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http://dx.doi.org/10.4014/mbl.1912.12001

Comparative Genomics Study of Candidatus Carsonella Ruddii; an Endosymbiont of Economically Important Psyllids  

Mondal, Shakhinur Islam (Genetic Engineering and Biotechnology Department, Shahjalal University of Science and Technology)
Akter, Elma (Genetic Engineering and Biotechnology Department, Shahjalal University of Science and Technology)
Akter, Arzuba (Biochemistry and Molecular Biology Department, Shahjalal University of Science and Technology)
Khan, Md Tahsin (Genetic Engineering and Biotechnology Department, Shahjalal University of Science and Technology)
Jewel, Nurnabi Azad (Genetic Engineering and Biotechnology Department, Shahjalal University of Science and Technology)
Publication Information
Microbiology and Biotechnology Letters / v.48, no.3, 2020 , pp. 373-382 More about this Journal
Abstract
Candidatus Carsonella ruddii is an endosymbiont that resides in specialized cells within the body cavity of plant sap-feeding insects called psyllids. The establishment of symbiotic associations is considered one of the key factors for the evolutionary success of psyllids, as it may have helped them adapt to imbalanced food resources like plant sap. Although C. ruddii is defined as a psyllid primary symbiont, the genes for some essential amino acid pathways are absent. Complete genome sequences of several C. ruddii strains have been published. However, in-depth intra-species comparison of C. ruddii strains has not yet been done. This study therefore aimed to perform a comparative genome analysis of six C. ruddii strains, allowing the interrogation of phylogenetic group, functional category of genes, and biosynthetic pathway analysis. Accordingly, overall genome size, number of genes, and GC content of C. ruddii strains were reduced. Phylogenetic analysis based on the whole genome proteomes of 30 related bacterial strains revealed that the six C. ruddii strains form a cluster in same clade. Biosynthetic pathway analysis showed that complete sets of genes for biosynthesis of essential amino acids, except tryptophan, are absent in six C. ruddii strains. All genes for tryptophan biosynthesis are present in three C. ruddii strains (BC, BT, and YCCR). It is likely that the host may depend on a secondary symbiont to complement its deficient diet. Overall, it is therefore possible that C. ruddii is being driven to extinction and replacement by new symbionts.
Keywords
Carsonella; endosymbiont; comparative genomics; pathway analysis;
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1 Gray SM, Banerjee N. 1999. Mechanisms of arthropod transmission of plant and animal viruses. Microbiol. Mol. Biol. Rev. MMBR. 63: 128-148.   DOI
2 Blackman RL, Eastop VF. 1984. Aphids on the World's Crops: An Identification and Information Guide, pp. 476. 1st Ed. John Wiley Sons, London.
3 Sylvester ES. 1985. Multiple acquisition of viruses and vectordependent prokaryotes: consequences on transmission. Ann. Rev. Entomol. 30: 71-88.   DOI
4 Lo N, Bandi C, Watanabe H, Nalepa C, Beninati T. 2003. Evidence for cocladogenesis between diverse dictyopteran lineages and their intracellular endosymbionts. Mol. Biol. Evol. 20: 907-913.   DOI
5 Conord C, Despres L, Vallier A, Balmand S, Miquel C, Zundel S, et al. 2008. Long-term evolutionary stability of bacterial endosymbiosis in curculionoidea: additional evidence of symbiont replacement in the dryophthoridae family. Mol. Biol. Evol. 25: 859-868.   DOI
6 Chaumot A, Da Lage JL, Maestro O, Martin D, Iwema T, Brunet F, et al. 2012. Molecular adaptation and resilience of the insect's nuclear receptor USP. BMC Evol. Biol. 12: 199.   DOI
7 Moran NA, Bennett GM. 2014. The tiniest tiny genomes. Ann. Rev. Microbiol. 68: 195-215.   DOI
8 Baumann P. 2005. Biology bacteriocyte-associated endosymbionts of plant sap-sucking insects. Ann. Rev. Microbiol. 59: 155-189.   DOI
9 Gil R, Silva FJ, Pereto J, Moya A. 2004. Determination of the core of a minimal bacterial gene set. Microbiol. Mol. Biol. Rev. 68: 518.   DOI
10 Perez-Brocal V, Gil R, Ramos S, Lamelas A, Postigo M, Michelena JM, et al. 2006. A small microbial genome: the end of a long symbiotic relationship? Science 314: 312-313.   DOI
11 Thao ML, Clark MA, Baumann L, Brennan EB, Moran NA, Baumann P. 2000. Secondary endosymbionts of psyllids have been acquired multiple times. Curr. Microbiol. 41: 300-304.   DOI
12 Brown JK, Rehman M, Rogan D, Martin RR, Idris AM. 2010. First report of "Candidatus Liberibacter psyllaurous" (synonym "Ca. L. solanacearum") associated with 'Tomato Vein-Greening' and 'Tomato Psyllid Yellows' diseases in commercial greenhouses in Arizona. Plant Dis. 94: 376.
13 Munyaneza J, Buchman J, Upton J, Goolsby J, Crosslin J, Bester G, et al. 2008. Impact of different potato psyllid populations on zebra chip disease incidence, severity, and potato yield. Subtropical Plant Sci. 60: 27-37.
14 Dan H, Ikeda N, Fujikami M, Nakabachi A. 2017. Behavior of bacteriome symbionts during transovarial transmission and development of the Asian citrus psyllid. PLoS One. 12: e0189779.   DOI
15 Baumann P, Moran NA, Baumann L. 2006. Bacteriocyte-Associated Endosymbionts of Insects, pp. 403-438. In Dworkin M, Falkow S, Rosenberg E, Schleifer K-HandStackebrandt E (eds.), Ed. Springer New York, New York, NY.
