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Kawakami SM, Kawakami S. Unreduced spore formation in a spontaneous chimeric pinnule in an artificially produced haploid Anisocampium niponicum (Athyriaceae, Polypodiales). JOURNAL OF PLANT RESEARCH 2024; 137:161-165. [PMID: 38194203 DOI: 10.1007/s10265-023-01511-2] [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: 05/02/2023] [Accepted: 11/23/2023] [Indexed: 01/10/2024]
Abstract
Haploid sporophytes of Anisocampium niponicum with 2n = 40, were produced artificially by induced apogamy in vitro. They were subsequently transplanted into pots and two of them have been cultivated for the investigation of sporogenesis and/or production of chimera for more than 20 years. Haploid A. niponicum is sterile, but an abnormal chimeric pinnule that developed spontaneously in a single frond produced sporangia with spores. Each sporangium bore approximately 32 spores that were almost uniform in size. Sowing of these spores resulted in 50 gametophytes. Of 20 gametophytes cultured individually, five produced sporophytes apogamously after eight months. Both the gametophytes and subsequent apogamous sporophytes showed a chromosome number of 2n = 40. Our study demonstrates that a haploid sporophyte offspring can be produced from a haploid mother sporophyte via haploid spores. Since asexual reproduction is a prominent evolutionary process in ferns, the reproduction of a haploid A. niponicum sporophyte by unreduced spore formation might help to elucidate how apogamous ferns occur and evolve.
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Affiliation(s)
- Suzue M Kawakami
- Kuwana Nursing College, Honganji, Kuwana, Mie, 511-0835, Japan.
- , 1-6-16, Shiratori, Togo-cho, Aichi-gun, Aichi, 470-0155, Japan.
| | - Shogo Kawakami
- Faculty of Education, Aichi University of Education, Igaya, Kariya, Aichi, 448-8542, Japan
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Kim HT, Park SH, Kim JS. Dynamic hybridization between two spleenworts, Asplenium incisum and Asplenium ruprechtii in Korea. FRONTIERS IN PLANT SCIENCE 2023; 14:1116040. [PMID: 37476173 PMCID: PMC10354290 DOI: 10.3389/fpls.2023.1116040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Accepted: 05/31/2023] [Indexed: 07/22/2023]
Abstract
Natural hybridization between Asplenium incisum and A. ruprechtii has been observed in Northeast Asia and its allotetraploid species, A. castaneoviride, was reported. However, the hybridization process between the parental species and the origin of the allotetraploid taxon remains obscure. Additionally, the systematic affinities of the recently described hybrid A. bimixtum, considered to have originated from the hybridization of A. ruprechtii, A. trichomanes, and A. incisum, is unresolved owing to its similarity to A. castaneoviride. The goals of this study were to (1) investigate the hybridization between A. ruprechtii and A. incisum; (2) verify the origin of A. castaneoviride occurring in Korea, whether it independently arose from 2x sterile hybrids; and (3) elucidate the reliability of identifying A. bimixtum. Three genotypes, A. incisum, A. ruprechtii, and their hybrid, were identified based on the nuclear gene pgiC sequence and finally divided them into six types by ploidy levels: diploid A. incisum, A. ruprechtii, and four hybrid types (diploid A. × castaneoviride, triploid A. × castaneoviride, allotetraploid A. castaneoviride, and A. bimixtum). In the analyses of plastid DNA, all hybrids had an A. ruprechtii-type rbcL gene. In addition, the four plastomes of A. ruprechtii and the hybrids had high pairwise sequence identities greater than 98.48%. They increased up to 99.88% when a large deletion of A. x castaneoriviride (2x) collected from Buramsan populations was ignored. Notably, this large deletion was also found in triploid A. × castaneoviride and allotetraploid A. castaneoviride in the same populations. Sequence data of the nuclear and plastid genes showed that hybridization is unidirectional, and A. ruprechtii is the maternal parent. The large deletion of rpoC2-rps2 commonly found in the different ploidy hybrids of the Buramsan population suggests that the allotetraploid A. castaneoviride can be created independently from sterile hybrids. We assume that both polyploidization driving allopolyploidy and minority cytotype exclusion took place independently in the population, since A castaenoviride co-occurs with A. ruprechtii in small populations. Furthermore, it was also observed that an enlarged noncoding region in fern organelle (ENRIFO) of the plastome was found in the genus Asplenium.
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Affiliation(s)
- Hyoung Tae Kim
- Department of Ecological and Environmental System, Kyungpook National University, Sangju, Republic of Korea
| | - Sang Hee Park
- Department of Forest Science, Chungbuk National University, Cheongju, Republic of Korea
| | - Jung Sung Kim
- Department of Forest Science, Chungbuk National University, Cheongju, Republic of Korea
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Ojosnegros S, Alvarez JM, Grossmann J, Gagliardini V, Quintanilla LG, Grossniklaus U, Fernández H. The Shared Proteome of the Apomictic Fern Dryopteris affinis ssp. affinis and Its Sexual Relative Dryopteris oreades. Int J Mol Sci 2022; 23:ijms232214027. [PMID: 36430514 PMCID: PMC9693225 DOI: 10.3390/ijms232214027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Revised: 11/09/2022] [Accepted: 11/10/2022] [Indexed: 11/16/2022] Open
Abstract
Ferns are a diverse evolutionary lineage, sister to the seed plants, which is of great ecological importance and has a high biotechnological potential. Fern gametophytes represent one of the simplest autotrophic, multicellular plant forms and show several experimental advantages, including a simple and space-efficient in vitro culture system. However, the molecular basis of fern growth and development has hardly been studied. Here, we report on a proteomic study that identified 417 proteins shared by gametophytes of the apogamous fern Dryopteris affinis ssp. affinis and its sexual relative Dryopteris oreades. Most proteins are predicted to localize to the cytoplasm, the chloroplast, or the nucleus, and are linked to enzymatic, binding, and structural activities. A subset of 145 proteins are involved in growth, reproduction, phytohormone signaling and biosynthesis, and gene expression, including homologs of SHEPHERD (SHD), HEAT SHOCK PROTEIN 90-5 (CR88), TRP4, BOBBER 1 (BOB1), FLAVONE 3'-O-METHYLTRANSFERASE 1 (OMT1), ZEAXANTHIN EPOXIDASE (ABA1), GLUTAMATE DESCARBOXYLASE 1 (GAD), and dsRNA-BINDING DOMAIN-LIKE SUPERFAMILY PROTEIN (HLY1). Nearly 25% of the annotated proteins are associated with responses to biotic and abiotic stimuli. As for biotic stress, the proteins PROTEIN SGT1 HOMOLOG B (SGT1B), SUPPRESSOR OF SA INSENSITIVE2 (SSI2), PHOSPHOLIPASE D ALPHA 1 (PLDALPHA1), SERINE/THREONINE-PROTEIN KINASE SRK2E (OST1), ACYL CARRIER PROTEIN 4 (ACP4), and NONHOST RESISTANCE TO P. S. PHASEOLICOLA1 (GLPK) are worth mentioning. Regarding abiotic stimuli, we found proteins associated with oxidative stress: SUPEROXIDE DISMUTASE[CU-ZN] 1 (CSD1), and GLUTATHIONE S-TRANSFERASE U19 (GSTU19), light intensity SERINE HYDROXYMETHYLTRANSFERASE 1 (SHM1) and UBIQUITIN-CONJUGATING ENZYME E2 35 (UBC35), salt and heavy metal stress included MITOCHONDRIAL PHOSPHATE CARRIER PROTEIN 3 (PHT3;1), as well as drought and thermotolerance: LEA7, DEAD-BOX ATP-DEPENDENT RNA HELICASE 38 (LOS4), and abundant heat-shock proteins and other chaperones. In addition, we identified interactomes using the STRING platform, revealing protein-protein associations obtained from co-expression, co-occurrence, text mining, homology, databases, and experimental datasets. By focusing on ferns, this proteomic study increases our knowledge on plant development and evolution, and may inspire future applications in crop species.
