genus Caenorhabditis. Sci Rep 2021; 11:6720. [PMID: 33762598 PMCID: PMC7991662 DOI: 10.1038/s41598-021-85967-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Accepted: 03/08/2021] [Indexed: 01/31/2023] Open
Abstract
Caenorhabditis auriculariae, which was morphologically described in 1999, was re-isolated from a Platydema mushroom-associated beetle. Based on the re-isolated materials, some morphological characteristics were re-examined and ascribed to the species. In addition, to clarify phylogenetic relationships with other Caenorhabditis species and biological features of the nematode, the whole genome was sequenced and assembled into 109.5 Mb with 16,279 predicted protein-coding genes. Molecular phylogenetic analyses based on ribosomal RNA and 269 single-copy genes revealed the species is closely related to C. sonorae and C. monodelphis placing them at the most basal clade of the genus. C. auriculariae has morphological characteristics clearly differed from those two species and harbours a number of species-specific gene families, indicating its usefulness as a new outgroup species for Caenorhabditis evolutionary studies. A comparison of carbohydrate-active enzyme (CAZy) repertoires in genomes, which we found useful to speculate about the lifestyle of Caenorhabditis nematodes, suggested that C. auriculariae likely has a life-cycle with tight-association with insects.
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Affiliation(s)
- Mehmet Dayi
- Department of Infectious Disease, Faculty of Medicine, University of Miyazaki, 5200 Kiyotakecho Kihara, Miyazaki-City, Miyazaki, 889-1692, Japan
- Forestry Vocational School, Duzce University, 81620, Duzce, Turkey
| | - Natsumi Kanzaki
- Kansai Research Center, Forestry and Forest Products Research Institute, 68 Nagaikyutaroh, Momoyama, Fushimi, Kyoto, 612-0855, Japan
| | - Simo Sun
- Department of Infectious Disease, Faculty of Medicine, University of Miyazaki, 5200 Kiyotakecho Kihara, Miyazaki-City, Miyazaki, 889-1692, Japan
| | - Tatsuya Ide
- Department of Zoology, National Museum of Nature and Science, 4-1-1 Amakubo, Tsukuba, Ibaraki, 305-0005, Japan
| | - Ryusei Tanaka
- Department of Infectious Disease, Faculty of Medicine, University of Miyazaki, 5200 Kiyotakecho Kihara, Miyazaki-City, Miyazaki, 889-1692, Japan
| | - Hayato Masuya
- Forestry and Forest Products Research Institute, 1 Matsunosato, Tsukuba, Ibaraki, 305-8687, Japan
| | - Kimiko Okabe
- Forestry and Forest Products Research Institute, 1 Matsunosato, Tsukuba, Ibaraki, 305-8687, Japan
| | - Hisashi Kajimura
- Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8601, Japan
| | - Taisei Kikuchi
- Department of Infectious Disease, Faculty of Medicine, University of Miyazaki, 5200 Kiyotakecho Kihara, Miyazaki-City, Miyazaki, 889-1692, Japan.
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4
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Crombie TA, Zdraljevic S, Cook DE, Tanny RE, Brady SC, Wang Y, Evans KS, Hahnel S, Lee D, Rodriguez BC, Zhang G, van der Zwagg J, Kiontke K, Andersen EC. Deep sampling of Hawaiian Caenorhabditis elegans reveals high genetic diversity and admixture with global populations. eLife 2019; 8:50465. [PMID: 31793880 PMCID: PMC6927746 DOI: 10.7554/elife.50465] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Accepted: 12/02/2019] [Indexed: 01/04/2023] Open
Abstract
Hawaiian isolates of the nematode species Caenorhabditis elegans have long been known to harbor genetic diversity greater than the rest of the worldwide population, but this observation was supported by only a small number of wild strains. To better characterize the niche and genetic diversity of Hawaiian C. elegans and other Caenorhabditis species, we sampled different substrates and niches across the Hawaiian islands. We identified hundreds of new Caenorhabditis strains from known species and a new species, Caenorhabditis oiwi. Hawaiian C. elegans are found in cooler climates at high elevations but are not associated with any specific substrate, as compared to other Caenorhabditis species. Surprisingly, admixture analysis revealed evidence of shared ancestry between some Hawaiian and non-Hawaiian C. elegans strains. We suggest that the deep diversity we observed in Hawaii might represent patterns of ancestral genetic diversity in the C. elegans species before human influence.
