A New Chromosome-level Genome Assembly and Annotation of

Overview

Journal bioRxiv

Date 2024 Feb 26

PMID 38405792

Authors

Lasya R Penumarthi

Rodrigo P Baptista

Megan S Beaudry

Travis C Glenn

Jessica C Kissinger

Affiliations

Soon will be listed here.

Abstract

spp. are medically and scientifically relevant protozoan parasites that cause severe diarrheal illness in infants and immunosuppressed populations as well as animals. Although most human infections are caused by and , there are several other human-infecting species including , which is commonly observed in developing countries. Here, we polished and annotated a long-read genome sequence assembly for TU1867, a species which infects birds and humans. The genome sequence was generated using a combination of whole genome amplification (WGA) and long-read Oxford Nanopore Technologies sequencing. The assembly was then polished with Illumina data. The chromosome-level genome assembly is 9.2 Mbp with a contig N50 of 1.1 Mb. Annotation revealed 3,923 protein-coding genes. A BUSCO analysis indicates a completeness of 96.6% (n=446), including 430 (96.4%) single-copy and 1 (0.224%) duplicated apicomplexan conserved gene(s). The new genome assembly is nearly gap-free and provides a valuable new resource for the community and future studies on evolution and host-specificity.

References

Schattner P, Brooks A, Lowe T . The tRNAscan-SE, snoscan and snoGPS web servers for the detection of tRNAs and snoRNAs. Nucleic Acids Res. 2005; 33(Web Server issue):W686-9. PMC: 1160127. DOI: 10.1093/nar/gki366. View

Fayer R . Taxonomy and species delimitation in Cryptosporidium. Exp Parasitol. 2009; 124(1):90-7. DOI: 10.1016/j.exppara.2009.03.005. View

Girma M, Teshome W, Petros B, Endeshaw T . Cryptosporidiosis and Isosporiasis among HIV-positive individuals in south Ethiopia: a cross sectional study. BMC Infect Dis. 2014; 14:100. PMC: 3936862. DOI: 10.1186/1471-2334-14-100. View

Chen C, Chen H, Zhang Y, Thomas H, Frank M, He Y . TBtools: An Integrative Toolkit Developed for Interactive Analyses of Big Biological Data. Mol Plant. 2020; 13(8):1194-1202. DOI: 10.1016/j.molp.2020.06.009. View

Putignani L, Tait A, Smith H, Horner D, Tovar J, Tetley L . Characterization of a mitochondrion-like organelle in Cryptosporidium parvum. Parasitology. 2004; 129(Pt 1):1-18. DOI: 10.1017/s003118200400527x. View

Kotloff K, Nataro J, Blackwelder W, Nasrin D, Farag T, Panchalingam S . Burden and aetiology of diarrhoeal disease in infants and young children in developing countries (the Global Enteric Multicenter Study, GEMS): a prospective, case-control study. Lancet. 2013; 382(9888):209-22. DOI: 10.1016/S0140-6736(13)60844-2. View

Kearse M, Moir R, Wilson A, Stones-Havas S, Cheung M, Sturrock S . Geneious Basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics. 2012; 28(12):1647-9. PMC: 3371832. DOI: 10.1093/bioinformatics/bts199. View

Astashyn A, Tvedte E, Sweeney D, Sapojnikov V, Bouk N, Joukov V . Rapid and sensitive detection of genome contamination at scale with FCS-GX. Genome Biol. 2024; 25(1):60. PMC: 10898089. DOI: 10.1186/s13059-024-03198-7. View

Slavin D . Cryptosporidium meleagridis (sp. nov.). J Comp Pathol. 1955; 65(3):262-6. DOI: 10.1016/s0368-1742(55)80025-2. View

10.

Conesa A, Gotz S, Garcia-Gomez J, Terol J, Talon M, Robles M . Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics. 2005; 21(18):3674-6. DOI: 10.1093/bioinformatics/bti610. View

11.

Gremme G, Steinbiss S, Kurtz S . GenomeTools: a comprehensive software library for efficient processing of structured genome annotations. IEEE/ACM Trans Comput Biol Bioinform. 2013; 10(3):645-56. DOI: 10.1109/TCBB.2013.68. View

12.

Gilbert I, Vinayak S, Striepen B, Manjunatha U, Khalil I, Van Voorhis W . Safe and effective treatments are needed for cryptosporidiosis, a truly neglected tropical disease. BMJ Glob Health. 2023; 8(8). PMC: 10407372. DOI: 10.1136/bmjgh-2023-012540. View

13.

Lee E, Helt G, Reese J, Munoz-Torres M, Childers C, Buels R . Web Apollo: a web-based genomic annotation editing platform. Genome Biol. 2013; 14(8):R93. PMC: 4053811. DOI: 10.1186/gb-2013-14-8-r93. View

14.

Emms D, Kelly S . OrthoFinder: solving fundamental biases in whole genome comparisons dramatically improves orthogroup inference accuracy. Genome Biol. 2015; 16:157. PMC: 4531804. DOI: 10.1186/s13059-015-0721-2. View

15.

Hulsen T, Huynen M, de Vlieg J, Groenen P . Benchmarking ortholog identification methods using functional genomics data. Genome Biol. 2006; 7(4):R31. PMC: 1557999. DOI: 10.1186/gb-2006-7-4-r31. View

16.

Akiyoshi D, Dilo J, Pearson C, Chapman S, Tumwine J, Tzipori S . Characterization of Cryptosporidium meleagridis of human origin passaged through different host species. Infect Immun. 2003; 71(4):1828-32. PMC: 152090. DOI: 10.1128/IAI.71.4.1828-1832.2003. View

17.

Sun J, Lu F, Luo Y, Bie L, Xu L, Wang Y . OrthoVenn3: an integrated platform for exploring and visualizing orthologous data across genomes. Nucleic Acids Res. 2023; 51(W1):W397-W403. PMC: 10320085. DOI: 10.1093/nar/gkad313. View

18.

Baptista R, Li Y, Sateriale A, Sanders M, Brooks K, Tracey A . Long-read assembly and comparative evidence-based reanalysis of genome sequences reveal expanded transporter repertoire and duplication of entire chromosome ends including subtelomeric regions. Genome Res. 2021; 32(1):203-213. PMC: 8744675. DOI: 10.1101/gr.275325.121. View

19.

Li H, Durbin R . Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics. 2009; 25(14):1754-60. PMC: 2705234. DOI: 10.1093/bioinformatics/btp324. View

20.

Darling A, Mau B, Perna N . progressiveMauve: multiple genome alignment with gene gain, loss and rearrangement. PLoS One. 2010; 5(6):e11147. PMC: 2892488. DOI: 10.1371/journal.pone.0011147. View