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He Y, He J, Zhao Y, Zhang S, Rao X, Wang H, Wang Z, Song A, Jiang J, Chen S, Chen F. Divergence of 10 satellite repeats in Artemisia (Asteraceae: Anthemideae) based on sequential fluorescence in situ hybridization analysis: evidence for species identification and evolution. Chromosome Res 2024; 32:5. [PMID: 38502277 DOI: 10.1007/s10577-024-09749-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2024] [Revised: 03/01/2024] [Accepted: 03/07/2024] [Indexed: 03/21/2024]
Abstract
Artemisia is a large genus encompassing about 400 diverse species, many of which have considerable medicinal and ecological value. However, complex morphological information and variation in ploidy level and nuclear DNA content have presented challenges for evolution studies of this genus. Consequently, taxonomic inconsistencies within the genus persist, hindering the utilization of such large plant resources. Researchers have utilized satellite DNAs to aid in chromosome identification, species classification, and evolutionary studies due to their significant sequence and copy number variation between species and close relatives. In the present study, the RepeatExplorer2 pipeline was utilized to identify 10 satellite DNAs from three species (Artemisia annua, Artemisia vulgaris, Artemisia viridisquama), and fluorescence in situ hybridization confirmed their distribution on chromosomes in 24 species, including 19 Artemisia species with 5 outgroup species from Ajania and Chrysanthemum. Signals of satellite DNAs exhibited substantial differences between species. We obtained one genus-specific satellite from the sequences. Additionally, molecular cytogenetic maps were constructed for Artemisia vulgaris, Artemisia leucophylla, and Artemisia viridisquama. One species (Artemisia verbenacea) showed a FISH distribution pattern suggestive of an allotriploid origin. Heteromorphic FISH signals between homologous chromosomes in Artemisia plants were observed at a high level. Additionally, the relative relationships between species were discussed by comparing ideograms. The results of the present study provide new insights into the accurate identification and taxonomy of the Artemisia genus using molecular cytological methods.
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Affiliation(s)
- Yanze He
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jun He
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yong Zhao
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Shuangshuang Zhang
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xinyu Rao
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Haibin Wang
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
- Zhongshan Biological Breeding Laboratory, No. 50 Zhongling Street, Nanjing, 210014, China
| | - Zhenxing Wang
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
- Zhongshan Biological Breeding Laboratory, No. 50 Zhongling Street, Nanjing, 210014, China
| | - Aiping Song
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
- Zhongshan Biological Breeding Laboratory, No. 50 Zhongling Street, Nanjing, 210014, China
| | - Jiafu Jiang
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
- Zhongshan Biological Breeding Laboratory, No. 50 Zhongling Street, Nanjing, 210014, China
| | - Sumei Chen
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
- Zhongshan Biological Breeding Laboratory, No. 50 Zhongling Street, Nanjing, 210014, China
| | - Fadi Chen
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China.
- Zhongshan Biological Breeding Laboratory, No. 50 Zhongling Street, Nanjing, 210014, China.
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Hussain M, Thakur RK, Khazir J, Ahmed S, Khan MI, Rahi P, Peer LA, Shanmugam PV, Kaur S, Raina SN, Reshi ZA, Sehgal D, Rajpal VR, Mir BA. Traditional uses, Phytochemistry, Pharmacology, and Toxicology of the Genus Artemisia L. (Asteraceae): A High-value Medicinal Plant. Curr Top Med Chem 2024; 24:301-342. [PMID: 37711006 DOI: 10.2174/1568026623666230914104141] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 08/15/2023] [Accepted: 08/23/2023] [Indexed: 09/16/2023]
Abstract
Biologically active secondary metabolites, essential oils, and volatile compounds derived from medicinal and aromatic plants play a crucial role in promoting human health. Within the large family Asteraceae, the genus Artemisia consists of approximately 500 species. Artemisia species have a rich history in traditional medicine worldwide, offering remedies for a wide range of ailments, such as malaria, jaundice, toothache, gastrointestinal problems, wounds, inflammatory diseases, diarrhoea, menstrual pains, skin disorders, headache, and intestinal parasites. The therapeutic potential of Artemisia species is derived from a multitude of phytoconstituents, including terpenoids, phenols, flavonoids, coumarins, sesquiterpene lactones, lignans, and alkaloids that serve as active pharmaceutical ingredients (API). The remarkable antimalarial, antimicrobial, anthelmintic, antidiabetic, anti-inflammatory, anticancer, antispasmodic, antioxidative and insecticidal properties possessed by the species are attributed to these APIs. Interestingly, several commercially utilized pharmaceutical drugs, including arglabin, artemisinin, artemether, artesunate, santonin, and tarralin have also been derived from different Artemisia species. However, despite the vast medicinal potential, only a limited number of Artemisia species have been exploited commercially. Further, the available literature on traditional and pharmacological uses of Artemisia lacks comprehensive reviews. Therefore, there is an urgent need to bridge the existing knowledge gaps and provide a scientific foundation for future Artemisia research endeavours. It is in this context, the present review aims to provide a comprehensive account of the traditional uses, phytochemistry, documented biological properties and toxicity of all the species of Artemisia and offers useful insights for practitioners and researchers into underutilized species and their potential applications. This review aims to stimulate further exploration, experimentation and collaboration to fully realize the therapeutic potential of Artemisia in augmenting human health and well-being.
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Affiliation(s)
- Manzoor Hussain
- Department of Botanical & Environmental Sciences, Guru Nanak Dev University, Amritsar, India
| | - Rakesh Kr Thakur
- Amity Institute of Biotechnology, Amity University, Noida, U.P, 201313, India
| | - Jabeena Khazir
- Department of Chemistry, HKM Govt. Degree College Eidgah, Srinagar, J&K, India
| | - Sajad Ahmed
- Department of Plant Biotechnology, Indian Institute of Integrative Medicine, Canal Road Jammu, 180001, J&K, India
| | | | - Praveen Rahi
- Biological Resources Center, Institut Pasteur, University de Paris, Paris, 75015, France
| | - Latif Ahmad Peer
- Department of Botany, University of Kashmir, Srinagar, Jammu & Kashmir, 190006, India
| | | | - Satwinderjeet Kaur
- Department of Botanical & Environmental Sciences, Guru Nanak Dev University, Amritsar, India
| | - Soom Nath Raina
- Amity Institute of Biotechnology, Amity University, Noida, U.P, 201313, India
| | - Zafar Ahmad Reshi
- Department of Botany, University of Kashmir, Srinagar, Jammu & Kashmir, 190006, India
| | - Deepmala Sehgal
- Syngenta, Jeolett's Hill International Research Centre, Bracknell, Berkshire, UK
| | - Vijay Rani Rajpal
- Department of Botany, HansRaj College, University of Delhi, Delhi, 110007, India
| | - Bilal Ahmad Mir
- Department of Botany, University of Kashmir, Srinagar, Jammu & Kashmir, 190006, India
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Shivappagowda Kruthika H, Srikanta Rukmangada M, Girish Naik V. Genome size, chromosome number variation and its correlation with stomatal characters for assessment of ploidy levels in a core subset of mulberry (Morus spp.) germplasm. Gene 2023:147637. [PMID: 37442306 DOI: 10.1016/j.gene.2023.147637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 06/15/2023] [Accepted: 07/10/2023] [Indexed: 07/15/2023]
Abstract
The large size of the germplasm collection along with scanty information on their cytological and genome constitution have hindered well-planned breeding schemes in mulberry. To address the issue, a study was undertaken to investigate the variability in DNA content and genome size, chromosome number, ploidy and its relation with important stomatal characteristics among 162 mulberry germplasm. These germplasm comprise a core subset of 150 collections along with a representative collection of different mulberry species including the wild. Among the germplasm belonging to 16 species, we identified 122 diploids (2n = 28), 4 aneuploids (2n = 30), 13 triploids (2n = 42), 15 tetraploids (2n = 56), 7 hexaploids (2n = 84) and 1 dodecosaploid (2n = 308) based on the chromosome count. Most of the cultivated mulberries are found to be diploids. The mean nuclear 2C DNA content estimated by Flow cytometry, varied from 0.723±0.006 pg (M. australis, 2n = 2x) to 7.732 pg (M. nigra, 2n = 22x). The 2C DNA content positively correlated with the ploidy status and stomatal length (r = 0.814, p<0.001). Based on the 1Cx value, the study also suggests that the majority of the polyploid species have experienced genome downsizing in relation to their diploid progenitors. This study provides the most essential information on chromosome number, ploidy and DNA content to facilitate the utilization of a core subset of germplasm in the mulberry breeding program.
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Affiliation(s)
- Hampapura Shivappagowda Kruthika
- Molecular Biology Laboratory - 1, Central Sericultural Research and Training Institute, Srirampura, Manandavadi Road, Mysuru - 570 008, India
| | - Martikyathnahalli Srikanta Rukmangada
- Molecular Biology Laboratory - 1, Central Sericultural Research and Training Institute, Srirampura, Manandavadi Road, Mysuru - 570 008, India; Department of Plant Sciences, UC Davis, California, 95616, USA
| | - Vorkady Girish Naik
- Molecular Biology Laboratory - 1, Central Sericultural Research and Training Institute, Srirampura, Manandavadi Road, Mysuru - 570 008, India.
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Grossfurthner LP, Milano ER, Hohenlohe PA, Waits LP, Richardson BA. Population structure and hybridization under contemporary and future climates in a heteroploid foundational shrub species ( Artemisia tridentata). FRONTIERS IN PLANT SCIENCE 2023; 14:1155868. [PMID: 37284723 PMCID: PMC10239881 DOI: 10.3389/fpls.2023.1155868] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 04/20/2023] [Indexed: 06/08/2023]
Abstract
Current and past climatic changes can shift plant climatic niches, which may cause spatial overlap or separation between related taxa. The former often leads to hybridization and introgression, which may generate novel variation and influence the adaptive capacity of plants. An additional mechanism facilitating adaptations to novel environments and an important evolutionary driver in plants is polyploidy as the result of whole genome duplication. Artemisia tridentata (big sagebrush) is a landscape-dominating foundational shrub in the western United States which occupies distinct ecological niches, exhibiting diploid and tetraploid cytotypes. Tetraploids have a large impact on the species' landscape dominance as they occupy a preponderance of the arid spectrum of A. tridentata range. Three distinct subspecies are recognized, which co-occur in ecotones - the transition zone between two or more distinct ecological niches - allowing for hybridization and introgression. Here we assess the genomic distinctiveness and extent of hybridization among subspecies at different ploidies under both contemporary and predicted future climates. We sampled five transects throughout the western United States where a subspecies overlap was predicted using subspecies-specific climate niche models. Along each transect, we sampled multiple plots representing the parental and the potential hybrid habitats. We performed reduced representation sequencing and processed the data using a ploidy-informed genotyping approach. Population genomic analyses revealed distinct diploid subspecies and at least two distinct tetraploid gene pools, indicating independent origins of the tetraploid populations. We detected low levels of hybridization (2.5%) between the diploid subspecies, while we found evidence for increased admixture between ploidy levels (18%), indicating hybridization has an important role in the formation of tetraploids. Our analyses highlight the importance of subspecies co-occurrence within these ecotones to maintain gene exchange and potential formation of tetraploid populations. Genomic confirmations of subspecies in the ecotones support the subspecies overlap predicted by the contemporary climate niche models. However, future mid-century projections of subspecies niches predict a substantial loss in range and subspecies overlap. Thus, reductions in hybridization potential could affect new recruitment of genetically variable tetraploids that are vital to this species' ecological role. Our results underscore the importance of ecotone conservation and restoration.