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Affiliation(s)
- Sara Ojosnegros
- Area of Plant Physiology, Department of Organisms and Systems Biology, University of Oviedo, 33071 Oviedo, Spain
| | - José Manuel Alvarez
- Area of Plant Physiology, Department of Organisms and Systems Biology, University of Oviedo, 33071 Oviedo, Spain
| | - Jonas Grossmann
- Functional Genomic Center Zurich, University and ETH Zurich, 8092 Zurich, Switzerland
- SIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Valeria Gagliardini
- Department of Plant and Microbial Biology & Zurich-Basel Plant Science Center, University of Zurich, 8006 Zurich, Switzerland
| | - Luis G. Quintanilla
- Department of Biology and Geology, Physics and Inorganic Chemistry, University Rey Juan Carlos, 28933 Móstoles, Spain
| | - Ueli Grossniklaus
- Department of Plant and Microbial Biology & Zurich-Basel Plant Science Center, University of Zurich, 8006 Zurich, Switzerland
| | - Helena Fernández
- Area of Plant Physiology, Department of Organisms and Systems Biology, University of Oviedo, 33071 Oviedo, Spain
- Correspondence: ; Tel.: +34-985-104-811
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Park SH, Kim JS, Kim HT. Asplenium pseudocapillipes (Aspleniaceae), a New Fern Species from South Korea. PLANTS (BASEL, SWITZERLAND) 2022; 11:3089. [PMID: 36432818 PMCID: PMC9696321 DOI: 10.3390/plants11223089] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 11/04/2022] [Accepted: 11/11/2022] [Indexed: 06/16/2023]
Abstract
A new allotetraploid species of the genus Asplenium, A. pseudocapillipes, originated from the hybridization between A. capillipes and A. tenuicaule, has been newly discovered in two limestone areas of South Korea. A molecular phylogenetic analysis using one chloroplast region (rbcL) and three single- or low-copy nuclear regions (AK1, gapCp, pgiC) and a cytological analysis, including genome size measurements, were conducted to characterize this new species. From these results, the maternal origin of A. pseudocapillipes was confirmed to be A. capillipes, which has never been reported in Korea. All three nuclear data showed that this new species had genotypes of both A. capillipes and A. tenuicaule. The quantitative characteristics of the leaves showed values intermediate between the two parental species. The absence of gemma accorded with its paternal origin from A. tenuicaule, and 32 spores per sporangium accorded with its maternal origin from A. capillipes. Although A. pseudocapillipes has 32 spores per sporangium, it is considered to be a sexually reproducing, not an apomitic, fern.
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Affiliation(s)
- Sang Hee Park
- Department of Forest Science, Chungbuk National University, Chungdae-Ro 1, Seowon-Gu, Cheongju 28644, Chungbuk, Korea
| | - Jung Sung Kim
- Department of Forest Science, Chungbuk National University, Chungdae-Ro 1, Seowon-Gu, Cheongju 28644, Chungbuk, Korea
| | - Hyoung Tae Kim
- Department of Ecological and Environmental System, Kyungpook National University, Gyeongsang-Daero, Sangju-Si 37224, Gyeongsangbuk-Do, Korea
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Chang Y, Zhang G, Wang Z, Cao L. Molecular and morphological evidence reveals a new fern species of Hymenasplenium (Aspleniaceae) from south and southwestern China. PHYTOKEYS 2022; 211:93-106. [PMID: 36760732 PMCID: PMC9836484 DOI: 10.3897/phytokeys.211.90363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 09/20/2022] [Indexed: 06/18/2023]
Abstract
Hymenaspleniumobtusidentatum, a new fern species of the H.excisum subclade of Hymenasplenium (Aspleniaceae) from south and southwestern China was described. Molecular phylogenetic analyses and morphological observations of H.obtusidentatum and related species clearly indicated that this is a distinct taxonomic entity. Phylogenetically, H.obtusidentatum was confirmed to represent a diverging lineage in the H.excisum subclade of Hymenasplenium and was closely related to one lineage that includes accessions identified as H.obscurum, H.pseudobscurum and H.tholiformis. Morphologically, H.obtusidentatum can be distinguished by the combination of its lamina base truncate, stipe not shiny and with color of reddish brown to dark brown, and pinna marginal teeth that are not sharp, but blunt or rounded. A complete species description and comparison with related species in the H.excisum subclade were provided. The holotype of H.obtusidentatum was designated.
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Affiliation(s)
- Yanfen Chang
- College of Life Sciences, Hengyang Normal University, Hengyang 421008, Hunan, ChinaHengyang Normal UniversityHunanChina
- Hunan Key Laboratory for Conservation and Utilization of Biological Resources in the Nanyue Mountainous Region, Hunan, ChinaHunan Key Laboratory for Conservation and Utilization of Biological ResourcesHunanChina
| | - Guocheng Zhang
- College of Life Sciences, Hengyang Normal University, Hengyang 421008, Hunan, ChinaHengyang Normal UniversityHunanChina
- Hunan Key Laboratory for Conservation and Utilization of Biological Resources in the Nanyue Mountainous Region, Hunan, ChinaHunan Key Laboratory for Conservation and Utilization of Biological ResourcesHunanChina
| | - Zhixin Wang
- College of Life Sciences, Hengyang Normal University, Hengyang 421008, Hunan, ChinaHengyang Normal UniversityHunanChina
- Hunan Key Laboratory for Conservation and Utilization of Biological Resources in the Nanyue Mountainous Region, Hunan, ChinaHunan Key Laboratory for Conservation and Utilization of Biological ResourcesHunanChina
| | - Limin Cao
- College of Life Sciences, Hengyang Normal University, Hengyang 421008, Hunan, ChinaHengyang Normal UniversityHunanChina
- Hunan Key Laboratory for Conservation and Utilization of Biological Resources in the Nanyue Mountainous Region, Hunan, ChinaHunan Key Laboratory for Conservation and Utilization of Biological ResourcesHunanChina
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Hornych O, Férová A, Hori K, Košnar J, Ekrt L. Apomictic fern fathers: an experimental approach to the reproductive characteristics of sexual, apomict, and hybrid fern gametophytes. AMERICAN JOURNAL OF BOTANY 2022; 109:628-644. [PMID: 35072270 DOI: 10.1002/ajb2.1817] [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: 05/05/2021] [Revised: 01/05/2022] [Accepted: 01/13/2022] [Indexed: 06/14/2023]
Abstract
PREMISE Apomixis and hybridization are two essential and complementary factors in the evolution of plants, including ferns. Hybridization combines characteristics from different species, while apomixis conserves features within a lineage. When combined, these two processes result in apo-sex hybrids. The conditions leading to the formation of these hybrids are poorly understood in ferns. METHODS We cultivated spores from 66 fern samples (43 apomicts, 7 apo-sex hybrids, and 16 sexuals), and measured their development in vitro over 16 weeks. We evaluated germination, lateral meristem formation rates, sexual expression, and production of sporophytes and then compared ontogenetic patterns among the three groups. RESULTS The three examined groups formed antheridia (male gametangia) but differed in overall gametophyte development. Sexual species created archegonia (female, 86% of viable samples), but no sporophytes. Apomicts rarely created nonfunctional archegonia (8%) but usually produced apogamous sporophytes (75%). Surprisingly, apomictic and sexual species showed similar development speed. The sexually reproducing parents of viable studied hybrids formed about twice as many meristic gametophytes as the apomictic parents (39% vs. 20%, respectively). CONCLUSIONS We present the most thorough comparison of gametangial development of sexual and apomictic ferns, to date. Despite expectations, apomictic reproduction might not lead to earlier sporophyte formation. Apomicts produce functional sperm and thus can contribute this type of gamete to their hybrids. The development patterns found in the parents of hybrids indicate a possible increase of hybridization rates by antheridiogens. The apo-sex hybrids always inherit the apomictic reproductive strategy and are thus capable of self-perpetuation.
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Affiliation(s)
- Ondřej Hornych
- Department of Botany, Faculty of Science, University of South Bohemia, Branišovská 1760, České Budějovice, CZ-37005, Czech Republic
| | - Alžběta Férová
- Department of Botany, Faculty of Science, University of South Bohemia, Branišovská 1760, České Budějovice, CZ-37005, Czech Republic
| | - Kiyotaka Hori
- The Kochi prefectural Makino Botanical Garden, Godaisan 4200-6, Kochi, 781-8125, Japan
| | - Jiří Košnar
- Department of Botany, Faculty of Science, University of South Bohemia, Branišovská 1760, České Budějovice, CZ-37005, Czech Republic
| | - Libor Ekrt
- Department of Botany, Faculty of Science, University of South Bohemia, Branišovská 1760, České Budějovice, CZ-37005, Czech Republic
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Fernández H, Grossmann J, Gagliardini V, Feito I, Rivera A, Rodríguez L, Quintanilla LG, Quesada V, Cañal MJ, Grossniklaus U. Sexual and Apogamous Species of Woodferns Show Different Protein and Phytohormone Profiles. FRONTIERS IN PLANT SCIENCE 2021; 12:718932. [PMID: 34868105 PMCID: PMC8633544 DOI: 10.3389/fpls.2021.718932] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 09/23/2021] [Indexed: 06/13/2023]
Abstract
The gametophyte of ferns reproduces either by sexual or asexual means. In the latter, apogamy represents a peculiar case of apomixis, in which an embryo is formed from somatic cells. A proteomic and physiological approach was applied to the apogamous fern Dryopteris affinis ssp. affinis and its sexual relative D. oreades. The proteomic analysis compared apogamous vs. female gametophytes, whereas the phytohormone study included, in addition to females, three apogamous stages (filamentous, spatulate, and cordate). The proteomic profiles revealed a total of 879 proteins and, after annotation, different regulation was found in 206 proteins of D. affinis and 166 of its sexual counterpart. The proteins upregulated in D. affinis are mostly associated to protein metabolism (including folding, transport, and proteolysis), ribosome biogenesis, gene expression and translation, while in the sexual counterpart, they account largely for starch and sucrose metabolism, generation of energy and photosynthesis. Likewise, ultra-performance liquid chromatography-tandem spectrometry (UHPLC-MS/MS) was used to assess the levels of indol-3-acetic acid (IAA); the cytokinins: 6-benzylaminopurine (BA), trans-Zeatine (Z), trans-Zeatin riboside (ZR), dyhidrozeatine (DHZ), dyhidrozeatin riboside (DHZR), isopentenyl adenine (iP), isopentenyl adenosine (iPR), abscisic acid (ABA), the gibberellins GA3 and GA4, salicylic acid (SA), and the brassinosteroids: brassinolide (BL) and castasterone (CS). IAA, the cytokinins Z, ZR, iPR, the gibberellin GA4, the brassinosteoids castasterone, and ABA accumulated more in the sexual gametophyte than in the apogamous one. When comparing the three apogamous stages, BA and SA peaked in filamentous, GA3 and BL in spatulate and DHRZ in cordate gametophytes. The results point to the existence of large metabolic differences between apogamous and sexual gametophytes, and invite to consider the fern gametophyte as a good experimental system to deepen our understanding of plant reproduction.
