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Vignesh P, Mahadevaiah C, Selvamuthu K, Mahadeva Swamy HK, Sreenivasa V, Appunu C. Comparative genome-wide characterization of salt responsive micro RNA and their targets through integrated small RNA and de novo transcriptome profiling in sugarcane and its wild relative Erianthus arundinaceus. 3 Biotech 2024; 14:24. [PMID: 38162015 PMCID: PMC10756875 DOI: 10.1007/s13205-023-03867-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2023] [Accepted: 11/24/2023] [Indexed: 01/03/2024] Open
Abstract
Soil salinity and saline irrigation water are major constraints in sugarcane affecting the production of cane and sugar yield. To understand the salinity induced responses and to identify novel genomic resources, integrated de novo transcriptome and small RNA sequencing in sugarcane wild relative, Erianthus arundinaceus salt tolerant accession IND 99-907 and salt-sensitive sugarcane genotype Co 97010 were performed. A total of 362 known miRNAs belonging to 62 families and 353 miRNAs belonging to 63 families were abundant in IND 99-907 and Co 97010 respectively. The miRNA families such as miR156, miR160, miR166, miR167, miR169, miR171, miR395, miR399, miR437 and miR5568 were the most abundant with more than ten members in both genotypes. The differential expression analysis of miRNA reveals that 221 known miRNAs belonging to 48 families and 130 known miRNAs belonging to 42 families were differentially expressed in IND 99-907 and Co 97010 respectively. A total of 12,693 and 7982 miRNA targets against the monoploid mosaic genome and a total of 15,031 and 12,152 miRNA targets against the de novo transcriptome were identified for differentially expressed known miRNAs of IND 99-907 and Co 97010 respectively. The gene ontology (GO) enrichment analysis of the miRNA targets revealed that 24, 12 and 14 enriched GO terms (FDR < 0.05) for biological process, molecular function and cellular component respectively. These miRNAs have many targets that associated in regulation of biotic and abiotic stresses. Thus, the genomic resources generated through this study are useful for sugarcane crop improvement through biotechnological and advanced breeding approaches. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-023-03867-7.
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Affiliation(s)
- Palanisamy Vignesh
- Division of Crop Improvement, ICAR-Sugarcane Breeding Institute, Coimbatore, Tamil Nadu 641007 India
| | - Channappa Mahadevaiah
- Division of Crop Improvement, ICAR-Sugarcane Breeding Institute, Coimbatore, Tamil Nadu 641007 India
- ICAR-Indian Institute of Horticultural Research, Hesaraghatta Lake Post, Bangalore, 560089 India
| | - Kannan Selvamuthu
- Division of Crop Improvement, ICAR-Sugarcane Breeding Institute, Coimbatore, Tamil Nadu 641007 India
| | | | - Venkatarayappa Sreenivasa
- Division of Crop Improvement, ICAR-Sugarcane Breeding Institute, Coimbatore, Tamil Nadu 641007 India
| | - Chinnaswamy Appunu
- Division of Crop Improvement, ICAR-Sugarcane Breeding Institute, Coimbatore, Tamil Nadu 641007 India
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2
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Ling K, Yi-ning D, Majeed A, Zi-jiang Y, Jun-wen C, Li-lian H, Xian-hong W, Lu-feng L, Zhen-feng Q, Dan Z, Shu-jie G, Rong X, Lin-yan X, Fu X, Yang D, Fu-sheng L. Evaluation of genome size and phylogenetic relationships of the Saccharum complex species. 3 Biotech 2022; 12:327. [PMID: 36276474 PMCID: PMC9582063 DOI: 10.1007/s13205-022-03338-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 08/16/2022] [Indexed: 11/29/2022] Open
Abstract
"Saccharum complex" is a hypothetical group of species, which is supposed to be involved in the origin of modern sugarcane, and displays large genomes and complex chromosomal alterations. The utilization of restricted parents in breeding programs of modern cultivated sugarcane has resulted in a genetic blockage, which controlled its improvement because of the limited genetic diversity. The use of wild relatives is an effective way to broaden the genetic composition of cultivated sugarcane. Due to the infrequent characterization of genomes, the potential of wild relatives is diffused in improving the cultivated sugarcane. To characterize the genomes of the wild relatives, the genome size and phylogenetic relationships among eight species, including Saccharum spontaneum, Erianthus arundinaceus, E. fulvus, E. rockii, Narenga porphyrocoma, Miscanthus floridulus, Eulalia quadrinervis, and M. sinensis were evaluated based on flow cytometry, genome surveys, K-mer analysis, chloroplast genome sequencing, and whole-genome SNPs analysis. We observed highly heterozygous genomes of S. spontaneum, E. rockii, and E. arundinaceus and the highly repetitive genome of E. fulvus. The genomes of Eulalia quadrinervis, N. porphyrocoma, M. sinensis, and M. floridulus were highly complex. Phylogenetic results of the two approaches were dissimilar, however, both indicate E. fulvus displayed closer relationships to Miscanthus and Saccharum than other species of Saccharum complex. Eulalia quadrinervis was more closely related to M. floridulus than M. sinensis; E. arundinaceus differ significantly from Miscanthus, Narenga, and Saccharum, but was relatively close to Erianthus. We proved the point of E. rockii and E. fulvus should not be classified as one genus, and E. fulvus should be classified as the Saccharum genus. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-022-03338-5.
