Horizontal transfer of an adaptive chimeric photoreceptor from bryophytes to ferns

Li, Fay‐Wei; Villarreal, Juan Carlos; Kelly, Steven; Rothfels, Carl J.; Melkonian, Michael; Frangedakis, Eftychios; Ruhsam, Markus; Sigel, Erin M.; Der, Joshua P.; Pittermann, Jarmila; Bürge, Dylan O.; Pokorny, Lisa; Larsson, Anders; Chen, Tao; Weststrand, Stina; Thomas, Philip; Carpenter, Eric J.; Zhang, Yong; Tian, Zhendong; Chen, Li; Yan, Zhixiang; Zhu, Ying; Sun, Xiao; Wang, Jun; Stevenson, Dennis Wm.; Crandall‐Stotler, Barbara; Shaw, A. Jonathan; Deyholos, Michael K.; Soltis, Douglas E.; Graham, Sean W.; Windham, Michael D.; Langdale, Jane A.; Wong, Gane Ka‐Shu; Mathews, Sarah; Pryer, Kathleen M.

doi:10.1073/pnas.1319929111

Cited by 151 publications

(163 citation statements)

References 76 publications

Supporting

Mentioning

157

Contrasting

Order By: Relevance

“…The divergence times between species estimated from introgressed genes are expected to be younger than those estimated from other genes (e.g., Smith & Kronforst 2013; Li et al. 2014; Marcussen et al. 2014; Li et al.…”

Section: Methodsmentioning

confidence: 99%

Introgression and repeated co-option facilitated the recurrent emergence of C₄photosynthesis among close relatives

et al. 2017

View full text Add to dashboard Cite

The origins of novel traits are often studied using species trees and modeling phenotypes as different states of the same character, an approach that cannot always distinguish multiple origins from fewer origins followed by reversals. We address this issue by studying the origins of C4 photosynthesis, an adaptation to warm and dry conditions, in the grass Alloteropsis. We dissect the C4 trait into its components, and show two independent origins of the C4 phenotype via different anatomical modifications, and the use of distinct sets of genes. Further, inference of enzyme adaptation suggests that one of the two groups encompasses two transitions to a full C4 state from a common ancestor with an intermediate phenotype that had some C4 anatomical and biochemical components. Molecular dating of C4 genes confirms the introgression of two key C4 components between species, while the inheritance of all others matches the species tree. The number of origins consequently varies among C4 components, a scenario that could not have been inferred from analyses of the species tree alone. Our results highlight the power of studying individual components of complex traits to reconstruct trajectories toward novel adaptations.

show abstract

Section: Methodsmentioning

confidence: 99%

Introgression and repeated co-option facilitated the recurrent emergence of C₄photosynthesis among close relatives

et al. 2017

View full text Add to dashboard Cite

show abstract

“…Several horizontally transferred genes have been shown to be correlated with the occurrence of a specific phenotype. Examples include the transfer of carotenoid biosynthetic genes from fungi to aphids that results in the red or green coloration of the aphids (5), or the transfer of genes from hornworts to ferns that results in a more efficient photoreceptor (6). HGT from microbes to plants is well documented.…”

mentioning

confidence: 99%

The genome of cultivated sweet potato contains Agrobacterium T-DNAs with expressed genes: An example of a naturally transgenic food crop

