The role of cis-elements in the evolution of crassulacean acid metabolism photosynthesis

Chen, Li Yu; Xin, Yinghui; Wai, Ching Man; Liu, Juan; Ming, Ray

doi:10.1038/s41438-019-0229-0

Cited by 30 publications

(25 citation statements)

References 60 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Gene duplication and expansion was initially proposed to be the driven force for the evolution of the CAM pathway [ 45 ]. However, it is still controversial, many studies have shown that CAM pathway should be evolved by differential expression of CAM-related genes or neofunctionalization rather than gene dosage [ 7 , 10 , 11 ].…”

Section: Discussionmentioning

confidence: 99%

“…The benefits of this system are that CAM plants reduce water loss by closing stomata during the day and also have increased photosynthetic efficiency. The mechanism and evolution of CAM have been extensively investigated [6][7][8][9][10]. For instance, many genes putatively involved in the carbon fixation module of CAM in pineapple have been identified [6], and many of them are differentially regulated in different leaf tissues [11].…”

mentioning

confidence: 99%

See 1 more Smart Citation

Integrated analysis of DNA methylome and transcriptome reveals epigenetic regulation of CAM photosynthesis in pineapple

et al. 2021

View full text Add to dashboard Cite

Background Crassulacean acid metabolism (CAM) photosynthesis is an important carbon fixation pathway especially in arid environments because it leads to higher water-use efficiency compared to C3 and C4 plants. However, the role of DNA methylation in regulation CAM photosynthesis is not fully understood. Results Here, we performed temporal DNA methylome and transcriptome analysis of non-photosynthetic (white base) and photosynthetic (green tip) tissues of pineapple leaf. The DNA methylation patterns and levels in these two tissues were generally similar for the CG and CHG cytosine sequence contexts. However, CHH methylation was reduced in white base leaf tissue compared with green tip tissue across diel time course in both gene and transposon regions. We identified thousands of local differentially methylated regions (DMRs) between green tip and white base at different diel periods. We also showed that thousands of genes that overlapped with DMRs were differentially expressed between white base and green tip leaf tissue across diel time course, including several important CAM pathway-related genes, such as beta-CA, PEPC, PPCK, and MDH. Conclusions Together, these detailed DNA methylome and transcriptome maps provide insight into DNA methylation changes and enhance our understanding of the relationships between DNA methylation and CAM photosynthesis.

show abstract

Section: Discussionmentioning

confidence: 99%

mentioning

confidence: 99%

Integrated analysis of DNA methylome and transcriptome reveals epigenetic regulation of CAM photosynthesis in pineapple

et al. 2021

View full text Add to dashboard Cite

show abstract

“…3), which was also found in orchids [56]. In other words, PEPC gene duplications were very important for the evolutionary origination of C4 photosynthesis, but not for CAM pathways, in which posttranslational regulation of PEPC possibly played key roles [19,27,57].…”

Section: Pepc Was Convergent In C4 But Not In Cam Photosynthesismentioning

confidence: 74%

Convergent Molecular Evolution of PEPC Gene Family in C4 and CAM Plants

Shu¹,

Yan²,

Wang³

2020

Preprint

View full text Add to dashboard Cite

Background: Phosphoenolpyruvate carboxylase (PEPC), as the key enzyme in initial carbon fixation of C4 and crassulacean acid mechanism (CAM) pathways, was thought to undergo convergent adaptive changes resulted in the convergent evolution of C4 and CAM photosynthesis in vascular plants. However, the integral evolutionary history and convergence of PEPC in plants remained lack of understanding. Results: In present study, we identified the members of PEPC gene family across green plants with genomic data, found ten conserved motifs and modeled three-dimensional protein structures of 90 plant-type PEPC genes. After reconstructed PEPC gene family tree and reconciled with species tree, we found PEPC genes occurred 71 gene duplications and 16 gene losses, which might result from whole-genome duplication events in plants. Based on the integral phylogenetic tree of PEPC gene family, we detected four convergent evolution sites of PEPC in C4 species but no one in CAM species. Conclusions: PEPC gene family was ubiquitous and highly conservative in green plants. After originated from gene duplication of ancestral C3-PEPC, C4-PEPC isoforms underwent convergent molecular substitution that facilitated the convergent evolution of C4 photosynthesis in Angiosperms, but PEPC gene did not exist molecular convergence corresponded to the multiple independent evolution of CAM photosynthesis. Our findings help to understand the origin and evolution of C4 and CAM pathways and shed new light on the adaptation of plants in drought and high-temperature habitats.

show abstract

“…Another important feature in the Bromeliad1776 set is the inclusion of genes putatively associated with key innovative traits in Bromeliaceae with a focus on C3/CAM shifts. Little is known about the molecular basis of the CAM pathway, an adaptation to arid environments which evolved independently and repeatedly in over 36 plant families (Heyduk, Moreno-Villena, Gilman, Christin, & Edwards, 2019; Chen, Xin, Wai, Liu, & Ming, 2020; Silvera et al, 2010). CAM phenotypes are considered key adaptations in Bromeliaceae, associated with expansion into novel ecological niches.…”

Section: Discussionmentioning

confidence: 99%

Taxon-specific or universal? Using target capture to study the evolutionary history of rapid radiations

Yardeni

Viruel

Paris

et al. 2021

Preprint

View full text Add to dashboard Cite

Target capture emerged as an important tool for phylogenetics and population genetics in non-model taxa. Whereas developing taxon-specific capture probes requires sustained efforts, available universal kits may have a lower power to reconstruct relationships at shallow phylogenetic scales and within rapidly radiating clades. We present here a newly-developed target capture set for Bromeliaceae, a large and ecologically-diverse plant family with highly variable diversification rates. The set targets 1,776 coding regions, including genes putatively involved in key innovations, with the aim to empower testing of a wide range of evolutionary hypotheses. We compare the relative power of this taxon-specific set, Bromeliad1776, to the universal Angiosperms353 kit. The taxon-specific set results in higher enrichment success across the entire family. However, the overall performance of both kits to reconstruct phylogenetic trees is relatively comparable, highlighting the vast potential of universal kits for resolving evolutionary relationships. For more detailed phylogenetic or population genetic analyses, e.g. the exploration of gene tree concordance, nucleotide diversity or population structure, the taxon-specific capture set presents clear benefits. We discuss the potential lessons that this comparative study provides for future phylogenetic and population genetic investigations, in particular for the study of evolutionary radiations.

show abstract

The role of cis-elements in the evolution of crassulacean acid metabolism photosynthesis

Cited by 30 publications

References 60 publications

Integrated analysis of DNA methylome and transcriptome reveals epigenetic regulation of CAM photosynthesis in pineapple

Integrated analysis of DNA methylome and transcriptome reveals epigenetic regulation of CAM photosynthesis in pineapple

Convergent Molecular Evolution of PEPC Gene Family in C4 and CAM Plants

Taxon-specific or universal? Using target capture to study the evolutionary history of rapid radiations

Contact Info

Product

Resources

About