scholarly journals The Coordination and Jumps along C4 Photosynthesis Evolution in the Genus Flaveria

2021 ◽  
Author(s):  
Amy Lyu ◽  
Udo Gowik ◽  
Steve Kelly ◽  
Sarah Covshoff ◽  
Harmony Clayton ◽  
...  
Keyword(s):  
Gene Expression ◽  
Phylogenetic Tree ◽  
Protein Sequence ◽  
C4 Photosynthesis ◽  
Correlation Coefficients ◽  
Complex Trait ◽  
Transcript Abundance ◽  
Morphological Features ◽  
Evolutionary Trajectory ◽  
C4 Species

Abstract C4 photosynthesis is a remarkable complex trait, elucidations of the evolutionary trajectory of C4 photosynthesis from its ancestral C3 pathway can help us better understand the generic principles of the evolution of complex trait and guide the engineering of C3 crops for higher yields. Here, we used the genus Flaveria that contains C3, C3-C4, C4-like and C4 species as a system to study the evolution of C4 photosynthesis. We first mapped transcript abundance, protein sequence, and morphological features to the phylogenetic tree of the genus Flaveria, and calculated the evolutionary correlation of different features; we then predicted the relative changes of ancestral nodes of those features to illustrate the key stages during the evolution of C4 photosynthesis. We found that gene expression and protein sequence showed consistent modification pattern along the phylogenetic tree. High correlation coefficients ranging from 0.46 to 0.9 among gene expression, protein sequence and morphology were observed, and the greatest modification of those different features consistently occurred at the transition between C3-C4 species and C4-like species. Our results show highly coordinated changes in gene expression, protein sequence and morphological features, which support an obviously evolutionary jump during the evolution of C4 metabolism.

scholarly journals The Coordination and Jumps along C4 Photosynthesis Evolution in the Genus Flaveria

2018 ◽  
Author(s):  
Ming-Ju Amy Lyu ◽  
Udo Gowik ◽  
Peter Westhoff ◽  
Yimin Tao ◽  
Steve Kelly ◽  
...  
Keyword(s):  
Gene Expression ◽  
Phylogenetic Tree ◽  
Protein Sequence ◽  
C4 Photosynthesis ◽  
Correlation Coefficients ◽  
Complex Trait ◽  
Transcript Abundance ◽  
Morphological Features ◽  
Evolutionary Trajectory ◽  
Photosynthesis Gene

AbstractBackgroundC4 photosynthesis is a remarkable complex trait, elucidations of the evolutionary trajectory of C4 photosynthesis from its ancestral C3 pathway can help us to better understand the generic principles of complex trait evolution and guide engineering of C3 crops for higher yields. We used the genus Flaveria that contains C3, C3-C4, C4-like and C4 species as a system to study the evolution of C4 photosynthesis.ResultsWe mapped transcript abundance, protein sequence, and morphological features to the phylogenetic tree of the genus Flaveria, and calculated the evolutionary correlation of different features. Besides, we predicted the relative changes of ancestral nodes of those features to illustrate the key stages during the evolution of C4 photosynthesis. Gene expression and protein sequence showed consistent modification pattern along the phylogenetic tree. High correlation coefficients ranging from 0.46 to 0.9 among gene expression, protein sequence and morphology were observed, and the greatest modification of those different features consistently occurred at the transition between C3-C4 species and C4-like species.ConclusionsOur data shows highly coordinated changes in gene expression, protein sequence and morphological features. Besides, our results support an obviously evolutionary jump during the evolution of C4 metabolism.

scholarly journals The coordination of major events in C4 photosynthesis evolution in the genus Flaveria

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Ming-Ju Amy Lyu ◽  
Udo Gowik ◽  
Steve Kelly ◽  
Sarah Covshoff ◽  
Julian M. Hibberd ◽  
...  
Keyword(s):  
Gene Expression ◽  
Phylogenetic Tree ◽  
Protein Sequence ◽  
Complex Traits ◽  
C4 Photosynthesis ◽  
Correlation Coefficients ◽  
Complex Trait ◽  
Transcript Abundance ◽  
Morphological Features ◽  
Evolutionary Trajectory