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Affiliation(s)
- Tim A Crombie
- Department of Molecular Biosciences, Northwestern University, Evanston, United States
| | - Stefan Zdraljevic
- Department of Molecular Biosciences, Northwestern University, Evanston, United States.,Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, United States
| | - Daniel E Cook
- Department of Molecular Biosciences, Northwestern University, Evanston, United States.,Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, United States
| | - Robyn E Tanny
- Department of Molecular Biosciences, Northwestern University, Evanston, United States
| | - Shannon C Brady
- Department of Molecular Biosciences, Northwestern University, Evanston, United States.,Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, United States
| | - Ye Wang
- Department of Molecular Biosciences, Northwestern University, Evanston, United States
| | - Kathryn S Evans
- Department of Molecular Biosciences, Northwestern University, Evanston, United States.,Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, United States
| | - Steffen Hahnel
- Department of Molecular Biosciences, Northwestern University, Evanston, United States
| | - Daehan Lee
- Department of Molecular Biosciences, Northwestern University, Evanston, United States
| | - Briana C Rodriguez
- Department of Molecular Biosciences, Northwestern University, Evanston, United States
| | - Gaotian Zhang
- Department of Molecular Biosciences, Northwestern University, Evanston, United States
| | - Joost van der Zwagg
- Department of Molecular Biosciences, Northwestern University, Evanston, United States
| | - Karin Kiontke
- Department of Biology, New York University, New York, United States
| | - Erik C Andersen
- Department of Molecular Biosciences, Northwestern University, Evanston, United States
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5
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Specific Interactions Between Autosome and X Chromosomes Cause Hybrid Male Sterility in Caenorhabditis Species. Genetics 2019; 212:801-813. [PMID: 31064822 DOI: 10.1534/genetics.119.302202] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Accepted: 05/03/2019] [Indexed: 11/18/2022] Open
Abstract
Hybrid male progeny from interspecies crosses are more prone to sterility or inviability than hybrid female progeny, and the male sterility and inviability often demonstrate parent-of-origin asymmetry. However, the underlying genetic mechanism of asymmetric sterility or inviability remains elusive. We previously established a genome-wide hybrid incompatibility (HI) landscape between Caenorhabditis briggsae and C. nigoni by phenotyping a large collection of C. nigoni strains each carrying a C. briggsae introgression. In this study, we systematically dissect the genetic mechanism of asymmetric sterility and inviability in both hybrid male and female progeny between the two species. Specifically, we performed reciprocal crosses between C . briggsae and different C. nigoni strains that each carry a GFP-labeled C. briggsae genomic fragment referred to as introgression, and scored the HI phenotypes in the F1 progeny. The aggregated introgressions cover 94.6% of the C. briggsae genome, including 100% of the X chromosome. Surprisingly, we observed that two C. briggsae X fragments that produce C. nigoni male sterility as an introgression rescued hybrid F1 sterility in males fathered by C. briggsae Subsequent backcrossing analyses indicated that a specific interaction between the X-linked interaction and one autosome introgression is required to rescue the hybrid male sterility. In addition, we identified another two C. briggsae genomic intervals on chromosomes II and IV that can rescue the inviability, but not the sterility, of hybrid F1 males fathered by C. nigoni, suggesting the involvement of differential epistatic interactions in the asymmetric hybrid male fertility and inviability. Importantly, backcrossing of the rescued sterile males with C. nigoni led to the isolation of a 1.1-Mb genomic interval that specifically interacts with an X-linked introgression, which is essential for hybrid male fertility. We further identified three C. briggsae genomic intervals on chromosome I, II, and III that produced inviability in all F1 progeny, dependent on or independent of the parent-of-origin. Taken together, we identified multiple independent interacting loci that are responsible for asymmetric hybrid male and female sterility, and inviability, which lays a foundation for their molecular characterization.
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6
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Stevens L, Félix M, Beltran T, Braendle C, Caurcel C, Fausett S, Fitch D, Frézal L, Gosse C, Kaur T, Kiontke K, Newton MD, Noble LM, Richaud A, Rockman MV, Sudhaus W, Blaxter M. Comparative genomics of 10 new Caenorhabditis species. Evol Lett 2019; 3:217-236. [PMID: 31007946 PMCID: PMC6457397 DOI: 10.1002/evl3.110] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Revised: 02/08/2019] [Accepted: 02/25/2019] [Indexed: 01/29/2023] Open
Abstract
The nematode Caenorhabditis elegans has been central to the understanding of metazoan biology. However, C. elegans is but one species among millions and the significance of this important model organism will only be fully revealed if it is placed in a rich evolutionary context. Global sampling efforts have led to the discovery of over 50 putative species from the genus Caenorhabditis, many of which await formal species description. Here, we present species descriptions for 10 new Caenorhabditis species. We also present draft genome sequences for nine of these new species, along with a transcriptome assembly for one. We exploit these whole-genome data to reconstruct the Caenorhabditis phylogeny and use this phylogenetic tree to dissect the evolution of morphology in the genus. We reveal extensive variation in genome size and investigate the molecular processes that underlie this variation. We show unexpected complexity in the evolutionary history of key developmental pathway genes. These new species and the associated genomic resources will be essential in our attempts to understand the evolutionary origins of the C. elegans model.
