Gene count from target sequence capture places three whole genome duplication events in Hibiscus L. (Malvaceae)
Open Access
- 2 June 2021
- journal article
- research article
- Published by Springer Science and Business Media LLC in BMC Ecology and Evolution
- Vol. 21 (1), 1-13
- https://doi.org/10.1186/s12862-021-01751-7
Abstract
Background: The great diversity in plant genome size and chromosome number is partly due to polyploidization (i.e. genome doubling events). The differences in genome size and chromosome number among diploid plant species can be a window into the intriguing phenomenon of past genome doubling that may be obscured through time by the process of diploidization. The genus Hibiscus L. (Malvaceae) has a wide diversity of chromosome numbers and a complex genomic history. Hibiscus is ideal for exploring past genomic events because although two ancient genome duplication events have been identified, more are likely to be found due to its diversity of chromosome numbers. To reappraise the history of whole-genome duplication events in Hibiscus, we tested three alternative scenarios describing different polyploidization events. Results: Using target sequence capture, we designed a new probe set for Hibiscus and generated 87 orthologous genes from four diploid species. We detected paralogues in > 54% putative single-copy genes. 34 of these genes were selected for testing three different genome duplication scenarios using gene counting. All species of Hibiscus sampled shared one genome duplication with H. syriacus, and one whole genome duplication occurred along the branch leading to H. syriacus. Conclusions: Here, we corroborated the independent genome doubling previously found in the lineage leading to H. syriacus and a shared genome doubling of this lineage and the remainder of Hibiscus. Additionally, we found a previously undiscovered genome duplication shared by the /Pavonia and /Malvaviscus clades (both nested within Hibiscus) with the occurrences of two copies in what were otherwise single-copy genes. Our results highlight the complexity of genomic diversity in some plant groups, which makes orthology assessment and accurate phylogenomic inference difficult.Keywords
Funding Information
- Vetenskapsrådet (2009-5206, 2019-05191)
- Stiftelsen Lars Hiertas Minne
- Kungliga Fysiografiska Sällskapet i Lund
- Helge Ax:son Johnsons Stiftelse
- Lundgrenska
- Stiftelsen för Strategisk Forskning (FFL15-0196)
- Royal Botanical Gardens, Kew
This publication has 77 references indexed in Scilit:
- CD-HIT: accelerated for clustering the next-generation sequencing dataBioinformatics, 2012
- Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence dataBioinformatics, 2012
- Haplotype phasing: existing methods and new developmentsNature Reviews Genetics, 2011
- Differentiation of the maize subgenomes by genome dominance and both ancient and ongoing gene lossProceedings of the National Academy of Sciences of the United States of America, 2011
- The frequency of polyploid speciation in vascular plantsProceedings of the National Academy of Sciences of the United States of America, 2009
- The Sequence Alignment/Map format and SAMtoolsBioinformatics, 2009
- Fast and accurate short read alignment with Burrows–Wheeler transformBioinformatics, 2009
- Plants with double genomes might have had a better chance to survive the Cretaceous–Tertiary extinction eventProceedings of the National Academy of Sciences of the United States of America, 2009
- The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phylaNature, 2007
- Legume genome evolution viewed through the Medicago truncatula and Lotus japonicus genomesProceedings of the National Academy of Sciences of the United States of America, 2006