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Affiliation(s)
- Helena Fernández
- Area of Plant Physiology, Department of Organisms and Systems Biology, Oviedo University, Oviedo, Spain
| | - Jonas Grossmann
- Functional Genomics Center, Zurich, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Valeria Gagliardini
- Department of Plant and Microbial Biology & Zurich and Basel Plant Science Center, University of Zurich, Zurich, Switzerland
| | - Isabel Feito
- Servicio Regional de Investigación y Desarrollo Agroalimentario (SERIDA), Finca Experimental La Mata, Grado, Spain
| | - Alejandro Rivera
- Area of Plant Physiology, Department of Organisms and Systems Biology, Oviedo University, Oviedo, Spain
| | - Lucía Rodríguez
- Servicio Regional de Investigación y Desarrollo Agroalimentario (SERIDA), Finca Experimental La Mata, Grado, Spain
| | - Luis G. Quintanilla
- Department of Biology and Geology, Physics and Inorganic Chemistry, Rey Juan Carlos University, Móstoles, Spain
| | - Víctor Quesada
- Department of Biochemistry and Molecular Biology, Institute of Oncology of the Principality of Asturias, Oviedo University, Móstoles, Spain
| | - Mª Jesús Cañal
- Area of Plant Physiology, Department of Organisms and Systems Biology, Oviedo University, Oviedo, Spain
| | - Ueli Grossniklaus
- Department of Plant and Microbial Biology & Zurich and Basel Plant Science Center, University of Zurich, Zurich, Switzerland
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Picard KT, Ranft H, Grusz AL, Windham MD, Schuettpelz E. When it only takes one to tango: assessing the impact of apomixis in the fern genus Pteris. AMERICAN JOURNAL OF BOTANY 2021; 108:2220-2234. [PMID: 34618360 PMCID: PMC9298017 DOI: 10.1002/ajb2.1761] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 07/30/2021] [Accepted: 08/12/2021] [Indexed: 05/14/2023]
Abstract
PREMISE Apomixis (asexual reproduction by seed, spore, or egg) has evolved repeatedly across the tree of life. Studies of animals and angiosperms show that apomictic lineages are often evolutionarily short-lived and frequently exhibit different distributions than their sexual relatives. However, apomixis is rare in these groups. Less is known about the role of apomixis in the evolution and biogeography of ferns, in which ~10% of species are apomictic. Apomixis is especially common in the fern genus Pteris (34-39% of species); however, because of the limited taxonomic and geographic sampling of previous studies, the true frequency of apomixis and its associations with geography and phylogeny in this lineage remain unclear. METHODS We used spore analyses of herbarium specimens to determine reproductive mode for 127 previously unsampled Pteris species. Then we leveraged biogeographic and phylogenetic analyses to estimate the global distribution and evolution of apomixis in Pteris. RESULTS Among all Pteris species examined, we found that 21% are exclusively apomictic, 71% are exclusively sexual, and 8% have conflicting reports. Apomixis is unevenly distributed across the range of the genus, with the Paleotropics exhibiting the highest frequency, and has evolved numerous times across the Pteris phylogeny, with predominantly East Asian and South Asian clades containing the most apomictic species. CONCLUSIONS Apomixis arises frequently in Pteris, but apomictic species do not appear to diversify. Species that encompass both apomictic and sexual populations have wider ranges than exclusively sexual or apomictic species, which suggests that sexual and apomictic ferns could occupy separate ecological niches.
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Affiliation(s)
- Kathryn T. Picard
- Department of Botany, National Museum of Natural HistorySmithsonian InstitutionWashingtonDC20560USA
| | - Hannah Ranft
- Department of Botany, National Museum of Natural HistorySmithsonian InstitutionWashingtonDC20560USA
- Johns Hopkins UniversityBaltimoreMaryland21218USA
- Department of BiologyUniversity of Minnesota DuluthDuluthMinnesota55812USA
| | - Amanda L. Grusz
- Department of BiologyUniversity of Minnesota DuluthDuluthMinnesota55812USA
| | | | - Eric Schuettpelz
- Department of Botany, National Museum of Natural HistorySmithsonian InstitutionWashingtonDC20560USA
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Xu KW, Wang LL, Zhang LB. Taxonomic revision of the Asplenium wrightii complex (Aspleniaceae) with reinstatement of A. alatulum and A. subcrenatum. PHYTOKEYS 2021; 172:75-91. [PMID: 33633487 PMCID: PMC7895818 DOI: 10.3897/phytokeys.172.62511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Accepted: 01/27/2021] [Indexed: 06/12/2023]
Abstract
The Asplenium wrightii complex is morphologically variable and difficult in species delimitation. Owing to lack of comprehensive sampling in phylogenetic studies, the taxonomy of this complex remains unresolved. Based on extensive field observations, specimen examination and our recent molecular data, the present study aims to clarify the identities of three species of Asplenium in this complex from Asia. Our study revealed that A. alatulum and A. subcrenatum, previously treated as synonyms of A. wrightii, should be reinstated. A taxonomic revision of the three species, including their type information, detailed descriptions, voucher specimens, distribution, ecology, as well as taxonomic notes, is carried out.
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Affiliation(s)
- Ke-Wang Xu
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing; 510275, ChinaNanjing Forestry UniversityNanjingChina
| | - Lu-Lu Wang
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing; 510275, ChinaNanjing Forestry UniversityNanjingChina
| | - Li-Bing Zhang
- Missouri Botanical Garden, P.O. Box 299, St. Louis, Missouri 63166-0299, USAMissouri Botanical GardenSt. LouisChina
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Barrington DS, Patel NR, Southgate MW. Inferring the impacts of evolutionary history and ecological constraints on spore size and shape in the ferns. APPLICATIONS IN PLANT SCIENCES 2020; 8:e11339. [PMID: 32351800 PMCID: PMC7186895 DOI: 10.1002/aps3.11339] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Accepted: 02/03/2020] [Indexed: 05/27/2023]
Abstract
PREMISE In the ferns, cell size has been explored with spores, which are largely uniform within species, produced in abundance, and durable. However, spore size and shape have been variously defined, and the relationship of these traits to genome size has not been well established. Here, we explore the variation in fern spore size and shape by ploidy level and genome size. METHODS Measurements of spore dimensions for two study sets of ferns, Polystichum and Adiantum, both including diploid and tetraploid taxa, provided the basis for computing estimates of shape and size as defined here. These traits were compared between and within ploidy levels and regressed with genome size estimates from flow cytometry analysis. RESULTS All size traits were strongly correlated with genome size; the shape trait was weakly correlated. Tetraploids were larger than diploids as expected; the spores of some closely related diploid species were also significantly different in size. DISCUSSION Researchers with access to a student-grade compound microscope can develop a valid estimate of relative genome size for ferns. These estimates provide enough resolution to infer ploidy level and explore the relationship between genome size, habitat, and physiological constraints for species within ploidy level.
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Affiliation(s)
- David S. Barrington
- Pringle HerbariumUniversity of Vermont111 Jeffords HallBurlingtonVermont05405‐1737USA
| | - Nikisha R. Patel
- Ecology and Evolutionary BiologyUniversity of Connecticut75 North Eagleville RoadStorrsConnecticut06269USA
| | - Morgan W. Southgate
- Pringle HerbariumUniversity of Vermont111 Jeffords HallBurlingtonVermont05405‐1737USA
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Wyder S, Rivera A, Valdés AE, Cañal MJ, Gagliardini V, Fernández H, Grossniklaus U. Differential gene expression profiling of one- and two-dimensional apogamous gametophytes of the fern Dryopteris affinis ssp. affinis. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2020; 148:302-311. [PMID: 32000107 DOI: 10.1016/j.plaphy.2020.01.021] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 12/16/2019] [Accepted: 01/15/2020] [Indexed: 05/01/2023]
Abstract
Apomixis was originally defined as the replacement of sexual reproduction by an asexual process that does not involve fertilization but, in angiosperms, it is often used in the more restricted sense of asexual reproduction through seeds. In ferns, apomixis combines the production of unreduced spores (diplospory) and the formation of sporophytes from somatic cells of the prothallium (apogamy). The genes that control the onset of apogamy in ferns are largely unknown. In this study, we describe the gametophyte transcriptome of the apogamous fern Dryopteris affinis ssp. affinis using an RNA-Seq approach to compare the gene expression profiles of one- and two-dimensional gametophytes, the latter containing apogamic centers. After collapsing highly similar de novo transcripts, we obtained 166,191 unigenes, of which 30% could be annotated using public databases. Multiple quality metrics indicate a good quality of the de novo transcriptome with a low level of fragmentation. Our data show a total of 10,679 genes (6% of all genes) to be differentially expressed between gametophytes of filamentous (one-dimensional) and prothallial (two-dimensional) architecture. 6,110 genes were up-regulated in two-dimensional relative to one-dimensional gametophytes, some of which are implicated in the regulation of meristem growth, auxin signaling, reproduction, and sucrose metabolism. 4,570 genes were down-regulated in two-dimensional versus one-dimensional gametophytes, which are enriched in stimulus and defense genes, as well as genes involved in epigenetic gene regulation and ubiquitin degradation. Our results provide insights into free-living gametophyte development, focusing on the filamentous-to-prothallus growth transition, and provide a useful resource for further investigations of asexual reproduction.
