Whole-genome Sequencing of Dog-specific Assemblages C and D of from Single and Pooled Cysts Indicates Host-associated Genes

Overview

Journal Microb Genom

Specialties Genetics
Microbiology

Date 2019 Dec 11

PMID 31821130

Citations 13

Authors

Frans N J Kooyman

Jaap A Wagenaar

Aldert Zomer

Affiliations

Soon will be listed here.

Abstract

(syn. or ) infSAects over 280 million people each year and numerous animals. can be subdivided into eight assemblages with different host specificity. Unculturable assemblages have so far resisted genome sequencing efforts. In this study, we isolated single and pooled cysts of assemblages C and D from dog faeces by FACS, and sequenced them using multiple displacement amplification and Illumina paired-end sequencing. The genomes of assemblages C and D were compared with genomes of assemblages A and B from humans and assemblage E from ruminants and pigs. The genomes obtained from the pooled cysts and from the single cysts were considered complete (>99 % marker genes observed) and the allelic sequence heterozygosity (ASH) values of assemblages C and D were 0.89 and 0.74 %, respectively. These ASH values were slightly higher than for assemblage B (>0.43 %) and much higher than for assemblages A and E, which ranged from 0.002 to 0.037 %. The flavohaemoglobin and 4Fe-4S binding domain family encoding genes involved in O and NO detoxification were only present in assemblages A, B and E. Cathepsin B orthologs were found in all genomes. Six clades of cathepsin B orthologs contained one gene of each genome, while in three clades not all assemblages were represented. We conclude that whole-genome sequencing from a single cyst results in complete draft genomes, making the genomes of unculturable assemblages accessible. Observed differences between the genomes of assemblages C and D on one hand and the assemblages A, B and E on the other hand are possibly associated with host specificity.

Citing Articles

Zoonotic Cryptosporidium and Giardia in marsupials-an update.

Barbosa A, Egan S, Feng Y, Xiao L, Balogun S, Ryan U Parasitol Res. 2024; 123(1):107.

PMID: 38253768 PMC: 10803519. DOI: 10.1007/s00436-024-08129-w.

Genomic survey maps differences in the molecular complement of vesicle formation machinery between Giardia intestinalis assemblages.

Pipaliya S, Dacks J, Croxen M PLoS Negl Trop Dis. 2023; 17(12):e0011837.

PMID: 38109380 PMC: 10758263. DOI: 10.1371/journal.pntd.0011837.

and in cats and dogs: What is the real zoonotic risk?.

Barbosa A, Egan S, Feng Y, Xiao L, Ryan U Curr Res Parasitol Vector Borne Dis. 2023; 4:100158.

PMID: 38089689 PMC: 10714218. DOI: 10.1016/j.crpvbd.2023.100158.

Highly contiguous genomes of human clinical isolates of reveal assemblage- and sub-assemblage-specific presence-absence variation in protein-coding genes.

Klotz C, Schmid M, Winter K, Ignatius R, Weisz F, Saghaug C Microb Genom. 2023; 9(3).

PMID: 36976254 PMC: 10132058. DOI: 10.1099/mgen.0.000963.

Role of rodents in the zoonotic transmission of giardiasis.

Li J, Qin H, Li X, Zhang L One Health. 2023; 16:100500.

PMID: 36844973 PMC: 9947413. DOI: 10.1016/j.onehlt.2023.100500.

References

Bhargava A, Cotton J, Dixon B, Gedamu L, Yates R, Buret A . Giardia duodenalis Surface Cysteine Proteases Induce Cleavage of the Intestinal Epithelial Cytoskeletal Protein Villin via Myosin Light Chain Kinase. PLoS One. 2015; 10(9):e0136102. PMC: 4559405. DOI: 10.1371/journal.pone.0136102. View

Jain C, Rodriguez-R L, Phillippy A, Konstantinidis K, Aluru S . High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries. Nat Commun. 2018; 9(1):5114. PMC: 6269478. DOI: 10.1038/s41467-018-07641-9. View

Lasken R . Single-cell genomic sequencing using Multiple Displacement Amplification. Curr Opin Microbiol. 2007; 10(5):510-6. DOI: 10.1016/j.mib.2007.08.005. View

Ankarklev J, Lebbad M, Einarsson E, Franzen O, Ahola H, Troell K . A novel high-resolution multilocus sequence typing of Giardia intestinalis Assemblage A isolates reveals zoonotic transmission, clonal outbreaks and recombination. Infect Genet Evol. 2018; 60:7-16. DOI: 10.1016/j.meegid.2018.02.012. View