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Affiliation(s)
- Kui Ling
- The Key Laboratory for Crop Production and Intelligent Agriculture of Yunnan Province, Kunming, 650201 Yunnan China
- Shenzhen Qianhai Shekou Free Trade Zone Hospital, Shenzhen, 518067 China
| | - Di Yi-ning
- The Key Laboratory for Crop Production and Intelligent Agriculture of Yunnan Province, Kunming, 650201 Yunnan China
| | - Aasim Majeed
- School of Agricultural Biotechnology, Punjab Agriculture University, Ludhiana, 141004 India
| | - Yang Zi-jiang
- Applied Genomics Technology Laboratory, Yunnan Agricultural University, Kunming, 650201 Yunnan China
| | - Chen Jun-wen
- The Key Laboratory for Crop Production and Intelligent Agriculture of Yunnan Province, Kunming, 650201 Yunnan China
| | - He Li-lian
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, 650201 Yunnan China
| | - Wang Xian-hong
- The Key Laboratory for Crop Production and Intelligent Agriculture of Yunnan Province, Kunming, 650201 Yunnan China
| | - Liu Lu-feng
- Sugarcane Research Institute, Yunnan Agricultural University, Kunming, 650201 Yunnan China
| | - Qian Zhen-feng
- The Key Laboratory for Crop Production and Intelligent Agriculture of Yunnan Province, Kunming, 650201 Yunnan China
| | - Zeng Dan
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, 650201 Yunnan China
| | - Gu Shu-jie
- The Key Laboratory for Crop Production and Intelligent Agriculture of Yunnan Province, Kunming, 650201 Yunnan China
| | - Xu Rong
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, 650201 Yunnan China
| | - Xie Lin-yan
- The Key Laboratory for Crop Production and Intelligent Agriculture of Yunnan Province, Kunming, 650201 Yunnan China
| | - Xu Fu
- Sugarcane Research Institute, Yunnan Agricultural University, Kunming, 650201 Yunnan China
| | - Dong Yang
- Applied Genomics Technology Laboratory, Yunnan Agricultural University, Kunming, 650201 Yunnan China
| | - Li Fu-sheng
- The Key Laboratory for Crop Production and Intelligent Agriculture of Yunnan Province, Kunming, 650201 Yunnan China
- Sugarcane Research Institute, Yunnan Agricultural University, Kunming, 650201 Yunnan China
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, 650201 Yunnan China
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3
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Comparative Analysis of Chloroplast Genome in Saccharum spp. and Related Members of ‘Saccharum Complex’. Int J Mol Sci 2022; 23:ijms23147661. [PMID: 35887005 PMCID: PMC9315705 DOI: 10.3390/ijms23147661] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 07/05/2022] [Accepted: 07/05/2022] [Indexed: 02/04/2023] Open
Abstract
High ploids of the sugarcane nuclear genome limit its genomic studies, whereas its chloroplast genome is small and conserved, which is suitable for phylogenetic studies and molecular marker development. Here, we applied whole genome sequencing technology to sequence and assemble chloroplast genomes of eight species of the ‘Saccharum Complex’, and elucidated their sequence variations. In total, 19 accessions were sequenced, and 23 chloroplast genomes were assembled, including 6 species of Saccharum (among them, S. robustum, S. sinense, and S. barberi firstly reported in this study) and 2 sugarcane relative species, Tripidium arundinaceum and Narenga porphyrocoma. The plastid phylogenetic signal demonstrated that S. officinarum and S. robustum shared a common ancestor, and that the cytoplasmic origins of S. sinense and S. barberi were much more ancient than the S. offcinarum/S. robustum linage. Overall, 14 markers were developed, including 9 InDel markers for distinguishing Saccharum from its relative species, 4 dCAPS markers for distinguishing S. officinarum from S. robustum, and 1 dCAPS marker for distinguishing S. sinense and S. barberi from other species. The results obtained from our studies will contribute to the understanding of the classification and plastome evolution of Saccharinae, and the molecular markers developed have demonstrated their highly discriminatory power in Saccharum and relative species.
