Genome-Wide Comparative Analysis of Five Amaranthaceae Species Reveals a Large Amount of Repeat Content

Singh, Akshay and Maurya, A and Rajkumar, S and Singh, A K and Bhardwaj, R and Kaushik, S K and Kumar, Sandeep and Singh, K and Singh, G P and Singh, R (2024) Genome-Wide Comparative Analysis of Five Amaranthaceae Species Reveals a Large Amount of Repeat Content. Plants (TSI), 13 (6). pp. 1-26. ISSN 2223-7747

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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.

Item Type:	Article
Divisions:	Genebank
CRP:	UNSPECIFIED
Uncontrolled Keywords:	comparative analysis, repetitive elements, single-copy orthologs, phylogenetic analysis, LTR elements
Subjects:	Others > Genetics and Genomics
Depositing User:	Mr Nagaraju T
Date Deposited:	04 Jun 2024 10:48
Last Modified:	04 Jun 2024 10:48
URI:	http://oar.icrisat.org/id/eprint/12690
Official URL:	https://www.mdpi.com/2223-7747/13/6/824
Projects:	UNSPECIFIED
Funders:	Government of India - Department of Biotechnology
Acknowledgement:	We are thankful to the Director, ICAR-NBPGR, New Delhi, for providing the necessary facilities to carry out this research work.
Links:	Google Scholar

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