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Affiliation(s)
- Stefan Wyder
- Department of Plant and Microbial Biology & Zurich-Basel Plant Science Center, University of Zurich, Zollikerstrasse 107, CH-8008, Zurich, Switzerland
| | - Alejandro Rivera
- Area of Plant Physiology, Department of Organisms and Systems Biology, University of Oviedo, c) Catedrático R Uría s/n, 33071, Oviedo, Spain
| | - Ana E Valdés
- Department of Ecology, Environment and Plant Sciences, Stockholm University, SE-106 91, Stockholm, Sweden
| | - María Jesús Cañal
- Area of Plant Physiology, Department of Organisms and Systems Biology, University of Oviedo, c) Catedrático R Uría s/n, 33071, Oviedo, Spain
| | - Valeria Gagliardini
- Department of Plant and Microbial Biology & Zurich-Basel Plant Science Center, University of Zurich, Zollikerstrasse 107, CH-8008, Zurich, Switzerland
| | - Helena Fernández
- Area of Plant Physiology, Department of Organisms and Systems Biology, University of Oviedo, c) Catedrático R Uría s/n, 33071, Oviedo, Spain.
| | - Ueli Grossniklaus
- Department of Plant and Microbial Biology & Zurich-Basel Plant Science Center, University of Zurich, Zollikerstrasse 107, CH-8008, Zurich, Switzerland
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13
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Xu K, Zhang L, Rothfels CJ, Smith AR, Viane R, Lorence D, Wood KR, Chen C, Knapp R, Zhou L, Lu NT, Zhou X, Wei H, Fan Q, Chen S, Cicuzza D, Gao X, Liao W, Zhang L. A global plastid phylogeny of the fern genusAsplenium(Aspleniaceae). Cladistics 2019; 36:22-71. [DOI: 10.1111/cla.12384] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/11/2019] [Indexed: 01/20/2023] Open
Affiliation(s)
- Ke‐Wang Xu
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources School of Life Sciences Sun Yat‐sen University Guangzhou
- Missouri Botanical Garden 4344 Shaw Blvd St. Louis MO 63110
| | - Liang Zhang
- Key Laboratory for Plant Diversity and Biogeography of East Asia Kunming Institute of Botany Chinese Academy of Sciences Kunming
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization Chengdu Institute of Biology Chinese Academy of Sciences P.O. Box 416 Chengdu
| | - Carl J. Rothfels
- University Herbarium and Department of Integrative Biology University of California 1001 Valley Life Sciences Building Berkeley CA 94720
| | - Alan R. Smith
- University Herbarium and Department of Integrative Biology University of California 1001 Valley Life Sciences Building Berkeley CA 94720
| | - Ronald Viane
- Department of Biology Ghent University 9000 Gent
| | - David Lorence
- National Tropical Botanical Garden 3530 Papalina Road Kalāheo HI 96741
| | - Kenneth R. Wood
- National Tropical Botanical Garden 3530 Papalina Road Kalāheo HI 96741
| | - Cheng‐Wei Chen
- Division of Silviculture Taiwan Forestry Research Institute Taipei
| | - Ralf Knapp
- Muséum national d'Histoire naturelle (MNHN, Paris, France) Steigestrasse 78 69412 Eberbach
| | - Lin Zhou
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization Chengdu Institute of Biology Chinese Academy of Sciences P.O. Box 416 Chengdu
| | - Ngan Thi Lu
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization Chengdu Institute of Biology Chinese Academy of Sciences P.O. Box 416 Chengdu
- University of Chinese Academy of Sciences Beijing
- Department of Biology Vietnam National Museum of Nature Vietnam Academy of Science and Technology 18th Hoang Quoc Viet Road Ha Noi
| | - Xin‐Mao Zhou
- Laboratory of Ecology and Evolutionary Biology State Key Laboratory for Conservation and Utilization of Bio‐Resources in Yunnan Yunnan University Kunming
| | - Hong‐Jin Wei
- Shanghai Chenshan Botanical Garden Shanghai 201602
| | - Qiang Fan
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources School of Life Sciences Sun Yat‐sen University Guangzhou
| | - Su‐Fang Chen
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources School of Life Sciences Sun Yat‐sen University Guangzhou
| | - Daniele Cicuzza
- Faculty of Science Universiti Brunei Darussalam Bandar Seri Begawan
| | - Xin‐Fen Gao
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization Chengdu Institute of Biology Chinese Academy of Sciences P.O. Box 416 Chengdu
| | - Wen‐Bo Liao
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources School of Life Sciences Sun Yat‐sen University Guangzhou
| | - Li‐Bing Zhang
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization Chengdu Institute of Biology Chinese Academy of Sciences P.O. Box 416 Chengdu
- Missouri Botanical Garden 4344 Shaw Blvd St. Louis MO 63110
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14
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Ahmed D, Comte A, Curk F, Costantino G, Luro F, Dereeper A, Mournet P, Froelicher Y, Ollitrault P. Genotyping by sequencing can reveal the complex mosaic genomes in gene pools resulting from reticulate evolution: a case study in diploid and polyploid citrus. ANNALS OF BOTANY 2019; 123:1231-1251. [PMID: 30924905 PMCID: PMC6612944 DOI: 10.1093/aob/mcz029] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Revised: 01/17/2019] [Accepted: 02/18/2019] [Indexed: 05/21/2023]
Abstract
BACKGROUND AND AIMS Reticulate evolution, coupled with reproductive features limiting further interspecific recombinations, results in admixed mosaics of large genomic fragments from the ancestral taxa. Whole-genome sequencing (WGS) data are powerful tools to decipher such complex genomes but still too costly to be used for large populations. The aim of this work was to develop an approach to infer phylogenomic structures in diploid, triploid and tetraploid individuals from sequencing data in reduced genome complexity libraries. The approach was applied to the cultivated Citrus gene pool resulting from reticulate evolution involving four ancestral taxa, C. maxima, C. medica, C. micrantha and C. reticulata. METHODS A genotyping by sequencing library was established with the restriction enzyme ApeKI applying one base (A) selection. Diagnostic single nucleotide polymorphisms (DSNPs) for the four ancestral taxa were mined in 29 representative varieties. A generic pipeline based on a maximum likelihood analysis of the number of read data was established to infer ancestral contributions along the genome of diploid, triploid and tetraploid individuals. The pipeline was applied to 48 diploid, four triploid and one tetraploid citrus accessions. KEY RESULTS Among 43 598 mined SNPs, we identified a set of 15 946 DSNPs covering the whole genome with a distribution similar to that of gene sequences. The set efficiently inferred the phylogenomic karyotype of the 53 analysed accessions, providing patterns for common accessions very close to that previously established using WGS data. The complex phylogenomic karyotypes of 21 cultivated citrus, including bergamot, triploid and tetraploid limes, were revealed for the first time. CONCLUSIONS The pipeline, available online, efficiently inferred the phylogenomic structures of diploid, triploid and tetraploid citrus. It will be useful for any species whose reproductive behaviour resulted in an interspecific mosaic of large genomic fragments. It can also be used for the first generations of interspecific breeding schemes.