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Affiliation(s)
- Lewis Stevens
- Institute of Evolutionary Biology, Ashworth Laboratories, School of Biological SciencesUniversity of EdinburghEdinburghEH9 3JTUnited Kingdom
| | - Marie‐Anne Félix
- Institut de Biologie de l'Ecole Normale Supérieure, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, École Normale SupérieureParis Sciences et Lettres75005ParisFrance
| | - Toni Beltran
- MRC London Institute of Medical SciencesLondonW12 0NNUnited Kingdom
| | - Christian Braendle
- Université Côte d'Azur, Centre National de la Recherche Scientifique, InsermInstitute of Biology Valrose06108NiceFrance
| | - Carlos Caurcel
- Institute of Evolutionary Biology, Ashworth Laboratories, School of Biological SciencesUniversity of EdinburghEdinburghEH9 3JTUnited Kingdom
| | - Sarah Fausett
- Université Côte d'Azur, Centre National de la Recherche Scientifique, InsermInstitute of Biology Valrose06108NiceFrance
| | - David Fitch
- Department of BiologyNew York UniversityNew YorkNew York10003
| | - Lise Frézal
- Institut de Biologie de l'Ecole Normale Supérieure, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, École Normale SupérieureParis Sciences et Lettres75005ParisFrance
| | - Charlie Gosse
- Institut de Biologie de l'Ecole Normale Supérieure, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, École Normale SupérieureParis Sciences et Lettres75005ParisFrance
| | - Taniya Kaur
- Center for Genomics and Systems Biology, Department of BiologyNew York UniversityNew YorkNew York10003
| | - Karin Kiontke
- Department of BiologyNew York UniversityNew YorkNew York10003
| | - Matthew D. Newton
- MRC London Institute of Medical SciencesLondonW12 0NNUnited Kingdom
- Molecular Virology, Department of MedicineImperial College LondonDu Cane RoadLondonW12 0NNUnited Kingdom
| | - Luke M. Noble
- Center for Genomics and Systems Biology, Department of BiologyNew York UniversityNew YorkNew York10003
| | - Aurélien Richaud
- Institut de Biologie de l'Ecole Normale Supérieure, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, École Normale SupérieureParis Sciences et Lettres75005ParisFrance
| | - Matthew V. Rockman
- Center for Genomics and Systems Biology, Department of BiologyNew York UniversityNew YorkNew York10003
| | - Walter Sudhaus
- Institut für Biologie/ZoologieFreie Universität BerlinBerlinD‐14195Germany
| | - Mark Blaxter
- Institute of Evolutionary Biology, Ashworth Laboratories, School of Biological SciencesUniversity of EdinburghEdinburghEH9 3JTUnited Kingdom
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Abolafia J, Peña-Santiago R. Morphological and Molecular Characterization of Oscheius saproxylicus sp. n. (Rhabditida, Rhabditidae) From Decaying Wood in Spain, With New Insights into the Phylogeny of the Genus and a Revision of its Taxonomy. J Nematol 2019; 51:e2019-53. [PMID: 34179804 PMCID: PMC6909031 DOI: 10.21307/jofnem-2019-053] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Indexed: 11/11/2022] Open
Affiliation(s)
- Joaquín Abolafia
- Departamento de Biología Animal, Biología Vegetal y Ecología, Universidad de Jaén. Campus “Las Lagunillas” s/n. 23071-Jaén, Spain
- * E-mail:
| | - Reyes Peña-Santiago
- Departamento de Biología Animal, Biología Vegetal y Ecología, Universidad de Jaén. Campus “Las Lagunillas” s/n. 23071-Jaén, Spain
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Haag ES, Fitch DHA, Delattre M. From "the Worm" to "the Worms" and Back Again: The Evolutionary Developmental Biology of Nematodes. Genetics 2018; 210:397-433. [PMID: 30287515 PMCID: PMC6216592 DOI: 10.1534/genetics.118.300243] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Accepted: 08/03/2018] [Indexed: 12/13/2022] Open
Abstract
Since the earliest days of research on nematodes, scientists have noted the developmental and morphological variation that exists within and between species. As various cellular and developmental processes were revealed through intense focus on Caenorhabditis elegans, these comparative studies have expanded. Within the genus Caenorhabditis, they include characterization of intraspecific polymorphisms and comparisons of distinct species, all generally amenable to the same laboratory culture methods and supported by robust genomic and experimental tools. The C. elegans paradigm has also motivated studies with more distantly related nematodes and animals. Combined with improved phylogenies, this work has led to important insights about the evolution of nematode development. First, while many aspects of C. elegans development are representative of Caenorhabditis, and of terrestrial nematodes more generally, others vary in ways both obvious and cryptic. Second, the system has revealed several clear examples of developmental flexibility in achieving a particular trait. This includes developmental system drift, in which the developmental control of homologous traits has diverged in different lineages, and cases of convergent evolution. Overall, the wealth of information and experimental techniques developed in C. elegans is being leveraged to make nematodes a powerful system for evolutionary cellular and developmental biology.