16 Baumann P, Baumann L, Lai CY, Rouhbakhsh D, Moran NA, Clark MA. 1995. Genetics, physiology, and evolutionary relationships of the genus Buchnera: intracellular symbionts of aphids. Ann. Rev. Microbiol. 49: 55-94.   DOI
17 Engel P, Moran NA. 2013. The gut microbiota of insects - diversity in structure and function. FEMS Microbiol. Rev. 37: 699-735.   DOI
18 Thao ML, Moran NA, Abbot P, Brennan EB, Burckhardt DH, Baumann P. 2000. Cospeciation of psyllids and their primary prokaryotic endosymbionts. Appl. Environ. Microbiol. 66: 2898-2905.   DOI
19 Sacchi L, Genchi M, Clementi E, Negri I, Alma A, Ohler S, et al. 2010. Bacteriocyte-like cells harbour Wolbachia in the ovary of Drosophila melanogaster (Insecta, Diptera) and Zyginidia pullula (Insecta, Hemiptera). Tissue Cell 42: 328-333.   DOI
20 Sloan DB, Moran NA. 2012. Genome reduction and co-evolution between the primary and secondary bacterial symbionts of psyllids. Mol. Biol. Evol. 29: 3781-3792.   DOI
21 Tamames J, Gil R, Latorre A, Pereto J, Silva FJ, Moya A. 2007. The frontier between cell and organelle: genome analysis of Candidatus Carsonella ruddii. BMC Evol. Biol. 7: 181.   DOI
22 Alikhan NF, Petty NK, Ben Zakour NL, Beatson SA. 2011. BLAST Ring Image Generator (BRIG): simple prokaryote genome comparisons. BMC Genomics 12: 402.   DOI
23 Zuo G, Hao B. 2015. CVTree3 web server for whole-genome-based and alignment-free prokaryotic phylogeny and taxonomy. Genomics Proteomics Bioinformatics 13: 321-331.   DOI
24 Ogata H, Goto S, Sato K, Fujibuchi W, Bono H, Kanehisa M. 1999. KEGG: Kyoto encyclopedia of genes and genomes. Nucleic Acids Res. 27: 29-34.   DOI
25 Kanehisa M, Sato Y, Morishima K. 2016. BlastKOALA and Ghost-KOALA: KEGG Tools for functional characterization of genome and metagenome sequences. J. Mol. Biol. 428: 726-731.   DOI
26 Xu L, Dong Z, Fang L, Luo Y, Wei Z, Guo H, et al. 2019. Ortho-Venn2: a web server for whole-genome comparison and annotation of orthologous clusters across multiple species. Nucleic Acids Res. 47: W52-w58.   DOI
27 Li L, Stoeckert CJ, Jr., Roos DS. 2003. OrthoMCL: identification of ortholog groups for eukaryotic genomes. Genome Res. 13: 2178-2189.   DOI
28 Nakabachi A, Yamashita A, Toh H, Ishikawa H, Dunbar HE, Moran NA, et al. 2006. The 160-kilobase genome of the bacterial endosymbiont Carsonella. Science 314: 267.   DOI
29 Enright AJ, Van Dongen S, Ouzounis CA. 2002. An efficient algorithm for large-scale detection of protein families. Nucleic Acids Res. 30: 1575-1584.   DOI
30 Wu F, Deng X, Liang G, Huang J, Cen Y, Chen J. 2015. Wholegenome sequence of "Candidatus Profftella armatura" from diaphorina citri in Guangdong, China. Genome Announc. 3: e01282-01215.
31 Riley AB, Kim D, Hansen AK. 2017. Genome sequence of "Candidatus Carsonella ruddii" strain BC, a nutritional endosymbiont of bactericera cockerelli. Genome Announc. 5: e00236-17.
32 Katsir L, Zhepu R, Piasezky A, Jiang J, Sela N, Freilich S, et al. 2018. Genome sequence of "Candidatus Carsonella ruddii" strain BT from the psyllid bactericera trigonica. Genome Announc. 6: e01466-01417.
33 Wernegreen JJ. 2005. For better or worse: genomic consequences of intracellular mutualism and parasitism. Curr. Opin. Genet. Dev. 15: 572-583.   DOI
34 Tamas I, Klasson L, Canback B, Naslund AK, Eriksson AS, Wernegreen JJ, et al. 2002. 50 million years of genomic stasis in endosymbiotic bacteria. Science (New York, N.Y.). 296: 2376-2379.   DOI
35 Moran NA, Plague GR. 2004. Genomic changes following host restriction in bacteria. Curr. Opin. Genet. Dev. 14: 627-633.   DOI
36 Audic S, Robert C, Campagna B, Parinello H, Claverie JM, Raoult D, et al. 2007. Genome analysis of Minibacterium massiliensis highlights the convergent evolution of water-living bacteria. PLoS Genet. 3: e138.   DOI
37 Moran NA. 2002. Microbial minimalism: genome reduction in bacterial pathogens. Cell 108: 583-586.   DOI
38 Darby AC, Cho NH, Fuxelius HH, Westberg J, Andersson SG. 2007. Intracellular pathogens go extreme: genome evolution in the Rickettsiales. Trends Genet. 23: 511-520.   DOI
39 Williams KP, Gillespie JJ, Sobral BWS, Nordberg EK, Snyder EE, Shallom JM, et al. 2010. Phylogeny of Gammaproteobacteria. J. Bacteriol. 192: 2305.   DOI