1
|
Moore‐Pollard ER, Jones DS, Mandel JR. Compositae-ParaLoss-1272: A complementary sunflower-specific probe set reduces paralogs in phylogenomic analyses of complex systems. APPLICATIONS IN PLANT SCIENCES 2024; 12:e11568. [PMID: 38369976 PMCID: PMC10873820 DOI: 10.1002/aps3.11568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 10/30/2023] [Accepted: 11/12/2023] [Indexed: 02/20/2024]
Abstract
Premise A family-specific probe set for sunflowers, Compositae-1061, enables family-wide phylogenomic studies and investigations at lower taxonomic levels, but may lack resolution at genus to species levels, especially in groups complicated by polyploidy and hybridization. Methods We developed a Hyb-Seq probe set, Compositae-ParaLoss-1272, that targets orthologous loci in Asteraceae. We tested its efficiency across the family by simulating target enrichment sequencing in silico. Additionally, we tested its effectiveness at lower taxonomic levels in the historically complex genus Packera. We performed Hyb-Seq with Compositae-ParaLoss-1272 for 19 Packera taxa that were previously studied using Compositae-1061. The resulting sequences from each probe set, plus a combination of both, were used to generate phylogenies, compare topologies, and assess node support. Results We report that Compositae-ParaLoss-1272 captured loci across all tested Asteraceae members, had less gene tree discordance, and retained longer loci than Compositae-1061. Most notably, Compositae-ParaLoss-1272 recovered substantially fewer paralogous sequences than Compositae-1061, with only ~5% of the recovered loci reporting as paralogous, compared to ~59% with Compositae-1061. Discussion Given the complexity of plant evolutionary histories, assigning orthology for phylogenomic analyses will continue to be challenging. However, we anticipate Compositae-ParaLoss-1272 will provide improved resolution and utility for studies of complex groups and lower taxonomic levels in the sunflower family.
Collapse
Affiliation(s)
- Erika R. Moore‐Pollard
- Department of Biological SciencesUniversity of Memphis3700 Walker Ave.MemphisTennessee38152USA
| | - Daniel S. Jones
- Department of Biological SciencesAuburn University101 Rouse Life SciencesAuburnAlabama36849USA
| | - Jennifer R. Mandel
- Department of Biological SciencesUniversity of Memphis3700 Walker Ave.MemphisTennessee38152USA
| |
Collapse
|
2
|
Ventimiglia M, Castellacci M, Usai G, Vangelisti A, Simoni S, Natali L, Cavallini A, Mascagni F, Giordani T. Discovering the Repeatome of Five Species Belonging to the Asteraceae Family: A Computational Study. PLANTS (BASEL, SWITZERLAND) 2023; 12:1405. [PMID: 36987093 PMCID: PMC10058865 DOI: 10.3390/plants12061405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 03/08/2023] [Accepted: 03/20/2023] [Indexed: 06/19/2023]
Abstract
Genome divergence by repeat proliferation and/or loss is a process that plays a crucial role in species evolution. Nevertheless, knowledge of the variability related to repeat proliferation among species of the same family is still limited. Considering the importance of the Asteraceae family, here we present a first contribution towards the metarepeatome of five Asteraceae species. A comprehensive picture of the repetitive components of all genomes was obtained by genome skimming with Illumina sequence reads and by analyzing a pool of full-length long terminal repeat retrotransposons (LTR-REs). Genome skimming allowed us to estimate the abundance and variability of repetitive components. The structure of the metagenome of the selected species was composed of 67% repetitive sequences, of which LTR-REs represented the bulk of annotated clusters. The species essentially shared ribosomal DNA sequences, whereas the other classes of repetitive DNA were highly variable among species. The pool of full-length LTR-REs was retrieved from all the species and their age of insertion was established, showing several lineage-specific proliferation peaks over the last 15-million years. Overall, a large variability of repeat abundance at superfamily, lineage, and sublineage levels was observed, indicating that repeats within individual genomes followed different evolutionary and temporal dynamics, and that different events of amplification or loss of these sequences may have occurred after species differentiation.