AbstractC4 photosynthesis is a remarkable complex trait, elucidations of the evolutionary trajectory of C4 photosynthesis from its ancestral C3 pathway can help us better understand the generic principles of the evolution of complex traits and guide the engineering of C3 crops for higher yields. Here, we used the genus Flaveria that contains C3, C3–C4, C4-like and C4 species as a system to study the evolution of C4 photosynthesis. We first mapped transcript abundance, protein sequence and morphological features onto the phylogenetic tree of the genus Flaveria, and calculated the evolutionary correlation of different features; we then predicted the relative changes of ancestral nodes of those features to illustrate the major events during the evolution of C4 photosynthesis. We found that gene expression and protein sequence showed consistent modification patterns in the phylogenetic tree. High correlation coefficients ranging from 0.46 to 0.9 among gene expression, protein sequence and morphology were observed. The greatest modification of those different features consistently occurred at the transition between C3-C4 species and C4-like species. Our results show highly coordinated changes in gene expression, protein sequence and morphological features, which support evolutionary major events during the evolution of C4 metabolism.

scholarly journals Key changes in gene expression identified for different stages of C4 evolution in Alloteropsis semialata

2019 ◽  
Vol 70 (12) ◽  
pp. 3255-3268 ◽  
Author(s):  
Luke T Dunning ◽  
Jose J Moreno-Villena ◽  
Marjorie R Lundgren ◽  
Jacqueline Dionora ◽  
Paolo Salazar ◽  
...  
Keyword(s):  
Gene Expression ◽  
Phosphoenolpyruvate Carboxykinase ◽  
C4 Photosynthesis ◽  
Complex Trait ◽  
Single Species ◽  
Isolated Populations ◽  
Adaptive Landscapes ◽  
Pyruvate Orthophosphate Dikinase ◽  
Gradual Process ◽  
Tropical Conditions

Abstract C4 photosynthesis is a complex trait that boosts productivity in tropical conditions. Compared with C3 species, the C4 state seems to require numerous novelties, but species comparisons can be confounded by long divergence times. Here, we exploit the photosynthetic diversity that exists within a single species, the grass Alloteropsis semialata, to detect changes in gene expression associated with different photosynthetic phenotypes. Phylogenetically informed comparative transcriptomics show that intermediates with a weak C4 cycle are separated from the C3 phenotype by increases in the expression of 58 genes (0.22% of genes expressed in the leaves), including those encoding just three core C4 enzymes: aspartate aminotransferase, phosphoenolpyruvate carboxykinase, and phosphoenolpyruvate carboxylase. The subsequent transition to full C4 physiology was accompanied by increases in another 15 genes (0.06%), including only the core C4 enzyme pyruvate orthophosphate dikinase. These changes probably created a rudimentary C4 physiology, and isolated populations subsequently improved this emerging C4 physiology, resulting in a patchwork of expression for some C4 accessory genes. Our work shows how C4 assembly in A. semialata happened in incremental steps, each requiring few alterations over the previous step. These create short bridges across adaptive landscapes that probably facilitated the recurrent origins of C4 photosynthesis through a gradual process of evolution.

