Comparative genome analysis of Phyllosticta citricarpa and Phyllosticta capitalensis, two fungi species that share the same host

Rodrigues, Carolina M.; Takita, Marco Aurélio; Silva, Nicholas Vinícius; Ribeiro-Alves, Marcelo; Machado, Marcos Antônio

doi:10.1186/s12864-019-5911-y

Cited by 20 publications

(11 citation statements)

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“…During preparing this manuscript, we noticed that a paper describing the genomic sequencing of P. citricarpa and P. capitalensis was published (Rodrigues et al, 2019). However, the general features of their genome sequences are of great difference from ours.…”

Section: Genome Assembly and General Featuresmentioning

confidence: 78%

Genomic Sequencing of Phyllosticta citriasiana Provides Insight Into Its Conservation and Diversification With Two Closely Related Phyllosticta Species Associated With Citrus

et al. 2020

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Phyllosticta capitalensis, Phyllosticta citricarpa, and Phyllosticta citriasiana are three very important Phyllosticta species associated with citrus. P. capitalensis is an endophyte fungus of citrus while P. citricarpa can cause black spot of citrus (e.g., oranges and mandarins). P. citriasiana was identified recently which is the causal agent of the pomelo tan spot. Here, we present the ∼34 Mb genome of P. citriasiana. The genome is organized in 92 contigs, encompassing 9202 predicted genes. Comparative genomic analyses with two other Phyllosticta species (P. citricarpa and P. capitalensis) associated with citrus was conducted to understand their evolutionary conservation and diversification. Pair-wise genome alignments revealed that these species are highly syntenic. All species encode similar numbers of CAZymes and secreted proteins. However, the molecular functions of the secretome showed that each species contains some enzymes with distinct activities. The three Phyllosticta species investigated shared a core set of 7261 protein families. P. capitalensis had the largest set of orphan genes (1991), in complete contrast to that of P. citriasiana (364) and P. citricarpa (262). Most of the orphan genes are functionally unknown, but they contain a certain number of species-specific secreted proteins. A total of 23 secondary metabolites biosynthesis clusters were identified in the three Phyllosticta species, 21 of them being highly conserved among these species while the remaining two showed whole cluster gain and loss polymorphisms or gene content polymorphisms. Taken together, our study reveals insights into the genetic mechanisms of host adaptation of three species of Phyllosticta associated with citrus and paves the way to identify effectors that function in infection of citrus plants.

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Section: Genome Assembly and General Featuresmentioning

confidence: 78%

Genomic Sequencing of Phyllosticta citriasiana Provides Insight Into Its Conservation and Diversification With Two Closely Related Phyllosticta Species Associated With Citrus

et al. 2020

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“…Differences in terms of pathogenesis-related proteins have been confirmed after the genome sequencing of the two species, disclosing a higher number of coding sequences in P. citricarpa (15,206 versus 14,797). Such a difference has been interpreted considering the presence of growth and developmental genes involved in the expression of pathogenicity [23].The issue of detection of contaminated material imported from areas where the pathogen is endemic has also prompted investigations concerning the assortment of Phyllosticta spp. able to colonize citrus plants in either symptomatic or latent courses.…”

