De novo transcriptome assembly and comparison of C3, C3-C4, and C4 species of tribe Salsoleae (Chenopodiaceae)

Publikationstyp:
Zeitschriftenaufsatz
Metadaten:
Autoren
  • Maximilian Lauterbach
  • Hanno Schmidt
  • Kumari Billakurthi
  • Thomas Hankeln
  • Peter Westhoff
  • Udo Gowik
  • Gudrun Kadereit
Sammlungen
  • metadata
ISSN
1664-462X
Zeitschrift
Frontiers in plant science
Schlüsselwörter
  • 570 Biowissenschaften
  • 570 Life sciences
Sprache
eng
Paginierung
Art. 1939
Datum der Veröffentlichung
2017
Herausgeber
Frontiers Media
Herausgeber URL
http://dx.doi.org/10.3389/fpls.2017.01939
Datum der Datenerfassung
2020
Datum, an dem der Datensatz öffentlich gemacht wurde
2020
Zugang
Public
Titel
De novo transcriptome assembly and comparison of C3, C3-C4, and C4 species of tribe Salsoleae (Chenopodiaceae)
Ausgabe der Zeitschrift
8

Datenquelle: METADATA.UB

Andere Metadatenquellen:
Autoren
  • Maximilian Lauterbach
  • Hanno Schmidt
  • Kumari Billakurthi
  • Thomas Hankeln
  • Peter Westhoff
  • Udo Gowik
  • Gudrun Kadereit
Autoren-URL
https://www.webofscience.com/api/gateway?GWVersion=2&SrcApp=fis-test-1&SrcAuth=WosAPI&KeyUT=WOS:000415039800001&DestLinkType=FullRecord&DestApp=WOS_CPL
DOI
10.3389/fpls.2017.01939
Externe Identifier
  • Clarivate Analytics Document Solution ID: FM4ZX
  • PubMed Identifier: 29184562
ISSN
1664-462X
Zeitschrift
FRONTIERS IN PLANT SCIENCE
Schlüsselwörter
  • Caryophyllales
  • evolution
  • leaf
  • photorespiration
  • photosynthesis
  • RNA-Seq
  • Salsola
Artikelnummer
ARTN 1939
Datum der Veröffentlichung
2017
Status
Published
Titel
<i>De</i> <i>novo</i> Transcriptome Assembly and Comparison of C<sub>3</sub>, C<sub>3</sub>-C<sub>4</sub>, and C<sub>4</sub> Species of Tribe Salsoleae (Chenopodiaceae)
Sub types
  • Article
Ausgabe der Zeitschrift
8

Datenquelle: Web of Science (Lite)

Autoren
  • Maximilian Lauterbach
  • Hanno Schmidt
  • Kumari Billakurthi
  • Thomas Hankeln
  • Peter Westhoff
  • Udo Gowik
  • Gudrun Kadereit
DOI
10.3389/fpls.2017.01939
eISSN
1664-462X
Zeitschrift
Frontiers in Plant Science
Online publication date
2017
Status
Published online
Herausgeber
Frontiers Media SA
Herausgeber URL
http://dx.doi.org/10.3389/fpls.2017.01939
Datum der Datenerfassung
2023
Titel
De novo Transcriptome Assembly and Comparison of C3, C3-C4, and C4 Species of Tribe Salsoleae (Chenopodiaceae)
Ausgabe der Zeitschrift
8