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Pompidor N, Charron C, Hervouet C, Bocs S, Droc G, Rivallan R, Manez A, Mitros T, Swaminathan K, Glaszmann JC, Garsmeur O, D’Hont A. Three founding ancestral genomes involved in the origin of sugarcane. ANNALS OF BOTANY 2021; 127:827-840. [PMID: 33637991 PMCID: PMC8103802 DOI: 10.1093/aob/mcab008] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Accepted: 02/25/2021] [Indexed: 05/11/2023]
Abstract
BACKGROUND AND AIMS Modern sugarcane cultivars (Saccharum spp.) are high polyploids, aneuploids (2n = ~12x = ~120) derived from interspecific hybridizations between the domesticated sweet species Saccharum officinarum and the wild species S. spontaneum. METHODS To analyse the architecture and origin of such a complex genome, we analysed the sequences of all 12 hom(oe)ologous haplotypes (BAC clones) from two distinct genomic regions of a typical modern cultivar, as well as the corresponding sequence in Miscanthus sinense and Sorghum bicolor, and monitored their distribution among representatives of the Saccharum genus. KEY RESULTS The diversity observed among haplotypes suggested the existence of three founding genomes (A, B, C) in modern cultivars, which diverged between 0.8 and 1.3 Mya. Two genomes (A, B) were contributed by S. officinarum; these were also found in its wild presumed ancestor S. robustum, and one genome (C) was contributed by S. spontaneum. These results suggest that S. officinarum and S. robustum are derived from interspecific hybridization between two unknown ancestors (A and B genomes). The A genome contributed most haplotypes (nine or ten) while the B and C genomes contributed one or two haplotypes in the regions analysed of this typical modern cultivar. Interspecific hybridizations likely involved accessions or gametes with distinct ploidy levels and/or were followed by a series of backcrosses with the A genome. The three founding genomes were found in all S. barberi, S. sinense and modern cultivars analysed. None of the analysed accessions contained only the A genome or the B genome, suggesting that representatives of these founding genomes remain to be discovered. CONCLUSIONS This evolutionary model, which combines interspecificity and high polyploidy, can explain the variable chromosome pairing affinity observed in Saccharum. It represents a major revision of the understanding of Saccharum diversity.
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Affiliation(s)
- Nicolas Pompidor
- CIRAD, UMR AGAP, Montpellier, France
- AGAP, Université de Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Carine Charron
- CIRAD, UMR AGAP, Montpellier, France
- AGAP, Université de Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Catherine Hervouet
- CIRAD, UMR AGAP, Montpellier, France
- AGAP, Université de Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Stéphanie Bocs
- CIRAD, UMR AGAP, Montpellier, France
- AGAP, Université de Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Gaëtan Droc
- CIRAD, UMR AGAP, Montpellier, France
- AGAP, Université de Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Ronan Rivallan
- CIRAD, UMR AGAP, Montpellier, France
- AGAP, Université de Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Aurore Manez
- CIRAD, UMR AGAP, Montpellier, France
- AGAP, Université de Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Therese Mitros
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | | | - Jean-Christophe Glaszmann
- CIRAD, UMR AGAP, Montpellier, France
- AGAP, Université de Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Olivier Garsmeur
- CIRAD, UMR AGAP, Montpellier, France
- AGAP, Université de Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Angélique D’Hont
- CIRAD, UMR AGAP, Montpellier, France
- AGAP, Université de Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
- For correspondence. E-mail
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5
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Grace OM, Pérez-Escobar OA, Lucas EJ, Vorontsova MS, Lewis GP, Walker BE, Lohmann LG, Knapp S, Wilkie P, Sarkinen T, Darbyshire I, Lughadha EN, Monro A, Woudstra Y, Demissew S, Muasya AM, Díaz S, Baker WJ, Antonelli A. Botanical Monography in the Anthropocene. TRENDS IN PLANT SCIENCE 2021; 26:433-441. [PMID: 33579621 DOI: 10.1016/j.tplants.2020.12.018] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 12/15/2020] [Accepted: 12/23/2020] [Indexed: 06/12/2023]
Abstract
Unprecedented changes in the Earth's biota are prompting urgent efforts to describe and conserve plant diversity. For centuries, botanical monographs - comprehensive systematic treatments of a family or genus - have been the gold standard for disseminating scientific information to accelerate research. The lack of a monograph compounds the risk that undiscovered species become extinct before they can be studied and conserved. Progress towards estimating the Tree of Life and digital information resources now bring even the most ambitious monographs within reach. Here, we recommend best practices to complete monographs urgently, especially for tropical plant groups under imminent threat or with expected socioeconomic benefits. We also highlight the renewed relevance and potential impact of monographies for the understanding, sustainable use, and conservation of biodiversity.
