Adaptation and codon-usage preference of apple and pear-infecting apple stem grooving viruses

Jaedeok Kim; Aamir Lal; Eui Joon Kil; Hae Ryun Kwak; Hwan Su Yoon; Hong Soo Choi; Mikyeong Kim; Muhammad Ali; Sukchan Lee

doi:10.3390/microorganisms9061111

Adaptation and codon-usage preference of apple and pear-infecting apple stem grooving viruses

Jaedeok Kim, Aamir Lal, Eui Joon Kil, Hae Ryun Kwak, Hwan Su Yoon, Hong Soo Choi, Mikyeong Kim, Muhammad Ali, Sukchan Lee

Research output: Contribution to journal › Article › peer-review

9 Scopus citations

Abstract

Apple stem grooving virus (ASGV; genus Capillovirus) is an economically important virus. It has an approx. 6.5 kb, monopartite, linear, positive-sense, single-stranded RNA genome. The present study includes identification of 24 isolates—13 isolates from apple (Pyrus malus L.) and 11 isolates from pear (Pyrus communis L.)—from different agricultural fields in South Korea. The coat protein (CP) gene of the corresponding 23 isolates were amplified, sequenced, and analyzed. The CP sequences showed phylogenetic separation based on their host species, and not on the geography, indicating host adaptation. Further analysis showed that the ASGV isolated in this study followed host adaptation influenced and preferred by the host codon-usage.

Original language	English
Article number	1111
Journal	Microorganisms
Volume	9
Issue number	6
DOIs	https://doi.org/10.3390/microorganisms9061111
State	Published - Jun 2021

Keywords

ASGV
Coat protein
Host adaptation
RNA virus
Virus evolution

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10.3390/microorganisms9061111

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title = "Adaptation and codon-usage preference of apple and pear-infecting apple stem grooving viruses",

abstract = "Apple stem grooving virus (ASGV; genus Capillovirus) is an economically important virus. It has an approx. 6.5 kb, monopartite, linear, positive-sense, single-stranded RNA genome. The present study includes identification of 24 isolates—13 isolates from apple (Pyrus malus L.) and 11 isolates from pear (Pyrus communis L.)—from different agricultural fields in South Korea. The coat protein (CP) gene of the corresponding 23 isolates were amplified, sequenced, and analyzed. The CP sequences showed phylogenetic separation based on their host species, and not on the geography, indicating host adaptation. Further analysis showed that the ASGV isolated in this study followed host adaptation influenced and preferred by the host codon-usage.",

keywords = "ASGV, Coat protein, Host adaptation, RNA virus, Virus evolution",

author = "Jaedeok Kim and Aamir Lal and Kil, \{Eui Joon\} and Kwak, \{Hae Ryun\} and Yoon, \{Hwan Su\} and Choi, \{Hong Soo\} and Mikyeong Kim and Muhammad Ali and Sukchan Lee",

note = "Publisher Copyright: {\textcopyright} 2021 by the authors. Licensee MDPI, Basel, Switzerland.",

year = "2021",

month = jun,

doi = "10.3390/microorganisms9061111",

language = "English",

volume = "9",

journal = "Microorganisms",

issn = "2076-2607",

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TY - JOUR

T1 - Adaptation and codon-usage preference of apple and pear-infecting apple stem grooving viruses

AU - Kim, Jaedeok

AU - Lal, Aamir

AU - Kil, Eui Joon

AU - Kwak, Hae Ryun

AU - Yoon, Hwan Su

AU - Choi, Hong Soo

AU - Kim, Mikyeong

AU - Ali, Muhammad

AU - Lee, Sukchan

PY - 2021/6

Y1 - 2021/6

N2 - Apple stem grooving virus (ASGV; genus Capillovirus) is an economically important virus. It has an approx. 6.5 kb, monopartite, linear, positive-sense, single-stranded RNA genome. The present study includes identification of 24 isolates—13 isolates from apple (Pyrus malus L.) and 11 isolates from pear (Pyrus communis L.)—from different agricultural fields in South Korea. The coat protein (CP) gene of the corresponding 23 isolates were amplified, sequenced, and analyzed. The CP sequences showed phylogenetic separation based on their host species, and not on the geography, indicating host adaptation. Further analysis showed that the ASGV isolated in this study followed host adaptation influenced and preferred by the host codon-usage.

AB - Apple stem grooving virus (ASGV; genus Capillovirus) is an economically important virus. It has an approx. 6.5 kb, monopartite, linear, positive-sense, single-stranded RNA genome. The present study includes identification of 24 isolates—13 isolates from apple (Pyrus malus L.) and 11 isolates from pear (Pyrus communis L.)—from different agricultural fields in South Korea. The coat protein (CP) gene of the corresponding 23 isolates were amplified, sequenced, and analyzed. The CP sequences showed phylogenetic separation based on their host species, and not on the geography, indicating host adaptation. Further analysis showed that the ASGV isolated in this study followed host adaptation influenced and preferred by the host codon-usage.

KW - ASGV

KW - Coat protein

KW - Host adaptation

KW - RNA virus

KW - Virus evolution

UR - https://www.scopus.com/pages/publications/85106274640

U2 - 10.3390/microorganisms9061111

DO - 10.3390/microorganisms9061111

M3 - Article

AN - SCOPUS:85106274640

SN - 2076-2607

VL - 9

JO - Microorganisms

JF - Microorganisms

IS - 6

M1 - 1111

ER -

Adaptation and codon-usage preference of apple and pear-infecting apple stem grooving viruses

Abstract

Keywords

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