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Affiliation(s)
- Eric S Haag
- Department of Biology, University of Maryland, College Park, Maryland 20742
| | | | - Marie Delattre
- Laboratoire de Biologie Moléculaire de la Cellule, CNRS, INSERM, Ecole Normale Supérieure de Lyon, 69007, France
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9
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Woodruff GC, Phillips PC. Field studies reveal a close relative of C. elegans thrives in the fresh figs of Ficus septica and disperses on its Ceratosolen pollinating wasps. BMC Ecol 2018; 18:26. [PMID: 30129423 PMCID: PMC6102938 DOI: 10.1186/s12898-018-0182-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Accepted: 07/30/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Biotic interactions are ubiquitous and require information from ecology, evolutionary biology, and functional genetics in order to be understood. However, study systems that are amenable to investigations across such disparate fields are rare. Figs and fig wasps are a classic system for ecology and evolutionary biology with poor functional genetics; Caenorhabditis elegans is a classic system for functional genetics with poor ecology. In order to help bridge these disciplines, here we describe the natural history of a close relative of C. elegans, Caenorhabditis inopinata, that is associated with the fig Ficus septica and its pollinating Ceratosolen wasps. RESULTS To understand the natural context of fig-associated Caenorhabditis, fresh F. septica figs from four Okinawan islands were sampled, dissected, and observed under microscopy. C. inopinata was found in all islands where F. septica figs were found. C.i nopinata was routinely found in the fig interior and almost never observed on the outside surface. C. inopinata was only found in pollinated figs, and C. inopinata was more likely to be observed in figs with more foundress pollinating wasps. Actively reproducing C. inopinata dominated early phase figs, whereas late phase figs with emerging wasp progeny harbored C. inopinata dauer larvae. Additionally, C. inopinata was observed dismounting from Ceratosolen pollinating wasps that were placed on agar plates. C. inopinata was not found on non-pollinating, parasitic Philotrypesis wasps. Finally, C. inopinata was only observed in F. septica figs among five Okinawan Ficus species sampled. CONCLUSION These are the first detailed field observations of C. inopinata, and they suggest a natural history where this species proliferates in early phase F. septica figs and disperses from late phase figs on Ceratosolen pollinating fig wasps. While consistent with other examples of nematode diversification in the fig microcosm, the fig and wasp host specificity of C. inopinata is highly divergent from the life histories of its close relatives and frames hypotheses for future investigations. This natural co-occurrence of the fig/fig wasp and C. inopinata study systems sets the stage for an integrated research program that can help to explain the evolution of interspecific interactions.
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Affiliation(s)
- Gavin C Woodruff
- Forest Pathology Laboratory, Forestry and Forest Products Research Institute, Tsukuba, Japan.
- Department of Biology, Institute of Ecology and Evolution, University of Oregon, Eugene, OR, USA.
| | - Patrick C Phillips
- Department of Biology, Institute of Ecology and Evolution, University of Oregon, Eugene, OR, USA
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10
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Woodruff GC, Willis JH, Phillips PC. Dramatic evolution of body length due to postembryonic changes in cell size in a newly discovered close relative of Caenorhabditis elegans. Evol Lett 2018; 2:427-441. [PMID: 30283693 PMCID: PMC6121821 DOI: 10.1002/evl3.67] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Revised: 06/08/2018] [Accepted: 06/11/2018] [Indexed: 12/24/2022] Open
Abstract
Understanding morphological diversity-and morphological constraint-has been a central question in evolutionary biology since its inception. Nematodes of the genus Caenorhabditis, which contains the well-studied model organism C. elegans, display remarkable morphological consistency in the face of extensive genetic divergence. Here, we provide a description of the broad developmental patterns of a newly discovered species, C. sp. 34, which was isolated from fresh figs in Okinawa and which is among the closest known relatives of C. elegans. C. sp. 34 displays an extremely large body size; it can grow to be nearly twice as long as C. elegans and all other known members of the genus. Observations of the timing of developmental milestones reveal that C. sp. 34 develops about twice as slowly as C. elegans. Measurements of embryonic and larval size show that the size difference between C. sp. 34 and C. elegans is largely due to postembryonic events, particularly during the transition from larval to adult stages. This difference in size is not attributable to differences in germ line chromosome number or the number of somatic cells. The overall difference in body size is therefore largely attributable to changes in cell size via increased cytoplasmic volume. Because of its close relationship to C. elegans, the distinctness of C. sp. 34 provides an ideal system for the detailed analysis of evolutionary diversification. The context of over 40 years of C. elegans developmental genetics also reveals clues into how natural selection and developmental constraint act jointly to promote patterns of morphological stasis and divergence in this group.
