Genome-wide comparative and evolutionary analysis of transposable elements in eight different legume plants

Pawan Kumar Jayaswal; Asheesh Shanker; Nagendra Kumar Singh

doi:10.56093/ijas.v90i5.104388

Authors

Pawan Kumar Jayaswal ICAR-National Institute for Plant Biotechnology, Pusa, New Delhi 110 012, India
Asheesh Shanker ICAR-National Institute for Plant Biotechnology, Pusa, New Delhi 110 012, India
Nagendra Kumar Singh ICAR-National Institute for Plant Biotechnology, Pusa, New Delhi 110 012, India

https://doi.org/10.56093/ijas.v90i5.104388

Keywords:

Comparative analysis, Divergence analysis, Legume species, Phylogenetic tree

Abstract

Transposable elements (TEs) are a major component of the eukaryotic genomes, which are highly dynamic in nature and significantly contribute in the expansion of genome. We have genome sequence information on several legume species but there is limited information regarding the evolutionary pattern of TEs in these. To understand the expansion of the genomes, we did comparative analysis of TEs in eight different legume species, viz. Arachis durensis (Adu,2.7Gb), Arachis ipaensis (Aip,2.7Gb), Cicer arietinum (Car,738.09 Mb), Cajanus cajan (Cca,858 Mb), Glycine max (Gma,1115 Mb), Lotus japonicas (Lja,472Mb), Medicago truncatula (Mtr,465 Mb) and Vignaan gularis (Van,612 Mb). Our analysis showed that, the TEs in legume genome varied between 27.86% (Lja) to 70.62% (Aip) and LTR was the most dominant category over other TEs. Two Arachis species from Dalbergia tribe differ significantly in their total TEs content (Adu: 60.23%, Aip:70.62%). Comparative analysis indicated that despite the abundance of species-specific TEs in these genome, total 2,850 copies of repeat elements were conserved among all eight selected legume species. These belonged to LTR (n=2,514), non-LTR (n=14), and DNA transposons (n= 133). Evolutionary analysis revealed that most of the conserved TEs belonging tothe same tribe were clustered together, indicating introgression of repeats via horizontal transfer process. Intra and inter tribe divergence time analysis of conserved TEs provided evidence of single and multiple duplication events in the eight legume species.

Downloads

Download data is not yet available.

References

Benson G.1999. Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Research 27: 573–80. DOI: https://doi.org/10.1093/nar/27.2.573

Bertioli D J. 2016. The genome sequences of Arachis duranensis and Arachis ipaensis, the diploid ancestors of cultivated peanut. Nature Genetics 48: 438–46. DOI: https://doi.org/10.1038/ng.3517

Bao Z and Eddy S R. 2002. Automated de novo identification of repeats sequence families in sequenced genomes. Genome Research 12: 1269–76. DOI: https://doi.org/10.1101/gr.88502

Gaiero P. 2019. Comparative analysis of repetitive sequences among species from the potato and the tomato clades. Annals of Botany 123(3): 521–32. DOI: https://doi.org/10.1093/aob/mcy186

Gao D. 2018. Horizontal Transfer of Non-LTR Retrotransposons from Arthropods to Flowering Plants. Molecular Biology and Evolution 35(2): 354–64. DOI: https://doi.org/10.1093/molbev/msx275

Gill N. 2010. Dynamic oryza genomes: Repetitive DNA sequences as genome modeling agents. Rice 3: 251–69. DOI: https://doi.org/10.1007/s12284-010-9054-7

Han Y and Wessler S R. 2010. MITE-Hunter: a program for discovering miniature inverted-repeat transposable elements from genomic sequences. Nucleic Acids Research 38(22): e199. DOI: https://doi.org/10.1093/nar/gkq862

Hirsch C D and Springer N M. 2017. Transposable element influences on gene expression in plants. Biochimica et Biophysica Acta 860: 157–65. DOI: https://doi.org/10.1016/j.bbagrm.2016.05.010

