Chromosomal scale assembly reveals localized structural variants in avian caecal coccidian parasite Eimeria tenella
Abstract Eimeria tenella is a major cause of caecal coccidiosis in commercial poultry chickens worldwide. Here, we report chromosomal scale assembly of Eimeria tenella strain APU2, a strain isolated from commercial broiler chickens in the U.S. We obtained 100× sequencing Oxford Nanopore Technology (...
| Main Authors: | , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Nature Portfolio
2023-12-01
|
| Series: | Scientific Reports |
| Online Access: | https://doi.org/10.1038/s41598-023-50117-0 |
| _version_ | 1797377001078652928 |
|---|---|
| author | Subodh K. Srivastava Carolyn Parker Celia N. O’Brien Matthew S. Tucker Peter C. Thompson Benjamin M. Rosenthal Jitender P. Dubey Asis Khan Mark C. Jenkins |
| author_facet | Subodh K. Srivastava Carolyn Parker Celia N. O’Brien Matthew S. Tucker Peter C. Thompson Benjamin M. Rosenthal Jitender P. Dubey Asis Khan Mark C. Jenkins |
| author_sort | Subodh K. Srivastava |
| collection | DOAJ |
| description | Abstract Eimeria tenella is a major cause of caecal coccidiosis in commercial poultry chickens worldwide. Here, we report chromosomal scale assembly of Eimeria tenella strain APU2, a strain isolated from commercial broiler chickens in the U.S. We obtained 100× sequencing Oxford Nanopore Technology (ONT) and more than 800× Coverage of Illumina Next-Seq. We created the assembly using the hybrid approach implemented in MaSuRCA, achieving a contiguous 51.34 Mb chromosomal-scale scaffolding enabling identification of structural variations. The AUGUSTUS pipeline predicted 8060 genes, and BUSCO deemed the genomes 99% complete; 6278 (78%) genes were annotated with Pfam domains, and 1395 genes were assigned GO-terms. Comparing E. tenella strains (APU2, US isolate and Houghton, UK isolate) derived Houghton strain of E. tenella revealed 62,905 high stringency differences, of which 45,322 are single nucleotide polymorphisms (SNPs) (0.088%). The rate of transitions/transversions among the SNPs are 1.63 ts/tv. The strains possess conserved gene order but have profound sequence heterogeneity in a several chromosomal segments (chr 2, 11 and 15). Genic and intergenic variation in defined gene families was evaluated between the two strains to possibly identify sequences under selection. The average genic nucleotide diversity of 2.8 with average 2 kb gene length (0.145%) at genic level. We examined population structure using available E. tenella sequences in NCBI, revealing that the two E. tenella isolates from the U.S. (E. tenella APU2 and Wisconsin, “ERR296879”) share a common maternal inheritance with the E. tenella Houghton. Our chromosomal level assembly promotes insight into Eimeria biology and evolution, hastening drug discovery and vaccine development. |
| first_indexed | 2024-03-08T19:47:42Z |
| format | Article |
| id | doaj.art-c15c1aa0871846a7ae959792e0fd7068 |
| institution | Directory Open Access Journal |
| issn | 2045-2322 |
| language | English |
| last_indexed | 2024-03-08T19:47:42Z |
| publishDate | 2023-12-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Scientific Reports |
| spelling | doaj.art-c15c1aa0871846a7ae959792e0fd70682023-12-24T12:18:25ZengNature PortfolioScientific Reports2045-23222023-12-0113111210.1038/s41598-023-50117-0Chromosomal scale assembly reveals localized structural variants in avian caecal coccidian parasite Eimeria tenellaSubodh K. Srivastava0Carolyn Parker1Celia N. O’Brien2Matthew S. Tucker3Peter C. Thompson4Benjamin M. Rosenthal5Jitender P. Dubey6Asis Khan7Mark C. Jenkins8USDA-ARS Animal Parasitic Diseases Laboratory, Beltsville Agricultural Research CenterUSDA-ARS Animal Parasitic Diseases Laboratory, Beltsville Agricultural Research CenterUSDA-ARS Animal Parasitic Diseases Laboratory, Beltsville Agricultural Research CenterUSDA-ARS Animal Parasitic Diseases Laboratory, Beltsville Agricultural Research CenterUSDA-ARS Animal Parasitic Diseases Laboratory, Beltsville Agricultural Research CenterUSDA-ARS Animal Parasitic Diseases Laboratory, Beltsville Agricultural Research CenterUSDA-ARS Animal Parasitic Diseases Laboratory, Beltsville Agricultural Research CenterUSDA-ARS Animal