Comparative genomics reveals insights into genetic variability and molecular evolution among sugarcane yellow leaf virus populations

Abstract Yellow leaf disease caused by sugarcane yellow leaf virus (SCYLV) is one of the most prevalent diseases worldwide. In this study, six near-complete genome sequences of SCYLV were determined to be 5775–5881 bp in length. Phylogenetic analysis revealed that the two SCYLV isolates from Réunion...

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Autores principales:	Jia-Ju Lu, Er-Qi He, Wen-Qing Bao, Jian-Sheng Chen, Sheng-Ren Sun, San-Ji Gao
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/ffb5fdd7d436485baf9010722d75a06d
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spelling	oai:doaj.org-article:ffb5fdd7d436485baf9010722d75a06d2021-12-02T18:17:41ZComparative genomics reveals insights into genetic variability and molecular evolution among sugarcane yellow leaf virus populations10.1038/s41598-021-86472-z2045-2322https://doaj.org/article/ffb5fdd7d436485baf9010722d75a06d2021-03-01T00:00:00Zhttps://doi.org/10.1038/s41598-021-86472-zhttps://doaj.org/toc/2045-2322Abstract Yellow leaf disease caused by sugarcane yellow leaf virus (SCYLV) is one of the most prevalent diseases worldwide. In this study, six near-complete genome sequences of SCYLV were determined to be 5775–5881 bp in length. Phylogenetic analysis revealed that the two SCYLV isolates from Réunion Island, France, and four from China were clustered into REU and CUB genotypes, respectively, based on 50 genomic sequences (this study = 6, GenBank = 44). Meanwhile, all 50 isolates were clustered into three phylogroups (G1–G3). Twelve significant recombinant events occurred in intra- and inter-phylogroups between geographical origins and host crops. Most recombinant hotspots were distributed in coat protein read-through protein (RTD), followed by ORF0 (P0) and ORF1 (P1). High genetic divergences of 12.4% for genomic sequences and 6.0–24.9% for individual genes were determined at nucleotide levels. The highest nucleotide diversity (π) was found in P0, followed by P1 and RdRP. In addition, purifying selection was a main factor restricting variability in SCYLV populations. Infrequent gene flow between Africa and the two subpopulations (Asia and America) were found, whereas frequent gene flow between Asia and America subpopulations was observed. Taken together, our findings facilitate understanding of genetic diversity and evolutionary dynamics of SCYLV.Jia-Ju LuEr-Qi HeWen-Qing BaoJian-Sheng ChenSheng-Ren SunSan-Ji GaoNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-11 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Jia-Ju Lu Er-Qi He Wen-Qing Bao Jian-Sheng Chen Sheng-Ren Sun San-Ji Gao Comparative genomics reveals insights into genetic variability and molecular evolution among sugarcane yellow leaf virus populations
description	Abstract Yellow leaf disease caused by sugarcane yellow leaf virus (SCYLV) is one of the most prevalent diseases worldwide. In this study, six near-complete genome sequences of SCYLV were determined to be 5775–5881 bp in length. Phylogenetic analysis revealed that the two SCYLV isolates from Réunion Island, France, and four from China were clustered into REU and CUB genotypes, respectively, based on 50 genomic sequences (this study = 6, GenBank = 44). Meanwhile, all 50 isolates were clustered into three phylogroups (G1–G3). Twelve significant recombinant events occurred in intra- and inter-phylogroups between geographical origins and host crops. Most recombinant hotspots were distributed in coat protein read-through protein (RTD), followed by ORF0 (P0) and ORF1 (P1). High genetic divergences of 12.4% for genomic sequences and 6.0–24.9% for individual genes were determined at nucleotide levels. The highest nucleotide diversity (π) was found in P0, followed by P1 and RdRP. In addition, purifying selection was a main factor restricting variability in SCYLV populations. Infrequent gene flow between Africa and the two subpopulations (Asia and America) were found, whereas frequent gene flow between Asia and America subpopulations was observed. Taken together, our findings facilitate understanding of genetic diversity and evolutionary dynamics of SCYLV.
format	article
author	Jia-Ju Lu Er-Qi He Wen-Qing Bao Jian-Sheng Chen Sheng-Ren Sun San-Ji Gao
author_facet	Jia-Ju Lu Er-Qi He Wen-Qing Bao Jian-Sheng Chen Sheng-Ren Sun San-Ji Gao
author_sort	Jia-Ju Lu
title	Comparative genomics reveals insights into genetic variability and molecular evolution among sugarcane yellow leaf virus populations
title_short	Comparative genomics reveals insights into genetic variability and molecular evolution among sugarcane yellow leaf virus populations
title_full	Comparative genomics reveals insights into genetic variability and molecular evolution among sugarcane yellow leaf virus populations
title_fullStr	Comparative genomics reveals insights into genetic variability and molecular evolution among sugarcane yellow leaf virus populations
title_full_unstemmed	Comparative genomics reveals insights into genetic variability and molecular evolution among sugarcane yellow leaf virus populations
title_sort	comparative genomics reveals insights into genetic variability and molecular evolution among sugarcane yellow leaf virus populations
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/ffb5fdd7d436485baf9010722d75a06d
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Comparative genomics reveals insights into genetic variability and molecular evolution among sugarcane yellow leaf virus populations

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