Plant Systematics and Evolution

, Volume 302, Issue 4, pp 433–445 | Cite as

Gene dosage effects and signatures of purifying selection in lateral organ boundaries domain (LBD) genes LBD1 and LBD18

  • Roba Bdeir
  • Victor Busov
  • Yordan Yordanov
  • Oliver Gailing
Original Article
First Online:
Received:
Accepted:

Abstract

Wood formation is an economically and environmentally important process and has played a significant role in the evolution of terrestrial plants. Despite its significance, the molecular underpinnings of the process are still poorly understood. We have previously shown that four lateral organ boundaries (LBD) transcription factors have important roles in the regulation of secondary (woody) growth with two (LBD1 and LBD4) involved in secondary phloem and ray cell development and two (LBD15 and LBD18) in secondary xylem formation. We studied gene copy number and variation in DNA and amino acid sequences of the four LBDs in a wide range of woody and herbaceous plant taxa with fully sequenced and annotated genomes. LBD1 showed the highest gene copy number across species, and gene copy number was strongly and significantly correlated with tangential ray width. The climbing vines, cucumber and grape, with wide multiseriate rays (>10 cells wide) showed the highest gene copy number. Because the growth habit of woody lianas like grape requires significant twisting and bending, it was suggested that the unlignified ray parenchyma cells likely facilitate stem flexibility and maintenance of xylem conductivity. We further demonstrate conservation of amino acids in LBD18 protein sequences specific to woody taxa downstream of the LBD domain. Neutrality tests showed evidence for strong purifying selection on these regions across various orders, indicating important functional roles in woody taxa. Additionally, structural modeling demonstrates that these regions have a significant impact on tertiary protein structure and thus are likely of significant functional importance.

Keywords

Ray cells Secondary growth Vascular cambium Woody growth 
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Notes

Acknowledgments

Funding for the project was provided by the USDA-NIFA grant (2012-67013-19389) to VB, YY and OG. We would also like to thank the Biochemistry and Molecular Biology program at Michigan Technological University (MTU) which supported the research for one semester. Additional support was made available by MTU’s Ecosystem Science and Biotech Research Center. We would like to thank for the very constructive comments from two anonymous reviewers.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

Funding

This study was funded by the USDA-NIFA grant (grant number 2012-67013-19389).

Supplementary material

606_2015_1272_MOESM1_ESM.pdf (36 kb)
Neighbor-Joining tree based on complete protein sequences of all LBD genes from Arabidopsis thaliana and Brassica rapa. LBD homologs and gene copy numbers for each species are determined by the position in the phylogenetic tree relative to Arabidopsis thaliana LBD genes (PDF 35 kb)
606_2015_1272_MOESM2_ESM.pdf (395 kb)
Neighbor-Joining tree based on complete protein sequences of LBD1 genes. Bootstrap values above 50 and genes from woody species are highlighted in yellow (PDF 394 kb)
606_2015_1272_MOESM3_ESM.pdf (277 kb)
Neighbor-Joining tree based on complete protein sequences of LBD4 genes. Bootstrap values above 50 and genes from woody species are highlighted in yellow (PDF 277 kb)
606_2015_1272_MOESM4_ESM.pdf (288 kb)
Neighbor-Joining tree based on complete protein sequences of LBD15 genes. Bootstrap values above 50 and genes from woody species are highlighted in yellow (PDF 288 kb)
606_2015_1272_MOESM5_ESM.pdf (48 kb)
Neighbor-Joining tree based on complete protein sequences of LBD18 genes. Bootstrap values above 50 and genes from woody species are highlighted in yellow (PDF 47 kb)
606_2015_1272_MOESM6_ESM.pdf (48 kb)
Neighbor-Joining tree based on complete DNA coding sequences of LBD18 genes. Bootstrap values above 50 and genes from woody species are highlighted in yellow (PDF 47 kb)

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Copyright information

© Springer-Verlag Wien 2016

Authors and Affiliations

  • Roba Bdeir
    • 1
  • Victor Busov
    • 1
  • Yordan Yordanov
    • 1
    • 2
  • Oliver Gailing
    • 1
  1. 1.School of Forest Resources and Environmental ScienceMichigan Technological UniversityHoughtonUSA
  2. 2.Department of Biological SciencesEastern Illinois UniversityCharlestonUSA

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