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Coelho SM, Umen J. Switching it up: algal insights into sexual transitions. PLANT REPRODUCTION 2021; 34:287-296. [PMID: 34181073 PMCID: PMC8566403 DOI: 10.1007/s00497-021-00417-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Accepted: 06/02/2021] [Indexed: 05/03/2023]
Abstract
While the process of meiosis is highly conserved across eukaryotes, the sexual systems that govern life cycle phase transitions are surprisingly labile. Switches between sexual systems have profound evolutionary and ecological consequences, in particular for plants, but our understanding of the fundamental mechanisms and ultimate causes underlying these transitions is still surprisingly incomplete. We explore here the idea that brown and green algae may be interesting comparative models that can increase our understanding of relevant processes in plant reproductive biology, from evolution of gamete dimorphism, gametogenesis, sex determination and transitions in sex-determining systems.
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Affiliation(s)
- Susana M Coelho
- Max Planck Institute for Developmental Biology, Max-Planck-Ring 5, 72076, Tübingen, Germany.
| | - James Umen
- Donald Danforth Plant Science Center, St. Louis, MO, 63132, USA
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2
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Takahashi K, Kawai-Toyooka H, Ootsuki R, Hamaji T, Tsuchikane Y, Sekimoto H, Higashiyama T, Nozaki H. Three sex phenotypes in a haploid algal species give insights into the evolutionary transition to a self-compatible mating system. Evolution 2021; 75:2984-2993. [PMID: 34250602 PMCID: PMC9291101 DOI: 10.1111/evo.14306] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 05/17/2021] [Accepted: 06/01/2021] [Indexed: 01/01/2023]
Abstract
Mating systems of haploid species such as fungi, algae, and bryophytes are either heterothallic (self‐incompatible) with two sex phenotypes (male and female, or mating type minus and plus in isogamous species) or homothallic (self‐compatible) with only a bisexual phenotype producing zygotes within a clone. The anisogamous volvocine green alga Pleodorina starrii is a haploid species previously reported to have a heterothallic mating system. Here, we found that two additional culture strains originating from the same water system of P. starrii were taxonomically identified as P. starrii and produced male and female gametes and zygotes within a clone (bisexual). Sequences of rapidly evolving plastid genome regions were identical between the bisexual and unisexual (male or female) P. starrii strains. Intercrossings between the bisexual and unisexual strains demonstrated normal thick‐walled zygotes and high survivability of F1 strains. Thus, these strains belong to the same biological species. Pleodorina starrii has a new haploid mating system that is unique in having three sex phenotypes, namely, male, female, and bisexual. Genetic analyses suggested the existence of autosomal “bisexual factor” locus independent of volvocine male and female determining regions. The present findings increase our understanding of the initial evolutionary step of transition from heterothallism to homothallism.
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Affiliation(s)
- Kohei Takahashi
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, 113-0033, Japan
| | - Hiroko Kawai-Toyooka
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, 113-0033, Japan.,Current Address: Department of Frontier Bioscience, Faculty of Bioscience and Applied Chemistry, Hosei University, Kajinocho, Koganei-shi, Tokyo, 184-8584, Japan
| | - Ryo Ootsuki
- Department of Natural Sciences, Faculty of Arts and Sciences, Komazawa University, Tokyo, 154-8525, Japan.,Department of Chemical and Biological Sciences, Faculty of Science, Japan Women's University, Tokyo, 112-8681, Japan
| | - Takashi Hamaji
- Research and Development Initiative, Chuo University, Tokyo, 112-8551, Japan
| | - Yuki Tsuchikane
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, 113-0033, Japan.,Department of Chemical and Biological Sciences, Faculty of Science, Japan Women's University, Tokyo, 112-8681, Japan
| | - Hiroyuki Sekimoto
- Department of Chemical and Biological Sciences, Faculty of Science, Japan Women's University, Tokyo, 112-8681, Japan
| | - Tetsuya Higashiyama
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, 113-0033, Japan.,Institute of Transformative Bio-Molecules, Nagoya University, Nagoya, 464-8601, Japan.,Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya, 464-8602, Japan
| | - Hisayoshi Nozaki
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, 113-0033, Japan
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3
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Craig RJ, Hasan AR, Ness RW, Keightley PD. Comparative genomics of Chlamydomonas. THE PLANT CELL 2021; 33:1016-1041. [PMID: 33793842 PMCID: PMC8226300 DOI: 10.1093/plcell/koab026] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 01/22/2021] [Indexed: 05/06/2023]
Abstract
Despite its role as a reference organism in the plant sciences, the green alga Chlamydomonas reinhardtii entirely lacks genomic resources from closely related species. We present highly contiguous and well-annotated genome assemblies for three unicellular C. reinhardtii relatives: Chlamydomonas incerta, Chlamydomonas schloesseri, and the more distantly related Edaphochlamys debaryana. The three Chlamydomonas genomes are highly syntenous with similar gene contents, although the 129.2 Mb C. incerta and 130.2 Mb C. schloesseri assemblies are more repeat-rich than the 111.1 Mb C. reinhardtii genome. We identify the major centromeric repeat in C. reinhardtii as a LINE transposable element homologous to Zepp (the centromeric repeat in Coccomyxa subellipsoidea) and infer that centromere locations and structure are likely conserved in C. incerta and C. schloesseri. We report extensive rearrangements, but limited gene turnover, between the minus mating type loci of these Chlamydomonas species. We produce an eight-species core-Reinhardtinia whole-genome alignment, which we use to identify several hundred false positive and missing genes in the C. reinhardtii annotation and >260,000 evolutionarily conserved elements in the C. reinhardtii genome. In summary, these resources will enable comparative genomics analyses for C. reinhardtii, significantly extending the analytical toolkit for this emerging model system.