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Affiliation(s)
- Lukas P. Grossfurthner
- Bioinformatics and Computational Biology Graduate Program, University of Idaho, Moscow, ID, United States
- Department of Biological Sciences, University of Idaho, Moscow, ID, United States
| | - Elizabeth R. Milano
- Rocky Mountain Research Station, United States Department of Agriculture (USDA) Forest Service, Moscow, ID, United States
| | - Paul A. Hohenlohe
- Department of Biological Sciences, University of Idaho, Moscow, ID, United States
| | - Lisette P. Waits
- Department of Fish and Wildlife Sciences, University of Idaho, Moscow, ID, United States
| | - Bryce A. Richardson
- Rocky Mountain Research Station, United States Department of Agriculture (USDA) Forest Service, Moscow, ID, United States
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Chen H, Guo M, Dong S, Wu X, Zhang G, He L, Jiao Y, Chen S, Li L, Luo H. A chromosome-scale genome assembly of Artemisia argyi reveals unbiased subgenome evolution and key contributions of gene duplication to volatile terpenoid diversity. PLANT COMMUNICATIONS 2023; 4:100516. [PMID: 36597358 DOI: 10.1016/j.xplc.2023.100516] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 12/14/2022] [Accepted: 12/31/2022] [Indexed: 05/11/2023]
Abstract
Artemisia argyi Lévl. et Vant., a perennial Artemisia herb with an intense fragrance, is widely used in traditional medicine in China and many other Asian countries. Here, we present a chromosome-scale genome assembly of A. argyi comprising 3.89 Gb assembled into 17 pseudochromosomes. Phylogenetic and comparative genomic analyses revealed that A. argyi underwent a recent lineage-specific whole-genome duplication (WGD) event after divergence from Artemisia annua, resulting in two subgenomes. We deciphered the diploid ancestral genome of A. argyi, and unbiased subgenome evolution was observed. The recent WGD led to a large number of duplicated genes in the A. argyi genome. Expansion of the terpene synthase (TPS) gene family through various types of gene duplication may have greatly contributed to the diversity of volatile terpenoids in A. argyi. In particular, we identified a typical germacrene D synthase gene cluster within the expanded TPS gene family. The entire biosynthetic pathways of germacrenes, (+)-borneol, and (+)-camphor were elucidated in A. argyi. In addition, partial deletion of the amorpha-4,11-diene synthase (ADS) gene and loss of function of ADS homologs may have resulted in the lack of artemisinin production in A. argyi. Our study provides new insights into the genome evolution of Artemisia and lays a foundation for further improvement of the quality of this important medicinal plant.
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Affiliation(s)
- Hongyu Chen
- Key Laboratory of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China
| | - Miaoxian Guo
- Key Laboratory of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China
| | - Shuting Dong
- Key Laboratory of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China
| | - Xinling Wu
- Key Laboratory of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China; Shandong University of Traditional Chinese Medicine, Jinan 250355, China
| | - Guobin Zhang
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Taian 271018, China; College of Agronomy, Shandong Agricultural University, Taian 271018, China
| | - Liu He
- Key Laboratory of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China
| | - Yuannian Jiao
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Shilin Chen
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China; Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China.
| | - Li Li
- Robert W. Holley Center for Agriculture and Health, USDA-ARS, Cornell University, Ithaca, NY 14853, USA; Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA.
| | - Hongmei Luo
- Key Laboratory of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China.
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Luo D, Zeng Z, Wu Z, Chen C, Zhao T, Du H, Miao Y, Liu D. Intraspecific variation in genome size in Artemisia argyi determined using flow cytometry and a genome survey. 3 Biotech 2023; 13:57. [PMID: 36698769 PMCID: PMC9868218 DOI: 10.1007/s13205-022-03412-y] [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: 07/20/2022] [Accepted: 11/26/2022] [Indexed: 01/23/2023] Open
Abstract
Different collections and accessions of Artemisia argyi (Chinese mugwort) harbour considerable diversity in morphology and bioactive compounds, but no mechanisms have been reported that explain these variations. We studied genome size in A. argyi accessions from different regions of China by flow cytometry. Genome size was significantly distinct among origins of these 42 Chinese mugwort accessions, ranging from 8.428 to 11.717 pg. There were no significant intraspecific differences among the 42 accessions from the five regions of China. The clustering analysis showed that these 42 A. argyi accessions could be divided into three groups, which had no significant relationship with geographical location. In a genome survey, the total genome size of A. argyi (A15) was estimated to be 7.852 Gb (or 8.029 pg) by K-mer analysis. This indicated that the results from the two independent methods are consistent, and that the genome survey can be used as an adjunct to flow cytometry to compensate for its deficiencies. In addition, genome survey can provide the information about heterozygosity, repeat sequences, GC content and ploidy of A. argyi genome. The nuclear DNA contents determined here provide a new reference for intraspecific variation in genome size in A. argyi, and may also be a potential resource for the study of genetic diversity and for breeding new cultivar.
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Affiliation(s)
- Dandan Luo
- College of Pharmacy, Hubei University of Chinese Medicine, Wuhan, 430065 China
| | - Zeyi Zeng
- College of Pharmacy, Hubei University of Chinese Medicine, Wuhan, 430065 China
| | - Zongqi Wu
- College of Pharmacy, Hubei University of Chinese Medicine, Wuhan, 430065 China
| | - Changjie Chen
- College of Pharmacy, Hubei University of Chinese Medicine, Wuhan, 430065 China
| | - Tingting Zhao
- College of Pharmacy, Hubei University of Chinese Medicine, Wuhan, 430065 China
| | - Hongzhi Du
- College of Pharmacy, Hubei University of Chinese Medicine, Wuhan, 430065 China
| | - Yuhuan Miao
- College of Pharmacy, Hubei University of Chinese Medicine, Wuhan, 430065 China
| | - Dahui Liu
- College of Pharmacy, Hubei University of Chinese Medicine, Wuhan, 430065 China
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Miao Y, Luo D, Zhao T, Du H, Liu Z, Xu Z, Guo L, Chen C, Peng S, Li JX, Ma L, Ning G, Liu D, Huang L. Genome sequencing reveals chromosome fusion and extensive expansion of genes related to secondary metabolism in Artemisia argyi. PLANT BIOTECHNOLOGY JOURNAL 2022; 20:1902-1915. [PMID: 35689517 PMCID: PMC9491451 DOI: 10.1111/pbi.13870] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 05/27/2022] [Accepted: 06/07/2022] [Indexed: 05/25/2023]
Abstract
Artemisia argyi, as famous as Artemisia annua, is a medicinal plant with huge economic value in the genus of Artemisia and has been widely used in the world for about 3000 years. However, a lack of the reference genome severely hinders the understanding of genetic basis for the active ingredient synthesis of A. argyi. Here, we firstly report a complex chromosome-level genome assembly of A. argyi with a large size of 8.03 Gb, with features of high heterozygosity (2.36%), high repetitive sequences (73.59%) and a huge number of protein-coding genes (279 294 in total). The assembly reveals at least three rounds of whole-genome duplication (WGD) events, including a recent WGD event in the A. argyi genome, and a recent burst of transposable element, which may contribute to its large genome size. The genomic data and karyotype analyses confirmed that A. argyi is an allotetraploid with 34 chromosomes. Intragenome synteny analysis revealed that chromosomes fusion event occurred in the A. argyi genome, which elucidates the changes in basic chromosome numbers in Artemisia genus. Significant expansion of genes related to photosynthesis, DNA replication, stress responses and secondary metabolism were identified in A. argyi, explaining the extensive environmental adaptability and rapid growth characteristics. In addition, we analysed genes involved in the biosynthesis pathways of flavonoids and terpenoids, and found that extensive gene amplification and tandem duplication contributed to the high contents of metabolites in A. argyi. Overall, the reference genome assembly provides scientific support for evolutionary biology, functional genomics and breeding in A. argyi and other Artemisia species.
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Affiliation(s)
- Yuhuan Miao
- College of PharmacyHubei University of Chinese MedicineWuhanChina
| | - Dandan Luo
- College of PharmacyHubei University of Chinese MedicineWuhanChina
| | - Tingting Zhao
- College of PharmacyHubei University of Chinese MedicineWuhanChina
| | - Hongzhi Du
- College of PharmacyHubei University of Chinese MedicineWuhanChina
| | | | - Zhongping Xu
- Hubei Hongshan Laboratory, National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina
| | - Lanping Guo
- China Academy of Chinese Medical SciencesBeijingChina
| | - Changjie Chen
- College of PharmacyHubei University of Chinese MedicineWuhanChina
| | - Sainan Peng
- College of PharmacyHubei University of Chinese MedicineWuhanChina
| | - Jin Xin Li
- College of PharmacyHubei University of Chinese MedicineWuhanChina
| | - Lin Ma
- College of PharmacyHubei University of Chinese MedicineWuhanChina
| | - Guogui Ning
- Key laboratory of Horticultural Plant Biology, Ministry of EducationHuazhong Agricultural UniversityWuhanChina
| | - Dahui Liu
- College of PharmacyHubei University of Chinese MedicineWuhanChina
| | - Luqi Huang
- China Academy of Chinese Medical SciencesBeijingChina
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Trifan A, Zengin G, Sinan KI, Sieniawska E, Sawicki R, Maciejewska-Turska M, Skalikca-Woźniak K, Luca SV. Unveiling the Phytochemical Profile and Biological Potential of Five Artemisia Species. Antioxidants (Basel) 2022; 11:antiox11051017. [PMID: 35624882 PMCID: PMC9137812 DOI: 10.3390/antiox11051017] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 05/17/2022] [Accepted: 05/19/2022] [Indexed: 12/15/2022] Open
Abstract
The Artemisia L. genus comprises over 500 species with important medicinal and economic attributes. Our study aimed at providing a comprehensive metabolite profiling and bioactivity assessment of five Artemisia species collected from northeastern Romania (A. absinthium L., A. annua L., A. austriaca Jacq., A. pontica L. and A. vulgaris L.). Liquid chromatography–tandem high-resolution mass spectrometry (LC-HRMS/MS) analysis of methanol and chloroform extracts obtained from the roots and aerial parts of the plants led to the identification of 15 phenolic acids (mostly hydroxycinnamic acid derivatives), 26 flavonoids (poly-hydroxylated/poly-methoxylated flavone derivatives, present only in the aerial parts), 14 sesquiterpene lactones, 3 coumarins, 1 lignan and 7 fatty acids. Clustered image map (CIM) analysis of the phytochemical profiles revealed that A. annua was similar to A. absinthium and that A. pontica was similar to A. austriaca, whereas A. vulgaris represented a cluster of its own. Correlated with their total phenolic contents, the methanol extracts from both parts of the plants showed the highest antioxidant effects, as assessed by the DPPH and ABTS radical scavenging, CUPRAC, FRAP and total antioxidant capacity methods. Artemisia extracts proved to be promising sources of enzyme inhibitory agents, with the methanol aerial part extracts being the most active samples against acetylcholinesterase and glucosidase. All Artemisia samples displayed good antibacterial effects against Mycobacterium tuberculosis H37Ra, with MIC values of 64–256 mg/L. In conclusion, the investigated Artemisia species proved to be rich sources of bioactives endowed with antioxidant, enzyme inhibitory and anti-mycobacterial properties.
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Affiliation(s)
- Adriana Trifan
- Department of Pharmacognosy, Grigore T. Popa University of Medicine and Pharmacy Iasi, 700115 Iasi, Romania;
| | - Gokhan Zengin
- Physiology and Biochemistry Research Laboratory, Department of Biology, Science Faculty, Selcuk University, University Campus, 42130 Konya, Turkey; (G.Z.); (K.I.S.)
| | - Kouadio Ibrahime Sinan
- Physiology and Biochemistry Research Laboratory, Department of Biology, Science Faculty, Selcuk University, University Campus, 42130 Konya, Turkey; (G.Z.); (K.I.S.)
| | - Elwira Sieniawska
- Department of Natural Products Chemistry, Medical University of Lublin, 20-093 Lublin, Poland;
- Correspondence: (E.S.); (S.V.L.)
| | - Rafal Sawicki
- Department of Biochemistry and Biotechnology, Medical University of Lublin, 20-093 Lublin, Poland;
| | - Magdalena Maciejewska-Turska
- Department of Pharmacognosy with the Medicinal Plant Garden, Medical University of Lublin, 20-093 Lublin, Poland;
| | | | - Simon Vlad Luca
- Biothermodynamics, TUM School of Life Sciences, Technical University of Munich, 85354 Freising, Germany
- Correspondence: (E.S.); (S.V.L.)