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Affiliation(s)
| | | | | | | | | | | | - Lúcia G Lohmann
- Universidade de São Paulo, Instituto de Biociências, Departamento de Botânica, 05508-900, São Paulo, Brazil
| | - Sandra Knapp
- Department of Botany, Natural History Museum, Cromwell Road, London, SW7 5BD, UK
| | - Peter Wilkie
- Royal Botanic Garden Edinburgh, 20A Inverleith Row, Edinburgh, EH3 5LP, UK
| | - Tiina Sarkinen
- Royal Botanic Garden Edinburgh, 20A Inverleith Row, Edinburgh, EH3 5LP, UK
| | | | | | | | - Yannick Woudstra
- Royal Botanic Gardens, Kew, TW9 3AE, UK; Natural History Museum of Denmark, University of Copenhagen, Gothersgade 130, Copenhagen 1153, Denmark
| | - Sebsebe Demissew
- Department of Plant Biology and Biodiversity Management, National Herbarium, College of Natural Sciences, Addis Ababa University, PO Box 3434, Addis Ababa, Ethiopia
| | - A Muthama Muasya
- Department of Biological Sciences, University of Cape Town, Rondebosch, 7700, South Africa
| | - Sandra Díaz
- Instituto Multidisciplinario de Biología Vegetal (CONICET-UNC) and FCEFyN, Universidad Nacional de Córdoba, Casilla de Correo 495, 5000 Córdoba, Argentina
| | | | - Alexandre Antonelli
- Royal Botanic Gardens, Kew, TW9 3AE, UK; Gothenburg Global Biodiversity Centre, Department of Biological and Environmental Sciences, University of Gothenburg, 41319 Gothenburg, Sweden; Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK.
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6
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Cordobés FM, Robbiati FO, Anton AM, Scrivanti LR. Phylogeny, evolution and ecological speciation analyses of Imperata (Poaceae: Andropogoneae) in the Neotropics. SYST BIODIVERS 2021. [DOI: 10.1080/14772000.2021.1887959] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- Fernando Moro Cordobés
- Instituto Multidisciplinario de Biología Vegetal (IMBIV), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) – Universidad Nacional de Córdoba, Córdoba, Prov. de Córdoba, Argentina
| | - Federico Omar Robbiati
- Instituto Multidisciplinario de Biología Vegetal (IMBIV), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) – Universidad Nacional de Córdoba, Córdoba, Prov. de Córdoba, Argentina
| | - Ana María Anton
- Instituto Multidisciplinario de Biología Vegetal (IMBIV), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) – Universidad Nacional de Córdoba, Córdoba, Prov. de Córdoba, Argentina
| | - Lidia Raquel Scrivanti
- Instituto Multidisciplinario de Biología Vegetal (IMBIV), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) – Universidad Nacional de Córdoba, Córdoba, Prov. de Córdoba, Argentina
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7
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Bressan EA, de Carvalho IAS, Borges MTMR, Carneiro MS, da Silva EF, Gazaffi R, Shirasuna RT, Abreu V, Popin RV, Figueira A, Oliveira GCX. Assessment of Gene Flow to Wild Relatives and Nutritional Composition of Sugarcane in Brazil. Front Bioeng Biotechnol 2020; 8:598. [PMID: 32637401 PMCID: PMC7317034 DOI: 10.3389/fbioe.2020.00598] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Accepted: 05/15/2020] [Indexed: 11/13/2022] Open
Abstract
The commercial release of genetically modified organisms (GMO) requires a prior environmental and human/animal health risk assessment. In Brazil, the National Biotechnology Technical Commission (CTNBio) requires a survey of the area of natural occurrence of wild relatives of the GMO in the Brazilian ecosystems to evaluate the possibility of introgressive hybridization between sexually compatible species. Modern sugarcane cultivars, the focus of this study, derive from a series of hybridization and backcrossing events among Saccharum species. The so-called "Saccharum broad sense" group includes around 40 species from a few genera, including Erianthus, found in various tropical regions, particularly South-Eastern Asia. In Brazil, three native species, originally considered to belong to Erianthus, were reclassified as S. angustifolium (Nees) Trin., S. asperum (Nees) Steud., and S. villosum Steud., based on inflorescence morphology. Thus, we have investigated the potential occurrence of gene flow among the Brazilian Saccharum native species and commercial hybrids as a requisite for GMO commercial release. A comprehensive survey was carried out to map the occurrence of the three native Saccharum species in Brazil, concluding that they are sympatric with sugarcane cultivation only from around 14°S southwards, which precludes most Northeastern sugarcane-producing states from undergoing introgression. Based on phenology, we concluded that the Brazilian Saccharum species are unable to outcross naturally with commercial sugarcane since the overlap between the flowering periods of sugarcane and the native species is limited. A phylogenomic reconstruction based on the full plastid genome sequence showed that the three native Saccharum species are the taxa closest to sugarcane in Brazil, being closer than introduced Erianthus or Miscanthus. A 2-year study on eight nutritional composition traits of the 20 main sugarcane cultivars cultivated in Brazil was carried out in six environments. The minimum and maximum values obtained were, in percent: moisture (62.6-82.5); sucrose (9.65-21.76); crude fiber (8.06-21.03); FDN (7.20-20.68); FDA (4.55-16.90); lipids (0.06-1.59); ash (0.08-2.67); and crude protein (0.18-1.18). Besides a considerable amount of genetic variation and plastic responses, many instances of genotype-by-environment interaction were detected.