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Affiliation(s)
| | - Ahmed R Hasan
- Department of Biology, University of Toronto Mississauga, Mississauga, Onatrio, Canada L5L 1C6
| | - Rob W Ness
- Department of Biology, University of Toronto Mississauga, Mississauga, Onatrio, Canada L5L 1C6
| | - Peter D Keightley
- School of Biological Sciences, Institute of Evolutionary Biology, University of Edinburgh, EH9 3FL Edinburgh, UK
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4
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Three genomes in the algal genus Volvox reveal the fate of a haploid sex-determining region after a transition to homothallism. Proc Natl Acad Sci U S A 2021; 118:2100712118. [PMID: 34011609 PMCID: PMC8166075 DOI: 10.1073/pnas.2100712118] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Evolutionary transitions between species with separate sexes and species in which individuals have both sex functions have wide-ranging biological implications. It is largely unknown how such transitions occur in systems with haploid male- and female-determining chromosomes in algae and bryophytes. We investigated such a transition in the algal genus Volvox by making whole-genome sequences of two closely related species, one of which is heterothallic (with distinct males and females) and the other homothallic (with only bisexual, self-compatible individuals). The heterothallic species harbors a sex-determining region (SDR), while the homothallic species retains a nearly intact female-derived SDR-like region and separate regions containing key male genes. Thus, an ancestral female has probably become homothallic by acquiring genes that confer male functions. Transitions between separate sexes (dioecy) and other mating systems are common across eukaryotes. Here, we study a change in a haploid dioecious green algal species with male- and female-determining chromosomes (U and V). The genus Volvox is an oogamous (with large, immotile female gametes and small, motile male gametes) and includes both heterothallic species (with distinct male and female genotypes, associated with a mating-type system that prevents fusion of gametes of the same sex) and homothallic species (bisexual, with the ability to self-fertilize). We date the origin of an expanded sex-determining region (SDR) in Volvox to at least 75 Mya, suggesting that homothallism represents a breakdown of dioecy (heterothallism). We investigated the involvement of the SDR of the U and V chromosomes in this transition. Using de novo whole-genome sequences, we identified a heteromorphic SDR of ca 1 Mbp in male and female genotypes of the heterothallic species Volvox reticuliferus and a homologous region (SDLR) in the closely related homothallic species Volvox africanus, which retained several different hallmark features of an SDR. The V. africanus SDLR includes a large region resembling the female SDR of the presumptive heterothallic ancestor, whereas most genes from the male SDR are absent. However, we found a multicopy array of the male-determining gene, MID, in a different genomic location from the SDLR. Thus, in V. africanus, an ancestrally female genotype may have acquired MID and thereby gained male traits.
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Horinouchi Y, Togashi T. Identification of genomic differences between the sexes and sex-specific molecular markers in Monostroma angicava (Ulvophyceae). JOURNAL OF PHYCOLOGY 2021; 57:447-453. [PMID: 33450042 DOI: 10.1111/jpy.13128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 11/05/2020] [Accepted: 12/06/2020] [Indexed: 06/12/2023]
Abstract
There is little information available regarding genomic differences between sexes in ulvophycean green algae. The detection of these differences will enable the development of sex-discriminating molecular markers, which are useful for algae showing little apparent difference between sexes. In this study, we identified male- and female-specific DNA sequences in the ulvophycean marine green alga Monostroma angicava, which has a dioicous heteromorphic haplo-diplontic life cycle, via next-generation sequencing. Fluorescence in situ hybridization (FISH) showed that signals for the sex-specific sequences exist only in the nuclei of the corresponding sex, confirming the specificity of the sequences. Sex-specific molecular markers that targeted these sequences successfully distinguished the sex of gametophytes even in geographically distant populations, indicating that the sex-specific sequences are universal. These results consistently suggest that male and female gametophytes of M. angicava are genetically different, implying that sex may be determined genetically in this alga.