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Melton AE, Child AW, Beard RS, Dumaguit CDC, Forbey JS, Germino M, de Graaff MA, Kliskey A, Leitch IJ, Martinez P, Novak SJ, Pellicer J, Richardson BA, Self D, Serpe M, Buerki S. A haploid pseudo-chromosome genome assembly for a keystone sagebrush species of western North American rangelands. G3 (BETHESDA, MD.) 2022; 12:6585877. [PMID: 35567476 PMCID: PMC9258541 DOI: 10.1093/g3journal/jkac122] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Accepted: 05/03/2022] [Indexed: 11/14/2022]
Abstract
Increased ecological disturbances, species invasions, and climate change are creating severe conservation problems for several plant species that are widespread and foundational. Understanding the genetic diversity of these species and how it relates to adaptation to these stressors are necessary for guiding conservation and restoration efforts. This need is particularly acute for big sagebrush (Artemisia tridentata; Asteraceae), which was once the dominant shrub over 1,000,000 km2 in western North America but has since retracted by half and thus has become the target of one of the largest restoration seeding efforts globally. Here, we present the first reference-quality genome assembly for an ecologically important subspecies of big sagebrush (A. tridentata subsp. tridentata) based on short and long reads, as well as chromatin proximity ligation data analyzed using the HiRise pipeline. The final 4.2-Gb assembly consists of 5,492 scaffolds, with nine pseudo-chromosomal scaffolds (nine scaffolds comprising at least 90% of the assembled genome; n = 9). The assembly contains an estimated 43,377 genes based on ab initio gene discovery and transcriptional data analyzed using the MAKER pipeline, with 91.37% of BUSCOs being completely assembled. The final assembly was highly repetitive, with repeat elements comprising 77.99% of the genome, making the Artemisia tridentata subsp. tridentata genome one of the most highly repetitive plant genomes to be sequenced and assembled. This genome assembly advances studies on plant adaptation to drought and heat stress and provides a valuable tool for future genomic research.
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Affiliation(s)
- Anthony E Melton
- Corresponding author: Department of Biological Sciences, Boise State University, Boise, ID 83725, USA.
| | | | - Richard S Beard
- Department of Biological Sciences, Boise State University, Boise, ID 83725, USA
| | | | - Jennifer S Forbey
- Department of Biological Sciences, Boise State University, Boise, ID 83725, USA
| | - Matthew Germino
- Forest and Rangeland Ecosystem Science Center, United States Geological Survey, Boise, ID 83706, USA
| | | | | | | | - Peggy Martinez
- Department of Biological Sciences, Boise State University, Boise, ID 83725, USA
| | - Stephen J Novak
- Department of Biological Sciences, Boise State University, Boise, ID 83725, USA
| | - Jaume Pellicer
- Royal Botanic Gardens, Richmond TW9 3AE, UK,Institut Botànic de Barcelona (IBB, CSIC-Ajuntament de Barcelona), Barcelona 08038, Spain
| | - Bryce A Richardson
- Rocky Mountain Research Station, United States Forest Service, Moscow, ID 83843, USA
| | - Desiree Self
- Department of Biological Sciences, Boise State University, Boise, ID 83725, USA
| | - Marcelo Serpe
- Department of Biological Sciences, Boise State University, Boise, ID 83725, USA
| | - Sven Buerki
- Corresponding author: Department of Biological Sciences, Boise State University, Boise, ID 83725, USA.
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10
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He J, Yu Z, Jiang J, Chen S, Fang W, Guan Z, Liao Y, Wang Z, Chen F, Wang H. An Eruption of LTR Retrotransposons in the Autopolyploid Genomes of Chrysanthemum nankingense (Asteraceae). PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11030315. [PMID: 35161296 PMCID: PMC8839533 DOI: 10.3390/plants11030315] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 01/21/2022] [Accepted: 01/22/2022] [Indexed: 05/09/2023]
Abstract
Whole genome duplication, associated with the induction of widespread genetic changes, has played an important role in the evolution of many plant taxa. All extant angiosperm species have undergone at least one polyploidization event, forming either an auto- or allopolyploid organism. Compared with allopolyploidization, however, few studies have examined autopolyploidization, and few studies have focused on the response of genetic changes to autopolyploidy. In the present study, newly synthesized C. nankingense autotetraploids (Asteraceae) were employed to characterize the genome shock following autopolyploidization. Available evidence suggested that the genetic changes primarily involved the loss of old fragments and the gain of novel fragments, and some novel sequences were potential long terminal repeat (LTR) retrotransposons. As Ty1-copia and Ty3-gypsy elements represent the two main superfamilies of LTR retrotransposons, the dynamics of Ty1-copia and Ty3-gypsy were evaluated using RT-PCR, transcriptome sequencing, and LTR retrotransposon-based molecular marker techniques. Additionally, fluorescence in situ hybridization(FISH)results suggest that autopolyploidization might also be accompanied by perturbations of LTR retrotransposons, and emergence retrotransposon insertions might show more rapid divergence, resulting in diploid-like behaviour, potentially accelerating the evolutionary process among progenies. Our results strongly suggest a need to expand the current evolutionary framework to include a genetic dimension when seeking to understand genomic shock following autopolyploidization in Asteraceae.
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11
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Blonder B, Ray CA, Walton JA, Castaneda M, Chadwick KD, Clyne MO, Gaüzère P, Iversen LL, Lusk M, Strimbeck GR, Troy S, Mock KE. Cytotype and genotype predict mortality and recruitment in Colorado quaking aspen (Populus tremuloides). ECOLOGICAL APPLICATIONS : A PUBLICATION OF THE ECOLOGICAL SOCIETY OF AMERICA 2021; 31:e02438. [PMID: 34374163 DOI: 10.1002/eap.2438] [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: 12/13/2020] [Revised: 02/27/2021] [Accepted: 04/16/2021] [Indexed: 06/13/2023]
Abstract
Species responses to climate change depend on environment, genetics, and interactions among these factors. Intraspecific cytotype (ploidy level) variation is a common type of genetic variation in many species. However, the importance of intraspecific cytotype variation in determining demography across environments is poorly known. We studied quaking aspen (Populus tremuloides), which occurs in diploid and triploid cytotypes. This widespread tree species is experiencing contractions in its western range, which could potentially be linked to cytotype-dependent drought tolerance. We found that interactions between cytotype and environment drive mortality and recruitment across 503 plots in Colorado. Triploids were more vulnerable to mortality relative to diploids and had reduced recruitment on more drought-prone and disturbed plots relative to diploids. Furthermore, there was substantial genotype-dependent variation in demography. Thus, cytotype and genotype variation are associated with decline in this foundation species. Future assessment of demographic responses to climate change will benefit from knowledge of how genetic and environmental mosaics interact to determine species' ecophysiology and demography.
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Affiliation(s)
- Benjamin Blonder
- School of Life Sciences, Arizona State University, Tempe, Arizona, 85281, USA
- Rocky Mountain Biological Laboratory, Crested Butte, Colorado, 81224, USA
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, California, 94720, USA
| | - Courtenay A Ray
- School of Life Sciences, Arizona State University, Tempe, Arizona, 85281, USA
- Rocky Mountain Biological Laboratory, Crested Butte, Colorado, 81224, USA
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, California, 94720, USA
| | - James A Walton
- Department of Wildland Resources and Ecology Center, Utah State University, Logan, Utah, 84322-5230, USA
| | - Marco Castaneda
- Rocky Mountain Biological Laboratory, Crested Butte, Colorado, 81224, USA
- East Los Angeles College, Monterey Park, California, 91754, USA
| | - K Dana Chadwick
- Department of Earth System Science, Stanford University, Stanford, California, 94305, USA
- Climate and Ecosystems Division, Lawrence Berkeley National Laboratory, Berkeley, California, 94720, USA
| | - Michael O Clyne
- School of Life Sciences, Arizona State University, Tempe, Arizona, 85281, USA
| | - Pierre Gaüzère
- School of Life Sciences, Arizona State University, Tempe, Arizona, 85281, USA
| | - Lars L Iversen
- School of Life Sciences, Arizona State University, Tempe, Arizona, 85281, USA
| | - Madison Lusk
- School of Life Sciences, Arizona State University, Tempe, Arizona, 85281, USA
| | - G Richard Strimbeck
- Department of Biology, Norwegian University of Science and Technology, Trondheim, 7491, Norway
| | - Savannah Troy
- Rocky Mountain Biological Laboratory, Crested Butte, Colorado, 81224, USA
| | - Karen E Mock
- Department of Wildland Resources and Ecology Center, Utah State University, Logan, Utah, 84322-5230, USA
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12
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Oyundelger K, Harpke D, Herklotz V, Troeva E, Zheng Z, Li Z, Oyuntsetseg B, Wagner V, Wesche K, Ritz CM. Phylogeography of Artemisia frigida (Anthemideae, Asteraceae) based on genotyping-by-sequencing and plastid DNA data: Migration through Beringia. J Evol Biol 2021; 35:64-80. [PMID: 34792226 DOI: 10.1111/jeb.13960] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 11/03/2021] [Accepted: 11/10/2021] [Indexed: 12/20/2022]
Abstract
Artemisia frigida is a temperate grassland species that has the largest natural range among its genus, with occurrences across the temperate grassland biomes of Eurasia and North America. Despite its wide geographic range, we know little about the species' distribution history. Hence, we conducted a phylogeographical study to test the hypothesis that the species' distribution pattern is related to a potential historical migration over the 'Bering land bridge'. We applied two molecular approaches: genotyping-by-sequencing (GBS) and Sanger sequencing of the plastid intergenic spacer region (rpl32 - trnL) to investigate genetic differentiation and relatedness among 21 populations from North America, Middle Asia, Central Asia and the Russian Far East. Furthermore, we identified the ploidy level of individuals based on GBS data. Our results indicate that A. frigida originated in Asia, spread northwards to the Far East and then to North America across the Bering Strait. We found a pronounced genetic structuring between Middle and Central Asian populations with mixed ploidy levels, tetraploids in the Far East, and nearly exclusively diploids in North America except for one individual. According to phylogenetic analysis, two populations of Kazakhstan (KZ2 and KZ3) represent the most likely ancestral diploids that constitute the basally branching lineages, and subsequent polyploidization has occurred on several occasions independently. Mantel tests revealed weak correlations between genetic distance and geographical distance and climatic conditions, which indicates that paleoclimatic fluctuations may have more profoundly influenced A. frigida's spatial genetic structure and distribution than the current environment.
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Affiliation(s)
- Khurelpurev Oyundelger
- Chair of Biodiversity of Higher Plants, International Institute (IHI) Zittau, Technische Universität Dresden, Zittau, Germany.,Department of Botany, Senckenberg Museum of Natural History Görlitz, Görlitz, Germany
| | - Dörte Harpke
- Leibniz Institut für Pflanzengenetik und Kulturpflanzenforschung (IPK), Seeland, Germany
| | - Veit Herklotz
- Department of Botany, Senckenberg Museum of Natural History Görlitz, Görlitz, Germany
| | - Elena Troeva
- Institute for Biological Problems of Cryolithozone, Siberian Branch of the Russian Academy of Sciences, Yakutsk, Russia
| | - Zhenzhen Zheng
- College of Life Sciences, University of the Chinese Academy of Sciences, Beijing, China
| | - Zheng Li
- School of Life Sciences, Henan University, Kaifeng, China
| | - Batlai Oyuntsetseg
- Department of Biology, School of Arts and Sciences, National University of Mongolia, Ulaanbaatar, Mongolia
| | - Viktoria Wagner
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada
| | - Karsten Wesche
- Chair of Biodiversity of Higher Plants, International Institute (IHI) Zittau, Technische Universität Dresden, Zittau, Germany.,Department of Botany, Senckenberg Museum of Natural History Görlitz, Görlitz, Germany
| | - Christiane M Ritz
- Chair of Biodiversity of Higher Plants, International Institute (IHI) Zittau, Technische Universität Dresden, Zittau, Germany.,Department of Botany, Senckenberg Museum of Natural History Görlitz, Görlitz, Germany
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13
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Melton AE, Beck J, Galla SJ, Jenkins J, Handley L, Kim M, Grimwood J, Schmutz J, Richardson BA, Serpe M, Novak S, Buerki S. A draft genome provides hypotheses on drought tolerance in a keystone plant species in Western North America threatened by climate change. Ecol Evol 2021; 11:15417-15429. [PMID: 34765187 PMCID: PMC8571618 DOI: 10.1002/ece3.8245] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 08/12/2021] [Accepted: 10/01/2021] [Indexed: 11/17/2022] Open
Abstract
Climate change presents distinct ecological and physiological challenges to plants as extreme climate events become more common. Understanding how species have adapted to drought, especially ecologically important nonmodel organisms, will be crucial to elucidate potential biological pathways for drought adaptation and inform conservation strategies. To aid in genome-to-phenome research, a draft genome was assembled for a diploid individual of Artemisia tridentata subsp. tridentata, a threatened keystone shrub in western North America. While this taxon has few genetic resources available and genetic/genomics work has proven difficult due to genetic heterozygosity in the past, a draft genome was successfully assembled. Aquaporin (AQP) genes and their promoter sequences were mined from the draft genome to predict mechanisms regulating gene expression and generate hypotheses on key genes underpinning drought response. Fifty-one AQP genes were fully assembled within the draft genome. Promoter and phylogenetic analyses revealed putative duplicates of A. tridentata subsp. tridentata AQPs which have experienced differentiation in promoter elements, potentially supporting novel biological pathways. Comparison with nondrought-tolerant congener supports enrichments of AQP genes in this taxon during adaptation to drought stress. Differentiation of promoter elements revealed that paralogues of some genes have evolved to function in different pathways, highlighting these genes as potential candidates for future research and providing critical hypotheses for future genome-to-phenome work.
