Phylogeography of Diaphorina citri (Hemiptera: Liviidae) and its primary endosymbiont, 'Candidatus Carsonella ruddii': an evolutionary approach to host-endosymbiont interaction

Pan-Genome Analysis of Wolbachia, Endosymbiont of Diaphorina citri, Reveals Independent Origin in Asia and North America

Wolbachia, a group of Gram-negative symbiotic bacteria, infects nematodes and a wide range of arthropods. Diaphorina citri Kuwayama, the vector of Candidatus Liberibacter asiaticus (CLas) that causes citrus greening disease, is naturally infected with Wolbachia (wDi). However, the interaction between wDi and D. citri remains poorly understood. In this study, we performed a pan-genome analysis using 65 wDi genomes to gain a comprehensive understanding of wDi. Based on average nucleotide identity (ANI) analysis, we classified the wDi strains into Asia and North America strains. The ANI analysis, principal coordinates analysis (PCoA), and phylogenetic tree analysis supported that the D. citri in Florida did not originate from China. Furthermore, we found that a significant number of core genes were associated with metabolic pathways. Pathways such as thiamine metabolism, type I secretion system, biotin transport, and phospholipid transport were highly conserved across all analyzed wDi genomes. The variation analysis between Asia and North America wDi showed that there were 39,625 single-nucleotide polymorphisms (SNPs), 2153 indels, 10 inversions, 29 translocations, 65 duplications, 10 SV-based insertions, and 4 SV-based deletions. The SV-based insertions and deletions involved genes encoding transposase, phage tail tube protein, ankyrin repeat (ANK) protein, and group II intron-encoded protein. Pan-genome analysis of wDi contributes to our understanding of the geographical population of wDi, the origin of hosts of D. citri, and the interaction between wDi and its host, thus facilitating the development of strategies to control the insects and huanglongbing (HLB).

Comparative Genomics Reveals Three Genetic Groups of the Whitefly Obligate Endosymbiont Candidatus Portiera aleyrodidarum

Maternally inherited obligate endosymbionts codiverge with their invertebrate hosts and reflect their host's evolutionary history. Whiteflies (Hemiptera: Aleyrodidae) harbor one obligate endosymbiont, Candidatus Portiera aleyrodidarum (hereafter Portiera). Portiera was anciently acquired by whitefly and has been coevolving with its host ever since. Uncovering the divergence of endosymbionts provides a fundamental basis for inspecting the coevolutionary processes between the bacteria and their hosts. To illustrate the divergence of Portiera lineages across different whitefly species, we sequenced the Portiera genome from Aleyrodes shizuokensis and conducted a comparative analysis on the basic features and gene evolution with bacterial genomes from five whitefly genera, namely Aleurodicus, Aleyrodes, Bemisia, Pealius, and Trialeurodes. The results indicated that Portiera from Bemisia possessed significantly larger genomes, fewer coding sequences (CDSs), and a lower coding density. Their gene arrangement differed notably from those of other genera. The phylogeny of the nine Portiera lineages resembled that of their hosts. Moreover, the lineages were classified into three distinct genetic groups based on the genetic distance, one from Aleurodicus (Aleurodicinae), one from Bemisia (Aleyrodinae), and another from Aleyrodes, Pealius, and Trialeurrodes (Aleyrodinae). Synonymous and nonsynonymous rate analyses, parity rule 2 plot analyses, neutrality plot analyses, and effective number of codons analyses supported the distinction of the three genetic groups. Our results indicated that Portiera from distant hosts exhibit distinct genomic contents, implying codivergence between hosts and their endosymbionts. This work will enhance our understanding of coevolution between hosts and their endosymbionts.

Report on the first detection of Asian citrus psyllid Diaphorina citri Kuwayama (Hemiptera: Liviidae) in the Republic of Benin, West Africa

