Synteny and Collinearity in Plant Genomes

By Haibao Tang, John E. Bowers, Xiyin Wang, R. Ming, Maqsudul Alam, Andrew H. Paterson. Science, 2008

1,390 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/9eef3dc9644989e805ead9f99694b9a0e1560ea1

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Citations in the corpus

JBrowse 2: a modular genome browser with views of synteny and structural variation (2022, neutral): “These views can display data from Synteny Tracks, which themselves can load data from formats including MUMmer [22], minimap2 [21], MashMap [23], UCSC chain files [26], and MCScan [24].”
The genome of the domesticated apple (Malus × domestica Borkh.) (2010, background): “This provides further evidence for a paleohexaploid state shared by most eudicot”
Polyploidy and angiosperm diversification. (2009, background): “Such alignments have also revealed patterns of differential gene loss following genome duplication, differential gene retention associated with evolution of some morphological complexity, and unexpectedly large variation among taxa in DNA substitution rates ( Tang et al., 2008 ).”
The genome of Theobroma cacao (2011, background): “cacao genome paleo-history Angiosperms have been shown to evolve through rounds of paleo-polyploid”
The tomato genome sequence provides insights into fleshy fruit evolution (2012, positive): “These genes, which have been preserved in paleo-duplicated locations for more than 100 Myr 10,11 are more constrained than ‘average’ genes and are enriched for transcription factors and genes otherwise related to gene regulation (Supplementary Tables 3-4).”
JCVI: A versatile toolkit for comparative genomics analysis (2024, methodology): “Most notable features include the “ compara ” module for comparative genomics analysis, offering tools for synteny block reconstruction [20], gene loss cataloging [21], quota ‐ based synteny alignment [22], pedigree visualization [23], and K s calculations and visualizations, among others.”
Genome sequence of the cultivated cotton Gossypium arboreum (2014, positive): “Intact LTRs were predicted using LTR_STRUC 47 Windows-based software, and solo LTRs were predicted on the basis of comparison with intact ancestor LTRs. Single-copy gene families were used to construct the phylogenetic tree, and syntenic blocks were identified by MCscan 48 .”
Unraveling ancient hexaploidy through multiply-aligned angiosperm gene maps. (2008, background): “2007), uncovering one-to-one best matching regions during pairwise genome comparisons, are relatively straightforward in vertebrates yet difficult in angiosperms because of additional challenges that are more prominent in angiosperm genomes (Tang et al. 2008).”
Unfurling Fern Biology in the Genomics Age (2010, background): “Ancient polyploidy, or paleopolyploidy, is now recognized as a major force in the evolution of flowering plants (Blanc and Wolfe 2004, Cui et al. 2006, Barker et al. 2008, Tang et al. 2008), but its full role in fern genome evolution remains unresolved.”
The genome of the pear (Pyrus bretschneideri Rehd.) (2013, methodology): “MCscan (Tang et al. 2008) was used to identify collinearity blocks using paralog gene pairs, which were then identified by BLASTP (Altschul et al.”