Monis P, Andrews R, Mayrhofer G, Ey P . Molecular systematics of the parasitic protozoan Giardia intestinalis. Mol Biol Evol. 1999; 16(9):1135-44. DOI: 10.1093/oxfordjournals.molbev.a026204. View

Emery S, Mirzaei M, Vuong D, Pascovici D, Chick J, Lacey E . Induction of virulence factors in Giardia duodenalis independent of host attachment. Sci Rep. 2016; 6:20765. PMC: 4751611. DOI: 10.1038/srep20765. View

Poxleitner M, Carpenter M, Mancuso J, Wang C, Dawson S, Cande W . Evidence for karyogamy and exchange of genetic material in the binucleate intestinal parasite Giardia intestinalis. Science. 2008; 319(5869):1530-3. DOI: 10.1126/science.1153752. View

Thompson R, Monis P . Giardia--from genome to proteome. Adv Parasitol. 2012; 78:57-95. DOI: 10.1016/B978-0-12-394303-3.00003-7. View

Jerlstrom-Hultqvist J, Ankarklev J, Svard S . Is human giardiasis caused by two different Giardia species?. Gut Microbes. 2011; 1(6):379-82. PMC: 3056102. DOI: 10.4161/gmic.1.6.13608. View

10.

Xu F, Jerlstrom-Hultqvist J, Einarsson E, Astvaldsson A, Svard S, Andersson J . The genome of Spironucleus salmonicida highlights a fish pathogen adapted to fluctuating environments. PLoS Genet. 2014; 10(2):e1004053. PMC: 3916229. DOI: 10.1371/journal.pgen.1004053. View

11.

Bankevich A, Nurk S, Antipov D, Gurevich A, Dvorkin M, Kulikov A . SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol. 2012; 19(5):455-77. PMC: 3342519. DOI: 10.1089/cmb.2012.0021. View

12.

Buchfink B, Xie C, Huson D . Fast and sensitive protein alignment using DIAMOND. Nat Methods. 2014; 12(1):59-60. DOI: 10.1038/nmeth.3176. View

13.

Uiterwijk M, Nijsse R, Kooyman F, Wagenaar J, Mughini-Gras L, Koop G . Comparing four diagnostic tests for Giardia duodenalis in dogs using latent class analysis. Parasit Vectors. 2018; 11(1):439. PMC: 6069568. DOI: 10.1186/s13071-018-3014-2. View

14.

Sprong H, Caccio S, van der Giessen J . Identification of zoonotic genotypes of Giardia duodenalis. PLoS Negl Trop Dis. 2009; 3(12):e558. PMC: 2777335. DOI: 10.1371/journal.pntd.0000558. View

15.

Caccio S, Beck R, Lalle M, Marinculic A, Pozio E . Multilocus genotyping of Giardia duodenalis reveals striking differences between assemblages A and B. Int J Parasitol. 2008; 38(13):1523-31. DOI: 10.1016/j.ijpara.2008.04.008. View

16.

Bernander R, PALM J, Svard S . Genome ploidy in different stages of the Giardia lamblia life cycle. Cell Microbiol. 2001; 3(1):55-62. DOI: 10.1046/j.1462-5822.2001.00094.x. View

17.

Liu J, Maayeh S, Peirasmaki D, Lundstrom-Stadelmann B, Hellman L, Svard S . Secreted Giardia intestinalis cysteine proteases disrupt intestinal epithelial cell junctional complexes and degrade chemokines. Virulence. 2018; 9(1):879-894. PMC: 5955458. DOI: 10.1080/21505594.2018.1451284. View

18.

Troell K, Hallstrom B, Divne A, Alsmark C, Arrighi R, Huss M . Cryptosporidium as a testbed for single cell genome characterization of unicellular eukaryotes. BMC Genomics. 2016; 17:471. PMC: 4917956. DOI: 10.1186/s12864-016-2815-y. View

19.

Ekseth O, Kuiper M, Mironov V . orthAgogue: an agile tool for the rapid prediction of orthology relations. Bioinformatics. 2013; 30(5):734-6. DOI: 10.1093/bioinformatics/btt582. View

20.

Feng Y, Xiao L . Zoonotic potential and molecular epidemiology of Giardia species and giardiasis. Clin Microbiol Rev. 2011; 24(1):110-40. PMC: 3021202. DOI: 10.1128/CMR.00033-10. View