Housekeeping genes for RT-qPCR in ovine preimplantation embryos

Zygote ◽  
2020 ◽  
Vol 28 (5) ◽  
pp. 432-439
Author(s):  
Pábola Santos Nascimento ◽  
Marcelo Tigre Moura ◽  
Roberta Lane Oliveira Silva ◽  
Pamela Ramos-Deus ◽  
José Carlos Ferreira-Silva ◽  
...  
Keyword(s):  
Gene Expression ◽  
Expression Analysis ◽  
Gene Expression Analysis ◽  
Developmental Stages ◽  
Zinc Finger Protein ◽  
Correlation Coefficients ◽  
Housekeeping Genes ◽  
Transcript Abundance ◽  
Preimplantation Development ◽  
Preimplantation Embryos

SummaryHousekeeping genes (HKG) are paramount for accurate gene expression analysis during preimplantation development. Markedly, quantitative reverse transcription polymerase chain reaction (RT-qPCR) in ovine embryos currently lacks HKGs. Therefore, we tested 11 HKGs for RT-qPCR normalization during ovine parthenogenetic preimplantation development. Seven HKGs reached the qPCR efficiency threshold (97.20–105.96%), with correlation coefficients ranging from −0.922 to −0.998 and slopes from −3.22 to −3.59. GeNorm ranked glyceraldehyde 3-phosphate dehydrogenase (GAPDH) and TATA-binding protein (TBP) as the best HKG pair, while H3 histone, family 3A (H3F3A) was the third HKG. Relative gene expression was measured for zinc finger protein X-linked (ZFX) and developmental pluripotency-associated 3 (DPPA3) transcripts during ovine parthenogenetic preimplantation development. ZFX did not show any transcript abundance fluctuation among oocytes, cleavage-stage embryos, and morulae. DPPA3 transcript abundance was also similar among all developmental stages, therefore suggesting that it may not display a maternal gene expression profile. In silico analysis of ovine DPPA3 mRNA and protein showed high conservation to bovine orthologues. However, DPPA3 orthologues differed in regulatory motifs. In conclusion, GAPDH, TBP and H3F3A are stable HKGs in ovine parthenogenetic embryos and allow accurate RT-qPCR-based gene expression analysis.

scholarly journals Evolutionary changes of phosphoenolpyruvate transporter (PPT) during the emergence of C4 photosynthesis

2019 ◽  
Author(s):  
Ming-Ju Amy Lyu ◽  
Yaling Wang ◽  
Jianjun Jiang ◽  
Genyun Chen ◽  
Xin-Guang Zhu
Keyword(s):  
Evolutionary History ◽  
C4 Photosynthesis ◽  
Mesophyll Cell ◽  
Complex Trait ◽  
Transcript Abundance ◽  
Sheath Cell ◽  
Loss Of Function ◽  
Evolutionary Changes ◽  
Transport Direction ◽  
History Of

AbstractC4 photosynthesis is a complex trait, which evolved from its ancestral C3 photosynthesis by recruiting pre-existing genes. The evolutionary history of enzymes involved in the C4 shuttle has been extensively studied. Here we analyze the evolutionary changes of phosphoenolpyruvate (PEP) transporter (PPT) during its recruitment from C3 to C4 photosynthesis. Our analysis shows that 1) among the two PPT paralogs, i.e. PPT1 and PPT2, PPT1 is an ancestral copy while PPT2 is a derived copy; 2) during C4 evolution, PPT1 shifted its expression from predominantly in root to in leaf, and from bundle sheath cell to mesophyll cell, supporting that PPT1 was recruited into C4 photosynthesis; 3) PPT1 gained increased transcript abundance, gained more rapid and long-lasting responses to light during C3 to C4 evolution, while PPT2 lost its responsiveness to light; 4) PPT1 gained a number of new cis-elements during C4 evolution; 5) C4 PPT1 can complement the phenotype of Arabidopsis PPT1 loss-of-function mutant, suggesting that it is a bidirectional transporter and its transport direction did not alter during C4 evolution. We finally discuss mechanistic linkages between these observed changes in PPT1 and C4 photosynthesis evolution.High lightDuring the process of C4 photosynthesis evolution, PPT not only experienced changes in its expression location and transcript abundance, but also acquired new cis-elements in its promoter region and accumulated protein variations.

scholarly journals Protein Sequence Editing of SKN-1A/Nrf1 by Peptide:N-Glycanase Controls Proteasome Gene Expression

