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Singh A, Maurya A, Rajkumar S, Singh AK, Bhardwaj R, Kaushik SK, Kumar S, Singh K, Singh GP, Singh R. Genome-Wide Comparative Analysis of Five Amaranthaceae Species Reveals a Large Amount of Repeat Content. PLANTS (BASEL, SWITZERLAND) 2024; 13:824. [PMID: 38592842 PMCID: PMC10975975 DOI: 10.3390/plants13060824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Revised: 02/20/2024] [Accepted: 02/26/2024] [Indexed: 04/11/2024]
Abstract
Amaranthus is a genus of C4 dicotyledonous herbaceous plant species that are widely distributed in Asia, Africa, Australia, and Europe and are used as grain, vegetables, forages, and ornamental plants. Amaranth species have gained significant attention nowadays as potential sources of nutritious food and industrial products. In this study, we performed a comparative genome analysis of five amaranth species, namely, Amaranthus hypochondriacus, Amaranthus tuberculatus, Amaranthus hybridus, Amaranthus palmeri, and Amaranthus cruentus. The estimated repeat content ranged from 54.49% to 63.26% and was not correlated with the genome sizes. Out of the predicted repeat classes, the majority of repetitive sequences were Long Terminal Repeat (LTR) elements, which account for about 13.91% to 24.89% of all amaranth genomes. Phylogenetic analysis based on 406 single-copy orthologous genes revealed that A. hypochondriacus is most closely linked to A. hybridus and distantly related to A. cruentus. However, dioecious amaranth species, such as A. tuberculatus and A. palmeri, which belong to the subgenera Amaranthus Acnida, have formed their distinct clade. The comparative analysis of genomic data of amaranth species will be useful to identify and characterize agronomically important genes and their mechanisms of action. This will facilitate genomics-based, evolutionary studies, and breeding strategies to design faster, more precise, and predictable crop improvement programs.
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Affiliation(s)
- Akshay Singh
- Division of Genomic Resources, ICAR-National Bureau of Plant Genetic Resources, Pusa, New Delhi 110012, India; (A.S.); (A.M.); (S.R.); (A.K.S.)
| | - Avantika Maurya
- Division of Genomic Resources, ICAR-National Bureau of Plant Genetic Resources, Pusa, New Delhi 110012, India; (A.S.); (A.M.); (S.R.); (A.K.S.)
| | - Subramani Rajkumar
- Division of Genomic Resources, ICAR-National Bureau of Plant Genetic Resources, Pusa, New Delhi 110012, India; (A.S.); (A.M.); (S.R.); (A.K.S.)
| | - Amit Kumar Singh
- Division of Genomic Resources, ICAR-National Bureau of Plant Genetic Resources, Pusa, New Delhi 110012, India; (A.S.); (A.M.); (S.R.); (A.K.S.)
| | - Rakesh Bhardwaj
- Division of Germplasm Evaluation, ICAR-National Bureau of Plant Genetic Resources, Pusa, New Delhi 110012, India; (R.B.); (S.K.K.); (S.K.)
| | - Surinder Kumar Kaushik
- Division of Germplasm Evaluation, ICAR-National Bureau of Plant Genetic Resources, Pusa, New Delhi 110012, India; (R.B.); (S.K.K.); (S.K.)
| | - Sandeep Kumar
- Division of Germplasm Evaluation, ICAR-National Bureau of Plant Genetic Resources, Pusa, New Delhi 110012, India; (R.B.); (S.K.K.); (S.K.)
| | - Kuldeep Singh
- International Crop Research Institute for the Semi-Arid Tropics, Hyderabad 502324, India;
| | | | - Rakesh Singh
- Division of Genomic Resources, ICAR-National Bureau of Plant Genetic Resources, Pusa, New Delhi 110012, India; (A.S.); (A.M.); (S.R.); (A.K.S.)