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Affiliation(s)
- Dalel Ahmed
- UMR AGAP, INRA, CIRAD, Montpellier SupAgro, Université de Montpellier, San Giuliano, France
| | - Aurore Comte
- IRD, CIRAD, Université de Montpellier, IPME, Montpellier, France
- South Green Bioinformatics Platform, Bioversity, CIRAD, INRA, IRD, Montpellier, France
| | - Franck Curk
- UMR AGAP, INRA, CIRAD, Montpellier SupAgro, Université de Montpellier, Montpellier, France
| | - Gilles Costantino
- UMR AGAP, INRA, CIRAD, Montpellier SupAgro, Université de Montpellier, San Giuliano, France
| | - François Luro
- UMR AGAP, INRA, CIRAD, Montpellier SupAgro, Université de Montpellier, San Giuliano, France
| | - Alexis Dereeper
- IRD, CIRAD, Université de Montpellier, IPME, Montpellier, France
- South Green Bioinformatics Platform, Bioversity, CIRAD, INRA, IRD, Montpellier, France
| | - Pierre Mournet
- UMR AGAP, INRA, CIRAD, Montpellier SupAgro, Université de Montpellier, Montpellier, France
- CIRAD, UMR AGAP, Montpellier, France
| | - Yann Froelicher
- UMR AGAP, INRA, CIRAD, Montpellier SupAgro, Université de Montpellier, Montpellier, France
- CIRAD, UMR AGAP, San Giuliano, France
| | - Patrick Ollitrault
- UMR AGAP, INRA, CIRAD, Montpellier SupAgro, Université de Montpellier, Montpellier, France
- CIRAD, UMR AGAP, San Giuliano, France
- For correspondence. E-mail
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15
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Hori K, Murakami N. Origin of the Diplaziumhachijoense complex (Athyriaceae). PHYTOKEYS 2019; 124:57-76. [PMID: 31258373 PMCID: PMC6592973 DOI: 10.3897/phytokeys.124.35242] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2019] [Accepted: 05/14/2019] [Indexed: 05/14/2023]
Abstract
We analyzed the phylogeny of the Diplaziumhachijoense complex using plastid trnL-F and low-copy nuclear marker AK1 DNA sequences. Based on allele constitution, triploid apogamous species of the D.hachijoense complex appeared to have originated from the hybridization of triploid apogamous species and diploid sexual species by recurrent hybridization events. These results suggested that triploid apogamous ferns can achieve hybridization with diploid sexual species by producing diploid spores with irregular meiosis in sporogenesis. Furthermore, the present study predicted the involvement of several unknown species associated with hybridization. More sampling of Callipteris species from China and adjacent areas is required to determine the relationships among unknown species and the D.hachijoense complex.
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Affiliation(s)
- Kiyotaka Hori
- The Kochi Prefectural Makino Botanical Garden 4200-6 Godaisan, Kochi 781-8125, JapanThe Kochi Prefectural Makino Botanical GardenKochiJapan
| | - Noriaki Murakami
- Makino Herbarium, Tokyo Metropolitan University, 1-1 Minami-osawa, Hachioji, Tokyo 192-0397, JapanTokyo Metropolitan UniversityHachiojiJapan
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16
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Fei X, Shi J, Liu Y, Niu J, Wei A. The steps from sexual reproduction to apomixis. PLANTA 2019; 249:1715-1730. [PMID: 30963237 DOI: 10.1007/s00425-019-03113-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Accepted: 02/18/2019] [Indexed: 05/03/2023]
Abstract
In this paper, an interaction model of apomixis-related genes was constructed to analyze the emergence of apomictic types. It is speculated that apomixis technology will be first implemented in gramineous plants. Apomixis (asexual seed formation) is a phenomenon in which a plant bypasses the most fundamental aspects of sexual reproduction-meiosis and fertilization-to form a viable seed. Plants can form seeds without fertilization, and the seed genotype is consistent with the female parent. The development of apomictic technology would be revolutionary for agriculture and for food production as it would reduce costs and breeding times and also avoid many complications typical of sexual reproduction (e.g. incompatibility barriers) and of vegetative propagation (e.g. viral transfer). The application of apomictic reproductive technology has the potential to revolutionize crop breeding. This article reviews recent advances in apomixis in cytology and molecular biology. The general idea of identifying apomixis was proposed and the process of the emergence of non-fusion types was discussed. To better understand the apomixis mechanism, an apomixis regulatory model was established. At the same time, the realization of apomixis technology is proposed, which provides reference for the research and application of apomixis.
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Affiliation(s)
- Xitong Fei
- College of Forestry, Northwest A&F University, Yangling, Shaanxi, China
| | - Jingwei Shi
- College of Forestry, Northwest A&F University, Yangling, Shaanxi, China
| | - Yulin Liu
- College of Forestry, Northwest A&F University, Yangling, Shaanxi, China
| | - Jinshuang Niu
- College of Forestry, Northwest A&F University, Yangling, Shaanxi, China
| | - Anzhi Wei
- College of Forestry, Northwest A&F University, Yangling, Shaanxi, China.
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17
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Hofstatter PG, Brown MW, Lahr DJG. Comparative Genomics Supports Sex and Meiosis in Diverse Amoebozoa. Genome Biol Evol 2018; 10:3118-3128. [PMID: 30380054 PMCID: PMC6263441 DOI: 10.1093/gbe/evy241] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/30/2018] [Indexed: 12/30/2022] Open
Abstract
Sex and reproduction are often treated as a single phenomenon in animals and plants, as in these organisms reproduction implies mixis and meiosis. In contrast, sex and reproduction are independent biological phenomena that may or may not be linked in the majority of other eukaryotes. Current evidence supports a eukaryotic ancestor bearing a mating type system and meiosis, which is a process exclusive to eukaryotes. Even though sex is ancestral, the literature regarding life cycles of amoeboid lineages depicts them as asexual organisms. Why would loss of sex be common in amoebae, if it is rarely lost, if ever, in plants and animals, as well as in fungi? One way to approach the question of meiosis in the "asexuals" is to evaluate the patterns of occurrence of genes for the proteins involved in syngamy and meiosis. We have applied a comparative genomic approach to study the occurrence of the machinery for plasmogamy, karyogamy, and meiosis in Amoebozoa, a major amoeboid supergroup. Our results support a putative occurrence of syngamy and meiotic processes in all major amoebozoan lineages. We conclude that most amoebozoans may perform mixis, recombination, and ploidy reduction through canonical meiotic processes. The present evidence indicates the possibility of sexual cycles in many lineages traditionally held as asexual.
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Affiliation(s)
- Paulo G Hofstatter
- Departamento de Zoologia, Instituto de Biociências, Universidade de São Paulo, Brazil
| | - Matthew W Brown
- Department of Biological Sciences, Mississippi State University
| | - Daniel J G Lahr
- Departamento de Zoologia, Instituto de Biociências, Universidade de São Paulo, Brazil
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18
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Fujiwara T, Serizawa S, Watano Y. Phylogenetic analysis reveals the origins of tetraploid and hexaploid species in the Japanese Lepisorus thunbergianus (Polypodiaceae) complex. JOURNAL OF PLANT RESEARCH 2018; 131:945-959. [PMID: 30167928 DOI: 10.1007/s10265-018-1061-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Accepted: 07/30/2018] [Indexed: 05/27/2023]
Abstract
The Japanese Lepisorus thunbergianus complex contains diploid and tetraploid races of L. thunbergianus and a hexaploid species, L. mikawanus. Here, we performed molecular phylogenetic analysis on this complex to delimit species and to elucidate the evolutionary origins of tetraploid and hexaploid species. Chloroplast DNA (cpDNA) phylogeny supported the monophyly of the complex. Based on a single-copy nuclear gene (PgiC) tree, the tetraploid L. thunbergianus samples could be classified into two variants: an allotetraploid of hybrid origin between diploid L. thunbergianus and Japanese L. angustus and another allotetraploid of hybrid origin between diploid L. thunbergianus and an unknown diploid race of L. tosaensis. These variants can be recognized morphologically and distinguished from their parent species. Hence, here we described these allopolyploids as new species, L. nigripes and L. kuratae, respectively. The hexaploid species L. mikawanus has three types of PgiC alleles, each of which was derived from diploid L. thunbergianus, L. tosaensis, and Japanese L. angustus, while cpDNA shows that it is included in Japanese L. thunbergianus clade. Based on the cpDNA phylogeny and PgiC nucleotide sequences, we therefore concluded that L. mikawanus is an allohexaploid that originated through hybridization between tetraploid species, L. nigripes and an unknown ancestral diploid race of L. tosaensis.
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Affiliation(s)
- Tao Fujiwara
- Department of Biology, Graduate School of Science, Chiba University, Yayoi-cho, Inage, Chiba, 263-8522, Japan.
- Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, 666303, Yunnan, China.
| | - Shunsuke Serizawa
- Aichi Green Association, Urahata 198-1, Nagamaki, Oharu-sho, Aichi, 490-1131, Japan
| | - Yasuyuki Watano
- Department of Biology, Graduate School of Science, Chiba University, Yayoi-cho, Inage, Chiba, 263-8522, Japan
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19
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Chang Y, Ebihara A, Lu S, Liu H, Schneider H. Integrated taxonomy of the Asplenium normale complex (Aspleniaceae) in China and adjacent areas. JOURNAL OF PLANT RESEARCH 2018; 131:573-587. [PMID: 29600315 DOI: 10.1007/s10265-018-1032-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Accepted: 02/27/2018] [Indexed: 06/08/2023]
Abstract
The Asplenium normale D. Don complex comprises several taxa that are either diploid or tetraploid. The tetraploids are assumed to have originated from diploid ancestors by relatively recent autopolyploidization or allopolyploidization. Some of the diploids are readily recognized morphologically but most of the taxa have until now been placed into a single species. However, phylogenetic studies have challenged this treatment and emphasized the notion that the taxonomic treatment of this complex needs to be revised. An integrative taxonomic approach was employed to delimit species in the complex using cytological, morphological, and DNA sequence data. Initially, we employed a diploid first approach to establish a robust taxonomic framework. Special efforts were made to collect and identify the diploid progenitors of each polyploid lineage identified in the plastid DNA based phylogenetic hypothesis. A total of six distinct diploid species were identified. The distinctive nature of the six diploids is strongly supported by sequence differences in plastid DNA and nuclear loci, as well as by the results of morphometric analysis. Diagnostic morphological characters were identified to distinguish the six diploid species, resulting in their revised taxonomy, which includes two novel species, namely, Asplenium normaloides and A. guangdongense. Further studies to strengthen the taxonomic classification of all of the tetraploid taxa are warranted.
