rKOMICS: an R package for processing mitochondrial minicircle assemblies in population-scale genome projects
Abstract Background The advent of population-scale genome projects has revolutionized our biological understanding of parasitic protozoa. However, while hundreds to thousands of nuclear genomes of parasitic protozoa have been generated and analyzed, information about the diversity, structure and evo...
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| Format: | Article |
| Language: | English |
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BMC
2021-09-01
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| Series: | BMC Bioinformatics |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s12859-021-04384-1 |
| _version_ | 1818885095667269632 |
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| author | Manon Geerts Achim Schnaufer Frederik Van den Broeck |
| author_facet | Manon Geerts Achim Schnaufer Frederik Van den Broeck |
| author_sort | Manon Geerts |
| collection | DOAJ |
| description | Abstract Background The advent of population-scale genome projects has revolutionized our biological understanding of parasitic protozoa. However, while hundreds to thousands of nuclear genomes of parasitic protozoa have been generated and analyzed, information about the diversity, structure and evolution of their mitochondrial genomes remains fragmentary, mainly because of their extraordinary complexity. Indeed, unicellular flagellates of the order Kinetoplastida contain structurally the most complex mitochondrial genome of all eukaryotes, organized as a giant network of homogeneous maxicircles and heterogeneous minicircles. We recently developed KOMICS, an analysis toolkit that automates the assembly and circularization of the mitochondrial genomes of Kinetoplastid parasites. While this tool overcomes the limitation of extracting mitochondrial assemblies from Next-Generation Sequencing datasets, interpreting and visualizing the genetic (dis)similarity within and between samples remains a time-consuming process. Results Here, we present a new analysis toolkit—rKOMICS—to streamline the analyses of minicircle sequence diversity in population-scale genome projects. rKOMICS is a user-friendly R package that has simple installation requirements and that is applicable to all 27 trypanosomatid genera. Once minicircle sequence alignments are generated, rKOMICS allows to examine, summarize and visualize minicircle sequence diversity within and between samples through the analyses of minicircle sequence clusters. We showcase the functionalities of the (r)KOMICS tool suite using a whole-genome sequencing dataset from a recently published study on the history of diversification of the Leishmania braziliensis species complex in Peru. Analyses of population diversity and structure highlighted differences in minicircle sequence richness and composition between Leishmania subspecies, and between subpopulations within subspecies. Conclusion The rKOMICS package establishes a critical framework to manipulate, explore and extract biologically relevant information from mitochondrial minicircle assemblies in tens to hundreds of samples simultaneously and efficiently. This should facilitate research that aims to develop new molecular markers for identifying species-specific minicircles, or to study the ancestry of parasites for complementary insights into their evolutionary history. |
| first_indexed | 2024-12-19T16:00:00Z |
| format | Article |
| id | doaj.art-8ef751dc6a4c491db8803820bfe28099 |
| institution | Directory Open Access Journal |
| issn | 1471-2105 |
| language | English |
| last_indexed | 2024-12-19T16:00:00Z |
| publishDate | 2021-09-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Bioinformatics |
| spelling | doaj.art-8ef751dc6a4c491db8803820bfe280992022-12-21T20:14:57ZengBMCBMC Bioinformatics1471-21052021-09-0122111410.1186/s12859-021-04384-1rKOMICS: an R package for processing mitochondrial minicircle assemblies in population-scale genome projectsManon Geerts0Achim Schnaufer1Frederik Van den Broeck2Department of Biomedical Sciences, Institute of Tropical MedicineInstitute of Immunology and Infection Research, University of EdinburghDepartment of Biomedical Sciences, Institute of Tropical MedicineAbstract Background The advent of population-scale genome projects has revolutionized our biological understanding of parasitic protozoa. However, while hundreds to thousands of nuclear genomes of parasitic protozoa have been generated and analyzed, information about the diversity, structure and evolution of their mitochondrial genomes remains fragmentary, mainly because of their extraordinary complexity. Indeed, unicellular flagellates of the order Kinetoplastida contain structurally the most complex mitochondrial genome of all eukaryotes, organized as a giant network of homogeneous maxicircles and heterogeneous minicircles. We recently developed KOMICS, an analysis toolkit that automates the assembly and circularization of the mitochondrial genomes of Kinetoplastid parasites. While this tool overcomes the limitation of extracting mitochondrial assemblies from Next-Generation Sequencing datasets, interpreting and visualizing the genetic (dis)similarity within and between samples remains a time-consuming process. Results Here, we present a new analysis toolkit—rKOMICS—to streamline the analyses of minicircle sequence diversity in population-scale genome projects. rKOMICS is a user-friendly R package that has simple installation requirements and that is applicable to all 27 trypanosomatid genera. Once minicircle sequence alignments are generated, rKOMICS allows to examine, summarize and visualize minicircle sequence diversity within and between samples through the analyses of minicircle sequence clusters. We showcase the functionalities of the (r)KOMICS tool suite using a whole-genome sequencing dataset from a recently published study on the history of diversification of the Leishmania braziliensis species complex in Peru. Analyses of population diversity and structure highlighted differences in minicircle sequence richness and composition between Leishmania subspecies, and between subpopulations within subspecies. Conclusion The rKOMICS package establishes a critical framework to manipulate, explore and extract biologically relevant information from mitochondrial minicircle assemblies in tens to hundreds of samples simultaneously and efficiently. This should facilitate research that aims to develop new molecular markers for identifying species-specific minicircles, or to study the ancestry of parasites for complementary insights into their evolutionary history.https://doi.org/10.1186/s12859-021-04384-1AssemblyClusteringMinicirclesSequencingKinetoplastLeishmania |
| spellingShingle | Manon Geerts Achim Schnaufer Frederik Van den Broeck rKOMICS: an R package for processing mitochondrial minicircle assemblies in population-scale genome projects BMC Bioinformatics Assembly Clustering Minicircles Sequencing Kinetoplast Leishmania |
| title | rKOMICS: an R package for processing mitochondrial minicircle assemblies in population-scale genome projects |
| title_full | rKOMICS: an R package for processing mitochondrial minicircle assemblies in population-scale genome projects |
| title_fullStr | rKOMICS: an R package for processing mitochondrial minicircle assemblies in population-scale genome projects |
| title_full_unstemmed | rKOMICS: an R package for processing mitochondrial minicircle assemblies in population-scale genome projects |
| title_short | rKOMICS: an R package for processing mitochondrial minicircle assemblies in population-scale genome projects |
| title_sort | rkomics an r package for processing mitochondrial minicircle assemblies in population scale genome projects |
| topic | Assembly Clustering Minicircles Sequencing Kinetoplast Leishmania |
| url | https://doi.org/10.1186/s12859-021-04384-1 |
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