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Affiliation(s)
- Anthony E. Melton
- Department of Biological SciencesBoise State UniversityBoiseIdahoUSA
| | - James Beck
- Department of ComputingBoise State UniversityBoiseIdahoUSA
| | | | - Jerry Jenkins
- HudsonAlpha Institute for BiotechnologyHuntsvilleAlabamaUSA
| | - Lori Handley
- HudsonAlpha Institute for BiotechnologyHuntsvilleAlabamaUSA
| | - Min Kim
- HudsonAlpha Institute for BiotechnologyHuntsvilleAlabamaUSA
| | - Jane Grimwood
- HudsonAlpha Institute for BiotechnologyHuntsvilleAlabamaUSA
| | - Jeremy Schmutz
- HudsonAlpha Institute for BiotechnologyHuntsvilleAlabamaUSA
| | | | - Marcelo Serpe
- Department of Biological SciencesBoise State UniversityBoiseIdahoUSA
| | - Stephen Novak
- Department of Biological SciencesBoise State UniversityBoiseIdahoUSA
| | - Sven Buerki
- Department of Biological SciencesBoise State UniversityBoiseIdahoUSA
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14
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Becher H, Powell RF, Brown MR, Metherell C, Pellicer J, Leitch IJ, Twyford AD. The nature of intraspecific and interspecific genome size variation in taxonomically complex eyebrights. ANNALS OF BOTANY 2021; 128:639-651. [PMID: 34318876 PMCID: PMC8422891 DOI: 10.1093/aob/mcab102] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 07/27/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND AND AIMS Genome size varies considerably across the diversity of plant life. Although genome size is, by definition, affected by genetic presence/absence variants, which are ubiquitous in population sequencing studies, genome size is often treated as an intrinsic property of a species. Here, we studied intra- and interspecific genome size variation in taxonomically complex British eyebrights (Euphrasia, Orobanchaceae). Our aim is to document genome size diversity and investigate underlying evolutionary processes shaping variation between individuals, populations and species. METHODS We generated genome size data for 192 individuals of diploid and tetraploid Euphrasia and analysed genome size variation in relation to ploidy, taxonomy, population affiliation and geography. We further compared the genomic repeat content of 30 samples. KEY RESULTS We found considerable intraspecific genome size variation, and observed isolation-by-distance for genome size in outcrossing diploids. Tetraploid Euphrasia showed contrasting patterns, with genome size increasing with latitude in outcrossing Euphrasia arctica, but with little genome size variation in the highly selfing Euphrasia micrantha. Interspecific differences in genome size and the genomic proportions of repeat sequences were small. CONCLUSIONS We show the utility of treating genome size as the outcome of polygenic variation. Like other types of genetic variation, such as single nucleotide polymorphisms, genome size variation may be affected by ongoing hybridization and the extent of population subdivision. In addition to selection on associated traits, genome size is predicted to be affected indirectly by selection due to pleiotropy of the underlying presence/absence variants.
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Affiliation(s)
- Hannes Becher
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | | | - Max R Brown
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
- Wellcome Trust Genome Campus, Hinxton, Saffron Walden, UK
| | - Chris Metherell
- Botanical Society of Britain and Ireland, Harpenden, Hertfordshire, UK
| | - Jaume Pellicer
- Royal Botanic Gardens, Kew, Richmond, Surrey, UK
- Institut Botànic de Barcelona (IBB, CSIC-Ajuntament de Barcelona), Barcelona, Spain
| | | | - Alex D Twyford
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
- Royal Botanic Garden Edinburgh, Edinburgh, UK
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15
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Garnatje T, Hidalgo O, Vallés J, Garcia S, Romo À, Vilatersana R. Primeras medidas del tamaño del genoma en Carduncellusy los géneros afines Femeniasia y Phonus (Asteraceae, Cardueae), con datos para 21 táxones. COLLECTANEA BOTANICA 2021. [DOI: 10.3989/collectbot.2021.v40.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
El tamaño del genoma de 18 especies del género Carduncellus, dos especies de los géneros relacionados, Phonus y el género monotípico Femeniasia (F. balearica) ha sido medido por primera vez mediante citometría de flujo. Los niveles de ploidía se asignaron utilizando datos de tamaño del genoma junto con los recuentos de cromosomas previamente reportados. Se construyó un marco filogenético para visualizar la distribución de las características citogenéticas de los táxones. Los resultados confirmaron tres niveles de ploidía (2x, 4x y 6x), con un predominio de los táxones diploides. Los valores de 2C oscilaron entre 3,24 pg en Carduncellus calvus y 11,16 pg en C. eriocephalus, mientras que el tamaño del genoma monoploide (1Cx) osciló entre 1,29 pg en C. duvauxii (4x) y 2,30 pg en Phonus rhiphaeus (2x). La media de los valores 1Cx para los tetraploides fue menor que para los diploides. Los valores de tamaño del genoma de Carduncellus, Femeniasia y Phonus fueron más elevados que los de Carthamus dentro del mismo nivel de ploidía. Este resultado concuerda con una tendencia frecuentemente observada en plantas en la que los táxones con ciclos de vida largos presentan tamaños del genoma más elevados que los táxones relacionados que poseen ciclos de vida cortos.
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16
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Contrasting effects of local environment and grazing pressure on the genetic diversity and structure of Artemisia frigida. CONSERV GENET 2021. [DOI: 10.1007/s10592-021-01375-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
AbstractDrylands count among the most globally extensive biomes, and while many desert and dry rangeland ecosystems are under threat, genetic structures of dryland species are still rarely studied. Artemisia frigida is one of the most widely distributed plant species in the temperate rangelands of Eurasia and North America, and it also dominates in many habitats of Mongolia due to its tolerance to low temperatures, drought and disturbance. Local environmental conditions and grazing pressure can influence species performance and affect spatial patterns of genetic diversity in contrasting ways, and our study set out to evaluate such effects on the genetic diversity and structure of A. frigida. We first developed new species-specific Simple Sequence Repeats (SSRs) markers using whole genome sequencing. We then analysed 11 populations of A. frigida that had been sampled along a large climatic gradient in Mongolia, which were sub-structured according to three levels of grazing intensity. Estimates of genetic diversity at the population level were high (HO = 0.56, HE = 0.73) and tended to increase with higher precipitation and soil nutrient availability. Grazing had no effect on genetic diversity, however, a high number of grazing-specific indicator alleles was found at grazed sites. Genetic differentiation among populations was extremely low (global GST = 0.034). Analysis of Molecular Variance revealed 5% variance between populations along the climatic gradient, with 3% of the variance being partitioned among different grazing intensity levels. We found no relationship between geographic and genetic distances, and thus no isolation by distance in this widely distributed species. The relatively low genetic structuring suggests that considerable gene flow exists among A. frigida populations across the rangelands of Mongolia, in spite of the pervasive grazing in the region.
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17
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Essential oil composition of five Artemisia (Compositae) species in regards to chemophenetics. BIOCHEM SYST ECOL 2019. [DOI: 10.1016/j.bse.2019.103960] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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18
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González SB, Gastaldi B, Catalán C, Di Leo Lira P, Retta D, van Baren CM, Bandoni AL. Artemisia magellanica. Chemical Composition of the Essential Oil from an Unexplored Endemic Species of Patagonia. Chem Biodivers 2019; 16:e1900125. [PMID: 31241852 DOI: 10.1002/cbdv.201900125] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Accepted: 05/13/2019] [Indexed: 11/12/2022]
Abstract
The essential oil composition of the aerial parts of Artemisia magellanica Sch. Bip. (Asteraceae), native to Patagonia, was analyzed by GC-FID-MS. This is the first report on the essential oil composition of A. magellanica. A total of 113 components were identified accounting for 95.6-95.7 % of the oil. The essential oil was characterized by a high percentage of γ-costol (21.0-43.5 %), selina-4,11-diene, (Z)-β-ocimene, (E)-β-farnesene, (Z)-en-yn-dicycloether and 23 different esters (28.7 %). In turn, Artemisia biennis, a species native to North America, which is considered by some authors to be conspecific with A. magellanica, yielded an essential oil that was rich in (Z)-β-ocimene (34.7 %), (E)-β-farnesene (40.0 %) and the acetylenes (Z)- and (E)-en-yn-dicycloethers (11.0 %). Thus, as A. biennis lacks the three main components present in A. magellanica, namely γ-costol, 2-methylbutyl 2-methylbutyrate and selina-4,11-diene, these compounds could be considered as potential chemical markers for A. magellanica since they are absent or only found as minor constituents in other members of the genus. The data presented herein is also useful for genus taxonomy.