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Affiliation(s)
- Yanfen Chang
- Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, 666303, Yunnan, China.
| | - Atsushi Ebihara
- Department of Botany, National Museum of Nature and Science, Tsukuba, Ibaraki, Japan
| | - Shugang Lu
- Institute of Ecology and Geobotany, Yunnan University, Kunming, 650091, Yunnan, China
| | - Hongmei Liu
- Gardening and Horticulture Department, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, 666303, Yunnan, China
| | - Harald Schneider
- Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, 666303, Yunnan, China
- Department of Life Sciences, Natural History Museum, London, SW7 5BD, UK
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20
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A global plastid phylogeny uncovers extensive cryptic speciation in the fern genus Hymenasplenium (Aspleniaceae). Mol Phylogenet Evol 2018; 127:203-216. [PMID: 29800652 DOI: 10.1016/j.ympev.2018.05.021] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2018] [Revised: 05/02/2018] [Accepted: 05/17/2018] [Indexed: 10/16/2022]
Abstract
The fern genus Hymenasplenium (Aspleniaceae) is one of the two genera in the family. It is generally recognized among modern pteridologists. However, its infrageneric relationships and species diversity have been unclear and controversial. The molecular studies so far have had small taxon and character sampling. In the present study, DNA sequences of six plastid markers of 158 accessions representing ca. 40 out of ca. 50 known species of Hymenasplenium, and 16 species of Asplenium were used to infer a phylogeny with maximum likelihood, Bayesian inference, and maximum parsimony approaches. Our major results include: (1) Hymenasplenium as currently defined is strongly supported as monophyletic; (2) three major clades representing early splits in Hymenasplenium are identified, with the Old World species being strongly supported as monophyletic; it is ambiguous if the New World species are monophyletic; (3) extensive cryptic speciation in the Old World is discovered demonstrating the complexity of evolution of the genus; and (4) six strongly or moderately supported subclades in the Old World clade are revealed, differing from one another in molecular, morphological, and geographical features.
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21
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Biodiversity and apomixis: Insights from the East-Asian holly ferns in Polystichum section Xiphopolystichum. Mol Phylogenet Evol 2018; 127:345-355. [PMID: 29763663 DOI: 10.1016/j.ympev.2018.05.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Revised: 04/30/2018] [Accepted: 05/03/2018] [Indexed: 11/24/2022]
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22
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Bui LT, Pandzic D, Youngstrom CE, Wallace S, Irish EE, Szövényi P, Cheng CL. A fern AINTEGUMENTA gene mirrors BABY BOOM in promoting apogamy in Ceratopteris richardii. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 90:122-132. [PMID: 28078730 DOI: 10.1111/tpj.13479] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2016] [Revised: 12/28/2016] [Accepted: 01/03/2017] [Indexed: 05/05/2023]
Abstract
Asexual reproduction is widespread in land plants, including ferns where 10% of all species are obligate asexuals. In these ferns, apogamous sporophytes are generated directly from gametophytes, bypassing fertilization. In the model fern Ceratopteris richardii, a sexual species, apogamy can be induced by culture on high sugar media. BABY BOOM (BBM) genes in angiosperms are known to promote somatic embryogenesis, which like apogamy produce sporophytes without fertilization. Here, a Brassica napus BBM (BnBBM) was used to investigate genetic similarity between apogamy in ferns and somatic embryogenesis in angiosperms. A C. richardii transcriptome was constructed from which one AINTEGUMENTA-LIKE unigene, CrANT, was identified. Whole mount in situ hybridization showed that CrANT is expressed in sperm and fertilized eggs. Phylogenetic analysis grouped CrANT with other non-seed-plant ANT genes to the euANT clade but in a branch separate from BBM genes. Overexpression of CrANT or BnBBM promotes apogamy in C. richardii without sugar supplement. CrANT knockdown gametophytes responded weakly to sugar for apogamy promotion. Theses results suggest some genetic conservation between apogamy and somatic embryogenesis and that such asexual reproduction may be ancient.
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Affiliation(s)
- Linh T Bui
- Department of Biology, University of Iowa, Iowa City, IA, 52242, USA
| | - Dzevida Pandzic
- Department of Biology, University of Iowa, Iowa City, IA, 52242, USA
| | | | - Simon Wallace
- Department of Biology, University of Iowa, Iowa City, IA, 52242, USA
| | - Erin E Irish
- Department of Biology, University of Iowa, Iowa City, IA, 52242, USA
| | - Péter Szövényi
- Department of Systematic and Evolutionary Botany, University of Zurich, Zurich, CH-8008, Switzerland
- Swiss Institute of Bioinformatics, Quartier Sorge-Batiment Genopode, Lausanne, Switzerland
- MTA ELTE-MTM Ecology Research Group, ELTE, Biological Institute, Budapest, Hungary
| | - Chi-Lien Cheng
- Department of Biology, University of Iowa, Iowa City, IA, 52242, USA
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23
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Rothfels CJ, Pryer KM, Li FW. Next-generation polyploid phylogenetics: rapid resolution of hybrid polyploid complexes using PacBio single-molecule sequencing. THE NEW PHYTOLOGIST 2017; 213:413-429. [PMID: 27463214 DOI: 10.1111/nph.14111] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2016] [Accepted: 06/14/2016] [Indexed: 05/27/2023]
Abstract
Difficulties in generating nuclear data for polyploids have impeded phylogenetic study of these groups. We describe a high-throughput protocol and an associated bioinformatics pipeline (Pipeline for Untangling Reticulate Complexes (Purc)) that is able to generate these data quickly and conveniently, and demonstrate its efficacy on accessions from the fern family Cystopteridaceae. We conclude with a demonstration of the downstream utility of these data by inferring a multi-labeled species tree for a subset of our accessions. We amplified four c. 1-kb-long nuclear loci and sequenced them in a parallel-tagged amplicon sequencing approach using the PacBio platform. Purc infers the final sequences from the raw reads via an iterative approach that corrects PCR and sequencing errors and removes PCR-mediated recombinant sequences (chimeras). We generated data for all gene copies (homeologs, paralogs, and segregating alleles) present in each of three sets of 50 mostly polyploid accessions, for four loci, in three PacBio runs (one run per set). From the raw sequencing reads, Purc was able to accurately infer the underlying sequences. This approach makes it easy and economical to study the phylogenetics of polyploids, and, in conjunction with recent analytical advances, facilitates investigation of broad patterns of polyploid evolution.
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Affiliation(s)
- Carl J Rothfels
- University Herbarium and Department of Integrative Biology, University of California, Berkeley, CA, 94720, USA
| | | | - Fay-Wei Li
- University Herbarium and Department of Integrative Biology, University of California, Berkeley, CA, 94720, USA
- Department of Biology, Duke University, Durham, NC, 27705, USA
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Applying DNA Barcodes to Identify Closely Related Species of Ferns: A Case Study of the Chinese Adiantum (Pteridaceae). PLoS One 2016; 11:e0160611. [PMID: 27603700 PMCID: PMC5014338 DOI: 10.1371/journal.pone.0160611] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2016] [Accepted: 07/21/2016] [Indexed: 11/19/2022] Open
Abstract
DNA barcoding is a fast-developing technique to identify species by using short and standard DNA sequences. Universal selection of DNA barcodes in ferns remains unresolved. In this study, five plastid regions (rbcL, matK, trnH-psbA, trnL-F and rps4-trnS) and eight nuclear regions (ITS, pgiC, gapC, LEAFY, ITS2, IBR3_2, DET1, and SQD1_1) were screened and evaluated in the fern genus Adiantum from China and neighboring areas. Due to low primer universality (matK) and/or the existence of multiple copies (ITS), the commonly used barcodes matK and ITS were not appropriate for Adiantum. The PCR amplification rate was extremely low in all nuclear genes except for IBR3_2. rbcL had the highest PCR amplification rate (94.33%) and sequencing success rate (90.78%), while trnH-psbA had the highest species identification rate (75%). With the consideration of discriminatory power, cost-efficiency and effort, the two-barcode combination of rbcL+ trnH-psbA seems to be the best choice for barcoding Adiantum, and perhaps basal polypod ferns in general. The nuclear IBR3_2 showed 100% PCR amplification success rate in Adiantum, however, it seemed that only diploid species could acquire clean sequences without cloning. With cloning, IBR3_2 can successfully distinguish cryptic species and hybrid species from their related species. Because hybridization and allopolyploidy are common in ferns, we argue for including a selected group of nuclear loci as barcodes, especially via the next-generation sequencing, as it is much more efficient to obtain single-copy nuclear loci without the cloning procedure.
