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ksrates: positioning whole-genome duplications relative to speciation events in KS distributions
[article]
2021
bioRxiv
pre-print
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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)
2021
Genome Biology and Evolution
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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]
2021
bioRxiv
pre-print
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2022; you can also visit the original URL.
The file type is application/pdf.
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
2022
Horticulture Research
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The file type is application/pdf.
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
2022
Frontiers in Plant Science
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The file type is application/pdf.
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