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Affiliation(s)
- Gavin C. Woodruff
- Forestry and Forest Products Research InstituteForest Pathology LaboratoryTsukubaJapan
- Department of Biology, Institute of Ecology and EvolutionUniversity of OregonEugeneOregon97403
| | - John H. Willis
- Department of Biology, Institute of Ecology and EvolutionUniversity of OregonEugeneOregon97403
| | - Patrick C. Phillips
- Department of Biology, Institute of Ecology and EvolutionUniversity of OregonEugeneOregon97403
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11
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Curran DM, Gilleard JS, Wasmuth JD. MIPhy: identify and quantify rapidly evolving members of large gene families. PeerJ 2018; 6:e4873. [PMID: 29868279 PMCID: PMC5983006 DOI: 10.7717/peerj.4873] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Accepted: 05/10/2018] [Indexed: 11/20/2022] Open
Abstract
After transitioning to a new environment, species often exhibit rapid phenotypic innovation. One of the fastest mechanisms for this is duplication followed by specialization of existing genes. When this happens to a member of a gene family, it tends to leave a detectable phylogenetic signature of lineage-specific expansions and contractions. These can be identified by analyzing the gene family across several species and identifying patterns of gene duplication and loss that do not correlate with the known relationships between those species. This signature, termed phylogenetic instability, has been previously linked to adaptations that change the way an organism samples and responds to its environment; conversely, low phylogenetic instability has been previously linked to proteins with endogenous functions. With the increase in genome-level data, there is a need to identify and quantify phylogenetic instability. Here, we present Minimizing Instability in Phylogenetics (MIPhy), a tool that solves this problem by quantifying the incongruence of a gene's evolutionary history. The motivation behind MIPhy was to produce a tool to aid in interpreting phylogenetic trees. It can predict which members of a gene family are under adaptive evolution, working only from a gene tree and the relationship between the species under consideration. While it does not conduct any estimation of positive selection-which is the typical indication of adaptive evolution-the results tend to agree. We demonstrate the usefulness of MIPhy by accurately predicting which members of the mammalian cytochrome P450 gene superfamily metabolize xenobiotics and which metabolize endogenous compounds. Our predictions correlate very well with known substrate specificities of the human enzymes. We also analyze the Caenorhabditis collagen gene family and use MIPhy to predict genes that produce an observable phenotype when knocked down in C. elegans, and show that our predictions correlate well with existing knowledge. The software can be downloaded and installed from https://github.com/dave-the-scientist/miphy and is also available as an online web tool at http://www.miphy.wasmuthlab.org.
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Affiliation(s)
- David M. Curran
- Department of Ecosystem and Public Health, Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
| | - John S. Gilleard
- Department of Comparative Biology and Experimental Medicine, Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
| | - James D. Wasmuth
- Department of Ecosystem and Public Health, Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
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Cytoplasmic-Nuclear Incompatibility Between Wild Isolates of Caenorhabditis nouraguensis. G3-GENES GENOMES GENETICS 2017; 7:823-834. [PMID: 28064190 PMCID: PMC5345712 DOI: 10.1534/g3.116.037101] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
How species arise is a fundamental question in biology. Species can be defined as populations of interbreeding individuals that are reproductively isolated from other such populations. Therefore, understanding how reproductive barriers evolve between populations is essential for understanding the process of speciation. Hybrid incompatibility (for example, hybrid sterility or lethality) is a common and strong reproductive barrier in nature. Here we report a lethal incompatibility between two wild isolates of the nematode Caenorhabditis nouraguensis Hybrid inviability results from the incompatibility between a maternally inherited cytoplasmic factor from each strain and a recessive nuclear locus from the other. We have excluded the possibility that maternally inherited endosymbiotic bacteria cause the incompatibility by treating both strains with tetracycline and show that hybrid death is unaffected. Furthermore, cytoplasmic-nuclear incompatibility commonly occurs between other wild isolates, indicating that this is a significant reproductive barrier within C. nouraguensis We hypothesize that the maternally inherited cytoplasmic factor is the mitochondrial genome and that mitochondrial dysfunction underlies hybrid death. This system has the potential to shed light on the dynamics of divergent mitochondrial-nuclear coevolution and its role in promoting speciation.
