Variability in P1 gene redefines phylogenetic relationships among cassava brown streak viruses

Mbewe, Willard; Tairo, Fred; Sseruwagi, Peter; Ndunguru, Joseph; Duffy, Siobain; Mukasa, Settumba B.; Benesi, I. R. M.; Sheat, Samar; Koerbler, M.; Winter, Stephan

doi:10.1186/s12985-017-0790-9

Cited by 13 publications

(14 citation statements)

References 33 publications

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“…However, primers based on HAM1 and CP may provide a very robust tool for general screening of CBSV for breeders, when there is no need to distinguish the strains or variants within CBSV clades. It was observed that HAM1 and CP were the most conserved genes between CBSV clades 1 and 2, in contrast to P1, which was the most variable gene, consistent with the observations of Mbewe et al (2017). The high conservation of HAM1 and CP among isolates of CBSV clades 1 and 2 observed here suggests that both were maintained during speciation within CBSV.…”

Section: Discussionsupporting

confidence: 89%

“…The two clades of CBSV have been previously reported, based on the P1 gene sequences (Mbewe et al ., ) and WGSs (Alicai et al ., ). This study presents molecular evidence that among the 10 gene sequences of CBSV, eight can be used to discriminate the two clades.…”

Section: Discussionmentioning

confidence: 97%

“…It was observed that HAM1 and CP were the most conserved genes between CBSV clades 1 and 2, in contrast to P1 , which was the most variable gene, consistent with the observations of Mbewe et al . (). The high conservation of HAM1 and CP among isolates of CBSV clades 1 and 2 observed here suggests that both were maintained during speciation within CBSV.…”

Section: Discussionmentioning

confidence: 97%

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Analyses of seven new whole genome sequences of cassava brown streak viruses in Mozambique reveals two distinct clades: evidence for new species

et al. 2019

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Cassava brown streak disease (CBSD) caused by Cassava brown streak virus (CBSV) and Uganda cassava brown streak virus (UCBSV) is a major constraint to cassava production in Mozambique. Full genome sequences of CBSD‐associated virus isolates contribute to the understanding of genetic diversity and the development of new diagnostic primers that can be used for early detection of the viruses for sustainable disease management. This study determined seven new whole CBSV genomes from total RNA isolated from cassava leaves with CBSD symptoms collected from Nampula and Zambezia in Mozambique. Phylogenetic analyses of the new genomes with published CBSV and UCBSV sequences in GenBank grouped the CBSV isolates from Mozambique into two distinct clades together with CBSV isolates from Tanzania. Clade 1 and 2 isolates shared low nucleotide (79.1–80.4%) and amino acid (86.5–88.2%) sequence identity. Further, comparisons within the seven new CBSV isolates, and between them and the single published complete CBSV sequence (CBSV_MO_83_FN434436) from Mozambique, revealed nucleotide sequence identities of 79.3–100% and 79.3–98%, respectively, and amino acid identities of 86.7–100% and 86.7–98.8%. In addition, using RDP4, a recombination analysis comprising all CBSV and UCBSV genome sequences from GenBank detect 11 recombination events. Using several comprehensive evolutionary models and statistical programs, it was confirmed that CBSV and UCBSV are distinct virus species, with an additional probable new species (clade 2).

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Section: Discussionsupporting

confidence: 89%

Section: Discussionmentioning

confidence: 97%

Section: Discussionmentioning

confidence: 97%

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Analyses of seven new whole genome sequences of cassava brown streak viruses in Mozambique reveals two distinct clades: evidence for new species

et al. 2019

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“…For convenience, we refer to the first class as the Common Class, since there is no significant divergence among any of the taxa; we refer to the second class as the UCBSV Class, since this class is characterised by the divergence between the CBSV and UCBSV replicates; and we refer to the third class as the CBSV-TZ Class. The reason for this is that the four CBSV replicates that diverge from the remainder in this class are also present in the study of the P1 gene (Mbewe et al, 2017) referred to earlier. These four replicates are found in the third clade which they tentatively labelled CBSV-TZ, and so it seems probable that the phylogenetic signal captured in the third class is related to the divergence of CBSV-TZ from CBSV.…”

Section: Resultsmentioning

confidence: 93%

“…This is not straightforward though, as it has already been shown that these viruses are fast-evolving (CBSV moreso than UCBSV) (Alicai et al, 2016). Mbewe et al (2017) showed that in the gene tree of the P1 gene, a third distinct clade is found in addition to CBSV and UCBSV, which they tentatively labelled Tanzanian CBSV (CBSV-TZ). Critical to winning the fight against CBSD is ongoing research into the evolutionary forces acting on these viruses, at both the molecular level and geographically.…”