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Affiliation(s)
- Eduardo Andrade Bressan
- Evolution Laboratory, Department of Genetics, “Luiz de Queiroz” Agricultural College, University of São Paulo, Piracicaba, Brazil
| | - Igor Araújo Santos de Carvalho
- Evolution Laboratory, Department of Genetics, “Luiz de Queiroz” Agricultural College, University of São Paulo, Piracicaba, Brazil
| | - Maria Teresa Mendes Ribeiro Borges
- Technological Analysis and Simulation Laboratory, Department of Agroindustrial Technology and Rural Socioeconomics, Center of Agricultural Sciences, Federal University of São Carlos, Araras, Brazil
| | - Monalisa Sampaio Carneiro
- Plant Biotechnology Laboratory, Department of Biotechnology, Vegetal and Animal Production, Center of Agricultural Sciences, Federal University of São Carlos, Araras, Brazil
| | - Edson Ferreira da Silva
- Plant Breeding Laboratory, Biology Department, Federal Rural University of Pernambuco, Recife, Brazil
| | - Rodrigo Gazaffi
- Department of Biotechnology, Vegetal and Animal Production, Center of Agricultural Sciences, Federal University of São Carlos, Araras, Brazil
| | - Regina Tomoko Shirasuna
- Herbarium Curatorship Research Nucleus, Vascular Plants Research Center, Institute of Botany, São Paulo, Brazil
| | - Vinícius Abreu
- Laboratory of Cell and Molecular Biology, Center of Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, Brazil
| | - Rafael V. Popin
- Laboratory of Cell and Molecular Biology, Center of Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, Brazil
| | - Antonio Figueira
- Plant Breeding Laboratory, Center of Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, Brazil
| | - Giancarlo Conde Xavier Oliveira
- Evolution Laboratory, Department of Genetics, “Luiz de Queiroz” Agricultural College, University of São Paulo, Piracicaba, Brazil
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Lloyd Evans D, Joshi SV, Wang J. Whole chloroplast genome and gene locus phylogenies reveal the taxonomic placement and relationship of Tripidium (Panicoideae: Andropogoneae) to sugarcane. BMC Evol Biol 2019; 19:33. [PMID: 30683070 PMCID: PMC6347779 DOI: 10.1186/s12862-019-1356-9] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2017] [Accepted: 01/03/2019] [Indexed: 11/13/2022] Open
Abstract
Background For over 50 years, attempts have been made to introgress agronomically useful traits from Erianthus sect. Ripidium (Tripidium) species into sugarcane based on both genera being part of the ‘Saccharum Complex’, an interbreeding group of species believed to be involved in the origins of sugarcane. However, recent low copy number gene studies indicate that Tripidium and Saccharum are more divergent than previously thought. The extent of genus Tripidium has not been fully explored and many species that should be included in Tripidium are still classified as Saccharum. Moreover, Tripidium is currently defined as incertae sedis within the Andropogoneae, though it has been suggested that members of this genus are related to the Germainiinae. Results Eight newly-sequenced chloroplasts from potential Tripidium species were combined in a phylogenetic study with 46 members of the Panicoideae, including seven Saccharum accessions, two Miscanthidium and three Miscanthus species. A robust chloroplast phylogeny was generated and comparison with a gene locus phylogeny clearly places a monophyletic Tripidium clade outside the bounds of the Saccharinae. A key to the currently identified Tripidium species is presented. Conclusion For the first time, we have undertaken a large-scale whole plastid study of eight newly assembled Tripidium accessions and a gene locus study of five Tripidium accessions. Our findings show that Tripidium and Saccharum are 8 million years divergent, last sharing a common ancestor 12 million years ago. We demonstrate that four species should be removed from Saccharum/Erianthus and included in genus Tripidium. In a genome context, we show that Tripidium evolved from a common ancestor with and extended Germainiinae clade formed from Germainia, Eriochrysis, Apocopis, Pogonatherum and Imperata. We re-define the ‘Saccharum complex’ to a group of genera that can interbreed in the wild and extend the Saccharinae to include Sarga along with Sorghastrum, Microstegium vimineum and Polytrias (but excluding Sorghum). Monophyly of genus Tripidium is confirmed and the genus is expanded to include Tripidium arundinaceum, Tripidium procerum, Tripidium kanashiroi and Tripidium rufipilum. As a consequence, these species are excluded from genus Saccharum. Moreover, we demonstrate that genus Tripidium is distinct from the Germainiinae. Electronic supplementary material The online version of this article (10.1186/s12862-019-1356-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Dyfed Lloyd Evans
- South African Sugarcane Research Institute, 170 Flanders Drive, Private Bag X02, Mount Edgecombe, Durban, 4300, South Africa. .,School of Life Sciences, College of Agriculture, Engineering and Science, University of Kwa-Zulu Natal, Private Bag X54001, Durban, 4000, South Africa. .,BeauSci Ltd., Waterbeach, Cambridge, CB25 9TL, UK.