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Affiliation(s)
- Silvia B González
- Universidad Nacional de la Patagonia San Juan Bosco sede Esquel, Facultad de Ciencias Naturales y Ciencias de la Salud, Ruta 259 km 16,41, Esquel, 9200, Chubut, Argentina
| | - Bruno Gastaldi
- Universidad Nacional de la Patagonia San Juan Bosco sede Esquel, Facultad de Ciencias Naturales y Ciencias de la Salud, Ruta 259 km 16,41, Esquel, 9200, Chubut, Argentina
| | - César Catalán
- INQUINOA-CONICET, Instituto de Química Orgánica, Facultad de Bioquímica, Química y Farmacia, Universidad Nacional de Tucumán, Ayacucho 471, S.M. de Tucumán, 4000, Argentina
| | - Paola Di Leo Lira
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Cátedra de Farmacognosia, Junín 956, 2° piso, 1113, C.A. de Buenos Aires, Argentina.,CONICET-Universidad de Buenos Aires, Instituto de Química y Metabolismo del Fármaco (IQUIMEFA), Junín 956, 2° piso, 1113, C.A. de Buenos Aires, Argentina
| | - Daiana Retta
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Cátedra de Farmacognosia, Junín 956, 2° piso, 1113, C.A. de Buenos Aires, Argentina.,CONICET-Universidad de Buenos Aires, Instituto de Química y Metabolismo del Fármaco (IQUIMEFA), Junín 956, 2° piso, 1113, C.A. de Buenos Aires, Argentina
| | - Catalina M van Baren
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Cátedra de Farmacognosia, Junín 956, 2° piso, 1113, C.A. de Buenos Aires, Argentina.,CONICET-Universidad de Buenos Aires, Instituto de Química y Metabolismo del Fármaco (IQUIMEFA), Junín 956, 2° piso, 1113, C.A. de Buenos Aires, Argentina
| | - Arnaldo L Bandoni
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Cátedra de Farmacognosia, Junín 956, 2° piso, 1113, C.A. de Buenos Aires, Argentina.,CONICET-Universidad de Buenos Aires, Instituto de Química y Metabolismo del Fármaco (IQUIMEFA), Junín 956, 2° piso, 1113, C.A. de Buenos Aires, Argentina
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19
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Srisuwan S, Sihachakr D, Martín J, Vallès J, Ressayre A, Brown SC, Siljak-Yakovlev S. Change in nuclear DNA content and pollen size with polyploidisation in the sweet potato (Ipomoea batatas, Convolvulaceae) complex. PLANT BIOLOGY (STUTTGART, GERMANY) 2019; 21:237-247. [PMID: 30468688 DOI: 10.1111/plb.12945] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Accepted: 11/16/2018] [Indexed: 05/12/2023]
Abstract
Genome size evolution and its relationship with pollen grain size has been investigated in sweet potato (Ipomoea batatas), an economically important crop which is closely related to diploid and tetraploid species, assessing the nuclear DNA content of 22 accessions from five Ipomoea species, ten sweet potato varieties and two outgroup taxa. Nuclear DNA amounts were determined using flow cytometry. Pollen grains were studied using scanning and transmission electron microscopy. 2C DNA content of hexaploid I. batatas ranged between 3.12-3.29 pg; the mean monoploid genome size being 0.539 pg (527 Mbp), similar to the related diploid accessions. In tetraploid species I. trifida and I. tabascana, 2C DNA content was, respectively, 2.07 and 2.03 pg. In the diploid species closely related to sweet potato e.g. I. ×leucantha, I. tiliacea, I. trifida and I. triloba, 2C DNA content was 1.01-1.12 pg. However, two diploid outgroup species, I. setosa and I. purpurea, were clearly different from the other diploid species, with 2C of 1.47-1.49 pg; they also have larger chromosomes. The I. batatas genome presents 60.0% AT bases. DNA content and ploidy level were positively correlated within this complex. In I. batatas and the more closely related species I. trifida, the genome size and ploidy levels were correlated with pollen size. Our results allow us to propose alternative or complementary hypotheses to that currently proposed for the formation of hexaploid Ipomoea batatas.
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Affiliation(s)
- S Srisuwan
- Ecologie, Systématique et Evolution, CNRS AgroParisTech, University of Paris-Sud, Université Paris-Saclay, Orsay, France
| | - D Sihachakr
- Ecologie, Systématique et Evolution, CNRS AgroParisTech, University of Paris-Sud, Université Paris-Saclay, Orsay, France
| | - J Martín
- Laboratori de Botànica (UB) - Unitat associada al CSIC, Facultat de Farmàcia i Ciències de l'Alimentació, Universitat de Barcelona, Barcelona, Catalonia, Spain
| | - J Vallès
- Laboratori de Botànica (UB) - Unitat associada al CSIC, Facultat de Farmàcia i Ciències de l'Alimentació, Universitat de Barcelona, Barcelona, Catalonia, Spain
| | - A Ressayre
- GQE- Le Moulon, INRA, University of Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, Gif-sur-Yvette, France
| | - S C Brown
- Institute for Integrative Biology of the Cell, UMR 9198, CNRS/Université Paris-Sud/CEA, Gif-sur-Yvette, France
| | - S Siljak-Yakovlev
- Ecologie, Systématique et Evolution, CNRS AgroParisTech, University of Paris-Sud, Université Paris-Saclay, Orsay, France
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20
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Artemisia campestris L.: review on taxonomical aspects, cytogeography, biological activities and bioactive compounds. Biomed Pharmacother 2018; 109:1884-1906. [PMID: 30551444 DOI: 10.1016/j.biopha.2018.10.149] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2018] [Revised: 10/14/2018] [Accepted: 10/24/2018] [Indexed: 11/23/2022] Open
Abstract
Artemisia campestris L. (Asteraceae) is a polymorphic species that consists of many subspecies and varieties. It is known for its medicinal, pharmacological, and culinary properties. This review is undertaken with the aim to highlight some aspects of this plant, specifically the taxonomy, the cytogeography, the phytochemistry with an emphasis on the structure-activity relationship (SAR) of the main bioactive compounds of A. campestris L. in addition to its biological properties and the food control properties. The bibliographic data compiled in this review allowed the revision of 146 papers, by using different databases and scientific engines, such as Scopus, ScienceDirect, Pubmed, and google scholar. The taxonomic analysis has embedded A. campestris L. in the tribe Anthemideae, and the genus Artemisia L. Also many subtaxa have been identified, and a subspecific classification of this species has been established on the basis of its botanical characters. The cytogenetic findings evidenced that A.campestris L. is prevailed by the chromosome number x = 9, with a polyploidization degree ranging from diploidy to hexaploidy according to the geographical distribution of the plant populations, while the genome size seems to be proportional to the ploidy level, suggesting an adaptive trait of the cytotypes to new environments. This plant is rich in polyphenols, flavonoids, and terpenic compounds, which substantiate the bioactivities attributed to its extracts and essential oil. Hence, the SAR of the main bioactive compounds of A. campestris L., mainly the prominent flavonoids, phenolic acids, and terpenes revealed a tight link between specific chemical entities of the bioactive compound and the respective biological activity. Many biological activities were approached in this review, mainly the antioxidant, antivenom, antidiabetic, antihyperlipidemic, anti-inflammatory, antihypertensive, anti-leishmaniasis, antinociceptive, wound healing, and analgesic activities in addition to the hepatoprotective, nephroprotective, neuroprotective, and gastroprotective actions. Finally, the food preservative ability of the extracts and essential oil obtained from A.campestris L. have been fully discussed. The present review contributes to the literature, by bringing more clarifications about the different aspects of A.campestris L., like taxonomy, cytogeography and biological interests of this species. The SAR approach of some constituents that occur in A.campestris L., gives a solid support that can be used to explore the bioactivity of components isolated from this species, while the preservative properties of this plant can be usefully exploited for the agrifood sector.
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21
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Pellicer J, Saslis-Lagoudakis CH, Carrió E, Ernst M, Garnatje T, Grace OM, Gras A, Mumbrú M, Vallès J, Vitales D, Rønsted N. A phylogenetic road map to antimalarial Artemisia species. JOURNAL OF ETHNOPHARMACOLOGY 2018; 225:1-9. [PMID: 29936053 DOI: 10.1016/j.jep.2018.06.030] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Accepted: 06/19/2018] [Indexed: 06/08/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE The discovery of the antimalarial agent artemisinin is considered one of the most significant success stories of ethnopharmacological research in recent times. The isolation of artemisinin was inspired by the use of Artemisia annua in traditional Chinese medicine (TCM) and was awarded a Nobel Prize in 2015. Antimalarial activity has since been demonstrated for a range of other Artemisia species, suggesting that the genus could provide alternative sources of antimalarial treatments. Given the stunning diversity of the genus (c. 500 species), a prioritisation of taxa to be investigated for their likely antimalarial properties is required. MATERIALS AND METHODS Here we use a phylogenetic approach to explore the potential for identifying species more likely to possess antimalarial properties. Ethnobotanical data from literature reports is recorded for 117 species. Subsequent phylogenetically informed analysis was used to identify lineages in which there is an overrepresentation of species used to treat malarial symptoms, and which could therefore be high priority for further investigation of antimalarial activity. RESULTS We show that these lineages indeed include several species with documented antimalarial activity. To further inform our approach, we use LC-MS/MS analysis to explore artemisinin content in fifteen species from both highlighted and not highlighted lineages. We detected artemisinin in nine species, in eight of them for the first time, doubling the number of Artemisia taxa known to content this molecule. CONCLUSIONS Our findings indicate that artemisinin may be widespread across the genus, providing an accessible local resource outside the distribution area of Artemisia annua.
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Affiliation(s)
- Jaume Pellicer
- Comparative Plant and Fungal Biology Department, Royal Botanic Gardens, Kew, Richmond TW9 3AE, United Kingdom
| | - C Haris Saslis-Lagoudakis
- Natural History Museum of Denmark, Faculty of Science, University of Copenhagen, Øster Farimagsgade 5A, Copenhagen 1353, Denmark
| | - Esperança Carrió
- Laboratori de Botànica - Unitat associada CSIC, Facultat de Farmàcia i Ciències de l'Alimentació, Universitat de Barcelona, Av. Joan XXIII 27-31, 08028 Barcelona, Catalonia, Spain
| | - Madeleine Ernst
- Natural History Museum of Denmark, Faculty of Science, University of Copenhagen, Øster Farimagsgade 5A, Copenhagen 1353, Denmark
| | - Teresa Garnatje
- Institut Botànic de Barcelona (IBB, CSIC-ICUB), Passeig del Migdia sn, 08038 Barcelona, Catalonia, Spain
| | - Olwen M Grace
- Comparative Plant and Fungal Biology Department, Royal Botanic Gardens, Kew, Richmond TW9 3AE, United Kingdom
| | - Airy Gras
- Laboratori de Botànica - Unitat associada CSIC, Facultat de Farmàcia i Ciències de l'Alimentació, Universitat de Barcelona, Av. Joan XXIII 27-31, 08028 Barcelona, Catalonia, Spain
| | - Màrius Mumbrú
- Departament de Biologia, Sanitat i Medi Ambient, Facultat de Farmàcia i Ciències de l'Alimentació, Universitat de Barcelona, Av. Joan XXIII 27-31, 08028 Barcelona, Catalonia, Spain
| | - Joan Vallès
- Laboratori de Botànica - Unitat associada CSIC, Facultat de Farmàcia i Ciències de l'Alimentació, Universitat de Barcelona, Av. Joan XXIII 27-31, 08028 Barcelona, Catalonia, Spain
| | - Daniel Vitales
- Institut Botànic de Barcelona (IBB, CSIC-ICUB), Passeig del Migdia sn, 08038 Barcelona, Catalonia, Spain
| | - Nina Rønsted
- Natural History Museum of Denmark, Faculty of Science, University of Copenhagen, Øster Farimagsgade 5A, Copenhagen 1353, Denmark.
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22
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Burchardt P, Souza-Chies TT, Chauveau O, Callegari-Jacques SM, Brisolara-Corrêa L, Inácio CD, Eggers L, Siljak-Yakovlev S, de Campos JMS, Kaltchuk-Santos E. Cytological and genome size data analyzed in a phylogenetic frame: Evolutionary implications concerning Sisyrinchium taxa (Iridaceae: Iridoideae). Genet Mol Biol 2018; 41:288-307. [PMID: 29505063 PMCID: PMC5913718 DOI: 10.1590/1678-4685-gmb-2017-0077] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Accepted: 08/24/2017] [Indexed: 11/22/2022] Open
Abstract
Sisyrinchium is the largest genus of Iridaceae in the Americas and has the greatest amount of cytological data available. This study aimed at investigating how genomes evolved in this genus. Chromosome number, genome size and altitude from species of sect. Viperella were analyzed in a phylogenetic context. Meiotic and pollen analyses were performed to assess reproductive success of natural populations, especially from those polyploid taxa. Character optimizations revealed that the common ancestor of sect. Viperella was probably diploid (2n = 2x =18) with two subsequent polyplodization events. Total DNA content (2C) varied considerably across the phylogeny with larger genomes detected mainly in polyploid species. Altitude also varied across the phylogeny, however no significant relationship was found between DNA content changes and altitude in our data set. All taxa presented regular meiosis and pollen viability (> 87%), except for S. sp. nov. aff. alatum (22.70%), suggesting a recent hybrid origin. Chromosome number is mostly constant within this section and polyploidy is the only source of modification. Although 2C varied considerably among the 20 taxa investigated, the diversity observed cannot be attributed only to polyploidy events because large variations of DNA content were also observed among diploids.