Section: Introductionmentioning

confidence: 99%

Characterising Genetic Diversity in Cassava Brown Streak Virus

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Rohrlach²,

Ndunguru

et al. 2018

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Plant viruses represent a significant threat to food security for many 23 global populations. Cassava Brown Streak Virus (CBSV) causes immense damage 24 to cassava crops in Eastern, Central and Southern Africa. The eradication of CBSV 25 is a difficult challenge, as it has been shown to be fast-evolving and it is 26 transmitted by flying insects that are ubiquitous in cassava growing regions. In this 27 paper we demonstrate the ability of two new developments in bioinformatics that 28 can be used to increase our understanding of CBSV and ultimately inform 29 strategies for its combat. We reconstruct the phylogeny of 29 whole-genome virus 30 isolates using the GHOST model. This phylogeny identifies three distinct clades 31 among the viruses and highlights a section of the genomes that is highly influential 32 in their divergence. We also perform Multiple Correspondence Analysis on the 33 alignment which is consistent in recovering the three clades, and offers insight on 34 the significance of the influence of a variety of external variables on the evolution of 35 the viruses. Knowledge and information from this analysis will be used as a base on 36 which to formulate sustainable Cassava Brown Streak Disease (CBSD) 37 management strategies in Africa. 38Introduction 39 It is difficult to overemphasize the importance of agriculture to people living in 40 3 sub-Saharan Africa. The population of sub-Saharan Africa exceeds one billion 41 people, and more than 60% of the population live in rural areas (United Nations, 42 2015). Beyond the obvious benefit of nutrition, agriculture is also the primary 43 source of income for the majority of sub-Saharan African families, and so access to 44 essentials such as health care and education depend indirectly on agriculture. As 45 such, the productivity of the agricultural industry in a given country and year is a 46 key indicator of the health and wellbeing of the population and the economy. 47 One of the major threats to agricultural productivity comes in the form of 48 crop pests and diseases. Of particular significance are the viruses of the genus 49 Ipomovirus. They have the potential to devastate crops, and they infect some of 50 the most economically important, commonly grown food staples across sub-Saharan 51 Africa, such as cassava and sweet potato. Cassava Brown Streak Disease (CBSD) is 52 caused by two closely related Ipomovirus species, Cassava Brown Streak Virus 53 (CBSV) and Ugandan Cassava Brown Streak Virus (UCBSV). CBSD is widespread 54 and causes significant reduction in both the quality and the yield of cassava crops, 55 making it a strong barrier to food security and economic prosperity in the regions 56 in which it is grown. 57 Efforts to combat CBSV and UCBSV are ongoing, but there are many 58 challenges. The viruses are transmitted between plants courtesy of whiteflies 59 4 (Bemesia tabaci ) and other potential vectors (Ateka et al., 2017), so it is critical 60 that infected plants are removed from crops swiftly. This indicates a critical need 61 fo...

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QTL associated with resistance to cassava brown streak and cassava mosaic diseases in a bi-parental cross of two Tanzanian farmer varieties, Namikonga and Albert

et al. 2017

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Key message QTL consistent across seasons were detected for resistance to cassava brown streak disease induced root necrosis and foliar symptoms. The CMD2 locus was detected in an East African landrace, and comprised two QTL.AbstractCassava production in Africa is compromised by cassava brown streak disease (CBSD) and cassava mosaic disease (CMD). To reduce costs and increase the precision of resistance breeding, a QTL study was conducted to identify molecular markers linked to resistance against these diseases. A bi-parental F1 mapping population was developed from a cross between the Tanzanian farmer varieties, Namikonga and Albert. A one-step genetic linkage map comprising 943 SNP markers and 18 linkage groups spanning 1776.2 cM was generated. Phenotypic data from 240 F1 progeny were obtained from two disease hotspots in Tanzania, over two successive seasons, 2013 and 2014. Two consistent QTLs linked to resistance to CBSD-induced root necrosis were identified in Namikonga on chromosomes II (qCBSDRNFc2Nm) and XI (qCBSDRNc11Nm) and a putative QTL on chromosome XVIII (qCBSDRNc18Nm). qCBSDRNFc2Nm was identified at Naliendele in both seasons. The same QTL was also associated with CBSD foliar resistance. qCBSDRNc11Nm was identified at Chambezi in both seasons, and was characterized by three peaks, spanning a distance of 253 kb. Twenty-seven genes were identified within this region including two LRR proteins and a signal recognition particle. In addition, two highly significant CMD resistance QTL (qCMDc12.1A and qCMDc12.2A) were detected in Albert, on chromosome 12. Both qCMDc12.1A and qCMDc12.2A lay within the range of markers reported earlier, defining the CMD2 locus. This is the first time that two loci have been identified within the CMD2 QTL, and in germplasm of apparent East African origin. Additional QTLs with minor effects on CBSD and CMD resistance were also identified.Electronic supplementary materialThe online version of this article (doi:10.1007/s00122-017-2943-z) contains supplementary material, which is available to authorized users.

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Variability in P1 gene redefines phylogenetic relationships among cassava brown streak viruses

Cited by 13 publications

References 33 publications

Analyses of seven new whole genome sequences of cassava brown streak viruses in Mozambique reveals two distinct clades: evidence for new species

Analyses of seven new whole genome sequences of cassava brown streak viruses in Mozambique reveals two distinct clades: evidence for new species

Characterising Genetic Diversity in Cassava Brown Streak Virus

QTL associated with resistance to cassava brown streak and cassava mosaic diseases in a bi-parental cross of two Tanzanian farmer varieties, Namikonga and Albert

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