| | - Shailesh V Joshi
- South African Sugarcane Research Institute, 170 Flanders Drive, Private Bag X02, Mount Edgecombe, Durban, 4300, South Africa.,School of Life Sciences, College of Agriculture, Engineering and Science, University of Kwa-Zulu Natal, Private Bag X54001, Durban, 4000, South Africa
| | - Jianping Wang
- Agronomy Department, University of Florida, Gainesville, FL, USA.,Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, China.,Plant Molecular and Biology Program, Genetics Institute, University of Florida, Gainesville, FL, USA
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9
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McAllister CA, McKain MR, Li M, Bookout B, Kellogg EA. Specimen-based analysis of morphology and the environment in ecologically dominant grasses: the power of the herbarium. Philos Trans R Soc Lond B Biol Sci 2018; 374:rstb.2017.0403. [PMID: 30455217 DOI: 10.1098/rstb.2017.0403] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/13/2018] [Indexed: 01/10/2023] Open
Abstract
Herbaria contain a cumulative sample of the world's flora, assembled by thousands of people over centuries. To capitalize on this resource, we conducted a specimen-based analysis of a major clade in the grass tribe Andropogoneae, including the dominant species of the world's grasslands in the genera Andropogon, Schizachyrium, Hyparrhenia and several others. We imaged 186 of the 250 named species of the clade, georeferenced the specimens and extracted climatic variables for each. Using semi- and fully automated image analysis techniques, we extracted spikelet morphological characters and correlated these with environmental variables. We generated chloroplast genome sequences to correct for phylogenetic covariance and here present a new phylogeny for 81 of the species. We confirm and extend earlier studies to show that Andropogon and Schizachyrium are not monophyletic. In addition, we find all morphological and ecological characters are homoplasious but variable among clades. For example, sessile spikelet length is positively correlated with awn length when all accessions are considered, but when separated by clade, the relationship is positive for three sub-clades and negative for three others. Climate variables showed no correlation with morphological variation in the spikelet pair; only very weak effects of temperature and precipitation were detected on macrohair density.This article is part of the theme issue 'Biological collections for understanding biodiversity in the Anthropocene'.
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Affiliation(s)
| | - Michael R McKain
- Donald Danforth Plant Science Center, 975 North Warson Road, St Louis, MO 63132, USA.,Department of Biological Sciences, The University of Alabama, Tuscaloosa, AL, USA
| | - Mao Li
- Donald Danforth Plant Science Center, 975 North Warson Road, St Louis, MO 63132, USA
| | - Bess Bookout
- Department of Biology and Natural Resources, Principia College, Elsah, IL, USA
| | - Elizabeth A Kellogg
- Donald Danforth Plant Science Center, 975 North Warson Road, St Louis, MO 63132, USA
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10
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Snyman SJ, Komape DM, Khanyi H, van den Berg J, Cilliers D, Lloyd Evans D, Barnard S, Siebert SJ. Assessing the Likelihood of Gene Flow From Sugarcane ( Saccharum Hybrids) to Wild Relatives in South Africa. Front Bioeng Biotechnol 2018; 6:72. [PMID: 29930938 PMCID: PMC5999724 DOI: 10.3389/fbioe.2018.00072] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Accepted: 05/17/2018] [Indexed: 01/17/2023] Open
Abstract
Pre-commercialization studies on environmental biosafety of genetically modified (GM) crops are necessary to evaluate the potential for sexual hybridization with related plant species that occur in the release area. The aim of the study was a preliminary assessment of factors that may contribute to gene flow from sugarcane (Saccharum hybrids) to indigenous relatives in the sugarcane production regions of Mpumalanga and KwaZulu-Natal provinces, South Africa. In the first instance, an assessment of Saccharum wild relatives was conducted based on existing phylogenies and literature surveys. The prevalence, spatial overlap, proximity, distribution potential, and flowering times of wild relatives in sugarcane production regions based on the above, and on herbaria records and field surveys were conducted for Imperata, Sorghum, Cleistachne, and Miscanthidium species. Eleven species were selected for spatial analyses based on their presence within the sugarcane cultivation region: four species in the Saccharinae and seven in the Sorghinae. Secondly, fragments of the nuclear internal transcribed spacer (ITS) regions of the 5.8s ribosomal gene and two chloroplast genes, ribulose-bisphosphate carboxylase (rbcL), and maturase K (matK) were sequenced or assembled from short read data to confirm relatedness between Saccharum hybrids and its wild relatives. Phylogenetic analyses of the ITS cassette showed that the closest wild relative species to commercial sugarcane were Miscanthidium capense, Miscanthidium junceum, and Narenga porphyrocoma. Sorghum was found to be more distantly related to Saccharum than previously described. Based on the phylogeny described in our study, the only species to highlight in terms of evolutionary divergence times from Saccharum are those within the genus Miscanthidium, most especially M. capense, and M. junceum which are only 3 million years divergent from Saccharum. Field assessment of pollen viability of 13 commercial sugarcane cultivars using two stains, iodine potassium iodide (IKI) and triphenyl tetrazolium chloride, showed decreasing pollen viability (from 85 to 0%) from the north to the south eastern regions of the study area. Future work will include other aspects influencing gene flow such as cytological compatibility and introgression between sugarcane and Miscanthidium species.
