Tick genomics through a Nanopore: a low-cost approach for tick genomics
Abstract Background The assembly of large and complex genomes can be costly since it typically requires the utilization of multiple sequencing technologies and access to high-performance computing, while creating a dependency on external service providers. The aim of this study was to independently...
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| Language: | English |
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BMC
2025-07-01
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| Series: | BMC Genomics |
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| Online Access: | https://doi.org/10.1186/s12864-025-11733-4 |
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| author | Christina Meiring Monique Eygelaar Josephus Fourie Michel Labuschagne |
| author_facet | Christina Meiring Monique Eygelaar Josephus Fourie Michel Labuschagne |
| author_sort | Christina Meiring |
| collection | DOAJ |
| description | Abstract Background The assembly of large and complex genomes can be costly since it typically requires the utilization of multiple sequencing technologies and access to high-performance computing, while creating a dependency on external service providers. The aim of this study was to independently generate draft genomes for the cattle ticks Rhipicephalus microplus and R. appendiculatus using Oxford Nanopore sequencing technology. Results Exclusively, Oxford Nanopore sequence data were assembled with Shasta and finalized on the Amazon Web Services cloud platform, capitalizing on the availability of up to 90% discounted Spot instances. The assembled and polished R. microplus and R. appendiculatus genomes from our study were comparable to published tick genomes where multiple sequencing technologies and costly bioinformatic resources were utilized that are not readily accessible to low-resource environments. We predicted 52,412 genes for R. appendiculatus, with 31,747 of them being functionally annotated. The R. microplus annotation consisted of 60,935 predicted genes, with 32,263 being functionally annotated in the final file. The sequence data were also used to assemble and annotate genetically distinct Coxiella-like endosymbiont genomes for each tick species. The results indicated that each of the endosymbionts exhibited genome reductions. The Nanopore Q20 + library kit and flow cell were used to sequence the > 80% AT-rich mitochondrial DNA of both tick species. The sequencing generated accurate mitochondrial genomes, encountering imperfect base calling only in homopolymer regions exceeding 10 bases. Conclusion This study presents an alternative approach for smaller laboratories with limited budgets to enter the field and participate in genomics without capital intensive investments, allowing for capacity building in a field normally exclusively accessible through collaboration and large funding opportunities. |
| format | Article |
| id | doaj-art-c101302f5dea461b8a855fb41e4a541e |
| institution | Kabale University |
| issn | 1471-2164 |
| language | English |
| publishDate | 2025-07-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj-art-c101302f5dea461b8a855fb41e4a541e2025-08-20T03:45:19ZengBMCBMC Genomics1471-21642025-07-0126112110.1186/s12864-025-11733-4Tick genomics through a Nanopore: a low-cost approach for tick genomicsChristina Meiring0Monique Eygelaar1Josephus Fourie2Michel Labuschagne3Clinglobal, B03/04, The Tamarin Commercial HubClinglobal, B03/04, The Tamarin Commercial HubClinvet International Pty (Ltd)Clinglobal, B03/04, The Tamarin Commercial HubAbstract Background The assembly of large and complex genomes can be costly since it typically requires the utilization of multiple sequencing technologies and access to high-performance computing, while creating a dependency on external service providers. The aim of this study was to independently generate draft genomes for the cattle ticks Rhipicephalus microplus and R. appendiculatus using Oxford Nanopore sequencing technology. Results Exclusively, Oxford Nanopore sequence data were assembled with Shasta and finalized on the Amazon Web Services cloud platform, capitalizing on the availability of up to 90% discounted Spot instances. The assembled and polished R. microplus and R. appendiculatus genomes from our study were comparable to published tick genomes where multiple sequencing technologies and costly bioinformatic resources were utilized that are not readily accessible to low-resource environments. We predicted 52,412 genes for R. appendiculatus, with 31,747 of them being functionally annotated. The R. microplus annotation consisted of 60,935 predicted genes, with 32,263 being functionally annotated in the final file. The sequence data were also used to assemble and annotate genetically distinct Coxiella-like endosymbiont genomes for each tick species. The results indicated that each of the endosymbionts exhibited genome reductions. The Nanopore Q20 + library kit and flow cell were used to sequence the > 80% AT-rich mitochondrial DNA of both tick species. The sequencing generated accurate mitochondrial genomes, encountering imperfect base calling only in homopolymer regions exceeding 10 bases. Conclusion This study presents an alternative approach for smaller laboratories with limited budgets to enter the field and participate in genomics without capital intensive investments, allowing for capacity building in a field normally exclusively accessible through collaboration and large funding opportunities.https://doi.org/10.1186/s12864-025-11733-4Genome assemblyLong readsNanoporeCloud computing, tick genomeDe novo |
| spellingShingle | Christina Meiring Monique Eygelaar Josephus Fourie Michel Labuschagne Tick genomics through a Nanopore: a low-cost approach for tick genomics BMC Genomics Genome assembly Long reads Nanopore Cloud computing, tick genome De novo |
| title | Tick genomics through a Nanopore: a low-cost approach for tick genomics |
| title_full | Tick genomics through a Nanopore: a low-cost approach for tick genomics |
| title_fullStr | Tick genomics through a Nanopore: a low-cost approach for tick genomics |
| title_full_unstemmed | Tick genomics through a Nanopore: a low-cost approach for tick genomics |
| title_short | Tick genomics through a Nanopore: a low-cost approach for tick genomics |
| title_sort | tick genomics through a nanopore a low cost approach for tick genomics |
| topic | Genome assembly Long reads Nanopore Cloud computing, tick genome De novo |
| url | https://doi.org/10.1186/s12864-025-11733-4 |
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