Datenquelle: Crossref

Abstract
C<sub>4</sub> photosynthesis is a carbon-concentrating mechanism that evolved independently more than 60 times in a wide range of angiosperm lineages. Among other alterations, the evolution of C<sub>4</sub> from ancestral C<sub>3</sub> photosynthesis requires changes in the expression of a vast number of genes. Differential gene expression analyses between closely related C<sub>3</sub> and C<sub>4</sub> species have significantly increased our understanding of C<sub>4</sub> functioning and evolution. In Chenopodiaceae, a family that is rich in C<sub>4</sub> origins and photosynthetic types, the anatomy, physiology and phylogeny of C<sub>4</sub>, C<sub>2</sub>, and C<sub>3</sub> species of Salsoleae has been studied in great detail, which facilitated the choice of six samples of five representative species with different photosynthetic types for transcriptome comparisons. mRNA from assimilating organs of each species was sequenced in triplicates, and sequence reads were <i>de novo</i> assembled. These novel genetic resources were then analyzed to provide a better understanding of differential gene expression between C<sub>3</sub>, C<sub>2</sub> and C<sub>4</sub> species. All three analyzed C<sub>4</sub> species belong to the NADP-ME type as most genes encoding core enzymes of this C<sub>4</sub> cycle are highly expressed. The abundance of photorespiratory transcripts is decreased compared to the C<sub>3</sub> and C<sub>2</sub> species. Like in other C<sub>4</sub> lineages of Caryophyllales, our results suggest that PEPC1 is the C<sub>4</sub>-specific isoform in Salsoleae. Two recently identified transporters from the PHT4 protein family may not only be related to the C<sub>4</sub> syndrome, but also active in C<sub>2</sub> photosynthesis in Salsoleae. In the two populations of the C<sub>2</sub> species <i>S. divaricata</i> transcript abundance of several C<sub>4</sub> genes are slightly increased, however, a C<sub>4</sub> cycle is not detectable in the carbon isotope values. Most of the core enzymes of photorespiration are highly increased in the C<sub>2</sub> species compared to both C<sub>3</sub> and C<sub>4</sub> species, confirming a successful establishment of the C<sub>2</sub> photosynthetic pathway. Furthermore, a function of PEP-CK in C<sub>2</sub> photosynthesis appears likely, since PEP-CK gene expression is not only increased in <i>S. divaricata</i> but also in C<sub>2</sub> species of other groups.
Addresses
  • Institute for Molecular Physiology, Johannes Gutenberg-University Mainz, Mainz, Germany.
Autoren
  • Maximilian Lauterbach
  • Hanno Schmidt
  • Kumari Billakurthi
  • Thomas Hankeln
  • Peter Westhoff
  • Udo Gowik
  • Gudrun Kadereit
DOI
10.3389/fpls.2017.01939
eISSN
1664-462X
Externe Identifier
  • PubMed Identifier: 29184562
  • PubMed Central ID: PMC5694442
Funding acknowledgements
  • Deutsche Forschungsgemeinschaft: KA1816/7-1
  • Deutsche Forschungsgemeinschaft: KA1816/9-1
Open access
true
ISSN
1664-462X
Zeitschrift
Frontiers in plant science
Sprache
eng
Medium
Electronic-eCollection
Online publication date
2017
Open access status
Open Access
Paginierung
1939
Datum der Veröffentlichung
2017
Status
Published
Publisher licence
CC BY
Datum der Datenerfassung
2017
Titel
<i>De novo</i> Transcriptome Assembly and Comparison of C<sub>3</sub>, C<sub>3</sub>-C<sub>4</sub>, and C<sub>4</sub> Species of Tribe Salsoleae (Chenopodiaceae).
Sub types
  • research-article
  • Journal Article
Ausgabe der Zeitschrift
8

Files

https://www.frontiersin.org/articles/10.3389/fpls.2017.01939/pdf https://europepmc.org/articles/PMC5694442?pdf=render