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Affiliation(s)
- Paula Burchardt
- Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Tatiana T Souza-Chies
- Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil.,Departamento de Botânica, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Olivier Chauveau
- Programa de Pós-Graduação em Botânica, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Sidia M Callegari-Jacques
- Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil.,Departamento de Estatística, Instituto de Matemática e Estatística, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Lauís Brisolara-Corrêa
- Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Camila Dellanhese Inácio
- Programa de Pós-Graduação em Botânica, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Lilian Eggers
- Departamento de Botânica, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil.,Programa de Pós-Graduação em Botânica, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Sonja Siljak-Yakovlev
- Ecologie Systématique Evolution, Université Paris-Sud, CNRS, AgroParisTech, Orsay, France
| | | | - Eliane Kaltchuk-Santos
- Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil.,Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
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23
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Gaynor KM, Solomon JW, Siller S, Jessell L, Duffy JE, Rubenstein DR. Development of genome- and transcriptome-derived microsatellites in related species of snapping shrimps with highly duplicated genomes. Mol Ecol Resour 2017; 17:e160-e173. [PMID: 28776934 DOI: 10.1111/1755-0998.12705] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Revised: 07/16/2017] [Accepted: 07/25/2017] [Indexed: 11/28/2022]
Abstract
Molecular markers are powerful tools for studying patterns of relatedness and parentage within populations and for making inferences about social evolution. However, the development of molecular markers for simultaneous study of multiple species presents challenges, particularly when species exhibit genome duplication or polyploidy. We developed microsatellite markers for Synalpheus shrimp, a genus in which species exhibit not only great variation in social organization, but also interspecific variation in genome size and partial genome duplication. From the four primary clades within Synalpheus, we identified microsatellites in the genomes of four species and in the consensus transcriptome of two species. Ultimately, we designed and tested primers for 143 microsatellite markers across 25 species. Although the majority of markers were disomic, many markers were polysomic for certain species. Surprisingly, we found no relationship between genome size and the number of polysomic markers. As expected, markers developed for a given species amplified better for closely related species than for more distant relatives. Finally, the markers developed from the transcriptome were more likely to work successfully and to be disomic than those developed from the genome, suggesting that consensus transcriptomes are likely to be conserved across species. Our findings suggest that the transcriptome, particularly consensus sequences from multiple species, can be a valuable source of molecular markers for taxa with complex, duplicated genomes.
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Affiliation(s)
- Kaitlyn M Gaynor
- Department of Ecology, Evolution and Environmental Biology, Columbia University, New York, NY, USA.,Department of Environmental Science, Policy and Management, University of California Berkeley, Berkeley, CA, USA
| | - Joseph W Solomon
- Department of Ecology, Evolution and Environmental Biology, Columbia University, New York, NY, USA
| | - Stefanie Siller
- Department of Ecology, Evolution and Environmental Biology, Columbia University, New York, NY, USA
| | - Linnet Jessell
- Department of Ecology, Evolution and Environmental Biology, Columbia University, New York, NY, USA
| | - J Emmett Duffy
- Tennenbaum Marine Observatories Network, Smithsonian Institution, Washington, DC, USA
| | - Dustin R Rubenstein
- Department of Ecology, Evolution and Environmental Biology, Columbia University, New York, NY, USA.,Department of Ornithology, Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, NY, USA
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24
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Genome size, cytogenetic data and transferability of EST-SSRs markers in wild and cultivated species of the genus Theobroma L. (Byttnerioideae, Malvaceae). PLoS One 2017; 12:e0170799. [PMID: 28187131 PMCID: PMC5302445 DOI: 10.1371/journal.pone.0170799] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2016] [Accepted: 01/11/2017] [Indexed: 11/19/2022] Open
Abstract
The genus Theobroma comprises several trees species native to the Amazon. Theobroma cacao L. plays a key economic role mainly in the chocolate industry. Both cultivated and wild forms are described within the genus. Variations in genome size and chromosome number have been used for prediction purposes including the frequency of interspecific hybridization or inference about evolutionary relationships. In this study, the nuclear DNA content, karyotype and genetic diversity using functional microsatellites (EST-SSR) of seven Theobroma species were characterized. The nuclear content of DNA for all analyzed Theobroma species was 1C = ~ 0.46 pg. These species presented 2n = 20 with small chromosomes and only one pair of terminal heterochromatic bands positively stained (CMA+/DAPI− bands). The small size of Theobroma ssp. genomes was equivalent to other Byttnerioideae species, suggesting that the basal lineage of Malvaceae have smaller genomes and that there was an expansion of 2C values in the more specialized family clades. A set of 20 EST-SSR primers were characterized for related species of Theobroma, in which 12 loci were polymorphic. The polymorphism information content (PIC) ranged from 0.23 to 0.65, indicating a high level of information per locus. Combined results of flow cytometry, cytogenetic data and EST-SSRs markers will contribute to better describe the species and infer about the evolutionary relationships among Theobroma species. In addition, the importance of a core collection for conservation purposes is highlighted.
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25
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Sosa MM, Angulo MB, Greppi JA, Bugallo V. Chromosome numbers and DNA content in some species of Mecardonia (Gratiolae, Plantaginaceae). COMPARATIVE CYTOGENETICS 2016; 10:769-780. [PMID: 28123693 PMCID: PMC5240523 DOI: 10.3897/compcytogen.v10i4.10362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Accepted: 11/04/2016] [Indexed: 06/06/2023]
Abstract
Cytogenetic characterization and determination of DNA content by flow cytometry of five species of Mecardonia Ruiz et Pavon, 1798 (Gratiolae, Plantaginaceae) was performed. This is the first study of nuclear DNA content carried out in the genus. Mitotic analysis revealed a base chromosome number x = 11 for all entities and different ploidy levels, ranging from diploid (2n = 2x = 22) to hexaploid (2n = 6x = 66). The results include the first report of the chromosome numbers for Mecardonia flagellaris (Chamisso & Schlechtendal, 1827) (2n = 22), Mecardonia grandiflora (Bentham) Pennell, 1946 (2n = 22), Mecardonia kamogawae Greppi & Hagiwara, 2011 (2n = 66), and Mecardonia sp. (2n = 44). The three ploidy levels here reported suggest that polyploidy is common in Mecardonia and appear to be an important factor in the evolution of this genus. The 2C- and 1Cx-values were also estimated in all the species. The 2C-values ranged from 1.91 to 5.29 pg. The 1Cx-values ranged from 0.88 to 1.03 pg. The general tendency indicated a decrease in the 1Cx-value with increasing ploidy level. The significance of the results is discussed in relation to taxonomy of the genus.
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Affiliation(s)
- María M. Sosa
- Instituto de Botánica del Nordeste (UNNE-CONICET). Sargento Cabral 2131. Facultad de Ciencias Exactas, Naturales y Agrimensura (UNNE). Av. Libertad 5460. 3400. Corrientes, Argentina
| | - María B. Angulo
- Instituto de Botánica del Nordeste (UNNE-CONICET). Sargento Cabral 2131. Facultad de Ciencias Exactas, Naturales y Agrimensura (UNNE). Av. Libertad 5460. 3400. Corrientes, Argentina
| | - Julián A. Greppi
- Instituto de Floricultura, Instituto Nacional de Tecnología Agropecuaria, Hurlingham 1686, Buenos Aires, Argentina
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26
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Yan H, Martin SL, Bekele WA, Latta RG, Diederichsen A, Peng Y, Tinker NA. Genome size variation in the genus Avena. Genome 2016; 59:209-20. [PMID: 26881940 DOI: 10.1139/gen-2015-0132] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Genome size is an indicator of evolutionary distance and a metric for genome characterization. Here, we report accurate estimates of genome size in 99 accessions from 26 species of Avena. We demonstrate that the average genome size of C genome diploid species (2C = 10.26 pg) is 15% larger than that of A genome species (2C = 8.95 pg), and that this difference likely accounts for a progression of size among tetraploid species, where AB < AC < CC (average 2C = 16.76, 18.60, and 21.78 pg, respectively). All accessions from three hexaploid species with the ACD genome configuration had similar genome sizes (average 2C = 25.74 pg). Genome size was mostly consistent within species and in general agreement with current information about evolutionary distance among species. Results also suggest that most of the polyploid species in Avena have experienced genome downsizing in relation to their diploid progenitors. Genome size measurements could provide additional quality control for species identification in germplasm collections, especially in cases where diploid and polyploid species have similar morphology.
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Affiliation(s)
- Honghai Yan
- a Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, 960 Carling Ave., Bldg. 20, C.E.F., Ottawa, ON K1A 0C6, Canada.,b Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu 611130, Sichuan, People's Republic of China
| | - Sara L Martin
- a Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, 960 Carling Ave., Bldg. 20, C.E.F., Ottawa, ON K1A 0C6, Canada
| | - Wubishet A Bekele
- a Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, 960 Carling Ave., Bldg. 20, C.E.F., Ottawa, ON K1A 0C6, Canada
| | - Robert G Latta
- c Department of Biology, Dalhousie University, 1355 Oxford St., Halifax, NS B3H 4R2, Canada
| | - Axel Diederichsen
- d Agriculture and Agri-Food Canada, Plant Gene Resources of Canada, 107 Science Place, Saskatoon, SK S7N 0X2, Canada
| | - Yuanying Peng
- b Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu 611130, Sichuan, People's Republic of China
| | - Nicholas A Tinker
- a Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, 960 Carling Ave., Bldg. 20, C.E.F., Ottawa, ON K1A 0C6, Canada
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27
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Olanj N, Garnatje T, Sonboli A, Vallès J, Garcia S. The striking and unexpected cytogenetic diversity of genus Tanacetum L. (Asteraceae): a cytometric and fluorescent in situ hybridisation study of Iranian taxa. BMC PLANT BIOLOGY 2015; 15:174. [PMID: 26152193 PMCID: PMC4494159 DOI: 10.1186/s12870-015-0564-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Accepted: 06/26/2015] [Indexed: 05/15/2023]
Abstract
BACKGROUND Although karyologically well studied, the genus Tanacetum (Asteraceae) is poorly known from the perspective of molecular cytogenetics. The prevalence of polyploidy, including odd ploidy warranted an extensive cytogenetic study. We studied several species native to Iran, one of the most important centres of diversity of the genus. We aimed to characterise Tanacetum genomes through fluorochrome banding, fluorescent in situ hybridisation (FISH) of rRNA genes and the assessment of genome size by flow cytometry. We appraise the effect of polyploidy and evaluate the existence of intraspecific variation based on the number and distribution of GC-rich bands and rDNA loci. Finally, we infer ancestral genome size and other cytogenetic traits considering phylogenetic relationships within the genus. RESULTS We report first genome size (2C) estimates ranging from 3.84 to 24.87 pg representing about 11 % of those recognised for the genus. We found striking cytogenetic diversity both in the number of GC-rich bands and rDNA loci. There is variation even at the population level and some species have undergone massive heterochromatic or rDNA amplification. Certain morphometric data, such as pollen size or inflorescence architecture, bear some relationship with genome size. Reconstruction of ancestral genome size, number of CMA+ bands and number of rDNA loci show that ups and downs have occurred during the evolution of these traits, although genome size has mostly increased and the number of CMA+ bands and rDNA loci have decreased in present-day taxa compared with ancestral values. CONCLUSIONS Tanacetum genomes are highly unstable in the number of GC-rich bands and rDNA loci, although some patterns can be established at the diploid and tetraploid levels. In particular, aneuploid taxa and some odd ploidy species show greater cytogenetic instability than the rest of the genus. We have also confirmed a linked rDNA arrangement for all the studied Tanacetum species. The labile scenario found in Tanacetum proves that some cytogenetic features previously regarded as relatively constant, or even diagnostic, can display high variability, which is better interpreted within a phylogenetic context.
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Affiliation(s)
- Nayyereh Olanj
- Department of Biology, Faculty of Basic Science, Malayer University, Malayer, Iran.
- Laboratori de Botànica - Unitat associada CSIC, Facultat de Farmàcia, Universitat de Barcelona, Avinguda Joan XXIII s/n, 08028, Barcelona, Catalonia, Spain.
| | - Teresa Garnatje
- Institut Botànic de Barcelona (IBB-CSIC-ICUB), Passeig del Migdia s/n, Parc de Montjuïc, 08038, Barcelona, Catalonia, Spain.
| | - Ali Sonboli
- Department of Biology, Medicinal Plants and Drugs Research Institute, Shahid Beheshti University, Evin, 1983963113, Tehran, Iran.
| | - Joan Vallès
- Laboratori de Botànica - Unitat associada CSIC, Facultat de Farmàcia, Universitat de Barcelona, Avinguda Joan XXIII s/n, 08028, Barcelona, Catalonia, Spain.
| | - Sònia Garcia
- Laboratori de Botànica - Unitat associada CSIC, Facultat de Farmàcia, Universitat de Barcelona, Avinguda Joan XXIII s/n, 08028, Barcelona, Catalonia, Spain.