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Affiliation(s)
- Yusuke Horinouchi
- Marine Biosystems Research Center, Chiba University, Kamogawa, 299-5502, Japan
| | - Tatsuya Togashi
- Marine Biosystems Research Center, Chiba University, Kamogawa, 299-5502, Japan
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6
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Desnitskiy AG. Advances in the Research of Sexual Reproduction in Colonial Volvocine Algae. Russ J Dev Biol 2019. [DOI: 10.1134/s1062360419050047] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Abstract
Algae are photosynthetic eukaryotes whose taxonomic breadth covers a range of life histories, degrees of cellular and developmental complexity, and diverse patterns of sexual reproduction. These patterns include haploid- and diploid-phase sex determination, isogamous mating systems, and dimorphic sexes. Despite the ubiquity of sexual reproduction in algae, their mating-type-determination and sex-determination mechanisms have been investigated in only a limited number of representatives. These include volvocine green algae, where sexual cycles and sex-determining mechanisms have shed light on the transition from mating types to sexes, and brown algae, which are a model for UV sex chromosome evolution in the context of a complex haplodiplontic life cycle. Recent advances in genomics have aided progress in understanding sexual cycles in less-studied taxa including ulvophyte, charophyte, and prasinophyte green algae, as well as in diatoms.
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Affiliation(s)
- James Umen
- Donald Danforth Plant Science Center, St. Louis, Missouri 63132, USA;
| | - Susana Coelho
- Algal Genetics Group, Integrative Biology of Marine Models, Station Biologique de Roscoff, Sorbonne Université, UPMC Université Paris 06, CNRS, CS 90074, F-29688 Roscoff, France;
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A streamlined and predominantly diploid genome in the tiny marine green alga Chloropicon primus. Nat Commun 2019; 10:4061. [PMID: 31492891 PMCID: PMC6731263 DOI: 10.1038/s41467-019-12014-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Accepted: 08/16/2019] [Indexed: 12/11/2022] Open
Abstract
Tiny marine green algae issued from two deep branches of the Chlorophyta, the Mamiellophyceae and Chloropicophyceae, dominate different regions of the oceans and play key roles in planktonic communities. Considering that the Mamiellophyceae is the sole lineage of prasinophyte algae that has been intensively investigated, the extent to which these two algal groups differ in their metabolic capacities and cellular processes is currently unknown. To address this gap of knowledge, we investigate here the nuclear genome sequence of a member of the Chloropicophyceae, Chloropicon primus. Among the main biological insights that emerge from this 17.4 Mb genome, we find an unexpected diploid structure for most chromosomes and a propionate detoxification pathway in green algae. Our results support the notion that separate events of genome minimization, which entailed differential losses of genes/pathways, have occurred in the Chloropicophyceae and Mamiellophyceae, suggesting different strategies of adaptation to oceanic environments.
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9
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Coelho SM, Gueno J, Lipinska AP, Cock JM, Umen JG. UV Chromosomes and Haploid Sexual Systems. TRENDS IN PLANT SCIENCE 2018; 23:794-807. [PMID: 30007571 PMCID: PMC6128410 DOI: 10.1016/j.tplants.2018.06.005] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Revised: 06/04/2018] [Accepted: 06/07/2018] [Indexed: 05/20/2023]
Abstract
The evolution of sex determination continues to pose major questions in biology. Sex-determination mechanisms control reproductive cell differentiation and development of sexual characteristics in all organisms, from algae to animals and plants. While the underlying processes defining sex (meiosis and recombination) are conserved, sex-determination mechanisms are highly labile. In particular, a flow of new discoveries has highlighted several fascinating features of the previously understudied haploid UV sex determination and related mating systems found in diverse photosynthetic taxa including green algae, bryophytes, and brown algae. Analyses integrating information from these systems and contrasting them with classical XY and ZW systems are providing exciting insights into both the universality and the diversity of sex-determining chromosomes across eukaryotes.
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Affiliation(s)
- Susana Margarida Coelho
- Sorbonne Université, Centre National de la Recherche Scientifique (CNRS), Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff (SBR), 29680 Roscoff, France.
| | - Josselin Gueno
- Sorbonne Université, Centre National de la Recherche Scientifique (CNRS), Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff (SBR), 29680 Roscoff, France
| | - Agnieszka Paulina Lipinska
- Sorbonne Université, Centre National de la Recherche Scientifique (CNRS), Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff (SBR), 29680 Roscoff, France
| | - Jeremy Mark Cock
- Sorbonne Université, Centre National de la Recherche Scientifique (CNRS), Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff (SBR), 29680 Roscoff, France
| | - James G Umen
- Donald Danforth Plant Science Center, St. Louis, MO 63132, USA.