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Horst NA, Reski R. Alternation of generations - unravelling the underlying molecular mechanism of a 165-year-old botanical observation. PLANT BIOLOGY (STUTTGART, GERMANY) 2016; 18:549-51. [PMID: 27094475 DOI: 10.1111/plb.12468] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Accepted: 04/15/2016] [Indexed: 05/02/2023]
Abstract
Characteristically, land plants exhibit a life cycle with an 'alternation of generations' and thus alternate between a haploid gametophyte and a diploid sporophyte. At meiosis and fertilisation the transitions between these two ontogenies take place in distinct single stem cells. The evolutionary invention of an embryo, and thus an upright multicellular sporophyte, in the ancestor of land plants formed the basis for the evolution of increasingly complex plant morphologies shaping Earth's ecosystems. Recent research employing the moss Physcomitrella patens revealed the homeotic gene BELL1 as a master regulator of the gametophyte-to-sporophyte transition. Here, we discuss these findings in the context of classical botanical observations.
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Affiliation(s)
- N A Horst
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - R Reski
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Freiburg, Germany
- BIOSS - Centre for Biological Signalling Studies, Freiburg, Germany
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Ekrt L, Koutecký P. Between sexual and apomictic: unexpectedly variable sporogenesis and production of viable polyhaploids in the pentaploid fern of the Dryopteris affinis agg. (Dryopteridaceae). ANNALS OF BOTANY 2016; 117:97-106. [PMID: 26476395 PMCID: PMC4701151 DOI: 10.1093/aob/mcv152] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Revised: 05/15/2015] [Accepted: 08/20/2015] [Indexed: 05/26/2023]
Abstract
BACKGROUND AND AIMS In ferns, apomixis is an important mode of asexual reproduction. Although the mechanisms of fern reproduction have been studied thoroughly, most previous work has focused on cases in which ferns reproduce either exclusively sexually or exclusively asexually. Reproduction of ferns with potentially mixed systems and inheritance of apomixis remains largely unknown. This study addresses reproduction of the pentaploid Dryopteris × critica, a hybrid of triploid apomictic D. borreri and tetraploid sexual D. filix-mas. METHODS Spore size, abortion percentage and number of spores per sporangium were examined in pentaploid plants of D. × critica grown in an experimental garden. The sporangial content of leaf segments was cultivated on an agar medium, and DNA ploidy levels were estimated by DAPI flow cytometry in 259 gametophytes or sporophytes arising from the F2 generation of the pentaploid hybrid. KEY RESULTS The hybrid is partly fertile (89-94% of aborted spores) and shows unstable sporogenesis with sexual and apomictic reproduction combined. The number of spores per sporangium varied from approx. 31 to 64. Within a single sporangium it was possible to detect formation of either only aborted spores or various mixtures of aborted and well-developed reduced spores and unreduced diplospores. The spores germinated in viable gametophytes with two ploidy levels: pentaploid (5x, from unreduced spores) and half of that (approx. 2·5x, from reduced spores). Moreover, 2-15% of gametophytes (both 2·5x and 5x) formed a viable sporophyte of the same ploidy level due to apogamy. CONCLUSIONS This study documents the mixed reproductive mode of a hybrid between apomictic and sexual ferns. Both sexual reduced and apomictic unreduced spores can be produced by a single individual, and even within a single sporangium. Both types of spores give rise to viable F2 generation gametophytes and sporophytes.
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Affiliation(s)
- Libor Ekrt
- Department of Botany, Faculty of Science, University of South Bohemia, Branišovská 1760, CZ-370 05 České Budějovice, Czech Republic
| | - Petr Koutecký
- Department of Botany, Faculty of Science, University of South Bohemia, Branišovská 1760, CZ-370 05 České Budějovice, Czech Republic
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27
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Rothfels CJ, Li FW, Sigel EM, Huiet L, Larsson A, Burge DO, Ruhsam M, Deyholos M, Soltis DE, Stewart CN, Shaw SW, Pokorny L, Chen T, dePamphilis C, DeGironimo L, Chen L, Wei X, Sun X, Korall P, Stevenson DW, Graham SW, Wong GKS, Pryer KM. The evolutionary history of ferns inferred from 25 low-copy nuclear genes. AMERICAN JOURNAL OF BOTANY 2015. [PMID: 26199366 DOI: 10.3732/ajb.1500089] [Citation(s) in RCA: 75] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
UNLABELLED • PREMISE OF THE STUDY Understanding fern (monilophyte) phylogeny and its evolutionary timescale is critical for broad investigations of the evolution of land plants, and for providing the point of comparison necessary for studying the evolution of the fern sister group, seed plants. Molecular phylogenetic investigations have revolutionized our understanding of fern phylogeny, however, to date, these studies have relied almost exclusively on plastid data.• METHODS Here we take a curated phylogenomics approach to infer the first broad fern phylogeny from multiple nuclear loci, by combining broad taxon sampling (73 ferns and 12 outgroup species) with focused character sampling (25 loci comprising 35877 bp), along with rigorous alignment, orthology inference and model selection.• KEY RESULTS Our phylogeny corroborates some earlier inferences and provides novel insights; in particular, we find strong support for Equisetales as sister to the rest of ferns, Marattiales as sister to leptosporangiate ferns, and Dennstaedtiaceae as sister to the eupolypods. Our divergence-time analyses reveal that divergences among the extant fern orders all occurred prior to ∼200 MYA. Finally, our species-tree inferences are congruent with analyses of concatenated data, but generally with lower support. Those cases where species-tree support values are higher than expected involve relationships that have been supported by smaller plastid datasets, suggesting that deep coalescence may be reducing support from the concatenated nuclear data.• CONCLUSIONS Our study demonstrates the utility of a curated phylogenomics approach to inferring fern phylogeny, and highlights the need to consider underlying data characteristics, along with data quantity, in phylogenetic studies.
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Affiliation(s)
- Carl J Rothfels
- Department of Zoology & Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia V6J 3S7, Canada
| | - Fay-Wei Li
- Department of Biology, Duke University, Durham, North Carolina 27708 USA
| | - Erin M Sigel
- Department of Botany (MRC 166), National Museum of Natural History, Smithsonian Institution, P.O. Box 37012 Washington, District of Columbia 20013-7012 USA
| | - Layne Huiet
- Department of Biology, Duke University, Durham, North Carolina 27708 USA
| | - Anders Larsson
- Systematic Biology, Department of Organismal Biology, Evolutionary Biology Centre, Uppsala University, Norbyv. 18D, SE-752 36 Uppsala, Sweden
| | - Dylan O Burge
- California Academy of Sciences, 55 Music Concourse Drive, San Francisco, California 94118 USA
| | - Markus Ruhsam
- Royal Botanic Garden Edinburgh, 20A Inverleith Row, Edinburgh EH3 5LR, Scotland, UK
| | - Michael Deyholos
- Department of Biology, University of British Columbia, Okanagan Campus, 1177 Research Road, Kelowna, British Columbia V1V 1V7, Canada
| | - Douglas E Soltis
- Florida Museum of Natural History, Department of Biology, and the Genetics Institute. University of Florida. Gainesville, Florida 32611 USA
| | - C Neal Stewart
- Department of Plant Sciences, University of Tennessee, Knoxville, Tennessee 37996, USA
| | | | - Lisa Pokorny
- Departamento de Biodiversidad y Conservación, Real Jardín Botánico-Consejo Superior de Investigaciones Científicas, 28014 Madrid, Spain
| | - Tao Chen
- Shenzhen Fairy Lake Botanical Garden, The Chinese Academy of Sciences, Shenzhen, Guangdong 518004, China
| | - Claude dePamphilis
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania 16802 USA
| | - Lisa DeGironimo
- The New York Botanical Garden, 2900 Southern Blvd., Bronx, New York 10458 USA
| | - Li Chen
- BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China
| | - Xiaofeng Wei
- BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China
| | - Xiao Sun
- BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China
| | - Petra Korall
- Systematic Biology, Department of Organismal Biology, Evolutionary Biology Centre, Uppsala University, Norbyv. 18D, SE-752 36 Uppsala, Sweden
| | - Dennis W Stevenson
- The New York Botanical Garden, 2900 Southern Blvd., Bronx, New York 10458 USA
| | - Sean W Graham
- Department of Botany & Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia V6J 3S7, Canada
| | - Gane K-S Wong
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta T6G 2E9, Canada Department of Medicine, University of Alberta, Edmonton, Alberta T6G 2E1, Canada
| | - Kathleen M Pryer
- Department of Biology, Duke University, Durham, North Carolina 27708 USA
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Pardi F, Scornavacca C. Reconstructible phylogenetic networks: do not distinguish the indistinguishable. PLoS Comput Biol 2015; 11:e1004135. [PMID: 25849429 PMCID: PMC4388854 DOI: 10.1371/journal.pcbi.1004135] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2014] [Accepted: 01/19/2015] [Indexed: 12/21/2022] Open
Abstract
Phylogenetic networks represent the evolution of organisms that have undergone reticulate events, such as recombination, hybrid speciation or lateral gene transfer. An important way to interpret a phylogenetic network is in terms of the trees it displays, which represent all the possible histories of the characters carried by the organisms in the network. Interestingly, however, different networks may display exactly the same set of trees, an observation that poses a problem for network reconstruction: from the perspective of many inference methods such networks are "indistinguishable". This is true for all methods that evaluate a phylogenetic network solely on the basis of how well the displayed trees fit the available data, including all methods based on input data consisting of clades, triples, quartets, or trees with any number of taxa, and also sequence-based approaches such as popular formalisations of maximum parsimony and maximum likelihood for networks. This identifiability problem is partially solved by accounting for branch lengths, although this merely reduces the frequency of the problem. Here we propose that network inference methods should only attempt to reconstruct what they can uniquely identify. To this end, we introduce a novel definition of what constitutes a uniquely reconstructible network. For any given set of indistinguishable networks, we define a canonical network that, under mild assumptions, is unique and thus representative of the entire set. Given data that underwent reticulate evolution, only the canonical form of the underlying phylogenetic network can be uniquely reconstructed. While on the methodological side this will imply a drastic reduction of the solution space in network inference, for the study of reticulate evolution this is a fundamental limitation that will require an important change of perspective when interpreting phylogenetic networks.