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Affiliation(s)
- Sandy J Snyman
- Crop Biology Resource Centre, South African Sugarcane Research Institute, Mount Edgecombe, South Africa.,Department of Biology, School of Life Sciences, University of KwaZulu-Natal, Westville, South Africa
| | - Dennis M Komape
- Unit for Environmental Sciences and Management, North-West University, Potchefstroom, South Africa
| | - Hlobisile Khanyi
- Unit for Environmental Sciences and Management, North-West University, Potchefstroom, South Africa
| | - Johnnie van den Berg
- Unit for Environmental Sciences and Management, North-West University, Potchefstroom, South Africa
| | - Dirk Cilliers
- Unit for Environmental Sciences and Management, North-West University, Potchefstroom, South Africa
| | - Dyfed Lloyd Evans
- Crop Biology Resource Centre, South African Sugarcane Research Institute, Mount Edgecombe, South Africa.,Department of Biology, School of Life Sciences, University of KwaZulu-Natal, Westville, South Africa.,BeauSci Ltd., Waterbeach, Cambridge, United Kingdom
| | - Sandra Barnard
- Unit for Environmental Sciences and Management, North-West University, Potchefstroom, South Africa
| | - Stefan J Siebert
- Unit for Environmental Sciences and Management, North-West University, Potchefstroom, South Africa
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11
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Complete Chloroplast Genomes of Erianthus arundinaceus and Miscanthus sinensis: Comparative Genomics and Evolution of the Saccharum Complex. PLoS One 2017; 12:e0169992. [PMID: 28125648 PMCID: PMC5268433 DOI: 10.1371/journal.pone.0169992] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Accepted: 12/27/2016] [Indexed: 11/19/2022] Open
Abstract
The genera Erianthus and Miscanthus, both members of the Saccharum complex, are of interest as potential resources for sugarcane improvement and as bioenergy crops. Recent studies have mainly focused on the conservation and use of wild accessions of these genera as breeding materials. However, the sequence data are limited, which hampers the studies of phylogenetic relationships, population structure, and evolution of these grasses. Here, we determined the complete chloroplast genome sequences of Erianthus arundinaceus and Miscanthus sinensis by using 454 GS FLX pyrosequencing and Sanger sequencing. Alignment of the E. arundinaceus and M. sinensis chloroplast genome sequences with the known sequence of Saccharum officinarum demonstrated a high degree of conservation in gene content and order. Using the data sets of 76 chloroplast protein-coding genes, we performed phylogenetic analysis in 40 taxa including E. arundinaceus and M. sinensis. Our results show that S. officinarum is more closely related to M. sinensis than to E. arundinaceus. We estimated that E. arundinaceus diverged from the subtribe Sorghinae before the divergence of Sorghum bicolor and the common ancestor of S. officinarum and M. sinensis. This is the first report of the phylogenetic and evolutionary relationships inferred from maternally inherited variation in the Saccharum complex. Our study provides an important framework for understanding the phylogenetic relatedness of the economically important genera Erianthus, Miscanthus, and Saccharum.
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12
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Evans DL, Joshi SV. Complete chloroplast genomes of Saccharum spontaneum, Saccharum officinarum and Miscanthus floridulus (Panicoideae: Andropogoneae) reveal the plastid view on sugarcane origins. SYST BIODIVERS 2016. [DOI: 10.1080/14772000.2016.1197336] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- Dyfed Lloyd Evans
- South African Sugarcane Research Institute, 170 Flanders Drive, Private Bag X02, Mount Edgecombe, Durban, 4300, South Africa
- School of Life Sciences, College of Agriculture, Engineering and Science, University of Kwa-Zulu Natal, Private Bag X54001, Durban, 4000, South Africa
| | - Shailesh Vinay Joshi
- South African Sugarcane Research Institute, 170 Flanders Drive, Private Bag X02, Mount Edgecombe, Durban, 4300, South Africa
- School of Life Sciences, College of Agriculture, Engineering and Science, University of Kwa-Zulu Natal, Private Bag X54001, Durban, 4000, South Africa
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13
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Kellogg EA. Has the connection between polyploidy and diversification actually been tested? CURRENT OPINION IN PLANT BIOLOGY 2016; 30:25-32. [PMID: 26855304 DOI: 10.1016/j.pbi.2016.01.002] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2015] [Revised: 01/09/2016] [Accepted: 01/17/2016] [Indexed: 05/07/2023]
Abstract
Many major clades of angiosperms have several whole genome duplications (polyploidization events) in their distant past, suggesting that polyploidy drives or at least permits diversification. However, data on recently diverged groups are more equivocal, finding little evidence of elevated diversification following polyploidy. The discrepancy may be attributable at least in part to methodology. Many studies use indirect methods, such as chromosome numbers, genome size, and Ks plots, to test polyploidy, although these approaches can be misleading, and often lack sufficient resolution. A direct test of diversification following polyploidy requires a sequence-based approach that traces the history of nuclear genomes rather than species. These methods identify the point of coalescence of ancestral genomes, but may be misleading about the time and thus the extent of diversification. Limitations of existing methods mean that the connection between polyploidy and diversification has not been rigorously tested and remains unknown.