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Kreiner JM, Hnatovska S, Stinchcombe JR, Wright SI. Quantifying the role of genome size and repeat content in adaptive variation and the architecture of flowering time in Amaranthus tuberculatus. PLoS Genet 2023; 19:e1010865. [PMID: 38150485 PMCID: PMC10775983 DOI: 10.1371/journal.pgen.1010865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 01/09/2024] [Accepted: 12/11/2023] [Indexed: 12/29/2023] Open
Abstract
Genome size variation, largely driven by repeat content, is poorly understood within and among populations, limiting our understanding of its significance for adaptation. Here we characterize intraspecific variation in genome size and repeat content across 186 individuals of Amaranthus tuberculatus, a ubiquitous native weed that shows flowering time adaptation to climate across its range and in response to agriculture. Sequence-based genome size estimates vary by up to 20% across individuals, consistent with the considerable variability in the abundance of transposable elements, unknown repeats, and rDNAs across individuals. The additive effect of this variation has important phenotypic consequences-individuals with more repeats, and thus larger genomes, show slower flowering times and growth rates. However, compared to newly-characterized gene copy number and polygenic nucleotide changes underlying variation in flowering time, we show that genome size is a marginal contributor. Differences in flowering time are reflected by genome size variation across sexes and marginally, habitats, while polygenic variation and a gene copy number variant within the ATP synthesis pathway show consistently stronger environmental clines than genome size. Repeat content nonetheless shows non-neutral distributions across the genome, and across latitudinal and environmental gradients, demonstrating the numerous governing processes that in turn influence quantitative genetic variation for phenotypes key to plant adaptation.
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Affiliation(s)
- Julia M. Kreiner
- Department of Botany, Biodiversity Research Centre, University of British Columbia
- Department of Ecology & Evolutionary Biology, University of Toronto
| | - Solomiya Hnatovska
- Department of Ecology & Evolutionary Biology, University of Toronto
- Department of Molecular Genetics, University of Toronto
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Bobadilla LK, Baek Y, Tranel PJ. Comparative transcriptomic analysis of male and females in the dioecious weeds Amaranthus palmeri and Amaranthus tuberculatus. BMC PLANT BIOLOGY 2023; 23:339. [PMID: 37365527 DOI: 10.1186/s12870-023-04286-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 05/16/2023] [Indexed: 06/28/2023]
Abstract
BACKGROUND Waterhemp (Amaranthus tuberculatus (Moq.) Sauer) and Palmer amaranth (Amaranthus palmeri S. Wats.) are two dioecious and important weed species in the world that can rapidly evolve herbicide-resistance traits. Understanding these two species' dioecious and sex-determination mechanisms could open opportunities for new tools to control them. This study aims to identify the differential expression patterns between males and females in A. tuberculatus and A. palmeri. Multiple analyses, including differential expression, co-expression, and promoter analyses, used RNA-seq data from multiple tissue types to identify putative essential genes for sex determination in both dioecious species. RESULTS Genes were identified as potential key players for sex determination in A. palmeri. Genes PPR247, WEX, and ACD6 were differentially expressed between the sexes and located at scaffold 20 within or near the male-specific Y (MSY) region. Multiple genes involved with flower development were co-expressed with these three genes. For A. tuberculatus, no differentially expressed gene was identified within the MSY region; however, multiple autosomal class B and C genes were identified as differentially expressed and possible candidate genes. CONCLUSIONS This is the first study comparing the global expression profile between males and females in dioecious weedy Amaranthus species. Results narrow down putative essential genes for sex-determination in A. palmeri and A. tuberculatus and also strengthen the hypothesis of two different evolutionary events for dioecy within the genus.
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Affiliation(s)
- Lucas K Bobadilla
- Department of Crop Sciences, University of Illinois, Urbana, IL, USA
| | - Yousoon Baek
- Department of Crop Sciences, University of Illinois, Urbana, IL, USA
| | - Patrick J Tranel
- Department of Crop Sciences, University of Illinois, Urbana, IL, USA.
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