Cell ◽  
2019 ◽  
Vol 177 (3) ◽  
pp. 737-750.e15 ◽  
Author(s):  
Nicolas J. Lehrbach ◽  
Peter C. Breen ◽  
Gary Ruvkun
Keyword(s):  
Gene Expression ◽  
Protein Sequence ◽  
Proteasome Gene

scholarly journals Zea mays RNA-seq estimated transcript abundances are strongly affected by read mapping bias

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Shuhua Zhan ◽  
Cortland Griswold ◽  
Lewis Lukens
Keyword(s):  
Gene Expression ◽  
Zea Mays ◽  
Reference Genome ◽  
Transcript Abundance ◽  
Gene Transcript ◽  
Rna Seq ◽  
Individual Genome ◽  
Abundance Estimates ◽  
Mapping Bias ◽  
Quantify Gene Expression

Abstract Background Genetic variation for gene expression is a source of phenotypic variation for natural and agricultural species. The common approach to map and to quantify gene expression from genetically distinct individuals is to assign their RNA-seq reads to a single reference genome. However, RNA-seq reads from alleles dissimilar to this reference genome may fail to map correctly, causing transcript levels to be underestimated. Presently, the extent of this mapping problem is not clear, particularly in highly diverse species. We investigated if mapping bias occurred and if chromosomal features associated with mapping bias. Zea mays presents a model species to assess these questions, given it has genotypically distinct and well-studied genetic lines. Results In Zea mays, the inbred B73 genome is the standard reference genome and template for RNA-seq read assignments. In the absence of mapping bias, B73 and a second inbred line, Mo17, would each have an approximately equal number of regulatory alleles that increase gene expression. Remarkably, Mo17 had 2–4 times fewer such positively acting alleles than did B73 when RNA-seq reads were aligned to the B73 reference genome. Reciprocally, over one-half of the B73 alleles that increased gene expression were not detected when reads were aligned to the Mo17 genome template. Genes at dissimilar chromosomal ends were strongly affected by mapping bias, and genes at more similar pericentromeric regions were less affected. Biased transcript estimates were higher in untranslated regions and lower in splice junctions. Bias occurred across software and alignment parameters. Conclusions Mapping bias very strongly affects gene transcript abundance estimates in maize, and bias varies across chromosomal features. Individual genome or transcriptome templates are likely necessary for accurate transcript estimation across genetically variable individuals in maize and other species.

A Study of Correlation between Morphology and Evolution of Euphorbiaceae s.l. using Taxonomic Congruence and Total Evidence

2021 ◽  
Vol 9 (1) ◽  
pp. 49-55
Author(s):  
Vanlal hruaia ◽  
◽  
Lal rinmuana ◽  
J Lalbiaknunga ◽  
Laldinfeli Ralte
Keyword(s):  
Phylogenetic Tree ◽  
Evolutionary Relationship ◽  
Cladistic Analysis ◽  
Morphological Characters ◽  
Flowering Plants ◽  
Morphological Features ◽  
Total Evidence ◽  
Pictorial Representation ◽  
Phenetic Analysis ◽  
Morphological Relationship

Euphorbiaceae is one of the largest family of flowering plants, in our study different species were collected from different localities of Mizoram, the collected specimens were studied and their morphological features noted. 34 genera of Euphorbiaceae s.l were used in the study. Cladistic analysis was performed in Mesquite software and Phenetic analysis was done in NTsys software. Both analyses produce a pictorial representation in a form of a tree; cladistic analysis produce phylogenetic tree (evolutionary relationship) while phenetic analysis produce phenogram (morphological relationship). The results of the aforementioned analyses were further analysed by total evidence technique and taxonomic congruence, a phylogenetic software PAUP is used for this purpose. The resultant trees were very different and comparison was done to find correlation between evolution and morphological characters. The research finds various correlation among characters like the number of locule in ovule, phyllanthoid branching and support the inclusion of genus like Breynia, Sauropus into Phyllanthus.

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