Biology subjects

Brockington, S.

Publications and source records attributed to Brockington, S..

3 recordsLinked to original sources

bioRxiv2022

Evolutionary blocks to anthocyanin accumulation and the loss of an anthocyanin carrier protein in betalain-pigmented Caryophyllales

{square} The order Caryophyllales exhibits complex pigment evolution, with mutual exclusion of anthocyanin and betalain pigments. Given recent evidence for multiple shifts to betalain pigmentation, we re-evaluated potential mechanisms underpinning the exclusion of anthocyanins from betalain-pigmented lineages. {square}We examined the evolution of the flavonoid pathway using transcriptomic and genomic datasets covering 309 species in 31 families. Orthologs and paralogs of known flavonoid synthesis genes were identified by sequence similarity, with gene duplication and gene loss inferred by phylogenetic and syntenic analysis. Relative transcript abundances were assessed to reveal broad-scale gene expression changes between betalain- and anthocyanin-pigmented lineages. {square}Most flavonoid genes are retained and transcribed in betalain-pigmented lineages, and many also show evidence of extensive gene duplication within betalain-pigmented lineages. However, expression of several flavonoid genes is reduced in betalain-pigmented lineages, especially the late-stage genes dihydroflavonol 4-reductase (DFR) and anthocyanidin synthase (ANS). Notably flavonoid 3',5'-hydroxylase (F3'5'H) homologs have been repeatedly lost in belatain-pigmented lineages, and Anthocyanin9 (AN9) homologs are undetectable in any betalain-pigmented lineages. {square}Down-regulation of ANS and DFR homolog expression (limiting synthesis) and reiterative loss of AN9 homologs (limiting transport), coincident with multiple shifts to betalain pigmentation, are likely crucial the loss of anthocyanins in betalain-pigmented Caryophyllales.

evolutionary biology↗

bioRxiv2019

Next generation sequencing to investigate genomic diversity in Caryophyllales

Caryophyllales are a highly diverse and large order of plants with a global distribution. While some species are important crops like Beta vulgaris, many others can survive under extreme conditions. This order is well known for the complex pigment evolution, because the pigments anthocyanins and betalains occur with mutual exclusion in species of the Caryophyllales. Here we report about genome assemblies of Kewa caespitosa (Kewaceae), Macarthuria australis (Macarthuriaceae), and Pharnaceum exiguum (Molluginaceae) which are representing different taxonomic groups in the Caryophyllales. The availability of these assemblies enhances molecular investigation of these species e.g. with respect to certain genes of interest.

genomics↗

bioRxiv2017

Improved Transcriptome Sampling Pinpoints 26 Paleopolyploidy Events In Caryophyllales, Including Two Paleo-Allopolyploidy Events

O_LIStudies of the macroevolutionary legacy of paleopolyploidy are limited by an incomplete sampling of these events across the tree of life. To better locate and understand these events, we need comprehensive taxonomic sampling as well as homology inference methods that accurately reconstruct the frequency and location of gene duplications.\nC_LIO_LIWe assembled a dataset of transcriptomes and genomes from 169 species in Caryophyllales, of which 43 were newly generated for this study, representing one of the densest sampled genomic-scale datasets yet available. We carried out phylogenomic analyses using a modified phylome strategy to reconstruct the species tree. We mapped phylogenetic distribution of paleopolyploidy events by both tree-based and distance-based methods, and explicitly tested scenarios for paleo-allopolyploidy.\nC_LIO_LIWe identified twenty-six paleopolyploidy events distributed throughout Caryophyllales, and using novel techniques inferred two to be paleo-allopolyploidy.\nC_LIO_LIThrough dense phylogenomic sampling, we show the propensity of paleo-polyploidy in the clade Caryophyllales. We also provide the first method for utilizing transcriptome data to detect paleo-allopolyploidy, which is important as it may have different macro-evolutionary implications compared to paleo-autopolyploidy.\nC_LI

evolutionary biology↗