Analysis of local genome rearrangement improves resolution of ancestral genomic maps in plants
Abstract Background Computationally inferred ancestral genomes play an important role in many areas of genome research. We present an improved workflow for the reconstruction from highly diverged genomes such as those of plants. Results Our work relies on an established workflow in the reconstructio...
| Main Authors: | , , , |
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| Format: | Article |
| Language: | English |
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BMC
2020-04-01
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| Series: | BMC Genomics |
| Subjects: | |
| Online Access: | http://link.springer.com/article/10.1186/s12864-020-6609-x |
| _version_ | 1818847243400118272 |
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| author | Diego P. Rubert Fábio V. Martinez Jens Stoye Daniel Doerr |
| author_facet | Diego P. Rubert Fábio V. Martinez Jens Stoye Daniel Doerr |
| author_sort | Diego P. Rubert |
| collection | DOAJ |
| description | Abstract Background Computationally inferred ancestral genomes play an important role in many areas of genome research. We present an improved workflow for the reconstruction from highly diverged genomes such as those of plants. Results Our work relies on an established workflow in the reconstruction of ancestral plants, but improves several steps of this process. Instead of using gene annotations for inferring the genome content of the ancestral sequence, we identify genomic markers through a process called genome segmentation. This enables us to reconstruct the ancestral genome from hundreds of thousands of markers rather than the tens of thousands of annotated genes. We also introduce the concept of local genome rearrangement, through which we refine syntenic blocks before they are used in the reconstruction of contiguous ancestral regions. With the enhanced workflow at hand, we reconstruct the ancestral genome of eudicots, a major sub-clade of flowering plants, using whole genome sequences of five modern plants. Conclusions Our reconstructed genome is highly detailed, yet its layout agrees well with that reported in Badouin et al. (2017). Using local genome rearrangement, not only the marker-based, but also the gene-based reconstruction of the eudicot ancestor exhibited increased genome content, evidencing the power of this novel concept. |
| first_indexed | 2024-12-19T05:58:21Z |
| format | Article |
| id | doaj.art-dd5ae9b9c0b3433ba95766c24c1d6aa6 |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-12-19T05:58:21Z |
| publishDate | 2020-04-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj.art-dd5ae9b9c0b3433ba95766c24c1d6aa62022-12-21T20:33:24ZengBMCBMC Genomics1471-21642020-04-0121S211110.1186/s12864-020-6609-xAnalysis of local genome rearrangement improves resolution of ancestral genomic maps in plantsDiego P. Rubert0Fábio V. Martinez1Jens Stoye2Daniel Doerr3Faculdade de Computação – FACOM, Universidade Federal de Mato Grosso do Sul – UFMSFaculdade de Computação – FACOM, Universidade Federal de Mato Grosso do Sul – UFMSFaculty of Technology and Center for Biotechnology (CeBiTec), Bielefeld UniversityFaculty of Technology and Center for Biotechnology (CeBiTec), Bielefeld UniversityAbstract Background Computationally inferred ancestral genomes play an important role in many areas of genome research. We present an improved workflow for the reconstruction from highly diverged genomes such as those of plants. Results Our work relies on an established workflow in the reconstruction of ancestral plants, but improves several steps of this process. Instead of using gene annotations for inferring the genome content of the ancestral sequence, we identify genomic markers through a process called genome segmentation. This enables us to reconstruct the ancestral genome from hundreds of thousands of markers rather than the tens of thousands of annotated genes. We also introduce the concept of local genome rearrangement, through which we refine syntenic blocks before they are used in the reconstruction of contiguous ancestral regions. With the enhanced workflow at hand, we reconstruct the ancestral genome of eudicots, a major sub-clade of flowering plants, using whole genome sequences of five modern plants. Conclusions Our reconstructed genome is highly detailed, yet its layout agrees well with that reported in Badouin et al. (2017). Using local genome rearrangement, not only the marker-based, but also the gene-based reconstruction of the eudicot ancestor exhibited increased genome content, evidencing the power of this novel concept.http://link.springer.com/article/10.1186/s12864-020-6609-xcomparative genomicsAncestral genome reconstructionEudicot phylogenyLocal genome rearrangement |
| spellingShingle | Diego P. Rubert Fábio V. Martinez Jens Stoye Daniel Doerr Analysis of local genome rearrangement improves resolution of ancestral genomic maps in plants BMC Genomics comparative genomics Ancestral genome reconstruction Eudicot phylogeny Local genome rearrangement |
| title | Analysis of local genome rearrangement improves resolution of ancestral genomic maps in plants |
| title_full | Analysis of local genome rearrangement improves resolution of ancestral genomic maps in plants |
| title_fullStr | Analysis of local genome rearrangement improves resolution of ancestral genomic maps in plants |
| title_full_unstemmed | Analysis of local genome rearrangement improves resolution of ancestral genomic maps in plants |
| title_short | Analysis of local genome rearrangement improves resolution of ancestral genomic maps in plants |
| title_sort | analysis of local genome rearrangement improves resolution of ancestral genomic maps in plants |
| topic | comparative genomics Ancestral genome reconstruction Eudicot phylogeny Local genome rearrangement |
| url | http://link.springer.com/article/10.1186/s12864-020-6609-x |
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