Finding and Comparing Syntenic Regions among Arabidopsis and the Outgroups Papaya, Poplar, and Grape: CoGe with Rosids

Lyons, Eric; Pedersen, Brent S.; Kane, Josh; Alam, Maqsudul; Ming, Ray; Tang, Haibao; Wang, Xiyin; Bowers, John E.; Paterson, Andrew D.; Lisch, Damon; Freeling, Michael

doi:10.1104/pp.108.124867

Cited by 375 publications

(306 citation statements)

References 55 publications

(52 reference statements)

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“…In contrast to functional enrichments of WGD duplicates, U. gibba genes filtered out by the blast_to_raw script in the QUOTA-ALIGN package [https://github.com/tanghaibao/quota-alignment (45), included in CoGe SynMap (29,30)] as tandem duplicates in the modern genome (and thus ignored in syntenic dot plot comparison) were enriched for many secondary metabolic functions, including specific functions that could be anticipated for a carnivorous plant (SI Appendix, Datasets S7 and S8). Arabidopsis tandems discovered in the same manner were similarly enriched for secondary metabolic activities, as anticipated based on earlier results (5).…”

Section: Significancementioning

confidence: 99%

Long-read sequencing uncovers the adaptive topography of a carnivorous plant genome

Lan

Renner

Ibarra-Laclette

et al. 2017

Proc. Natl. Acad. Sci. U.S.A.

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Utricularia gibba, the humped bladderwort, is a carnivorous plant that retains a tiny nuclear genome despite at least two rounds of whole genome duplication (WGD) since common ancestry with grapevine and other species. We used a third-generation genome assembly with several complete chromosomes to reconstruct the two most recent lineage-specific ancestral genomes that led to the modern U. gibba genome structure. Patterns of subgenome dominance in the most recent WGD, both architectural and transcriptional, are suggestive of allopolyploidization, which may have generated genomic novelty and led to instantaneous speciation. Syntenic duplicates retained in polyploid blocks are enriched for transcription factor functions, whereas gene copies derived from ongoing tandem duplication events are enriched in metabolic functions potentially important for a carnivorous plant. Among these are tandem arrays of cysteine protease genes with trap-specific expression that evolved within a protein family known to be useful in the digestion of animal prey. Further enriched functions among tandem duplicates (also with trap-enhanced expression) include peptide transport (intercellular movement of broken-down prey proteins), ATPase activities (bladder-trap acidification and transmembrane nutrient transport), hydrolase and chitinase activities (breakdown of prey polysaccharides), and cell-wall dynamic components possibly associated with active bladder movements. Whereas independently polyploid Arabidopsis syntenic gene duplicates are similarly enriched for transcriptional regulatory activities, Arabidopsis tandems are distinct from those of U. gibba, while still metabolic and likely reflecting unique adaptations of that species. Taken together, these findings highlight the special importance of tandem duplications in the adaptive landscapes of a carnivorous plant genome.

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Section: Significancementioning

confidence: 99%

Long-read sequencing uncovers the adaptive topography of a carnivorous plant genome

Lan

Renner

Ibarra-Laclette

et al. 2017

Proc. Natl. Acad. Sci. U.S.A.

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“…Here we report the first genome-wide high-resolution atlas of noncoding regions under selection in crucifers. Because the detection of CNSs is based on the comparison of a large number of closely related species, the sensitivity of this map is higher than that in previous studies based on pairs or sets of more distant species 20,65 or on intragenomic comparisons 22 , resulting in an eight to tenfold increase in the number of constrained regions identified.…”

Section: Discussionmentioning

confidence: 77%

An atlas of over 90,000 conserved noncoding sequences provides insight into crucifer regulatory regions

et al. 2013

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Despite the central importance of noncoding DNA to gene regulation and evolution, understanding of the extent of selection on plant noncoding DNA remains limited compared to that of other organisms. Here we report sequencing of genomes from three Brassicaceae species (Leavenworthia alabamica, Sisymbrium irio and Aethionema arabicum) and their joint analysis with six previously sequenced crucifer genomes. Conservation across orthologous bases suggests that at least 17% of the Arabidopsis thaliana genome is under selection, with nearly one-quarter of the sequence under selection lying outside of coding regions. Much of this sequence can be localized to approximately 90,000 conserved noncoding sequences (CNSs) that show evidence of transcriptional and post-transcriptional regulation. Population genomics analyses of two crucifer species, A. thaliana and Capsella grandiflora, confirm that most of the identified CNSs are evolving under medium to strong purifying selection. Overall, these CNSs highlight both similarities and several key differences between the regulatory DNA of plants and other species.

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“…The g WGD is probably shared by all core eudicots (Bowers et al, 2003;Jaillon et al, 2007;Lyons et al, 2008;Tang et al, 2008;Barker et al, 2009). Considering significant variation in molecular evolutionary rate and lack of precise estimate of nucleotide substitution rate among eudicots, the precise age of the g WGD could not be established.…”

Section: Ages Of Polyploidy Events Within the Brassicaceaementioning

confidence: 99%

Polyploid Evolution of the Brassicaceae during the Cenozoic Era

et al. 2014

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The Brassicaceae (Cruciferae) family, owing to its remarkable species, genetic, and physiological diversity as well as its significant economic potential, has become a model for polyploidy and evolutionary studies. Utilizing extensive transcriptome pyrosequencing of diverse taxa, we established a resolved phylogeny of a subset of crucifer species. We elucidated the frequency, age, and phylogenetic position of polyploidy and lineage separation events that have marked the evolutionary history of the Brassicaceae. Besides the well-known ancient a (47 million years ago [Mya]) and b (124 Mya) paleopolyploidy events, several species were shown to have undergone a further more recent (;7 to 12 Mya) round of genome multiplication. We identified eight whole-genome duplications corresponding to at least five independent neo/mesopolyploidy events. Although the Brassicaceae family evolved from other eudicots at the beginning of the Cenozoic era of the Earth (60 Mya), major diversification occurred only during the Neogene period (0 to 23 Mya). Remarkably, the widespread species divergence, major polyploidy, and lineage separation events during Brassicaceae evolution are clustered in time around epoch transitions characterized by prolonged unstable climatic conditions. The synchronized diversification of Brassicaceae species suggests that polyploid events may have conferred higher adaptability and increased tolerance toward the drastically changing global environment, thus facilitating species radiation.

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Finding and Comparing Syntenic Regions among Arabidopsis and the Outgroups Papaya, Poplar, and Grape: CoGe with Rosids

Cited by 375 publications

References 55 publications

Long-read sequencing uncovers the adaptive topography of a carnivorous plant genome

Long-read sequencing uncovers the adaptive topography of a carnivorous plant genome

An atlas of over 90,000 conserved noncoding sequences provides insight into crucifer regulatory regions

Polyploid Evolution of the Brassicaceae during the Cenozoic Era

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