TY - JOUR
T1 - Virome Analysis of Aphid Populations That Infest the Barley Field
T2 - The Discovery of Two Novel Groups of Nege/Kita-Like Viruses and Other Novel RNA Viruses
AU - Kondo, Hideki
AU - Fujita, Miki
AU - Hisano, Hiroshi
AU - Hyodo, Kiwamu
AU - Ida Bagus, Andika
AU - Suzuki, Nobuhiro
N1 - Funding Information:
We would like to thank Sakae Hisano, Kazuyuki Maruyama, Hideki Nishimura, Takakazu Matsuura, and Makoto Ishii for their helpful technical assistance. We also thank the handling editor and two reviewers for their assistances and valuable suggestions. Rhopalosiphum padi DNA sequencing data were obtained from AphidBase, which acknowledges funding from the European Research Council (Grant No. APHIDHOST-310190 to Dr. Jorunn Bos at the James Hutton Institute). The barley samples were provided by the National BioResource Project for barley (Principal Investigator Prof. Kazuhiro Sato), run by the Ministry of Education, Culture, Sports, Science and Technology (MEXT), Japan. We are also grateful to all researchers who have shared their sequence data deposited in publicly available databases before publication. Funding. This study was supported by the Grants-in-Aids for Scientific Research (C) (KAKENHI 15K07312) to HK and NS; and Scientific Research on Innovative Areas (16H06436, 16H06429, and 16H21723) to NS and HK from the Ministry of Education, Culture, Sports, Science and Technology (MEXT) of Japan; and a Joint Research Grant to HH and HK by the Ohara Foundation for Agriculture Research, Kurashiki, Japan.
Publisher Copyright:
© Copyright © 2020 Kondo, Fujita, Hisano, Hyodo, Andika and Suzuki.
PY - 2020/4/7
Y1 - 2020/4/7
N2 - Aphids (order Hemiptera) are important insect pests of crops and are also vectors of many plant viruses. However, little is known about aphid-infecting viruses, particularly their diversity and relationship to plant viruses. To investigate the aphid viromes, we performed deep sequencing analyses of the aphid transcriptomes from infested barley plants in a field in Japan. We discovered virus-like sequences related to nege/kita-, flavi-, tombus-, phenui-, mononega-, narna-, chryso-, partiti-, and luteoviruses. Using RT-PCR and sequence analyses, we determined almost complete sequences of seven nege/kitavirus-like virus genomes; one of which was a variant of the Wuhan house centipede virus (WHCV-1). The other six seem to belong to four novel viruses distantly related to Wuhan insect virus 9 (WhIV-9) or Hubei nege-like virus 4 (HVLV-4). We designated the four viruses as barley aphid RNA virus 1 to 4 (BARV-1 to -4). Moreover, some nege/kitavirus-like sequences were found by searches on the transcriptome shotgun assembly (TSA) libraries of arthropods and plants. Phylogenetic analyses showed that BARV-1 forms a clade with WHCV-1 and HVLV-4, whereas BARV-2 to -4 clustered with WhIV-9 and an aphid virus, Aphis glycines virus 3. Both virus groups (tentatively designated as Centivirus and Aphiglyvirus, respectively), together with arthropod virus-like TSAs, fill the phylogenetic gaps between the negeviruses and kitaviruses lineages. We also characterized the flavi/jingmen-like and tombus-like virus sequences as well as other RNA viruses, including six putative novel viruses, designated as barley aphid RNA viruses 5 to 10. Interestingly, we also discovered that some aphid-associated viruses, including nege/kita-like viruses, were present in different aphid species, raising a speculation that these viruses might be distributed across different aphid species with plants being the reservoirs. This study provides novel information on the diversity and spread of nege/kitavirus-related viruses and other RNA viruses that are associated with aphids.
AB - Aphids (order Hemiptera) are important insect pests of crops and are also vectors of many plant viruses. However, little is known about aphid-infecting viruses, particularly their diversity and relationship to plant viruses. To investigate the aphid viromes, we performed deep sequencing analyses of the aphid transcriptomes from infested barley plants in a field in Japan. We discovered virus-like sequences related to nege/kita-, flavi-, tombus-, phenui-, mononega-, narna-, chryso-, partiti-, and luteoviruses. Using RT-PCR and sequence analyses, we determined almost complete sequences of seven nege/kitavirus-like virus genomes; one of which was a variant of the Wuhan house centipede virus (WHCV-1). The other six seem to belong to four novel viruses distantly related to Wuhan insect virus 9 (WhIV-9) or Hubei nege-like virus 4 (HVLV-4). We designated the four viruses as barley aphid RNA virus 1 to 4 (BARV-1 to -4). Moreover, some nege/kitavirus-like sequences were found by searches on the transcriptome shotgun assembly (TSA) libraries of arthropods and plants. Phylogenetic analyses showed that BARV-1 forms a clade with WHCV-1 and HVLV-4, whereas BARV-2 to -4 clustered with WhIV-9 and an aphid virus, Aphis glycines virus 3. Both virus groups (tentatively designated as Centivirus and Aphiglyvirus, respectively), together with arthropod virus-like TSAs, fill the phylogenetic gaps between the negeviruses and kitaviruses lineages. We also characterized the flavi/jingmen-like and tombus-like virus sequences as well as other RNA viruses, including six putative novel viruses, designated as barley aphid RNA viruses 5 to 10. Interestingly, we also discovered that some aphid-associated viruses, including nege/kita-like viruses, were present in different aphid species, raising a speculation that these viruses might be distributed across different aphid species with plants being the reservoirs. This study provides novel information on the diversity and spread of nege/kitavirus-related viruses and other RNA viruses that are associated with aphids.
KW - RNA seq
KW - aphid
KW - barley
KW - diversity
KW - horizontal transmission
KW - kitavirus
KW - negevirus
KW - virome
UR - http://www.scopus.com/inward/record.url?scp=85083528240&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=85083528240&partnerID=8YFLogxK
U2 - 10.3389/fmicb.2020.00509
DO - 10.3389/fmicb.2020.00509
M3 - Article
AN - SCOPUS:85083528240
VL - 11
JO - Frontiers in Microbiology
JF - Frontiers in Microbiology
SN - 1664-302X
M1 - 509
ER -