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Jovelin R, Krizus A, Taghizada B, Gray JC, Phillips PC, Claycomb JM, Cutter AD. Comparative genomic analysis of upstream miRNA regulatory motifs in Caenorhabditis. RNA (NEW YORK, N.Y.) 2016; 22:968-978. [PMID: 27140965 PMCID: PMC4911920 DOI: 10.1261/rna.055392.115] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Accepted: 02/18/2016] [Indexed: 06/05/2023]
Abstract
MicroRNAs (miRNAs) comprise a class of short noncoding RNA molecules that play diverse developmental and physiological roles by controlling mRNA abundance and protein output of the vast majority of transcripts. Despite the importance of miRNAs in regulating gene function, we still lack a complete understanding of how miRNAs themselves are transcriptionally regulated. To fill this gap, we predicted regulatory sequences by searching for abundant short motifs located upstream of miRNAs in eight species of Caenorhabditis nematodes. We identified three conserved motifs across the Caenorhabditis phylogeny that show clear signatures of purifying selection from comparative genomics, patterns of nucleotide changes in motifs of orthologous miRNAs, and correlation between motif incidence and miRNA expression. We then validated our predictions with transgenic green fluorescent protein reporters and site-directed mutagenesis for a subset of motifs located in an enhancer region upstream of let-7 We demonstrate that a CT-dinucleotide motif is sufficient for proper expression of GFP in the seam cells of adult C. elegans, and that two other motifs play incremental roles in combination with the CT-rich motif. Thus, functional tests of sequence motifs identified through analysis of molecular evolutionary signatures provide a powerful path for efficiently characterizing the transcriptional regulation of miRNA genes.
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Affiliation(s)
- Richard Jovelin
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario M5S 3B2, Canada Informatics and Bio-Computing Program, Ontario Institute for Cancer Research, Toronto, Ontario M5G 0A3, Canada
| | - Aldis Krizus
- Department of Molecular Genetics, University of Toronto, Ontario M5S 1A8, Canada
| | - Bakhtiyar Taghizada
- Department of Molecular Genetics, University of Toronto, Ontario M5S 1A8, Canada
| | - Jeremy C Gray
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario M5S 3B2, Canada
| | - Patrick C Phillips
- Institute of Ecology and Evolution, University of Oregon, Oregon 97403, USA
| | - Julie M Claycomb
- Department of Molecular Genetics, University of Toronto, Ontario M5S 1A8, Canada
| | - Asher D Cutter
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario M5S 3B2, Canada
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14
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Du L, Tracy S, Rifkin SA. Mutagenesis of GATA motifs controlling the endoderm regulator elt-2 reveals distinct dominant and secondary cis-regulatory elements. Dev Biol 2016; 412:160-170. [PMID: 26896592 PMCID: PMC4814310 DOI: 10.1016/j.ydbio.2016.02.013] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Revised: 02/03/2016] [Accepted: 02/10/2016] [Indexed: 10/22/2022]
Abstract
Cis-regulatory elements (CREs) are crucial links in developmental gene regulatory networks, but in many cases, it can be difficult to discern whether similar CREs are functionally equivalent. We found that despite similar conservation and binding capability to upstream activators, different GATA cis-regulatory motifs within the promoter of the C. elegans endoderm regulator elt-2 play distinctive roles in activating and modulating gene expression throughout development. We fused wild-type and mutant versions of the elt-2 promoter to a gfp reporter and inserted these constructs as single copies into the C. elegans genome. We then counted early embryonic gfp transcripts using single-molecule RNA FISH (smFISH) and quantified gut GFP fluorescence. We determined that a single primary dominant GATA motif located 527bp upstream of the elt-2 start codon was necessary for both embryonic activation and later maintenance of transcription, while nearby secondary GATA motifs played largely subtle roles in modulating postembryonic levels of elt-2. Mutation of the primary activating site increased low-level spatiotemporally ectopic stochastic transcription, indicating that this site acts repressively in non-endoderm cells. Our results reveal that CREs with similar GATA factor binding affinities in close proximity can play very divergent context-dependent roles in regulating the expression of a developmentally critical gene in vivo.
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Affiliation(s)
- Lawrence Du
- Section of Ecology, Behavior, and Evolution, Division of Biological Sciences, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0116, United States
| | - Sharon Tracy
- Section of Ecology, Behavior, and Evolution, Division of Biological Sciences, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0116, United States
| | - Scott A Rifkin
- Section of Ecology, Behavior, and Evolution, Division of Biological Sciences, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0116, United States.
