Diversity and Phylogenetic Relationships of Full Genome Sequences of Cassava Brown Streak Viruses in Kenya

Cassava brown streak disease is caused by cassava brown streak virus (CBSV) and Uganda cassava brown streak virus (UCBSV). Many of the CBSV and UCBSV diversity studies utilize partial coat protein sequences due to the unavailability of representative full genome sequences. Hence, there is little information on the diversity of cassava brown streak viruses in the rest of the genomes of the two species that are present in the farmers’ fields. The aim of this study was to determine Kenyan full CBSV and UCBSV genomes, and their sequence diversity and phylogenetic relationships within various genome and genome segments. Twenty four CBSVs positive samples tested by RT PCR from major cassava producing regions in Kenya were sequenced using Illumina MiSeq. Quality assessment of the output reads was done using the CLC Genomics 5.5.1 software programs. Genome assembly was done by de novo and reference guided assembly. Nucleotide sequence similarity of CBSV and UCBSV was determined. Phylogenetic relationships between CBSV and UCBSV were determined by performing the neighbour-joining analysis using MEGA 6.0 software. Six CBSV and 9 UCBSV genomes were generated from this study. The coat protein of the CBSV sequences had nucleotide sequence similarity of 92-100% while P1 and P3 gene had 75-100% and 76-100%, respectively. The coat protein of the UCBSV sequences had nucleotide sequence similarity of 91-99%. P1 and P3 gene had 83-100% and 86-99%, respectively. The phylogenetic analysis of full genomes revealed two distinct clusters one for UCBSV and another cluster for CBSV. Individual gene segments phylogenetic tree resembled that of the whole genome by clustering the nucleotide sequences into two clusters, one belonging to UCBSV and the other CBSV. The study revealed an average genome nucleotide diversity of 21.5% and 15.8% in CBSV and UCBSV respectively. A vast genetic diversity observed in CBSV and UCBSV in this study portends a lot of challenges in developing molecular diagnostic techniques as well as control strategies against the viruses.

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Molecular characterization of the Cassava brown streak virus coat protein

Plant Pathology ◽

10.1046/j.1365-3059.2001.00589.x ◽

2001 ◽

Vol 50 (4) ◽

pp. 527-534 ◽

Cited By ~ 61

Author(s):

W. A. Monger ◽

S. Seal ◽

A. M. Isaac ◽

G. D. Foster

Keyword(s):

Coat Protein ◽

Molecular Characterization ◽

Streak Virus ◽

Virus Coat Protein ◽

Cassava Brown Streak Virus ◽

Virus Coat ◽

Brown Streak

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Genome Sequences of 19 Rhodococcus erythropolis Cluster CA Phages

Genome Announcements ◽

10.1128/genomea.01201-17 ◽

2017 ◽

Vol 5 (49) ◽

Cited By ~ 2

Author(s):

J. Alfred Bonilla ◽

Sharon Isern ◽

Ann M. Findley ◽

Karen K. Klyczek ◽

Scott F. Michael ◽

...

Keyword(s):

Nucleotide Sequence ◽

Complete Genome ◽

Environmental Samples ◽

Sequence Similarity ◽

Rhodococcus Erythropolis ◽

Genome Sequences ◽

Content Type ◽

Nucleotide Sequence Similarity

ABSTRACT We report the complete genome sequences of 19 cluster CA bacteriophages isolated from environmental samples using Rhodococcus erythropolis as a host. All of the phages are Siphoviridae, have similar genome lengths (46,314 to 46,985 bp) and G+C contents (58.5 to 58.8%), and share nucleotide sequence similarity.

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Genome Sequences of Newly Isolated Mycobacteriophages Forming Cluster S: TABLE 1

Genome Announcements ◽

10.1128/genomea.00933-16 ◽

2016 ◽

Vol 4 (5) ◽

Author(s):

Monique L. Mills ◽

Judd Bragg ◽

Asri Bruce ◽

Ari Dehn ◽

Jordan Drouin ◽

...

Keyword(s):

Nucleotide Sequence ◽

Single Nucleotide Polymorphisms ◽

Mycobacterium Smegmatis ◽

Sequence Similarity ◽

Nucleotide Polymorphisms ◽

Genome Sequences ◽

Single Nucleotide ◽

Nucleotide Sequence Similarity

We describe the genomes of two mycobacteriophages, MosMoris and Gattaca, newly isolated on Mycobacterium smegmatis . The two phages are very similar to each other, differing in 61 single nucleotide polymorphisms and six small insertion/deletions. Both have extensive nucleotide sequence similarity to mycobacteriophage Marvin and together form cluster S.