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Geng S, Miyagi A, Umen JG. Evolutionary divergence of the sex-determining gene MID uncoupled from the transition to anisogamy in volvocine algae. Development 2018; 145:dev.162537. [PMID: 29549112 DOI: 10.1242/dev.162537] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Accepted: 03/13/2018] [Indexed: 12/28/2022]
Abstract
Volvocine algae constitute a unique comparative model for investigating the evolution of oogamy from isogamous mating types. The sex- or mating type-determining gene MID encodes a conserved RWP-RK transcription factor found in either the MT- or male mating locus of dioecious volvocine species. We previously found that MID from the isogamous species Chlamydomonas reinhardtii (CrMID) could not induce ectopic spermatogenesis when expressed heterologously in Volvox carteri females, suggesting coevolution of Mid function with gamete dimorphism. Here we found that ectopic expression of MID from the anisogamous species Pleodorina starrii (PsMID) could efficiently induce spermatogenesis when expressed in V. carteri females and, unexpectedly, that GpMID from the isogamous species Gonium pectorale was also able to induce V. carteri spermatogenesis. Neither VcMID nor GpMID could complement a C. reinhardtii mid mutant, at least partly owing to instability of heterologous Mid proteins. Our data show that Mid divergence was not a major contributor to the transition between isogamy and anisogamy/oogamy in volvocine algae, and instead implicate changes in cis-regulatory interactions and/or trans-acting factors of the Mid network in the evolution of sexual dimorphism.
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Affiliation(s)
- Sa Geng
- Donald Danforth Plant Science Center, 975 N. Warson Rd., St. Louis, MO 63132, USA
| | - Ayano Miyagi
- Donald Danforth Plant Science Center, 975 N. Warson Rd., St. Louis, MO 63132, USA
| | - James G Umen
- Donald Danforth Plant Science Center, 975 N. Warson Rd., St. Louis, MO 63132, USA
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Hamaji T, Kawai-Toyooka H, Uchimura H, Suzuki M, Noguchi H, Minakuchi Y, Toyoda A, Fujiyama A, Miyagishima SY, Umen JG, Nozaki H. Anisogamy evolved with a reduced sex-determining region in volvocine green algae. Commun Biol 2018; 1:17. [PMID: 30271904 PMCID: PMC6123790 DOI: 10.1038/s42003-018-0019-5] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Accepted: 02/08/2018] [Indexed: 11/09/2022] Open
Abstract
Male and female gametes differing in size-anisogamy-emerged independently from isogamous ancestors in various eukaryotic lineages, although genetic bases of this emergence are still unknown. Volvocine green algae are a model lineage for investigating the transition from isogamy to anisogamy. Here we focus on two closely related volvocine genera that bracket this transition-isogamous Yamagishiella and anisogamous Eudorina. We generated de novo nuclear genome assemblies of both sexes of Yamagishiella and Eudorina to identify the dimorphic sex-determining chromosomal region or mating-type locus (MT) from each. In contrast to the large (>1 Mb) and complex MT of oogamous Volvox, Yamagishiella and Eudorina MT are smaller (7-268 kb) and simpler with only two sex-limited genes-the minus/male-limited MID and the plus/female-limited FUS1. No prominently dimorphic gametologs were identified in either species. Thus, the first step to anisogamy in volvocine algae presumably occurred without an increase in MT size and complexity.
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Affiliation(s)
- Takashi Hamaji
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo, 113-0033, Japan
- Department of Biological Sciences, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Hiroko Kawai-Toyooka
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo, 113-0033, Japan.
| | - Haruka Uchimura
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Masahiro Suzuki
- Kobe University Research Center for Inland Seas, Awaji, Hyogo, 656-2401, Japan
| | - Hideki Noguchi
- Center for Genome Informatics, Joint Support-Center for Data Science Research, Research Organization of Information and Systems, Mishima, Shizuoka, 411-8540, Japan
- Advanced Genomics Center, National Institute of Genetics, Mishima, Shizuoka, 411-8540, Japan
| | - Yohei Minakuchi
- Center for Information Biology, National Institute of Genetics, Mishima, Shizuoka, 411-8540, Japan
| | - Atsushi Toyoda
- Advanced Genomics Center, National Institute of Genetics, Mishima, Shizuoka, 411-8540, Japan
- Center for Information Biology, National Institute of Genetics, Mishima, Shizuoka, 411-8540, Japan
| | - Asao Fujiyama
- Advanced Genomics Center, National Institute of Genetics, Mishima, Shizuoka, 411-8540, Japan
| | - Shin-Ya Miyagishima
- Department of Cell Genetics, National Institute of Genetics, Mishima, Shizuoka, 411-8540, Japan
| | - James G Umen
- Donald Danforth Plant Science Center, 975 N Warson Rd, St. Louis, MO, 63132, USA
| | - Hisayoshi Nozaki
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo, 113-0033, Japan.
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