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ksrates: positioning whole-genome duplications relative to speciation events in KS distributions [article]

Cecilia Sensalari, Steven Maere, Rolf Lohaus
2021 bioRxiv   pre-print
AbstractSummaryWe present ksrates, a user-friendly command-line tool to position ancient whole-genome duplication (WGD) events with respect to speciation events in a phylogeny by comparing paralog and  ...  ortholog KS distributions derived from genomic or transcriptomic sequences, while adjusting for substitution rate differences among the lineages involved.Availability and implementationksrates is implemented  ...  Funding Research in the lab of S.M. is supported by VIB and Ghent University.  ... 
doi:10.1101/2021.02.28.433234 fatcat:3d6ky4d7lnbz3fsktlhnd5cz44

Chromosome level genome assembly and annotation of highly invasive Japanese stiltgrass (Microstegium vimineum)

Dhanushya Ramachandran, Cynthia D Huebner, Mark Daly, Jasmine Haimovitz, Thomas Swale, Craig F Barrett, Adam Eyre-Walker
2021 Genome Biology and Evolution  
We find corroborating evidence from Ks plots for a stiltgrass-specific duplication event, distinct from the more ancient grass-specific duplication event.  ...  The majority of LTR-retrotransposons are derived from a significant expansion in the past 1-2 million years, suggesting the presence of relatively young LTR-retrotransposon lineages.  ...  Acknowledgments Funding was provided by National Science Foundation Award OIA-1920858 and a Dovetail Genomics Tree of Life Grant to C.F.B.  ... 
doi:10.1093/gbe/evab238 pmid:34718556 pmcid:PMC8598173 fatcat:krquedzom5fdjl67qgeg5lswiu

Chromosome level genome assembly and annotation of highly invasive Japanese stiltgrass (Microstegium vimineum) [article]

Dhanushya Ramachandran, Cynthia D Huebner, Mark Daly, Jasmine Haimovitz, Thomas Swale, Craig F Barrett
2021 bioRxiv   pre-print
We find corroborating evidence from Ks plots for a stiltgrass-specific duplication event, distinct from the more ancient grass-specific duplication event.  ...  The majority of LTR-retrotransposons are derived from a significant expansion in the past 1-2 million years, suggesting the presence of relatively young LTR-retrotransposon lineages.  ...  Acknowledgments Funding was provided by National Science Foundation Award OIA-1920858 and a Dovetail Genomics Tree of Life Grant to CFB.  ... 
doi:10.1101/2021.09.16.460655 fatcat:zillpikycnclra2qnosccfrkbi

The genome of Hibiscus hamabo reveals its adaptation to saline and waterlogged habitat

Zhiquan Wang, Jia-Yu Xue, Shuai-Ya Hu, Fengjiao Zhang, Ranran Yu, Dijun Chen, Yves Van de Peer, Jiafu Jiang, Aiping Song, Longjie Ni, Jianfeng Hua, Zhiguo Lu (+3 others)
2022 Horticulture Research  
Our analyses suggested that H. hamabo has undergone two recent successive polyploidy events, a whole-genome duplication followed by a whole-genome triplication, resulting in an unusually large gene number  ...  In roots, genes that regulate ion channels involved in biosynthetic and metabolic processes responded quickly to adjust the ion concentration and provide metabolic products to protect root cells, whereas  ...  WGD (whole-genome duplication) event (E).  ... 
doi:10.1093/hr/uhac067 pmid:35480957 pmcid:PMC9039499 fatcat:acsxwb34pvf4do3vt4cuo6vwym

Phylotranscriptomics Illuminates the Placement of Whole Genome Duplications and Gene Retention in Ferns

Jessie A. Pelosi, Emily H. Kim, W. Brad Barbazuk, Emily B. Sessa
2022 Frontiers in Plant Science  
across the fern tree, the placement of whole genome duplications (WGDs), and gene retention patterns following WGDs.  ...  to stimuli, and certain organelles over-represented in paralogs while processes involved in transport, organelles derived from endosymbiotic events, and signaling were under-represented.  ...  their computing resources; Amanda Grusz for her help to identify species in Figure 1 ; and the Sessa and Barbazuk labs for insightful discussions.  ... 
doi:10.3389/fpls.2022.882441 pmid:35909764 pmcid:PMC9330400 fatcat:ic53tt2hp5hwfhv73za7c64h64