Collapse
|
3
|
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.
Collapse
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
| |
Collapse
|
4
|
Balant M, Rodríguez González R, Garcia S, Garnatje T, Pellicer J, Vallès J, Vitales D, Hidalgo O. Novel Insights into the Nature of Intraspecific Genome Size Diversity in Cannabis sativa L. PLANTS (BASEL, SWITZERLAND) 2022; 11:2736. [PMID: 36297761 PMCID: PMC9607409 DOI: 10.3390/plants11202736] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 10/08/2022] [Accepted: 10/11/2022] [Indexed: 06/16/2023]
Abstract
Cannabis sativa has been used for millennia in traditional medicine for ritual purposes and for the production of food and fibres, thus, providing important and versatile services to humans. The species, which currently has a worldwide distribution, strikes out for displaying a huge morphological and chemical diversity. Differences in Cannabis genome size have also been found, suggesting it could be a useful character to differentiate between accessions. We used flow cytometry to investigate the extent of genome size diversity across 483 individuals belonging to 84 accessions, with a wide range of wild/feral, landrace, and cultivated accessions. We also carried out sex determination using the MADC2 marker and investigated the potential of flow cytometry as a method for early sex determination. All individuals were diploid, with genome sizes ranging from 1.810 up to 2.152 pg/2C (1.189-fold variation), apart from a triploid, with 2.884 pg/2C. Our results suggest that the geographical expansion of Cannabis and its domestication had little impact on its overall genome size. We found significant differences between the genome size of male and female individuals. Unfortunately, differences were, however, too small to be discriminated using flow cytometry through the direct processing of combined male and female individuals.
Collapse
Affiliation(s)
- Manica Balant
- Institut Botànic de Barcelona (IBB, CSIC-Ajuntament de Barcelona), Passeig del Migdia s.n., 08038 Barcelona, Catalonia, Spain
| | - Roi Rodríguez González
- Institut Botànic de Barcelona (IBB, CSIC-Ajuntament de Barcelona), Passeig del Migdia s.n., 08038 Barcelona, Catalonia, Spain
| | - Sònia Garcia
- Institut Botànic de Barcelona (IBB, CSIC-Ajuntament de Barcelona), Passeig del Migdia s.n., 08038 Barcelona, Catalonia, Spain
| | - Teresa Garnatje
- Institut Botànic de Barcelona (IBB, CSIC-Ajuntament de Barcelona), Passeig del Migdia s.n., 08038 Barcelona, Catalonia, Spain
| | - Jaume Pellicer
- Institut Botànic de Barcelona (IBB, CSIC-Ajuntament de Barcelona), Passeig del Migdia s.n., 08038 Barcelona, Catalonia, Spain
- Royal Botanic Gardens, Kew, Kew Green, Richmond TW9 3AE, UK
| | - Joan Vallès
- Laboratori de Botànica (UB), Unitat Associada al CSIC, Facultat de Farmàcia i Ciències de l’Alimentació–Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Av. Joan XXIII 27–31, 08028 Barcelona, Catalonia, Spain
| | - Daniel Vitales
- Institut Botànic de Barcelona (IBB, CSIC-Ajuntament de Barcelona), Passeig del Migdia s.n., 08038 Barcelona, Catalonia, Spain
- Laboratori de Botànica (UB), Unitat Associada al CSIC, Facultat de Farmàcia i Ciències de l’Alimentació–Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Av. Joan XXIII 27–31, 08028 Barcelona, Catalonia, Spain
| | - Oriane Hidalgo
- Institut Botànic de Barcelona (IBB, CSIC-Ajuntament de Barcelona), Passeig del Migdia s.n., 08038 Barcelona, Catalonia, Spain
- Royal Botanic Gardens, Kew, Kew Green, Richmond TW9 3AE, UK
| |
Collapse
|