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Affiliation(s)
- Elizabeth A Kellogg
- Donald Danforth Plant Science Center, 975 North Warson Rd., St. Louis, MO 63132, USA.
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14
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Welker CAD, Souza-Chies TT, Longhi-Wagner HM, Peichoto MC, McKain MR, Kellogg EA. Multilocus phylogeny and phylogenomics of Eriochrysis P. Beauv. (Poaceae-Andropogoneae): Taxonomic implications and evidence of interspecific hybridization. Mol Phylogenet Evol 2016; 99:155-167. [PMID: 26947710 DOI: 10.1016/j.ympev.2016.02.022] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2015] [Revised: 02/24/2016] [Accepted: 02/25/2016] [Indexed: 01/04/2023]
Abstract
Species delimitation is a vital issue concerning evolutionary biology and conservation of biodiversity. However, it is a challenging task for several reasons, including the low interspecies variability of markers currently used in phylogenetic reconstructions and the occurrence of reticulate evolution and polyploidy in many lineages of flowering plants. The first phylogeny of the grass genus Eriochrysis is presented here, focusing on the New World species, in order to examine its relationships to other genera of the subtribe Saccharinae/tribe Andropogoneae and to define the circumscriptions of its taxonomically complicated species. Molecular cloning and sequencing of five regions of four low-copy nuclear genes (apo1, d8, ep2-ex7 and ep2-ex8, kn1) were performed, as well as complete plastome sequencing. Trees were reconstructed using maximum parsimony, maximum likelihood, and Bayesian inference analyses. The present phylogenetic analyses indicate that Eriochrysis is monophyletic and the Old World E. pallida is sister to the New World species. Subtribe Saccharinae is polyphyletic, as is the genus Eulalia. Based on nuclear and plastome sequences plus morphology, we define the circumscriptions of the New World species of Eriochrysis: E. laxa is distinct from E. warmingiana, and E. villosa is distinct from E. cayennensis. Natural hybrids occur between E. laxa and E. villosa. The hybrids are probably tetraploids, based on the number of paralogues in the nuclear gene trees. This is the first record of a polyploid taxon in the genus Eriochrysis. Some incongruities between nuclear genes and plastome analyses were detected and are potentially caused by incomplete lineage sorting and/or ancient hybridization. The set of low-copy nuclear genes used in this study seems to be sufficient to resolve phylogenetic relationships and define the circumscriptions of other species complexes in the grass family and relatives, even in the presence of polyploidy and reticulate evolution. Complete plastome sequencing is also a promising tool for phylogenetic inference.
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Affiliation(s)
- Cassiano A D Welker
- Universidade Federal do Rio Grande do Sul, Programa de Pós-Graduação em Botânica, Av. Bento Gonçalves 9500, CEP 91501-970 Porto Alegre, RS, Brazil.
| | - Tatiana T Souza-Chies
- Universidade Federal do Rio Grande do Sul, Programa de Pós-Graduação em Botânica, Av. Bento Gonçalves 9500, CEP 91501-970 Porto Alegre, RS, Brazil.
| | - Hilda M Longhi-Wagner
- Universidade Federal do Rio Grande do Sul, Programa de Pós-Graduação em Botânica, Av. Bento Gonçalves 9500, CEP 91501-970 Porto Alegre, RS, Brazil.
| | - Myriam Carolina Peichoto
- Instituto de Botánica del Nordeste (UNNE-CONICET), Facultad de Ciencias Agrarias (UNNE), Sargento Cabral 2131, Corrientes 3400, Argentina.
| | - Michael R McKain
- Donald Danforth Plant Science Center, 975 North Warson Road, St. Louis, MO 63132, USA.
| | - Elizabeth A Kellogg
- Donald Danforth Plant Science Center, 975 North Warson Road, St. Louis, MO 63132, USA.
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15
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Hyperspecialization in Some South American Endemic Ungulates Revealed by Long Bone Microstructure. J MAMM EVOL 2015. [DOI: 10.1007/s10914-015-9312-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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