Ibarra-Laclette. 2013. Architecture and evolution of a minute plant genome. Nature 498: 94–98. DOI: https://doi.org/10.1038/nature12132

Jayaswal P K. 2019. Phylogeny of actin and tubulin gene homologs in diverse eukaryotic species. Indian Journal of Genetics and Plant Breeding 79(1): 284–91. DOI: https://doi.org/10.31742/IJGPB.79S.1.20

Johnson L S. 2010. Hidden Markov model speed heuristic and iterative HMM search procedure. BMC Bioinformatics 11: 431. DOI: https://doi.org/10.1186/1471-2105-11-431

Karakülah G and Pavlopoulou A. 2018. In silico phylogenetic analysis of hAT transposable elements in plants. Genes (Basel) 9(6). DOI: https://doi.org/10.3390/genes9060284

Katoh K and Standley D M. 2013. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Molecular Biology and Evolution 30(4): 772–80. DOI: https://doi.org/10.1093/molbev/mst010

Librado P and Rozas J. 2009. DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics 25(11): 1451–52. DOI: https://doi.org/10.1093/bioinformatics/btp187

Lisch D. 2013. How important are transposons for plant evolution? Nature Reviews Genetics 14(1): 49–61. DOI: https://doi.org/10.1038/nrg3374

Ma J and Bennetzen J L.2004. Rapid recent growth and divergence of rice nuclear genomes. Proceedings of the National Academy of Sciences, USA 101(34): 12404-10. DOI: https://doi.org/10.1073/pnas.0403715101

Mao H and Wang H. 2017. SINE_scan: an efficient tool to discover short interspersed nuclear elements (SINEs) in large-scale genomic datasets. Bioinformatics 33(5): 743–45. DOI: https://doi.org/10.1093/bioinformatics/btw718

Nei M and Gojobori T.1986. Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. Molecular Biology and Evolution 3(5): 418–26.

Ronquist F. 2012. MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space. Systematic Biology 61(3): 539–42. DOI: https://doi.org/10.1093/sysbio/sys029

Sato S. 2008. Genome structure of the legume, Lotus japonicus. DNA Research. 15(4): 227–39. DOI: https://doi.org/10.1093/dnares/dsn008

Sarkar D. 2017. The draft genome of Corchorus olitorius cv. JRO-524 (Navin). Genomics Data 12: 151–54. DOI: https://doi.org/10.1016/j.gdata.2017.05.007

Schmutz J. 2010. Genome sequence of the palaeopolyploid soybean. Nature 463(7278): 178–83. DOI: https://doi.org/10.1038/nature08670

Schnable P S. 2009. The B73 maize genome: complexity, diversity, and dynamics. Science 326: 1112–15. DOI: https://doi.org/10.1126/science.1178534

Singh NK. 2012. The first draft of the pigeonpea genome sequence. Journal of Plant Biochemistry and Biotechnology 21: 98–112. DOI: https://doi.org/10.1007/s13562-011-0088-8

Varshney R K. 2013. Draft genome sequence of chickpea (Cicer arietinum) provides a resource for trait improvement. Nature Biotechnology 31(3): 240–46. DOI: https://doi.org/10.1038/nbt.2491

Xia E. 2019. The tea plant reference genome and improved gene annotation using long-read and paired-end sequencing data. Scientific Data 6(1): 122. DOI: https://doi.org/10.1038/s41597-019-0127-1

Yang K. 2015. Genome sequencing of adzuki bean (Vigna angularis) provides insight into high starch and low fat accumulation and domestication. Proceedings of the National Academy of Sciences, USA 112(43): 13213–18. DOI: https://doi.org/10.1073/pnas.1420949112

Young N D. 2011. The Medicago genome provides insight into the evolution of rhizobial symbioses. Nature 480(7378): 520–24. DOI: https://doi.org/10.1038/nature10625