Genetic diversity and spatial patterns of distribution of Citrus greening disease and its vectors in East Africa

Abstract

Citrus spp is an important cash crop supporting millions of households in East Africa. However, the crop faces challenges of infestation by pests and diseases that lead to substantial economic loss. Citrus greening disease is the most destructive disease on citrus worldwide. The disease is caused by a phloem-limited, bacteria of the “Candidatus” Liberibacter species. The Asian citrus greening also known as Huanglongbing (HLB), is associated with the pathogen “Candidatus Liberibacter asiaticus” (CLas) which is transmitted by the Asian citrus psyllid (Diaphorina citri Kuwayama). The African citrus greening disease (ACG) associated with “Candidatus Liberibacter africanus” (CLaf) is transmitted by the African citrus triozid (Trioza erytreae del Guercio). Trioza erytreae is widespread in Africa and has been reported in 21 countries in Africa while D. citri has been reported in Asia and the Americas with recent invasions into Kenya and Tanzania. Currently, management of the diseases rely on the control of the psyllid vectors. Furthermore, targeted control measures against the vectors are dependent on the knowledge of its biology and genetic diversity. Therefore, the objectives of this study were to i) To identify the Liberibacters associated with citrus greening disease in Eastern Africa, ii) determine current and predicted regional and global climate suitability of Liberibacter species associated with Huanglongbing, iii) unravel the genetic diversity of the greening disease vectors using microsatellite markers and mitochondrial genome analysis and iv) assess the microbiome diversity and genes for resistance to antibiotics within populations of D. citri. Field surveys were conducted in Ethiopia, Kenya and Uganda to assess the spatial distribution of the Liberibacters and vectors in the region. Quantitative PCR and Sanger sequencing were used to identify and characterise the Liberibacters. Future distribution of CLas in Africa and CLaf globally was predicted using an ensemble modelling approach. The genetic diversity of D. citri was assessed by analysing the complete mitochondrial genome of the African populations as well as assessing the simple sequence repeats within the genome of the psyllid. This provided the population structure and the possible route of invasion of D. citri into Africa. Finally, the bacterial microbiome diversity of the D. citri populations was assessed. Our findings showed that CLas was more widespread in Ethiopia than previously reported, CLas was detected in Kenya for the first time and D. citri was detected in Ethiopia for the first time. Furthermore, we found CLas in field populations of T. erytreae. The predictive modelling showed that most citrus producing countries in Africa are highly suitable for the establishment of CLas. The assessment of the genetic diversity revealed D. citri from Kenya and Tanzania had a close genetic relationship with D. citri from China while D. citri from Ethiopia had a close relationship with D. citri from the USA. Thus, two separate introduction events for D. citri into Africa was concluded. Finally, the microbiome analysis also showed that D. citri from Kenya and Tanzania had a similar microbiome composition to the D. citri from China.