The Asian citrus psyllid (ACP), Diaphorina citri, was detected for the first time in the Republic of Benin, West Africa. The ACP is a known vector of Candidatus Liberibacter asiaticus (CLas), the putative causal agent of the devastating Huanglongbing (HLB; citrus greening disease). During visual surveys, ACP was only observed on residential citrus trees in southern Benin, but not in residential areas or commercial groves in the central and northern parts of the country. Its identity was confirmed morphologically and molecularly via DNA barcoding with published primers. Analysis of the obtained sequences showed that the ACP recorded in Benin clustered with the ones previously reported from Nigeria, suggesting a common origin of both populations. The ACP samples from Benin also carried Ca. Carsonella ruddii and Ca. Profftella armatura, two commonly found ACP endosymbionts. However, all the sampled ACP individuals tested negative for Ca. Liberibacter africanus, Ca. Liberibacter americanus, and CLas by quantitative polymerase chain reaction. This is the second report of the ACP in West Africa after Nigeria, the eastern bordering country of the Republic of Benin. Benin has an expanding commercial citrus industry, especially in the southern part of the country. Although the ACP samples tested negative for the HLB associated bacteria, the detection of ACP in the country requires swift actions including area-wide surveys to determine the extent of spread of this pest and the implementation of eradication or control efforts to prevent its establishment and spread of HLB in the country.

Multilocus Genotyping and Intergenic Spacer Single Nucleotide Polymorphisms of Amylostereum areolatum (Russulales: Amylostereacea) Symbionts of Native and Non-Native Sirex Species

Sirex noctilio along with its mutualistic fungal symbiont, Amylostereum areolatum (a white rot fungus), is an invasive pest that causes excessive damage to Pinus plantations in Northeast China. In 2015, S. noctilio were found to attack Pinus sylvestris var. mongolica, and often share larval habitat with the native woodwasp, S. nitobei. The objective of this study was to determine the possible origin(s) of the introduced pest complex in China and analyse the genetic diversity between A. areolatum isolated from invasive S. noctilio, native S. nitobei and other woodwasps collected from Europe (native range) and other countries. Phylogenetic analyses were performed using the intergenic spacer (IGS) dataset and the combined 4-locus dataset (the internal transcribed spacer region (ITS), translation elongation factor alpha 1 (tef1), DNA-directed ribosomal polymerase II (RPB2), and mitochondrial small subunit (mtSSU)) of three Amylostereum taxa. The multilocus genotyping of nuclear ribosomal regions and protein coding genes revealed at least three distinct multilocus genotypes (MLGs) of the fungus associated with invasive S. noctilio populations in Northeast China, which may have come from North America or Europe. The IGS region of A. areolatum carried by S. noctilio from China was designated type B1D2. Our results showed a lack of fidelity (the paradigm of obligate fidelity to a single fungus per wasp species) between woodwasp hosts and A. areolatum. We found that the native S. nitobei predominantly carried A. areolatum IGS-D2, but a low percentage of females instead carried A. areolatum IGS-B1D2 (MLG A13), which was presumably due to horizontal transmission from S. noctilio, during the sequential use of the same wood for larval development. The precise identification of the A. areolatum genotypes provides valuable insight into co-evolution between Siricidae and their symbionts, as well as understanding of the geographical origin and history of both Sirex species and their associated fungi.

The first complete mitochondrial genome sequence of Cacopsylla citrisuga (Yang & Li), a new insect vector of Huanglongbing in Yunnan Province, China

Cacopsylla citrisuga (Yang & Li) is an important pest-threatening Citrus and Poncirus plants (Rutaceae) and a newly identified insect vector of citrus Huanglongbing. The complete mitochondrial genome of C. citrisuga was 14,906 bp in length, with 37 genes, including 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), two ribosomal RNA genes (rRNAs). The phylogenetic trees inferred from Bayesian inference and maximum likelihood analyses confirmed C. citrisuga as a member of the genus Cacopsylla. Our phylogenetic analyses suggested that the Cacopsylla is paraphyletic, and confirmed C. citrisuga as a member of clade-I under Cacopsylla. The complete mitochondrial genome of C. citrisuga will provide important information for the phylogeny and evolution analysis of Cacopsylla.

Co-haplotyping symbiont and host to unravel invasion pathways of the exotic pest Halyomorpha halys in Italy

The brown marmorated stink bug Halyomorpha halys (Stål) is a globally invasive species that harbours the primary bacterial symbiont ‘Candidatus Pantoea carbekii’. In this work, P. carbekii was used as another genetic marker to investigate the biodiversity and biogeographical patterns of this important pest, in native and newly invaded areas, especially in Italy. The correlation between the genetic structure of the symbiont and that of its host was studied through the analyses of one bacterial and one host marker, the putative pseudogene ΔybgF and the mitochondrial gene COI, respectively. As a result, five new P. carbekii haplotypes were identified, and an association pattern between host-symbiont haplotypes was observed. Host species showed higher haplotype diversity than symbiont, which can be expected in a long term host-symbiont association. Populations from the north-eastern Italy showed the highest values of genetic diversity for both markers, highlighting that this particular Italian area could be the result of multiple ongoing introductions. Moreover, some of the symbiont-host haplotypes observed were shared only by populations from north-eastern Italy and native areas, especially Japan, suggesting further introductions from this native country to Italy. Overall, our findings improve the understanding of the potential origin of multiple accidental introductions of H. halys in Italy.