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Affiliation(s)
- Fabio Pardi
- Laboratoire d’Informatique, de Robotique et de Microélectronique de Montpellier (LIRMM, UMR 5506) CNRS, Université de Montpellier, France
- Institut de Biologie Computationnelle, Montpellier, France
| | - Celine Scornavacca
- Institut des Sciences de l’Evolution de Montpellier (ISE-M, UMR 5554) CNRS, IRD, Université de Montpellier, France
- Institut de Biologie Computationnelle, Montpellier, France
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Hori K, Tono A, Fujimoto K, Kato J, Ebihara A, Watano Y, Murakami N. Reticulate evolution in the apogamous Dryopteris varia complex (Dryopteridaceae, subg. Erythrovariae, sect. Variae) and its related sexual species in Japan. JOURNAL OF PLANT RESEARCH 2014; 127:661-84. [PMID: 25064510 DOI: 10.1007/s10265-014-0652-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2014] [Accepted: 06/04/2014] [Indexed: 05/27/2023]
Abstract
Apogamous fern species are often difficult to distinguish from related species because of their continuous morphological variations. To clarify the genetic relationships among the members of the Dryopteris varia complex, we analyzed the nucleotide sequences of the plastid gene rbcL and the nuclear gene PgiC. We also analyzed the diploid sexual species D. caudipinna and D. chinensis, which have not been included in the complex, but were recently shown to be closely related to the complex in a molecular phylogenetic study. The PgiC sequences of the diploid sexual species, D. varia, D. saxifraga, D. sp. 'protobissetiana' (undescribed diploid sexual species), D. caudipinna, and D. chinensis, were well differentiated and hence designated A, B, C, D, and E, respectively. Thus, the PgiC constitution of apogamous species in the complex was as follows: D. bissetiana, B + C; D. kobayashii, B + C + E); D. pacifica, A + C, A + B + C, or A + C + D; D. sacrosancta, A + C + E; and D. saxifragivaria, B + C. These results suggest that these apogamous species are formed by hybridizations of species including not only the three diploid sexual species of the D. varia complex (A, B, and C) but also the two diploid sexual species D. caudipinna (D) and D. chinensis (E), which do not belong to the complex.
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Affiliation(s)
- Kiyotaka Hori
- Makino Herbarium, Tokyo Metropolitan University, 1-1 Minamiosawa, Hachioji, Tokyo, 192-0397, Japan,
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Dyer RJ, Pellicer J, Savolainen V, Leitch IJ, Schneider H. Genome size expansion and the relationship between nuclear DNA content and spore size in the Asplenium monanthes fern complex (Aspleniaceae). BMC PLANT BIOLOGY 2013; 13:219. [PMID: 24354467 PMCID: PMC3930065 DOI: 10.1186/1471-2229-13-219] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2013] [Accepted: 12/10/2013] [Indexed: 05/07/2023]
Abstract
BACKGROUND Homosporous ferns are distinctive amongst the land plant lineages for their high chromosome numbers and enigmatic genomes. Genome size measurements are an under exploited tool in homosporous ferns and show great potential to provide an overview of the mechanisms that define genome evolution in these ferns. The aim of this study is to investigate the evolution of genome size and the relationship between genome size and spore size within the apomictic Asplenium monanthes fern complex and related lineages. RESULTS Comparative analyses to test for a relationship between spore size and genome size show that they are not correlated. The data do however provide evidence for marked genome size variation between species in this group. These results indicate that Asplenium monanthes has undergone a two-fold expansion in genome size. CONCLUSIONS Our findings challenge the widely held assumption that spore size can be used to infer ploidy levels within apomictic fern complexes. We argue that the observed genome size variation is likely to have arisen via increases in both chromosome number due to polyploidy and chromosome size due to amplification of repetitive DNA (e.g. transposable elements, especially retrotransposons). However, to date the latter has not been considered to be an important process of genome evolution within homosporous ferns. We infer that genome evolution, at least in some homosporous fern lineages, is a more dynamic process than existing studies would suggest.
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Affiliation(s)
- Robert J Dyer
- Department of Botany, Natural History Museum, London SW7 5BD, UK
- Imperial College London, Silwood Park Campus, Ascot, Berkshire SL5 7PY, UK
- Centre for Ecology and Hydrology, Wallingford, Oxfordshire OX10 8BB, UK
| | - Jaume Pellicer
- Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AB, UK
| | - Vincent Savolainen
- Imperial College London, Silwood Park Campus, Ascot, Berkshire SL5 7PY, UK
- Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AB, UK
| | - Ilia J Leitch
- Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AB, UK
| | - Harald Schneider
- Department of Botany, Natural History Museum, London SW7 5BD, UK
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, The Chinese Academy of Sciences, Beijing, China
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31
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Rothfels CJ, Larsson A, Li FW, Sigel EM, Huiet L, Burge DO, Ruhsam M, Graham SW, Stevenson DW, Wong GKS, Korall P, Pryer KM. Transcriptome-mining for single-copy nuclear markers in ferns. PLoS One 2013; 8:e76957. [PMID: 24116189 PMCID: PMC3792871 DOI: 10.1371/journal.pone.0076957] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2013] [Accepted: 08/27/2013] [Indexed: 01/27/2023] Open
Abstract
BACKGROUND Molecular phylogenetic investigations have revolutionized our understanding of the evolutionary history of ferns-the second-most species-rich major group of vascular plants, and the sister clade to seed plants. The general absence of genomic resources available for this important group of plants, however, has resulted in the strong dependence of these studies on plastid data; nuclear or mitochondrial data have been rarely used. In this study, we utilize transcriptome data to design primers for nuclear markers for use in studies of fern evolutionary biology, and demonstrate the utility of these markers across the largest order of ferns, the Polypodiales. PRINCIPAL FINDINGS We present 20 novel single-copy nuclear regions, across 10 distinct protein-coding genes: ApPEFP_C, cryptochrome 2, cryptochrome 4, DET1, gapCpSh, IBR3, pgiC, SQD1, TPLATE, and transducin. These loci, individually and in combination, show strong resolving power across the Polypodiales phylogeny, and are readily amplified and sequenced from our genomic DNA test set (from 15 diploid Polypodiales species). For each region, we also present transcriptome alignments of the focal locus and related paralogs-curated broadly across ferns-that will allow researchers to develop their own primer sets for fern taxa outside of the Polypodiales. Analyses of sequence data generated from our genomic DNA test set reveal strong effects of partitioning schemes on support levels and, to a much lesser extent, on topology. A model partitioned by codon position is strongly favored, and analyses of the combined data yield a Polypodiales phylogeny that is well-supported and consistent with earlier studies of this group. CONCLUSIONS The 20 single-copy regions presented here more than triple the single-copy nuclear regions available for use in ferns. They provide a much-needed opportunity to assess plastid-derived hypotheses of relationships within the ferns, and increase our capacity to explore aspects of fern evolution previously unavailable to scientific investigation.
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Affiliation(s)
- Carl J. Rothfels
- Department of Biology, Duke University, Durham, North Carolina, United States of America
- Department of Zoology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Anders Larsson
- Systematic Biology, Department of Organismal Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Fay-Wei Li
- Department of Biology, Duke University, Durham, North Carolina, United States of America
| | - Erin M. Sigel
- Department of Biology, Duke University, Durham, North Carolina, United States of America
| | - Layne Huiet
- Department of Biology, Duke University, Durham, North Carolina, United States of America
| | - Dylan O. Burge
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
| | | | - Sean W. Graham
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
| | | | - Gane Ka-Shu Wong
- Department of Medicine, University of Alberta, Edmonton, Alberta, Canada
- BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen, China
| | - Petra Korall
- Systematic Biology, Department of Organismal Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Kathleen M. Pryer
- Department of Biology, Duke University, Durham, North Carolina, United States of America
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