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Comparative transcriptomics enables the identification of functional orthologous genes involved in early leaf growth

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Abstract
Leaf growth is a complex trait for which many similarities exist in different plant species, suggesting functional conservation of the underlying pathways. However, a global view of orthologous genes involved in leaf growth showing conserved expression in dicots and monocots is currently missing. Here, we present a genome-wide comparative transcriptome analysis between Arabidopsis and maize, identifying conserved biological processes and gene functions active during leaf growth. Despite the orthology complexity between these distantly related plants, 926 orthologous gene groups including 2829 Arabidopsis and 2974 maize genes with similar expression during leaf growth were found, indicating conservation of the underlying molecular networks. We found 65% of these genes to be involved in one-to-one orthology, whereas only 28.7% of the groups with divergent expression had one-to-one orthology. Within the pool of genes with conserved expression, 19 transcription factor families were identified, demonstrating expression conservation of regulators active during leaf growth. Additionally, 25 Arabidopsis and 25 maize putative targets of the TCP transcription factors with conserved expression were determined based on the presence of enriched transcription factor binding sites. Based on large-scale phenotypic data, we observed that genes with conserved expression have a higher probability to be involved in leaf growth and that leaf-related phenotypes are more frequently present for genes having orthologues between dicots and monocots than clade-specific genes. This study shows the power of integrating transcriptomic with orthology data to identify or select candidates for functional studies during leaf development in flowering plants.
Keywords
Biotechnology, Agronomy and Crop Science, Plant Science

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Citation

Please use this url to cite or link to this publication:

MLA
Vercruysse, Jasmien et al. “Comparative Transcriptomics Enables the Identification of Functional Orthologous Genes Involved in Early Leaf Growth.” Plant Biotechnology Journal (2019): n. pag. Print.
APA
Vercruysse, Jasmien, Van Bel, M., Osuna, C., Kulkarni, S. R., Van den Storme, V., Nelissen, H., Gonzalez Sanchez, N., et al. (2019). Comparative transcriptomics enables the identification of functional orthologous genes involved in early leaf growth. Plant Biotechnology Journal.
Chicago author-date
Vercruysse, Jasmien, Michiel Van Bel, Cristina Osuna, Shubhada Rajabhau Kulkarni, Véronique Van den Storme, Hilde Nelissen, Nathalie Gonzalez Sanchez, Dirk Inzé, and Klaas Vandepoele. 2019. “Comparative Transcriptomics Enables the Identification of Functional Orthologous Genes Involved in Early Leaf Growth.” Plant Biotechnology Journal.
Chicago author-date (all authors)
Vercruysse, Jasmien, Michiel Van Bel, Cristina Osuna, Shubhada Rajabhau Kulkarni, Véronique Van den Storme, Hilde Nelissen, Nathalie Gonzalez Sanchez, Dirk Inzé, and Klaas Vandepoele. 2019. “Comparative Transcriptomics Enables the Identification of Functional Orthologous Genes Involved in Early Leaf Growth.” Plant Biotechnology Journal.
Vancouver
1.
Vercruysse J, Van Bel M, Osuna C, Kulkarni SR, Van den Storme V, Nelissen H, et al. Comparative transcriptomics enables the identification of functional orthologous genes involved in early leaf growth. Plant Biotechnology Journal. 2019;
IEEE
[1]
J. Vercruysse et al., “Comparative transcriptomics enables the identification of functional orthologous genes involved in early leaf growth,” Plant Biotechnology Journal, 2019.
@article{8625712,
  abstract     = {Leaf growth is a complex trait for which many similarities exist in different plant species, suggesting functional conservation of the underlying pathways. However, a global view of orthologous genes involved in leaf growth showing conserved expression in dicots and monocots is currently missing. Here, we present a genome-wide comparative transcriptome analysis between Arabidopsis and maize, identifying conserved biological processes and gene functions active during leaf growth. Despite the orthology complexity between these distantly related plants, 926 orthologous gene groups including 2829 Arabidopsis and 2974 maize genes with similar expression during leaf growth were found, indicating conservation of the underlying molecular networks. We found 65% of these genes to be involved in one-to-one orthology, whereas only 28.7% of the groups with divergent expression had one-to-one orthology. Within the pool of genes with conserved expression, 19 transcription factor families were identified, demonstrating expression conservation of regulators active during leaf growth. Additionally, 25 Arabidopsis and 25 maize putative targets of the TCP transcription factors with conserved expression were determined based on the presence of enriched transcription factor binding sites. Based on large-scale phenotypic data, we observed that genes with conserved expression have a higher probability to be involved in leaf growth and that leaf-related phenotypes are more frequently present for genes having orthologues between dicots and monocots than clade-specific genes. This study shows the power of integrating transcriptomic with orthology data to identify or select candidates for functional studies during leaf development in flowering plants.},
  author       = {Vercruysse, Jasmien and Van Bel, Michiel and Osuna, Cristina and Kulkarni, Shubhada Rajabhau and Van den Storme, Véronique and Nelissen, Hilde and Gonzalez Sanchez, Nathalie and Inzé, Dirk and Vandepoele, Klaas},
  issn         = {1467-7644},
  journal      = {Plant Biotechnology Journal},
  keywords     = {Biotechnology,Agronomy and Crop Science,Plant Science},
  language     = {eng},
  title        = {Comparative transcriptomics enables the identification of functional orthologous genes involved in early leaf growth},
  url          = {http://dx.doi.org/10.1111/pbi.13223},
  year         = {2019},
}

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