First report of the occurrence of Asian citrus psyllid Diaphorina citri (Hemiptera: Liviidae), an invasive species in Nigeria, West Africa

The Asian citrus psyllid (ACP; Diaphorina citri) is the vector of Candidatus Liberibacter asiaticus (CLas) that is associated with the devastating Huanglongbing (HLB; citrus greening disease). This pest of Asian origin has spread into the Americas and more recently into a few countries in East Africa. During recent surveys, suspect ACP adults and nymphs were recorded for the first time infesting citrus trees in southwest Nigeria. Morphological identification and DNA barcoding confirmed the samples to be D. citri. Analysis of the obtained sequences revealed that the ACP recorded in Nigeria clustered with other taxa in the previously identified B1 clade that consists of populations from different continents. The presence of the endosymbionts Ca. Carsonella ruddii and Ca. Profftella armatura in ACP from Nigeria was also confirmed by PCR and Sanger sequencing. The ACP individuals were assayed for the presence of CLaf, CLam and CLas by qPCR, but none of the insects tested positive for any of the Liberibacters. The prolific nature of ACP and the tropical climate prevailing in the citrus-producing areas of Nigeria and other West African countries may favor its rapid spread and population increase, thus posing a grave threat to the sustainability of citriculture in these countries.

Predicting the potential distribution of the Asian citrus psyllid, Diaphorina citri (Kuwayama), in China using the MaxEnt model

Background

Citrus huanglongbing (HLB) is a destructive disease of citrus and a major threat to the citrus industry around the world. This disease accounts for substantial economic losses in China every year. Diaphorina citri Kuwayama is one of the major vectors by which citrus HLB is spread under natural conditions in China. Research is needed to identify the geographic distribution of D. citri and its major areas of occurrence and to formulate measures for early warning, monitoring, and control of this pest and citrus HLB.

Methods

In this study, the ecological niche modelling software MaxEnt (maximum entropy model) was combined with ArcGIS (a geographic information system) to predict the potential geographic distribution of D. citri in China. Key environmental factors and the appropriate ranges of their values were also investigated.

Results

Our results show that the training data provided a good forecast (AUC_mean = 0.988). The highly suitable areas for D. citri in China are mainly concentrated to the south of the Yangtze River, and the total area is 139.83 × 10⁴ km². The area of the moderately suitable areas is 27.71 × 10⁴ km², with a narrower distribution than that of the highly suitable area. The important environmental factors affecting the distribution of D. citri were min temperature of coldest month, mean temperature of coldest quarter, precipitation of wettest quarter, mean temperature of warmest quarter, precipitation of warmest quarter, max temperature of warmest month, and temperature seasonality. These results provide a valuable theoretical basis for risk assessments and control of D. citri.

Discussion

The predicted results showed that there were highly suitable areas for D. citri in Chongqing, Hubei, Anhui, and Jiangsu. Therefore, the possibility exists for the further spread of D. citri in China in the future. Extreme temperature variables, especially the min temperature of the coldest month, play an important role in the distribution of D. citri and are most closely related to the distribution of D. citri.

Diaphorina citri (Hemiptera: Psylloidea) in China: Two Invasion Routes and Three Transmission Paths

Diaphorina citri Kuwayama (Hemiptera: Liviidae) is one of the most common pests impacting citrus orchards in southern China. Samples of D. citri were collected in southern China in order to systematically explore the genetic architecture of the species. Mitochondrial cytochrome b (Cytb) and cytochrome coxidase subunit I (COI) were amplified by polymerase chain reaction (PCR) which allowed highlighting low haplotype and nucleotide diversities among the population. Two clades could be observed in the haplotype network. Moreover, Bayesian and maximum parsimony phylogenetic trees were constructed based on the sequences of Cytb and COI. Here, we report on the significant genetic variation of the species when comparing southwestern China with other regions of southern China (southern and southeastern). This analysis also suggested that the genetic structure of D. citri in China originates may from long-term climate fluctuations concomitant with recent disturbances resulting from human activity. Combined with previous data, the present work indicates that D. citri potentially entered China through two distinct invasion routes and spread within the country via three transmission paths.