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28
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Henry TA, Bainard JD, Newmaster SG. Genome size evolution in Ontario ferns (Polypodiidae): evolutionary correlations with cell size, spore size, and habitat type and an absence of genome downsizing. Genome 2015; 57:555-66. [PMID: 25727714 DOI: 10.1139/gen-2014-0090] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Genome size is known to correlate with a number of traits in angiosperms, but less is known about the phenotypic correlates of genome size in ferns. We explored genome size variation in relation to a suite of morphological and ecological traits in ferns. Thirty-six fern taxa were collected from wild populations in Ontario, Canada. 2C DNA content was measured using flow cytometry. We tested for genome downsizing following polyploidy using a phylogenetic comparative analysis to explore the correlation between 1Cx DNA content and ploidy. There was no compelling evidence for the occurrence of widespread genome downsizing during the evolution of Ontario ferns. The relationship between genome size and 11 morphological and ecological traits was explored using a phylogenetic principal component regression analysis. Genome size was found to be significantly associated with cell size, spore size, spore type, and habitat type. These results are timely as past and recent studies have found conflicting support for the association between ploidy/genome size and spore size in fern polyploid complexes; this study represents the first comparative analysis of the trend across a broad taxonomic group of ferns.
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Affiliation(s)
- Thomas A Henry
- Centre for Biodiversity Genomics, Department of Integrative Biology, University of Guelph, Guelph, ON N1G 2W1, Canada
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29
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The reticulate evolutionary history of the polyploid NW Iberian Leucanthemum pluriflorum clan (Compositae, Anthemideae) as inferred from nrDNA ETS sequence diversity and eco-climatological niche-modelling. Mol Phylogenet Evol 2014; 70:478-91. [DOI: 10.1016/j.ympev.2013.10.013] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2013] [Revised: 10/07/2013] [Accepted: 10/15/2013] [Indexed: 11/21/2022]
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30
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Wang H, Jiang J, Chen S, Fang W, Guan Z, Liao Y, Chen F. Rapid genomic and transcriptomic alterations induced by wide hybridization: Chrysanthemum nankingense × Tanacetum vulgare and C. crassum × Crossostephium chinense (Asteraceae). BMC Genomics 2013; 14:902. [PMID: 24350608 PMCID: PMC3878368 DOI: 10.1186/1471-2164-14-902] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2013] [Accepted: 12/13/2013] [Indexed: 11/22/2022] Open
Abstract
Background Hybridization is a major driver of evolution in plants. In a number of plant species, the process of hybridization has been revealed to be accompanied by wide-ranging genetic and epigenetic alterations, some of which have consequences on gene transcripts. The Asteraceae family includes a number of polyploid species, and wide crossing is seen as a viable means of genetically improving ornamental species such as Chrysanthemum spp. However, the consequences of hybridization in this taxon have yet to be characterized. Results Amplified fragment length polymorphism (AFLP), methylation sensitive amplification polymorphism (MSAP) and cDNA-AFLP profiling of the two intergeneric hybrids C. nankingense × Tanacetum vulgare and C. crassum × Crossostephium chinense were employed to characterize, respectively, the genomic, epigenomic and transcriptomic changes induced by the hybridization event. The hybrids’ AFLP profiles included both the loss of specific parental fragments and the gain of fragments not present in either parent’s profile. About 10% of the paternal fragments were not inherited by the hybrid, while the corresponding rate for the maternal parent fragments was around 4–5%. The novel fragments detected may have arisen either due to heterozygosity in one or other parent, or as a result of a deletion event following the hybridization. Around one half of the cDNA-AFLP fragments were common to both parents, about 30% were specific to the female parent, and somewhat under 20% specific to the male parent; the remainder (2.9-4.7%) of the hybrids’ fragments were not present in either parent’s profile. The MSAP fingerprinting demonstrated that the hybridization event also reduced the amount of global cytosine methylation, since > 50% of the parental fragments were methylated, while the corresponding frequencies for the two hybrids were 48.5% and 50.4%. Conclusions Combining two different Asteraceae genomes via hybridization clearly induced a range of genomic and epigenomic alterations, some of which had an effect on the transcriptome. The rapid genomic and transcriptomic alterations induced by hybridization may accelerate the evolutionary process among progenies.
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Affiliation(s)
| | - Jiafu Jiang
- College of Horticulture, Nanjing Agricultural University, No, 1 Weigang, Nanjing 210095, Jiangsu Province, China.
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Garcia S, Leitch IJ, Anadon-Rosell A, Canela MÁ, Gálvez F, Garnatje T, Gras A, Hidalgo O, Johnston E, Mas de Xaxars G, Pellicer J, Siljak-Yakovlev S, Vallès J, Vitales D, Bennett MD. Recent updates and developments to plant genome size databases. Nucleic Acids Res 2013; 42:D1159-66. [PMID: 24288377 PMCID: PMC3965065 DOI: 10.1093/nar/gkt1195] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Two plant genome size databases have been recently updated and/or extended: the Plant DNA C-values database (http://data.kew.org/cvalues), and GSAD, the Genome Size in Asteraceae database (http://www.asteraceaegenomesize.com). While the first provides information on nuclear DNA contents across land plants and some algal groups, the second is focused on one of the largest and most economically important angiosperm families, Asteraceae. Genome size data have numerous applications: they can be used in comparative studies on genome evolution, or as a tool to appraise the cost of whole-genome sequencing programs. The growing interest in genome size and increasing rate of data accumulation has necessitated the continued update of these databases. Currently, the Plant DNA C-values database (Release 6.0, Dec. 2012) contains data for 8510 species, while GSAD has 1219 species (Release 2.0, June 2013), representing increases of 17 and 51%, respectively, in the number of species with genome size data, compared with previous releases. Here we provide overviews of the most recent releases of each database, and outline new features of GSAD. The latter include (i) a tool to visually compare genome size data between species, (ii) the option to export data and (iii) a webpage containing information about flow cytometry protocols.
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Affiliation(s)
- Sònia Garcia
- Laboratori de Botànica-Unitat Associada CSIC, Facultat de Farmàcia, Universitat de Barcelona, 08028 Barcelona, Catalonia, Spain, Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AB, UK, Departament de Biologia Vegetal, Facultat de Biologia, Universitat de Barcelona, 08028 Barcelona, Catalonia, Spain, Department of Managerial Decision Sciences, IESE Business School, Universidad de Navarra, 08032 Barcelona, Catalonia, Spain, BioScripts - Centro de Investigación y Desarrollo de Recursos Científicos, 41012 Sevilla, Andalusia, Spain, Institut Botànic de Barcelona (IBB-CSIC-ICUB), 08038 Barcelona, Catalonia, Spain and Laboratoire d’Evolution et Systématique, Université Paris Sud, UMR8079 CNRS-UPS-AgroParis-Tech, 91405 Orsay Cedex, France
- *To whom correspondence should be addressed. Sònia Garcia: Tel: +34 934 024490; Fax: +34 934 025879;
| | - Ilia J. Leitch
- Laboratori de Botànica-Unitat Associada CSIC, Facultat de Farmàcia, Universitat de Barcelona, 08028 Barcelona, Catalonia, Spain, Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AB, UK, Departament de Biologia Vegetal, Facultat de Biologia, Universitat de Barcelona, 08028 Barcelona, Catalonia, Spain, Department of Managerial Decision Sciences, IESE Business School, Universidad de Navarra, 08032 Barcelona, Catalonia, Spain, BioScripts - Centro de Investigación y Desarrollo de Recursos Científicos, 41012 Sevilla, Andalusia, Spain, Institut Botànic de Barcelona (IBB-CSIC-ICUB), 08038 Barcelona, Catalonia, Spain and Laboratoire d’Evolution et Systématique, Université Paris Sud, UMR8079 CNRS-UPS-AgroParis-Tech, 91405 Orsay Cedex, France
- Correspondence may be also addressed to Ilia J. Leitch. Tel: +44 208 332 5329; Fax: +44 208 332 5310;
| | - Alba Anadon-Rosell
- Laboratori de Botànica-Unitat Associada CSIC, Facultat de Farmàcia, Universitat de Barcelona, 08028 Barcelona, Catalonia, Spain, Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AB, UK, Departament de Biologia Vegetal, Facultat de Biologia, Universitat de Barcelona, 08028 Barcelona, Catalonia, Spain, Department of Managerial Decision Sciences, IESE Business School, Universidad de Navarra, 08032 Barcelona, Catalonia, Spain, BioScripts - Centro de Investigación y Desarrollo de Recursos Científicos, 41012 Sevilla, Andalusia, Spain, Institut Botànic de Barcelona (IBB-CSIC-ICUB), 08038 Barcelona, Catalonia, Spain and Laboratoire d’Evolution et Systématique, Université Paris Sud, UMR8079 CNRS-UPS-AgroParis-Tech, 91405 Orsay Cedex, France
| | - Miguel Á. Canela
- Laboratori de Botànica-Unitat Associada CSIC, Facultat de Farmàcia, Universitat de Barcelona, 08028 Barcelona, Catalonia, Spain, Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AB, UK, Departament de Biologia Vegetal, Facultat de Biologia, Universitat de Barcelona, 08028 Barcelona, Catalonia, Spain, Department of Managerial Decision Sciences, IESE Business School, Universidad de Navarra, 08032 Barcelona, Catalonia, Spain, BioScripts - Centro de Investigación y Desarrollo de Recursos Científicos, 41012 Sevilla, Andalusia, Spain, Institut Botànic de Barcelona (IBB-CSIC-ICUB), 08038 Barcelona, Catalonia, Spain and Laboratoire d’Evolution et Systématique, Université Paris Sud, UMR8079 CNRS-UPS-AgroParis-Tech, 91405 Orsay Cedex, France
| | - Francisco Gálvez
- Laboratori de Botànica-Unitat Associada CSIC, Facultat de Farmàcia, Universitat de Barcelona, 08028 Barcelona, Catalonia, Spain, Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AB, UK, Departament de Biologia Vegetal, Facultat de Biologia, Universitat de Barcelona, 08028 Barcelona, Catalonia, Spain, Department of Managerial Decision Sciences, IESE Business School, Universidad de Navarra, 08032 Barcelona, Catalonia, Spain, BioScripts - Centro de Investigación y Desarrollo de Recursos Científicos, 41012 Sevilla, Andalusia, Spain, Institut Botànic de Barcelona (IBB-CSIC-ICUB), 08038 Barcelona, Catalonia, Spain and Laboratoire d’Evolution et Systématique, Université Paris Sud, UMR8079 CNRS-UPS-AgroParis-Tech, 91405 Orsay Cedex, France
| | - Teresa Garnatje
- Laboratori de Botànica-Unitat Associada CSIC, Facultat de Farmàcia, Universitat de Barcelona, 08028 Barcelona, Catalonia, Spain, Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AB, UK, Departament de Biologia Vegetal, Facultat de Biologia, Universitat de Barcelona, 08028 Barcelona, Catalonia, Spain, Department of Managerial Decision Sciences, IESE Business School, Universidad de Navarra, 08032 Barcelona, Catalonia, Spain, BioScripts - Centro de Investigación y Desarrollo de Recursos Científicos, 41012 Sevilla, Andalusia, Spain, Institut Botànic de Barcelona (IBB-CSIC-ICUB), 08038 Barcelona, Catalonia, Spain and Laboratoire d’Evolution et Systématique, Université Paris Sud, UMR8079 CNRS-UPS-AgroParis-Tech, 91405 Orsay Cedex, France
| | - Airy Gras