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Differential Tropism in Roots and Shoots of Resistant and Susceptible Cassava (Manihot esculenta Crantz) Infected by Cassava Brown Streak Viruses

Cells ◽

10.3390/cells10051221 ◽

2021 ◽

Vol 10 (5) ◽

pp. 1221

Author(s):

Samar Sheat ◽

Paolo Margaria ◽

Stephan Winter

Keyword(s):

Virus Replication ◽

Central Africa ◽

Streak Virus ◽

Virus Infections ◽

Long Distance ◽

Manihot Esculenta Crantz ◽

Cassava Brown Streak Virus ◽

Cassava Brown Streak Disease ◽

Long Distance Movement ◽

Brown Streak

Cassava brown streak disease (CBSD) is a destructive disease of cassava in Eastern and Central Africa. Because there was no source of resistance in African varieties to provide complete protection against the viruses causing the disease, we searched in South American germplasm and identified cassava lines that did not become infected with the cassava brown streak viruses. These findings motivated further investigations into the mechanism of virus resistance. We used RNAscope® in situ hybridization to localize cassava brown streak virus in cassava germplasm lines that were highly resistant (DSC 167, immune) or that restricted virus infections to stems and roots only (DSC 260). We show that the resistance in those lines is not a restriction of long-distance movement but due to preventing virus unloading from the phloem into parenchyma cells for replication, thus restricting the virus to the phloem cells only. When DSC 167 and DSC 260 were compared for virus invasion, only a low CBSV signal was found in phloem tissue of DSC 167, indicating that there is no replication in this host, while the presence of intense hybridization signals in the phloem of DSC 260 provided evidence for virus replication in companion cells. In neither of the two lines studied was there evidence of virus replication outside the phloem tissues. Thus, we conclude that in resistant cassava lines, CBSV is confined to the phloem tissues only, in which virus replication can still take place or is arrested.

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A time series transcriptome analysis of cassava (Manihot esculenta Crantz) varieties challenged with Ugandan cassava brown streak virus

Scientific Reports ◽

10.1038/s41598-017-09617-z ◽

2017 ◽

Vol 7 (1) ◽

Cited By ~ 15

Author(s):

T. Amuge ◽

D. K. Berger ◽

M. S. Katari ◽

A. A. Myburg ◽

S. L. Goldman ◽

...

Keyword(s):

Time Series ◽

Transcriptome Analysis ◽

Manihot Esculenta ◽

Streak Virus ◽

Manihot Esculenta Crantz ◽

Cassava Brown Streak Virus ◽

Brown Streak

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Cassava brown streak virus has a rapidly evolving genome: implications for virus speciation, variability, diagnosis and host resistance

Scientific Reports ◽

10.1038/srep36164 ◽

2016 ◽

Vol 6 (1) ◽

Cited By ~ 36

Author(s):

Titus Alicai ◽

Joseph Ndunguru ◽

Peter Sseruwagi ◽

Fred Tairo ◽

Geoffrey Okao-Okuja ◽

...

Keyword(s):

Host Resistance ◽

Streak Virus ◽

Cassava Brown Streak Virus ◽

Brown Streak

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Comparing the regional epidemiology of the cassava mosaic and cassava brown streak virus pandemics in Africa

Virus Research ◽

10.1016/j.virusres.2011.04.018 ◽

2011 ◽

Vol 159 (2) ◽

pp. 161-170 ◽

Cited By ~ 172

Author(s):

J.P. Legg ◽

S.C. Jeremiah ◽

H.M. Obiero ◽

M.N. Maruthi ◽

I. Ndyetabula ◽

...

Keyword(s):

Streak Virus ◽

Cassava Brown Streak Virus ◽

Brown Streak

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Expansion of the cassava brown streak disease epidemic in eastern Democratic Republic of Congo

Plant Disease ◽

10.1094/pdis-05-20-1135-re ◽

2020 ◽

Author(s):

Clérisse Mubasi Casinga ◽

Rudolph R Shirima ◽

N M Mahungu ◽

W Tata-Hangy ◽

Kalinga Benoit Bashizi ◽

...

Keyword(s):

Democratic Republic ◽

Democratic Republic Of Congo ◽

Smallholder Farmers ◽

Central Africa ◽

Virus Detection ◽

Streak Virus ◽

Republic Of Congo ◽

Cassava Brown Streak Virus ◽

Cassava Brown Streak Disease ◽

Brown Streak

Cassava plays a key role in assuring food security and generating income for smallholder farmers throughout central Africa, and particularly in the Democratic Republic of Congo (DRC). This status is threatened, however, by cassava brown streak disease (CBSD) which has recently expanded its incidence and range in eastern DRC. The study described here, comprises the first extensive assessment of temporal change in occurrence of CBSD and its causal viruses in DRC, based on surveys conducted during 2016 and 2018. Cassava fields were inspected in Ituri, Nord-Kivu, Sud-Kivu, Tanganyika and Haut-Katanga provinces within eastern DRC, to record foliar incidence and severity of CBSD. Leaf samples were collected for virus detection and species-level identification. New occurrences of CBSD, confirmed by virus diagnostic tests, were recorded in two provinces (Haut-Katanga and Sud-Kivu) and nine previously unaffected territories, covering an area of > 62,000 km2, and at up to 900 km from locations of previously published reports of CBSD in DRC. Overall, average CBSD incidence within fields was 13.2% in 2016 and 16.1% in 2018. In the new spread zone of Haut-Katanga, incidence increased from 1.7% to 15.9%. CBSD is now present in provinces covering 321,000 km2 which is approximately 14% of the total area of DRC. This represents a major expansion of the CBSD epidemic, which was only recorded from one province (Nord-Kivu) in 2012. Both cassava brown streak virus (CBSV) and Ugandan cassava brown streak virus (UCBSV) were detected in Ituri, Nord-Kivu and Sud-Kivu, but only CBSV was detected in Haut-Katanga. Considered overall, these results confirm the increasing threat that CBSD poses to cassava production in DRC and describe an important expansion in the African pandemic of CBSD.

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