Analysis of local genome rearrangement improves resolution of ancestral genomic maps in plants.
Ancestral genome reconstruction
Eudicot phylogeny
Local genome rearrangement
comparative genomics
Journal
BMC genomics
ISSN: 1471-2164
Titre abrégé: BMC Genomics
Pays: England
ID NLM: 100965258
Informations de publication
Date de publication:
16 Apr 2020
16 Apr 2020
Historique:
entrez:
18
4
2020
pubmed:
18
4
2020
medline:
14
1
2021
Statut:
epublish
Résumé
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. 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. 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.
Sections du résumé
BACKGROUND
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
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
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.
Identifiants
pubmed: 32299356
doi: 10.1186/s12864-020-6609-x
pii: 10.1186/s12864-020-6609-x
pmc: PMC7160886
doi:
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
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