Kyndt

Quispe

Zhai

et al. 2015

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

248

161

View full text Add to dashboard Cite

Agrobacterium rhizogenes and Agrobacterium tumefaciens are plant pathogenic bacteria capable of transferring DNA fragments [transfer DNA (T-DNA)] bearing functional genes into the host plant genome. This naturally occurring mechanism has been adapted by plant biotechnologists to develop genetically modified crops that today are grown on more than 10% of the world's arable land, although their use can result in considerable controversy. While assembling small interfering RNAs, or siRNAs, of sweet potato plants for metagenomic analysis, sequences homologous to T-DNA sequences from Agrobacterium spp. were discovered. Simple and quantitative PCR, Southern blotting, genome walking, and bacterial artificial chromosome library screening and sequencing unambiguously demonstrated that two different T-DNA regions (IbT-DNA1 and IbT-DNA2) are present in the cultivated sweet potato (Ipomoea batatas [L.] Lam.) genome and that these foreign genes are expressed at detectable levels in different tissues of the sweet potato plant. IbT-DNA1 was found to contain four open reading frames (ORFs) homologous to the tryptophan-2-monooxygenase (iaaM), indole-3-acetamide hydrolase (iaaH), C-protein (C-prot), and agrocinopine synthase (Acs) genes of Agrobacterium spp. IbT-DNA1 was detected in all 291 cultigens examined, but not in close wild relatives. IbT-DNA2 contained at least five ORFs with significant homology to the ORF14, ORF17n, rooting locus (Rol)B/RolC, ORF13, and ORF18/ ORF17n genes of A. rhizogenes. IbT-DNA2 was detected in 45 of 217 genotypes that included both cultivated and wild species. Our finding, that sweet potato is naturally transgenic while being a widely and traditionally consumed food crop, could affect the current consumer distrust of the safety of transgenic food crops.horizontal gene transfer | Agrobacterium spp. | food safety | sweet potato | transgenic crops

show abstract

“…In plants, the horizontal acquisition of genes from microbial sources has been hypothesized to play an important role in early land plant evolution (9). HGT among plant lineages may also occur; a notable example involves the adaptive transfer of a photoreceptor gene from bryophytes that enabled ferns to adapt to low-light conditions (10).…”

mentioning

confidence: 99%

Horizontal gene transfer is more frequent with increased heterotrophy and contributes to parasite adaptation

Yang

Zhang

Wafula

et al. 2016

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

View full text Add to dashboard Cite

Horizontal gene transfer (HGT) is the transfer of genetic material across species boundaries and has been a driving force in prokaryotic evolution. HGT involving eukaryotes appears to be much less frequent, and the functional implications of HGT in eukaryotes are poorly understood. We test the hypothesis that parasitic plants, because of their intimate feeding contacts with host plant tissues, are especially prone to horizontal gene acquisition. We sought evidence of HGTs in transcriptomes of three parasitic members of Orobanchaceae, a plant family containing species spanning the full spectrum of parasitic capabilities, plus the free-living Lindenbergia. Following initial phylogenetic detection and an extensive validation procedure, 52 highconfidence horizontal transfer events were detected, often from lineages of known host plants and with an increasing number of HGT events in species with the greatest parasitic dependence. Analyses of intron sequences in putative donor and recipient lineages provide evidence for integration of genomic fragments far more often than retro-processed RNA sequences. Purifying selection predominates in functionally transferred sequences, with a small fraction of adaptively evolving sites. HGT-acquired genes are preferentially expressed in the haustorium-the organ of parasitic plants-and are strongly biased in predicted gene functions, suggesting that expression products of horizontally acquired genes are contributing to the unique adaptive feeding structure of parasitic plants.

show abstract

Horizontal transfer of an adaptive chimeric photoreceptor from bryophytes to ferns

Cited by 151 publications

References 76 publications

Introgression and repeated co-option facilitated the recurrent emergence of C₄photosynthesis among close relatives

Introgression and repeated co-option facilitated the recurrent emergence of C₄photosynthesis among close relatives

The genome of cultivated sweet potato contains Agrobacterium T-DNAs with expressed genes: An example of a naturally transgenic food crop

Horizontal gene transfer is more frequent with increased heterotrophy and contributes to parasite adaptation

Contact Info

Product

Resources

About

Horizontal transfer of an adaptive chimeric photoreceptor from bryophytes to ferns

Cited by 151 publications

References 76 publications

Introgression and repeated co-option facilitated the recurrent emergence of C4photosynthesis among close relatives

Introgression and repeated co-option facilitated the recurrent emergence of C4photosynthesis among close relatives

The genome of cultivated sweet potato contains Agrobacterium T-DNAs with expressed genes: An example of a naturally transgenic food crop

Horizontal gene transfer is more frequent with increased heterotrophy and contributes to parasite adaptation

Contact Info

Product

Resources

About

Introgression and repeated co-option facilitated the recurrent emergence of C₄photosynthesis among close relatives

Introgression and repeated co-option facilitated the recurrent emergence of C₄photosynthesis among close relatives