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confidence: 99%

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confidence: 99%

Endophytic Fungi of Citrus Plants

Nicoletti

2019

Agriculture

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Besides a diffuse research activity on drug discovery and biodiversity carried out in natural contexts, more recently, investigations concerning endophytic fungi have started considering their occurrence in crops based on the major role that these microorganisms have been recognized to play in plant protection and growth promotion. Fruit growing is particularly involved in this new wave, by reason that the pluriannual crop cycle likely implies a higher impact of these symbiotic interactions. Aspects concerning occurrence and effects of endophytic fungi associated with citrus species are revised in the present paper.Agriculture 2019, 9, 247 2 of 13 similar but fast-growing, and producing conidia embedded within a thicker mucoid sheath [4][5][6][7][8]. The latter, characterized as a different species (Phyllosticta capitalensis), are known to be ubiquitous as endophytes in woody plants, having been reported from at least 70 botanical families [6,9,10]. Guignardia endophyllicola, treated as a separate species in a work also emphasizing its widespread endophytic occurrence [11], is at present recognized as a synonym. Differences between the two sister species also concern their metagenetic cycle. In fact, it has been ascertained that P. citricarpa is heterothallic, while P. capitalensis is homothallic [8]. This consolidated taxonomic distinction supports the exclusion from quarantine measures of plant material harbouring P. capitalensis. To this purpose, several rapid PCR assays have been developed [12][13][14][15][16][17][18][19][20]. The applicative use of these assays has enabled to exclude the presence of the pathogen in New Zealand, unlike what was previously assumed [21], and has supported the hypothesis of the possible endophytic occurrence of P. citricarpa in asymptomatic Citrus spp., as pointed out by several investigations (Table 1). Moreover, the two species have been clearly differentiated on account of their enzymatic profiles, with a higher expression of amylases, endoglucanases, and pectinases in P. citricarpa, suggesting a likely involvement of these enzymes in the pathogenic aptitude of the CBS agent [22]. Differences in terms of pathogenesis-related proteins have been confirmed after the genome sequencing of the two species, disclosing a higher number of coding sequences in P. citricarpa (15,206 versus 14,797). Such a difference has been interpreted considering the presence of growth and developmental genes involved in the expression of pathogenicity [23].The issue of detection of contaminated material imported from areas where the pathogen is endemic has also prompted investigations concerning the assortment of Phyllosticta spp. able to colonize citrus plants in either symptomatic or latent courses. Several revisions have been published [17,24], and novel species characterized, which consistently enlarge the citrus-associated consortium within this widespread genus. Particularly, the pathogenic P. citriasiana from south-east Asia [25], P. citrichinaensis from China [26], P. citrimaxima from Thailand...

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“…In that study, we found that the P. citricarpa genomic assembly consisted of 19,143 contigs with the N50 of 3049bp and the P. capitalensis genomic assembly contains 11,080 contigs with the N50 of 4925bp (Rodrigues et al, 2019). This means that their genome sequence was very fragmented and the incompleteness of the genome was also confirmed by their BUSCO analysis (Rodrigues et al, 2019). Thus, comparing with their genomic data, we believe that the data in this study is much better and more reliable.…”

Section: Resultsmentioning

confidence: 94%

Genomic sequencing ofPhyllosticta citriasianaprovide insight into its conservation and diversification with closely relatedPhyllostictaspecies associated with citrus

Wang

Liu

Ruan

et al. 2019

Preprint

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18Phyllosticta citriasiana is the causal agent of the pomelo tan spot. Here, we 19 presented the ~34Mb genome of P. citriasiana. The genome is organized in 92 20 contigs, encompassing 9202 predicted genes. Comparative genomic analyses with 21 other two Phyllosticta species (P. citricarpa and P. capitalensis) associated with citrus 22 was conducted to understand their evolutionary conservation and diversification. Pair-23 wise genome alignments revealed that these species are highly syntenic. All species 24 encode similar numbers of CAZymes and secreted proteins. However, the molecular 25 functions of the secretome showed that each species contains some enzymes with 26 distinct activities. Three Phyllosticta species shared a core set of 7261 protein 27 families. P. capitalensis had the largest set of orphan genes (2040), in complete 28 contrast to that of P. citriasiana (371) and P. citricarpa (262). Most of the orphan 29 genes were functionally unknown, but they contain a certain number of species-30 specific secreted proteins. A total of 23 secondary metabolites (SM) biosynthesis 31 clusters were identified in the three Phyllosticta species, 21 of them are highly 32 conserved among these species while the remaining 2 showed whole cluster gain and 33 loss polymorphisms or gene content polymorphisms. Taken together, our study 34 reveals insights into the genetic mechanisms of host adaptation of Phyllosticta species 35 associated with citrus and paves the way to identify effectors that function in infection 36 of citrus plants.37 38

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Comparative genome analysis of Phyllosticta citricarpa and Phyllosticta capitalensis, two fungi species that share the same host

Cited by 20 publications

References 59 publications

Genomic Sequencing of Phyllosticta citriasiana Provides Insight Into Its Conservation and Diversification With Two Closely Related Phyllosticta Species Associated With Citrus

Genomic Sequencing of Phyllosticta citriasiana Provides Insight Into Its Conservation and Diversification With Two Closely Related Phyllosticta Species Associated With Citrus

Endophytic Fungi of Citrus Plants

Genomic sequencing ofPhyllosticta citriasianaprovide insight into its conservation and diversification with closely relatedPhyllostictaspecies associated with citrus

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