Parasitic Diseases Laboratory, Beltsville Agricultural Research CenterUSDA-ARS Animal Parasitic Diseases Laboratory, Beltsville Agricultural Research CenterAbstract Eimeria tenella is a major cause of caecal coccidiosis in commercial poultry chickens worldwide. Here, we report chromosomal scale assembly of Eimeria tenella strain APU2, a strain isolated from commercial broiler chickens in the U.S. We obtained 100× sequencing Oxford Nanopore Technology (ONT) and more than 800× Coverage of Illumina Next-Seq. We created the assembly using the hybrid approach implemented in MaSuRCA, achieving a contiguous 51.34 Mb chromosomal-scale scaffolding enabling identification of structural variations. The AUGUSTUS pipeline predicted 8060 genes, and BUSCO deemed the genomes 99% complete; 6278 (78%) genes were annotated with Pfam domains, and 1395 genes were assigned GO-terms. Comparing E. tenella strains (APU2, US isolate and Houghton, UK isolate) derived Houghton strain of E. tenella revealed 62,905 high stringency differences, of which 45,322 are single nucleotide polymorphisms (SNPs) (0.088%). The rate of transitions/transversions among the SNPs are 1.63 ts/tv. The strains possess conserved gene order but have profound sequence heterogeneity in a several chromosomal segments (chr 2, 11 and 15). Genic and intergenic variation in defined gene families was evaluated between the two strains to possibly identify sequences under selection. The average genic nucleotide diversity of 2.8 with average 2 kb gene length (0.145%) at genic level. We examined population structure using available E. tenella sequences in NCBI, revealing that the two E. tenella isolates from the U.S. (E. tenella APU2 and Wisconsin, “ERR296879”) share a common maternal inheritance with the E. tenella Houghton. Our chromosomal level assembly promotes insight into Eimeria biology and evolution, hastening drug discovery and vaccine development.https://doi.org/10.1038/s41598-023-50117-0 |
| spellingShingle | Subodh K. Srivastava Carolyn Parker Celia N. O’Brien Matthew S. Tucker Peter C. Thompson Benjamin M. Rosenthal Jitender P. Dubey Asis Khan Mark C. Jenkins Chromosomal scale assembly reveals localized structural variants in avian caecal coccidian parasite Eimeria tenella Scientific Reports |
| title | Chromosomal scale assembly reveals localized structural variants in avian caecal coccidian parasite Eimeria tenella |
| title_full | Chromosomal scale assembly reveals localized structural variants in avian caecal coccidian parasite Eimeria tenella |
| title_fullStr | Chromosomal scale assembly reveals localized structural variants in avian caecal coccidian parasite Eimeria tenella |
| title_full_unstemmed | Chromosomal scale assembly reveals localized structural variants in avian caecal coccidian parasite Eimeria tenella |
| title_short | Chromosomal scale assembly reveals localized structural variants in avian caecal coccidian parasite Eimeria tenella |
| title_sort | chromosomal scale assembly reveals localized structural variants in avian caecal coccidian parasite eimeria tenella |
| url | https://doi.org/10.1038/s41598-023-50117-0 |
| work_keys_str_mv | AT subodhksrivastava chromosomalscaleassemblyrevealslocalizedstructuralvariantsinaviancaecalcoccidianparasiteeimeriatenella AT carolynparker chromosomalscaleassemblyrevealslocalizedstructuralvariantsinaviancaecalcoccidianparasiteeimeriatenella AT celianobrien chromosomalscaleassemblyrevealslocalizedstructuralvariantsinaviancaecalcoccidianparasiteeimeriatenella AT matthewstucker chromosomalscaleassemblyrevealslocalizedstructuralvariantsinaviancaecalcoccidianparasiteeimeriatenella AT petercthompson chromosomalscaleassemblyrevealslocalizedstructuralvariantsinaviancaecalcoccidianparasiteeimeriatenella AT benjaminmrosenthal chromosomalscaleassemblyrevealslocalizedstructuralvariantsinaviancaecalcoccidianparasiteeimeriatenella AT jitenderpdubey chromosomalscaleassemblyrevealslocalizedstructuralvariantsinaviancaecalcoccidianparasiteeimeriatenella AT asiskhan chromosomalscaleassemblyrevealslocalizedstructuralvariantsinaviancaecalcoccidianparasiteeimeriatenella AT markcjenkins chromosomalscaleassemblyrevealslocalizedstructuralvariantsinaviancaecalcoccidianparasiteeimeriatenella |