This work revisits a publication by Bean Our comparative analyses, with structural modelling, implicate numerous residues additional to those identified by Bean Multiple In summary, we were unable to replicate the
The evolution of To address this, we functionally characterised 23 distinct We find that low In the context of an updated organismal phylogeny and newly inferred pigment reconstructions, we argue that repeated convergent acquisition of elevated
- NSF-PAR ID:
- 10456853
- Publisher / Repository:
- Wiley-Blackwell
- Date Published:
- Journal Name:
- New Phytologist
- Volume:
- 227
- Issue:
- 3
- ISSN:
- 0028-646X
- Page Range / eLocation ID:
- p. 914-929
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
More Like this
-
Summary et al. (2018) that reports seven amino acid substitutions are essential for the evolution ofl ‐DOPA 4,5‐dioxygenase (DODA) activity in Caryophyllales. In this study, we explore several concerns which led us to replicate the analyses of Beanet al. (2018).et al. (2018), with many of these additional residues occurring around the active site of BvDODAα1. We therefore replicated the analyses of Beanet al. (2018) to re‐observe the effect of their original seven residue substitutions in a BvDODAα2 background, that is the BvDODAα2‐mut3 variant.in vivo assays, in bothSaccharomyces cerevisiae andNicotiana benthamiana , did not result in visible DODA activity in BvDODAα2‐mut3, with betalain production always 10‐fold below BvDODAα1.In vitro assays also revealed substantial differences in both catalytic activity and pH optima between BvDODAα1, BvDODAα2 and BvDODAα2‐mut3 proteins, explaining their differing performancein vivo .in vivo analyses of Beanet al. (2018 ), and our quantitativein vivo andin vitro analyses suggest a minimal effect of these seven residues in altering catalytic activity of BvDODAα2. We conclude that the evolutionary pathway to high DODA activity is substantially more complex than implied by Beanet al. (2018 ). -
Summary Plants mount coordinated immune responses to defend themselves against pathogens. However, the cellular components required for plant immunity are not fully understood. The jasmonate‐mimicking coronatine (
COR ) toxin produced byPseudomonas syringae pv.tomato (Pst )DC 3000 functions to overcome plant immunity. We previously isolated eight Arabidopsis (scord ) mutants that exhibit increased susceptibility to aCOR ‐deficient mutant ofPst DC 3000. Among them, thescord6 mutant exhibits defects both in stomatal closure response and in restricting bacterial multiplication inside the apoplast. However, the identity of remained elusive.SCORD 6In this study, we aim to identify the
gene.SCORD 6We identified
via next‐generation sequencing and found it to beSCORD 6 (MURUS 1 ), which is involved in the biosynthesis ofMUR 1GDP ‐l ‐fucose.Discovery of
asSCORD 6 led to a series of experiments that revealed a multi‐faceted role ofMUR 1l ‐fucose biosynthesis in stomatal and apoplastic defenses as well as in pattern‐triggered immunity and effector‐triggered immunity, including glycosylation of pattern‐recognition receptors. Furthermore, compromised stomatal and/or apoplastic defenses were observed in mutants of several fucosyltransferases with specific substrates (e.g.O ‐glycan,N ‐glycan or theDELLA transcriptional repressors). Collectively, these results uncover a novel and broad role ofl ‐fucose and protein fucosylation in plant immunity. -
Summary The tree of life is highly reticulate, with the history of population divergence emerging from populations of gene phylogenies that reflect histories of introgression, lineage sorting and divergence. In this study, we investigate global patterns of oak diversity and test the hypothesis that there are regions of the oak genome that are broadly informative about phylogeny.
We utilize fossil data and restriction‐site associated
DNA sequencing (RAD ‐seq) for 632 individuals representing nearly 250Quercus species to infer a time‐calibrated phylogeny of the world's oaks. We use a reversible‐jump Markov chain Monte Carlo method to reconstruct shifts in lineage diversification rates, accounting for among‐clade sampling biases. We then map the > 20 000RAD ‐seq loci back to an annotated oak genome and investigate genomic distribution of introgression and phylogenetic support across the phylogeny.Oak lineages have diversified among geographic regions, followed by ecological divergence within regions, in the Americas and Eurasia. Roughly 60% of oak diversity traces back to four clades that experienced increases in net diversification, probably in response to climatic transitions or ecological opportunity.
The strong support for the phylogeny contrasts with high genomic heterogeneity in phylogenetic signal and introgression. Oaks are phylogenomic mosaics, and their diversity may in fact depend on the gene flow that shapes the oak genome.
-
Summary In this study, we investigate the genetic mechanisms responsible for the loss of anthocyanins in betalain‐pigmented Caryophyllales, considering our hypothesis of multiple transitions to betalain pigmentation.
Utilizing transcriptomic and genomic datasets across 357 species and 31 families, we scrutinize 18 flavonoid pathway genes and six regulatory genes spanning four transitions to betalain pigmentation. We examined evidence for hypotheses of wholesale gene loss, modified gene function, altered gene expression, and degeneration of the MBW (MYB‐bHLH‐WD40) trasnscription factor complex, within betalain‐pigmented lineages.
Our analyses reveal that most flavonoid synthesis genes remain conserved in betalain‐pigmented lineages, with the notable exception of
TT19 orthologs, essential for the final step in anthocyanidin synthesis, which appear to have been repeatedly and entirely lost. Additional late‐stage flavonoid pathway genes upstream ofTT19 also manifest strikingly reduced expression in betalain‐pigmented species. Additionally, we find repeated loss and alteration in the MBW transcription complex essential for canonical anthocyanin synthesis.Consequently, the loss and exclusion of anthocyanins in betalain‐pigmented species appear to be orchestrated through several mechanisms: loss of a key enzyme, downregulation of synthesis genes, and degeneration of regulatory complexes. These changes have occurred iteratively in Caryophyllales, often coinciding with evolutionary transitions to betalain pigmentation.
-
Abstract Major habitat transitions, such as those from marine to freshwater habitats or from aquatic to terrestrial habitats, have occurred infrequently in animal evolution and may represent a barrier to diversification. Identifying genomic events associated with these transitions can help us better understand mechanisms that allow animals to cross these barriers and diversify in new habitats. Study of the
Capitella telata andHelobdella robusta genomes allows examination of one such habitat transition (marine to freshwater) in Annelida. Initial examination of these genomes indicated that the freshwater leechH. robusta contains many more copies (12) of the sodium–potassium pump alpha‐subunit (Na+/K+‐ATP ase) gene than does the marine polychaeteC. telata (2). The sodium–potassium pump plays a key role in maintenance of cellular ionic balance and osmoregulation, and Na+/K+‐ATP ase duplications may have helped annelids invade and diversify in freshwater habitats. To assess whether the timing of Na+/K+‐ATP ase duplications coincided with the marine‐to‐freshwater transition in Clitellata, we used transcriptomic data from 18 annelid taxa, along with the two genomes, to infer a species phylogeny and identified Na+/K+‐ATP ase gene transcripts in order to infer the timing of gene duplication events using tree‐based methods. The inferred timing of Na+/K+‐ATP ase duplication events is consistent with the timing of the initial marine‐to‐freshwater transition early in the history of clitellate annelids, supporting the hypothesis that gene duplications may have played a role in the annelid diversification into freshwater habitats.