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15
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Huang RE, Li R, Zhao Z. Discovery of a free-living nematode phylogenetically related to vertebrate parasites of the genus Strongyloides (Nematoda : Strongyloidoidea): morphological, anatomical and molecular characterisation. INVERTEBR SYST 2016. [DOI: 10.1071/is15048] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Nematodes are important, largely because they frequently act as parasites and threaten the health of plants, animals and even humans. Here, we describe an interesting free-living nematode from land snails on Luofu Mountain, Guangdong, China. Alloionema luofuensis, sp. nov. is phylogenetically related to slug-parasite A. appendiculatum and the well-known vertebrate parasites Strongyloides spp. based on small subunit (SSU) and the D2-D3 domain of large subunit (LSU) rDNA sequences. The new species possesses an extremely transparent body and is easily maintained using C. elegans culture media, suggesting a possible application prospect of this free-living nematode as a comparative model system for its related parasites. Morphology and anatomy of the gonochoristic A. luofuensis, sp. nov. adult were described and illustrated. The species is characterised by a filiform tail bisexually, ‘rhabditiform’ oesophagus and ‘rhabditid-like’ female anatomy, but its male caudal region is completely different from that of typical rhabditid nematodes, being absent from an enveloping bursa. It is the first marker taxon characterised morphologically as well as molecularly from the family Alloionematidae, a group of nematodes with hyperdiverse molecular genetic variations underlying highly conserved anatomy. Further molecular and genetic studies on A. luofuensis, sp. nov. populations hold promise to provide insight into evolution of the clade consisting of vertebrate parasites of the heterogonic nematode genus Strongyloides. This is because of its unusual high levels of heterozygosity maintained by the conserved rRNA genes of partial SSU and the D2-D3 domain of LSU for the type isolate of this species.
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Huang RE, Ye W, Ren X, Zhao Z. Morphological and Molecular Characterization of Phasmarhabditis huizhouensis sp. nov. (Nematoda: Rhabditidae), a New Rhabditid Nematode from South China. PLoS One 2015; 10:e0144386. [PMID: 26674768 PMCID: PMC4686017 DOI: 10.1371/journal.pone.0144386] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2015] [Accepted: 11/17/2015] [Indexed: 11/18/2022] Open
Abstract
The genus Phasmarhabditis is an economically important group of rhabditid nematodes, to which the well-known slug-parasite P. hermaphrodita belongs. Despite the commercial use of Phasmarhabditis species as an attractive and promising approach for pest control, the taxonomy and systematics of this group of rhabditids are poorly understood, largely because of the lack of diagnostic morphological features and DNA sequences for distinguishing species or inferring phylogenetic relationship. During a nematode sampling effort for identifying free-living relatives of Caenorhabditis elegans in Huizhou City, Guangdong, China, a novel species belonging to the genus Phasmarhabditis was isolated from rotting leaves. Detailed morphology of the gonochoristic P. huizhouensis sp. nov. was described and illustrated. The adult female has a robust body, a relatively short and wide buccal capsule conjoined by a rhabditiform pharynx. Females are characterized by a short cupola-shaped tail end bearing a slender pointed tip, with the junction flanked by a pair of ‘rod-like’ phasmids. Males have an open peloderan bursa that is supported by 9 pairs of genital papillae and 1 terminal pair of phasmids. P. huizhouensis sp. nov. is morphologically very similar to the type species Phasmarhabditis papillosa but is distinguishable by its male caudal traits. The new species is readily differentiated from other taxa in the genus by its female tail shape. Molecular phylogenetic inferences based on small subunit (SSU) and the D2-D3 domain of large subunit (LSU) ribosomal DNA genes reveal that P. huizhouensis sp. nov. forms a unique branch in both phylogenies which is genetically related to P. hermaphrodita and other parasites such as Angiostoma spp. The host associations of P. huizhouensis sp. nov. and its ability to parasitize slugs are unknown.
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Affiliation(s)
- Ren-E Huang
- School of Life Sciences, Tsinghua University, Beijing, China
- Department of Biology, Faculty of Science, Hong Kong Baptist University, Hong Kong, China
- * E-mail: (ZZ); (REH)
| | - Weimin Ye
- Nematode Assay Section, Agronomic Division, North Carolina Department of Agriculture & Consumer Services, Raleigh, North Carolina, United States of America
| | - Xiaoliang Ren
- Department of Biology, Faculty of Science, Hong Kong Baptist University, Hong Kong, China
| | - Zhongying Zhao
- Department of Biology, Faculty of Science, Hong Kong Baptist University, Hong Kong, China
- * E-mail: (ZZ); (REH)
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Bundus JD, Alaei R, Cutter AD. Gametic selection, developmental trajectories, and extrinsic heterogeneity in Haldane's rule. Evolution 2015; 69:2005-17. [PMID: 26102479 DOI: 10.1111/evo.12708] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2015] [Accepted: 06/01/2015] [Indexed: 12/31/2022]
Abstract
Deciphering the genetic and developmental causes of the disproportionate rarity, inviability, and sterility of hybrid males, Haldane's rule, is important for understanding the evolution of reproductive isolation between species. Moreover, extrinsic and prezygotic factors can contribute to the magnitude of intrinsic isolation experienced between species with partial reproductive compatibility. Here, we use the nematodes Caenorhabditis briggsae and C. nigoni to quantify the sensitivity of hybrid male viability to extrinsic temperature and developmental timing, and test for a role of mito-nuclear incompatibility as a genetic cause. We demonstrate that hybrid male inviability manifests almost entirely as embryonic, not larval, arrest and is maximal at the lowest rearing temperatures, indicating an intrinsic-by-extrinsic interaction to hybrid inviability. Crosses using mitochondrial substitution strains that have reciprocally introgressed mitochondrial and nuclear genomes show that mito-nuclear incompatibility is not a dominant contributor to postzygotic isolation and does not drive Haldane's rule in this system. Crosses also reveal that competitive superiority of X-bearing sperm provides a novel means by which postmating prezygotic factors exacerbate the rarity of hybrid males. These findings highlight the important roles of gametic, developmental, and extrinsic factors in modulating the manifestation of Haldane's rule.