Datenquelle: Europe PubMed Central

Abstract
C4 photosynthesis is a carbon-concentrating mechanism that evolved independently more than 60 times in a wide range of angiosperm lineages. Among other alterations, the evolution of C4 from ancestral C3 photosynthesis requires changes in the expression of a vast number of genes. Differential gene expression analyses between closely related C3 and C4 species have significantly increased our understanding of C4 functioning and evolution. In Chenopodiaceae, a family that is rich in C4 origins and photosynthetic types, the anatomy, physiology and phylogeny of C4, C2, and C3 species of Salsoleae has been studied in great detail, which facilitated the choice of six samples of five representative species with different photosynthetic types for transcriptome comparisons. mRNA from assimilating organs of each species was sequenced in triplicates, and sequence reads were de novo assembled. These novel genetic resources were then analyzed to provide a better understanding of differential gene expression between C3, C2 and C4 species. All three analyzed C4 species belong to the NADP-ME type as most genes encoding core enzymes of this C4 cycle are highly expressed. The abundance of photorespiratory transcripts is decreased compared to the C3 and C2 species. Like in other C4 lineages of Caryophyllales, our results suggest that PEPC1 is the C4-specific isoform in Salsoleae. Two recently identified transporters from the PHT4 protein family may not only be related to the C4 syndrome, but also active in C2 photosynthesis in Salsoleae. In the two populations of the C2 species S. divaricata transcript abundance of several C4 genes are slightly increased, however, a C4 cycle is not detectable in the carbon isotope values. Most of the core enzymes of photorespiration are highly increased in the C2 species compared to both C3 and C4 species, confirming a successful establishment of the C2 photosynthetic pathway. Furthermore, a function of PEP-CK in C2 photosynthesis appears likely, since PEP-CK gene expression is not only increased in S. divaricata but also in C2 species of other groups.
Date of acceptance
2017
Autoren
  • Maximilian Lauterbach
  • Hanno Schmidt
  • Kumari Billakurthi
  • Thomas Hankeln
  • Peter Westhoff
  • Udo Gowik
  • Gudrun Kadereit
Autoren-URL
https://www.ncbi.nlm.nih.gov/pubmed/29184562
DOI
10.3389/fpls.2017.01939
Externe Identifier
  • PubMed Central ID: PMC5694442
ISSN
1664-462X
Zeitschrift
Front Plant Sci
Schlüsselwörter
  • Caryophyllales
  • RNA-Seq
  • Salsola
  • evolution
  • leaf
  • photorespiration
  • photosynthesis
Sprache
eng
Country
Switzerland
Paginierung
1939
Datum der Veröffentlichung
2017
Status
Published online
Titel
De novo Transcriptome Assembly and Comparison of C3, C3-C4, and C4 Species of Tribe Salsoleae (Chenopodiaceae).
Sub types
  • Journal Article
Ausgabe der Zeitschrift
8

Datenquelle: PubMed

Author's licence
CC-BY
Autoren
  • Maximilian Lauterbach
  • Hanno Schmidt
  • Kumari Billakurthi
  • Thomas Hankeln
  • Peter Westhoff
  • Udo Gowik
  • Gudrun Kadereit
Hosting institution
Universitätsbibliothek Mainz
Sammlungen
  • DFG-OA-Publizieren (2012 - 2017)
Resource version
Published version
DOI
10.3389/fpls.2017.01939
Funding acknowledgements
  • DFG, Open Access-Publizieren Universität Mainz / Universitätsmedizin
File(s) embargoed
false
Open access
true
ISSN
1664-462X
Zeitschrift
Frontiers in plant science
Schlüsselwörter
  • 570 Biowissenschaften
  • 570 Life sciences
Sprache
eng
Open access status
Open Access
Paginierung
Art. 1939
Datum der Veröffentlichung
2017
Public URL
https://openscience.ub.uni-mainz.de/handle/20.500.12030/7378
Herausgeber
Frontiers Media
Herausgeber URL
http://dx.doi.org/10.3389/fpls.2017.01939
Datum der Datenerfassung
2022
Datum, an dem der Datensatz öffentlich gemacht wurde
2022
Zugang
Public
Titel
De novo transcriptome assembly and comparison of C3, C3-C4, and C4 species of tribe Salsoleae (Chenopodiaceae)
Ausgabe der Zeitschrift
8

Files

de_novo_transcriptome_assembl-20220710214650338.pdf

Datenquelle: OPENSCIENCE.UB

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