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Unraveling ancient hexaploidy through multiply-aligned angiosperm gene maps

H. Tang, X. Wang, J. E. Bowers, R. Ming, M. Alam, A. H. Paterson
2008 Genome Research  
Inferring the number and arrangement of genes in the ancestral angiosperm Top-down multiple alignments mitigate the fragmentation and decay of ancestral gene orders, improving our ability to deduce the  ...  In contrast to estimation of ancestral gene number, inference of ancestral gene order is a much harder problem, and our computationally reconstructed gene order should not be considered as truly "ancestral  ... 
doi:10.1101/gr.080978.108 pmid:18832442 pmcid:PMC2593578 fatcat:2fes7ym4bbfilnbptailwju54y

Ancient eudicot hexaploidy meets ancestral eurosid gene order

Chunfang Zheng, Eric Chen, Victor A Albert, Eric Lyons, David Sankoff
2013 BMC Genomics  
Results: We quantitatively trace the fate of gene triples originating in the hexaploidy across seven core eudicot flowering plants, and fit this to a two-stage model, pre-and post-radiation.  ...  We propose a new protocol for reconstructing ancestral gene order using only gene adjacency data from pairwise genomic analyses, based on repeating MAXIMUM WEIGHT MATCHING at two levels of resolution,  ...  order scrambling due to fractionation, i.e., the loss of duplicate genes from one or two of the three homeologous regions, more or less randomly, cause difficulty for the inference of ancestral gene order  ... 
doi:10.1186/1471-2164-14-s7-s3 pmid:24564362 pmcid:PMC3817805 fatcat:ow4kykqd4vfl7e32mobf4fhcou

Phylogenomic and Microsynteny Analysis Provides Evidence of Genome Arrangements of High-Affinity Nitrate Transporter Gene Families of Plants

Normig M. Zoghbi-Rodríguez, Samuel David Gamboa-Tuz, Alejandro Pereira-Santana, Luis C. Rodríguez-Zapata, Lorenzo Felipe Sánchez-Teyer, Ileana Echevarría-Machado
2021 International Journal of Molecular Sciences  
Our study provides novel information that could be used as guide for functional characterization of these gene families across plant lineages.  ...  In this study, we performed a microsynteny and orthology analysis on the NRT2 and NRT3 genes families across 132 plants (Sensu lato) to decipher their evolutionary history.  ...  Com2NRT2 was the most ancestral and was identified from the basal angiosperm (Figure 8 ).  ... 
doi:10.3390/ijms222313036 pmid:34884876 pmcid:PMC8658032 fatcat:fchp7ffcubbgvphrkixeeak4ea

Decoding Plant and Animal Genome Plasticity from Differential Paleo-Evolutionary Patterns and Processes

Florent Murat, Yves Van de Peer, Jérôme Salse
2012 Genome Biology and Evolution  
ancestor (seven protochromosomes followed by an ancestral 1R), with an n ¼ 21 intermediate (AEK for ancestral eudicot karyotype) common to all eudicots.  ...  on sequence alignment parameters, as well as gene order/orientation maintenance (table 1) .  ... 
doi:10.1093/gbe/evs066 pmid:22833223 pmcid:PMC3516226 fatcat:okmudaejszfofogpbdbbafmguy

Resurrected protein interaction networks reveal the innovation potential of ancient whole genome duplication [article]

Zhicheng Zhang, Heleen Coenen, Philip Ruelens, Rashmi Hazarika, Tareq Al Hindi, Georgianna Oguis, Vera Van Noort, Koen Geuten
2016 bioRxiv   pre-print
A good example is the γ triplication at the origin of core eudicots. Core eudicots comprise about 75% of flowering plants and are characterized by the canalization of reproductive development.  ...  We accurately inferred, resurrected and tested the interactions of ancestral proteins before and after the γ triplication and directly compared these ancestral networks to the networks of Arabidopsis and  ...  hexaploidy through multiply-aligned angiosperm gene maps.  ... 
doi:10.1101/074989 fatcat:wbt6imytgfcxbk3f5bmn6aji3a

Different Gene Families in Arabidopsis thaliana Transposed in Different Epochs and at Different Frequencies throughout the Rosids

M. R. Woodhouse, H. Tang, M. Freeling
2011 The Plant Cell  
Certain types of gene families, such as those encoding most families of transcription factors, maintain their chromosomal syntenic positions throughout angiosperm evolutionary time.  ...  gene families are under different selection pressure than syntenic genes.  ...  hexaploidy event (Wang et al., 2011) .  ... 
doi:10.1105/tpc.111.093567 pmid:22180627 pmcid:PMC3269863 fatcat:pjseyk2f7vha3enltogfgc6nbm

Fractionation Resistance of Duplicate Genes Following Whole Genome Duplication in Plants as a Function of Gene Ontology Category and Expression Level

Eric Chun-Hung Chen, Université D'Ottawa / University Of Ottawa, Université D'Ottawa / University Of Ottawa
2015
We use gene sequence similarity and gene order conservation to construct our gene fam- ilies.  ...  In this thesis we explore the effects of gene function and gene expression on duplicate gene loss and retention.  ...  Ancient eudicot hexaploidy meets ancestral eurosid gene order 37 originating in SynMap or omg!  ... 
doi:10.20381/ruor-4171 fatcat:7haec4347jc77eomz2e6gfp6um

Poplar Genomics: State of the Science

Xiaohan Yang, Udaya C. Kalluri, Stephen P. DiFazio, Stan D. Wullschleger, Timothy J. Tschaplinski, Max Zong-Ming Cheng, Gerald A. Tuskan
2009 Critical reviews in plant sciences  
of ancestral gene sets, as well as clade specific genes and gene expansions.  ...  Their phylogenetic analysis, together with kinetic data, suggest that xyloglucanase activity has evolved as a gain-of-function in an ancestral GH16 XET to meet specific biological requirements during seed  ...  ; a category tool for information about gene families, pathways, GO annotations; and a sequence tool for similarity searches and data downloads.  ... 
doi:10.1080/07352680903241014 fatcat:chdbixf5jzctnldd5xcb66j4s4

Fractionation in the Evolution of Syntenic Homology in Coffea Arabica

Zhe Yu, University, My
2021
Gene loss is the obverse of novel gene acquisition by a genome through a variety of evolutionary processes.  ...  A type of gene loss widespread in the lineages of plant genomes is "fractionation" after whole genome doubling or tripling, where one of a pair or triplet of paralogous genes in parallel syntenic contexts  ...  Chapter 4 Mechanisms of Gene Loss Introduction The alignment of the gene orders of homologous genes in two related genomes, or subgenomes of an (ancient) polyploid, such as that provided by the SynMap  ... 
doi:10.20381/ruor-26754 fatcat:l6iskbfz6jdhdcwvhxzpp6ifky

Effects of adaxial-abaxial signalling on leaf polarity

Julia S. Nowak
2012
Further, I studied the species relationships within the genus Populus in order to establish the ancestral state of leaf type. I determined that bifacial leaves are likely derived within the genus.  ...  YABBY, KANADI, and HD-ZIPIII genes are some of the major contributors to setting proper adaxial-abaxial polarity and I investigated the relationships of these genes by identifying the orthologs in Arabidopsis  ...  At -Arabidopsis, Eg -eucalyptus, Pt -poplar, X -denotes ancient hexaploidy event, * -denote whole genome duplication (WGD), ?  ... 
doi:10.14288/1.0072963 fatcat:yhpq2txgengupiq7r44zd2enbi