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Affiliation(s)
- Joanna D Bundus
- Department of Ecology & Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada, M5S 3B2
| | - Ravin Alaei
- Department of Ecology & Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada, M5S 3B2
| | - Asher D Cutter
- Department of Ecology & Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada, M5S 3B2.
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Fierst JL, Willis JH, Thomas CG, Wang W, Reynolds RM, Ahearne TE, Cutter AD, Phillips PC. Reproductive Mode and the Evolution of Genome Size and Structure in Caenorhabditis Nematodes. PLoS Genet 2015; 11:e1005323. [PMID: 26114425 PMCID: PMC4482642 DOI: 10.1371/journal.pgen.1005323] [Citation(s) in RCA: 75] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2014] [Accepted: 05/31/2015] [Indexed: 11/18/2022] Open
Abstract
The self-fertile nematode worms Caenorhabditis elegans, C. briggsae, and C. tropicalis evolved independently from outcrossing male-female ancestors and have genomes 20-40% smaller than closely related outcrossing relatives. This pattern of smaller genomes for selfing species and larger genomes for closely related outcrossing species is also seen in plants. We use comparative genomics, including the first high quality genome assembly for an outcrossing member of the genus (C. remanei) to test several hypotheses for the evolution of genome reduction under a change in mating system. Unlike plants, it does not appear that reductions in the number of repetitive elements, such as transposable elements, are an important contributor to the change in genome size. Instead, all functional genomic categories are lost in approximately equal proportions. Theory predicts that self-fertilization should equalize the effective population size, as well as the resulting effects of genetic drift, between the X chromosome and autosomes. Contrary to this, we find that the self-fertile C. briggsae and C. elegans have larger intergenic spaces and larger protein-coding genes on the X chromosome when compared to autosomes, while C. remanei actually has smaller introns on the X chromosome than either self-reproducing species. Rather than being driven by mutational biases and/or genetic drift caused by a reduction in effective population size under self reproduction, changes in genome size in this group of nematodes appear to be caused by genome-wide patterns of gene loss, most likely generated by genomic adaptation to self reproduction per se.
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Affiliation(s)
- Janna L. Fierst
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, United States of America
| | - John H. Willis
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, United States of America
| | - Cristel G. Thomas
- Department of Ecology and Evolutionary Biology and Centre for the Analysis of Genome Evolution and Function, University of Toronto, Ontario, Canada
| | - Wei Wang
- Department of Ecology and Evolutionary Biology and Centre for the Analysis of Genome Evolution and Function, University of Toronto, Ontario, Canada
| | - Rose M. Reynolds
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, United States of America
| | - Timothy E. Ahearne
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, United States of America
| | - Asher D. Cutter
- Department of Ecology and Evolutionary Biology and Centre for the Analysis of Genome Evolution and Function, University of Toronto, Ontario, Canada
| | - Patrick C. Phillips
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, United States of America
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Abstract
The roundworm Caenorhabditis elegans has risen to the status of a top model organism for biological research in the last fifty years. Among laboratory animals, this tiny nematode is one of the simplest and easiest organisms to handle. And its life outside the laboratory is beginning to be unveiled. Like other model organisms, C. elegans has a boom-and-bust lifestyle. It feasts on ephemeral bacterial blooms in decomposing fruits and stems. After resource depletion, its young larvae enter a migratory diapause stage, called the dauer. Organisms known to be associated with C. elegans include migration vectors (such as snails, slugs and isopods) and pathogens (such as microsporidia, fungi, bacteria and viruses). By deepening our understanding of the natural history of C. elegans, we establish a broader context and improved tools for studying its biology.
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Affiliation(s)
- Lise Frézal
- Institute of Biology of Ecole Normale Supérieure, Centre National de la Recherche Scientifique, Paris, France
| | - Marie-Anne Félix
- Institute of Biology of Ecole Normale Supérieure, Centre National de la Recherche Scientifique, Paris, France
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