- Laboratori de Botànica-Unitat Associada CSIC, Facultat de Farmàcia, Universitat de Barcelona, 08028 Barcelona, Catalonia, Spain, Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AB, UK, Departament de Biologia Vegetal, Facultat de Biologia, Universitat de Barcelona, 08028 Barcelona, Catalonia, Spain, Department of Managerial Decision Sciences, IESE Business School, Universidad de Navarra, 08032 Barcelona, Catalonia, Spain, BioScripts - Centro de Investigación y Desarrollo de Recursos Científicos, 41012 Sevilla, Andalusia, Spain, Institut Botànic de Barcelona (IBB-CSIC-ICUB), 08038 Barcelona, Catalonia, Spain and Laboratoire d’Evolution et Systématique, Université Paris Sud, UMR8079 CNRS-UPS-AgroParis-Tech, 91405 Orsay Cedex, France
| | - Oriane Hidalgo
- Laboratori de Botànica-Unitat Associada CSIC, Facultat de Farmàcia, Universitat de Barcelona, 08028 Barcelona, Catalonia, Spain, Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AB, UK, Departament de Biologia Vegetal, Facultat de Biologia, Universitat de Barcelona, 08028 Barcelona, Catalonia, Spain, Department of Managerial Decision Sciences, IESE Business School, Universidad de Navarra, 08032 Barcelona, Catalonia, Spain, BioScripts - Centro de Investigación y Desarrollo de Recursos Científicos, 41012 Sevilla, Andalusia, Spain, Institut Botànic de Barcelona (IBB-CSIC-ICUB), 08038 Barcelona, Catalonia, Spain and Laboratoire d’Evolution et Systématique, Université Paris Sud, UMR8079 CNRS-UPS-AgroParis-Tech, 91405 Orsay Cedex, France
| | - Emmeline Johnston
- Laboratori de Botànica-Unitat Associada CSIC, Facultat de Farmàcia, Universitat de Barcelona, 08028 Barcelona, Catalonia, Spain, Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AB, UK, Departament de Biologia Vegetal, Facultat de Biologia, Universitat de Barcelona, 08028 Barcelona, Catalonia, Spain, Department of Managerial Decision Sciences, IESE Business School, Universidad de Navarra, 08032 Barcelona, Catalonia, Spain, BioScripts - Centro de Investigación y Desarrollo de Recursos Científicos, 41012 Sevilla, Andalusia, Spain, Institut Botànic de Barcelona (IBB-CSIC-ICUB), 08038 Barcelona, Catalonia, Spain and Laboratoire d’Evolution et Systématique, Université Paris Sud, UMR8079 CNRS-UPS-AgroParis-Tech, 91405 Orsay Cedex, France
| | - Gemma Mas de Xaxars
- Laboratori de Botànica-Unitat Associada CSIC, Facultat de Farmàcia, Universitat de Barcelona, 08028 Barcelona, Catalonia, Spain, Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AB, UK, Departament de Biologia Vegetal, Facultat de Biologia, Universitat de Barcelona, 08028 Barcelona, Catalonia, Spain, Department of Managerial Decision Sciences, IESE Business School, Universidad de Navarra, 08032 Barcelona, Catalonia, Spain, BioScripts - Centro de Investigación y Desarrollo de Recursos Científicos, 41012 Sevilla, Andalusia, Spain, Institut Botànic de Barcelona (IBB-CSIC-ICUB), 08038 Barcelona, Catalonia, Spain and Laboratoire d’Evolution et Systématique, Université Paris Sud, UMR8079 CNRS-UPS-AgroParis-Tech, 91405 Orsay Cedex, France
| | - Jaume Pellicer
- Laboratori de Botànica-Unitat Associada CSIC, Facultat de Farmàcia, Universitat de Barcelona, 08028 Barcelona, Catalonia, Spain, Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AB, UK, Departament de Biologia Vegetal, Facultat de Biologia, Universitat de Barcelona, 08028 Barcelona, Catalonia, Spain, Department of Managerial Decision Sciences, IESE Business School, Universidad de Navarra, 08032 Barcelona, Catalonia, Spain, BioScripts - Centro de Investigación y Desarrollo de Recursos Científicos, 41012 Sevilla, Andalusia, Spain, Institut Botànic de Barcelona (IBB-CSIC-ICUB), 08038 Barcelona, Catalonia, Spain and Laboratoire d’Evolution et Systématique, Université Paris Sud, UMR8079 CNRS-UPS-AgroParis-Tech, 91405 Orsay Cedex, France
| | - Sonja Siljak-Yakovlev
- Laboratori de Botànica-Unitat Associada CSIC, Facultat de Farmàcia, Universitat de Barcelona, 08028 Barcelona, Catalonia, Spain, Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AB, UK, Departament de Biologia Vegetal, Facultat de Biologia, Universitat de Barcelona, 08028 Barcelona, Catalonia, Spain, Department of Managerial Decision Sciences, IESE Business School, Universidad de Navarra, 08032 Barcelona, Catalonia, Spain, BioScripts - Centro de Investigación y Desarrollo de Recursos Científicos, 41012 Sevilla, Andalusia, Spain, Institut Botànic de Barcelona (IBB-CSIC-ICUB), 08038 Barcelona, Catalonia, Spain and Laboratoire d’Evolution et Systématique, Université Paris Sud, UMR8079 CNRS-UPS-AgroParis-Tech, 91405 Orsay Cedex, France
| | - Joan Vallès
- Laboratori de Botànica-Unitat Associada CSIC, Facultat de Farmàcia, Universitat de Barcelona, 08028 Barcelona, Catalonia, Spain, Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AB, UK, Departament de Biologia Vegetal, Facultat de Biologia, Universitat de Barcelona, 08028 Barcelona, Catalonia, Spain, Department of Managerial Decision Sciences, IESE Business School, Universidad de Navarra, 08032 Barcelona, Catalonia, Spain, BioScripts - Centro de Investigación y Desarrollo de Recursos Científicos, 41012 Sevilla, Andalusia, Spain, Institut Botànic de Barcelona (IBB-CSIC-ICUB), 08038 Barcelona, Catalonia, Spain and Laboratoire d’Evolution et Systématique, Université Paris Sud, UMR8079 CNRS-UPS-AgroParis-Tech, 91405 Orsay Cedex, France
| | - Daniel Vitales
- Laboratori de Botànica-Unitat Associada CSIC, Facultat de Farmàcia, Universitat de Barcelona, 08028 Barcelona, Catalonia, Spain, Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AB, UK, Departament de Biologia Vegetal, Facultat de Biologia, Universitat de Barcelona, 08028 Barcelona, Catalonia, Spain, Department of Managerial Decision Sciences, IESE Business School, Universidad de Navarra, 08032 Barcelona, Catalonia, Spain, BioScripts - Centro de Investigación y Desarrollo de Recursos Científicos, 41012 Sevilla, Andalusia, Spain, Institut Botànic de Barcelona (IBB-CSIC-ICUB), 08038 Barcelona, Catalonia, Spain and Laboratoire d’Evolution et Systématique, Université Paris Sud, UMR8079 CNRS-UPS-AgroParis-Tech, 91405 Orsay Cedex, France
| | - Michael D. Bennett
- Laboratori de Botànica-Unitat Associada CSIC, Facultat de Farmàcia, Universitat de Barcelona, 08028 Barcelona, Catalonia, Spain, Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AB, UK, Departament de Biologia Vegetal, Facultat de Biologia, Universitat de Barcelona, 08028 Barcelona, Catalonia, Spain, Department of Managerial Decision Sciences, IESE Business School, Universidad de Navarra, 08032 Barcelona, Catalonia, Spain, BioScripts - Centro de Investigación y Desarrollo de Recursos Científicos, 41012 Sevilla, Andalusia, Spain, Institut Botànic de Barcelona (IBB-CSIC-ICUB), 08038 Barcelona, Catalonia, Spain and Laboratoire d’Evolution et Systématique, Université Paris Sud, UMR8079 CNRS-UPS-AgroParis-Tech, 91405 Orsay Cedex, France
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Neiman M, Kay AD, Krist AC. Can resource costs of polyploidy provide an advantage to sex? Heredity (Edinb) 2013; 110:152-9. [PMID: 23188174 PMCID: PMC3554456 DOI: 10.1038/hdy.2012.78] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2012] [Revised: 07/26/2012] [Accepted: 08/01/2012] [Indexed: 12/26/2022] Open
Abstract
The predominance of sexual reproduction despite its costs indicates that sex provides substantial benefits, which are usually thought to derive from the direct genetic consequences of recombination and syngamy. While genetic benefits of sex are certainly important, sexual and asexual individuals, lineages, or populations may also differ in physiological and life history traits that could influence outcomes of competition between sexuals and asexuals across environmental gradients. Here, we address possible phenotypic costs of a very common correlate of asexuality, polyploidy. We suggest that polyploidy could confer resource costs related to the dietary phosphorus demands of nucleic acid production; such costs could facilitate the persistence of sex in situations where asexual taxa are of higher ploidy level and phosphorus availability limits important traits like growth and reproduction. We outline predictions regarding the distribution of diploid sexual and polyploid asexual taxa across biogeochemical gradients and provide suggestions for study systems and empirical approaches for testing elements of our hypothesis.
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Affiliation(s)
- M Neiman
- Department of Biology, University of Iowa, Iowa City, IA 52242, USA.
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Garcia S, McArthur ED, Pellicer J, Sanderson SC, Vallès J, Garnatje T. A molecular phylogenetic approach to western North America endemic Artemisia and allies (Asteraceae): untangling the sagebrushes. AMERICAN JOURNAL OF BOTANY 2011; 98:638-653. [PMID: 21613164 DOI: 10.3732/ajb.1000386] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
PREMISE OF THE STUDY Artemisia subgenus Tridentatae plants characterize the North American Intermountain West. These are landscape-dominant constituents of important ecological communities and habitats for endemic wildlife. Together with allied species and genera (Picrothamnus and Sphaeromeria), they make up an intricate series of taxa whose limits are uncertain, likely the result of reticulate evolution. The objectives of this study were to resolve relations among Tridentatae species and their near relatives by delimiting the phylogenetic positions of subgenus Tridentatae species with particular reference to its New World geographic placement and to provide explanations for the relations of allied species and genera with the subgenus with an assessment of their current taxonomic placement. METHODS Bayesian inference and maximum parsimony analysis were based on 168 newly generated sequences (including the nuclear ITS and ETS and the plastid trnS(UGA)-trnfM(CAU) and trnS(GCU)-trnC(GCA)) and 338 previously published sequences (ITS and ETS). Genome size by flow cytometry of species from Sphaeromeria was also determined. KEY RESULTS The results support an expanded concept and reconfiguration of Tridentatae to accommodate additional endemic North American Artemisia species. The monotypic Picrothamnus and all Sphaeromeria species appear nested within subgenus Tridentatae clade. CONCLUSIONS A redefinition of subgenus Tridentatae to include other western North American endemics is supported. We propose a new circumscription of the subgenus and divide it into three sections: Tridentatae, Filifoliae, and Nebulosae. The position of the circumboreal and other North American species suggests that subgenus Artemisia is the ancestral stock for the New World endemics, including those native to South America.
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Affiliation(s)
- Sònia Garcia
- Institut Botànic de Barcelona (IBB-CSIC-ICUB). Passeig del Migdia s/n 08038 Barcelona, Catalonia, Spain.
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Abstract
The purpose of this study is to provide a new focus to contribute, from the perspective of genomic evolution, towards a better understanding of the Valerianaceae evolutionary history. Chromosome numbers were determined by Feulgen staining in 24 populations of 18 species (first count for Valerianella multidentata, 2n=2x=14–16), and DNA contents were assessed by flow cytometry in 74 populations of 35 species (first assessments in all taxa but Centranthus ruber). A molecular phylogeny based on the trnL-trnF and including 41 new sequences was established, with the first DNA sequence for Centranthus nevadensis, Valeriana rotundifolia, V. saxatilis, Valerianella multidentata, and V. turgida. This work is the first large genome size study devoted to the Valerianaceae, showing a range of DNA amounts from 2C=0.39 pg (Valerianella turgida) to 2C=8.32 pg (Valeriana officinalis). At the family level, changes in basic chromosome number and genome size coincide with or precede major shifts in the evolutionary history of the group, such as those concerning stamen number and floral symmetry.
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