Functional genomics of a generalist parasitic plant: Laser microdissection of host-parasite interface reveals host-specific patterns of parasite gene expression

Loren A. Honaas; Eric K. Wafula; Zhenzhen Yang; Joshua P. Der; Norman J. Wickett; Naomi S. Altman; Christopher G. Taylor; John I. Yoder; Michael P. Timko; James H. Westwood; Claude W. dePamphilis

doi:10.1186/1471-2229-13-9

Functional genomics of a generalist parasitic plant: Laser microdissection of host-parasite interface reveals host-specific patterns of parasite gene expression

Loren A. Honaas, Eric K. Wafula, Zhenzhen Yang, Joshua P. Der, Norman J. Wickett, Naomi S. Altman, Christopher G. Taylor, John I. Yoder, Michael P. Timko, James H. Westwood, Claude W. dePamphilis^*

^*Corresponding author for this work

Program in Biological Sciences

Research output: Contribution to journal › Article › peer-review

57 Scopus citations

Abstract

Background: Orobanchaceae is the only plant family with members representing the full range of parasitic lifestyles plus a free-living lineage sister to all parasitic lineages, Lindenbergia. A generalist member of this family, and an important parasitic plant model, Triphysaria versicolor regularly feeds upon a wide range of host plants. Here, we compare de novo assembled transcriptomes generated from laser micro-dissected tissues at the host-parasite interface to uncover details of the largely uncharacterized interaction between parasitic plants and their hosts.Results: The interaction of Triphysaria with the distantly related hosts Zea mays and Medicago truncatula reveals dramatic host-specific gene expression patterns. Relative to above ground tissues, gene families are disproportionally represented at the interface including enrichment for transcription factors and genes of unknown function. Quantitative Real-Time PCR of a T. versicolor β-expansin shows strong differential (120x) upregulation in response to the monocot host Z. mays; a result that is concordant with our read count estimates. Pathogenesis-related proteins, other cell wall modifying enzymes, and orthologs of genes with unknown function (annotated as such in sequenced plant genomes) are among the parasite genes highly expressed by T. versicolor at the parasite-host interface.Conclusions: Laser capture microdissection makes it possible to sample the small region of cells at the epicenter of parasite host interactions. The results of our analysis suggest that T. versicolor's generalist strategy involves a reliance on overlapping but distinct gene sets, depending upon the host plant it is parasitizing. The massive upregulation of a T. versicolor β-expansin is suggestive of a mechanism for parasite success on grass hosts. In this preliminary study of the interface transcriptomes, we have shown that T. versicolor, and the Orobanchaceae in general, provide excellent opportunities for the characterization of plant genes with unknown functions.

Original language	English (US)
Article number	9
Journal	BMC Plant Biology
Volume	13
Issue number	1
DOIs	https://doi.org/10.1186/1471-2229-13-9
State	Published - Jan 9 2013

Funding

The authors gratefully acknowledge partial funding for this project through NSF Plant Genome award DBI-0701748 to Westwood JH, dePamphilis CW, Timko MP, and Yoder JI, NSF award IOS-0821954 and IOS-1104334 to Taylor CG, McIntyre L and Koch, K, and the Intercollege Graduate Program in Plant Biology and Department of Biology of Penn State University. We thank Paula Ralph for lab assistance and Yongde Bao (University of Virginia) for Illumina sequencing. We also thank Daniel J. Cosgrove for helpful discussion and encouragement throughout the course of this research. We thank dePamphilis lab members past and present for their assistance with various aspects of this work, and two anonymous reviewers for helpful comments.

Keywords

Burkholderia
De novo assembly
Expansin
Generalist parasite
Illumina
Laser microdissection
Maize
Medicago
Orobanchaceae
Parasitic plant
RNA-Seq
Transcriptome
Triphysaria

ASJC Scopus subject areas

Plant Science

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10.1186/1471-2229-13-9

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Honaas, L. A., Wafula, E. K., Yang, Z., Der, J. P., Wickett, N. J., Altman, N. S., Taylor, C. G., Yoder, J. I., Timko, M. P., Westwood, J. H., & dePamphilis, C. W. (2013). Functional genomics of a generalist parasitic plant: Laser microdissection of host-parasite interface reveals host-specific patterns of parasite gene expression. BMC Plant Biology, 13(1), Article 9. https://doi.org/10.1186/1471-2229-13-9

@article{768e0eae4f3743c294d16eab5a00788a,

title = "Functional genomics of a generalist parasitic plant: Laser microdissection of host-parasite interface reveals host-specific patterns of parasite gene expression",

abstract = "Background: Orobanchaceae is the only plant family with members representing the full range of parasitic lifestyles plus a free-living lineage sister to all parasitic lineages, Lindenbergia. A generalist member of this family, and an important parasitic plant model, Triphysaria versicolor regularly feeds upon a wide range of host plants. Here, we compare de novo assembled transcriptomes generated from laser micro-dissected tissues at the host-parasite interface to uncover details of the largely uncharacterized interaction between parasitic plants and their hosts.Results: The interaction of Triphysaria with the distantly related hosts Zea mays and Medicago truncatula reveals dramatic host-specific gene expression patterns. Relative to above ground tissues, gene families are disproportionally represented at the interface including enrichment for transcription factors and genes of unknown function. Quantitative Real-Time PCR of a T. versicolor β-expansin shows strong differential (120x) upregulation in response to the monocot host Z. mays; a result that is concordant with our read count estimates. Pathogenesis-related proteins, other cell wall modifying enzymes, and orthologs of genes with unknown function (annotated as such in sequenced plant genomes) are among the parasite genes highly expressed by T. versicolor at the parasite-host interface.Conclusions: Laser capture microdissection makes it possible to sample the small region of cells at the epicenter of parasite host interactions. The results of our analysis suggest that T. versicolor's generalist strategy involves a reliance on overlapping but distinct gene sets, depending upon the host plant it is parasitizing. The massive upregulation of a T. versicolor β-expansin is suggestive of a mechanism for parasite success on grass hosts. In this preliminary study of the interface transcriptomes, we have shown that T. versicolor, and the Orobanchaceae in general, provide excellent opportunities for the characterization of plant genes with unknown functions.",

keywords = "Burkholderia, De novo assembly, Expansin, Generalist parasite, Illumina, Laser microdissection, Maize, Medicago, Orobanchaceae, Parasitic plant, RNA-Seq, Transcriptome, Triphysaria",

author = "Honaas, {Loren A.} and Wafula, {Eric K.} and Zhenzhen Yang and Der, {Joshua P.} and Wickett, {Norman J.} and Altman, {Naomi S.} and Taylor, {Christopher G.} and Yoder, {John I.} and Timko, {Michael P.} and Westwood, {James H.} and dePamphilis, {Claude W.}",

note = "Funding Information: The authors gratefully acknowledge partial funding for this project through NSF Plant Genome award DBI-0701748 to Westwood JH, dePamphilis CW, Timko MP, and Yoder JI, NSF award IOS-0821954 and IOS-1104334 to Taylor CG, McIntyre L and Koch, K, and the Intercollege Graduate Program in Plant Biology and Department of Biology of Penn State University. We thank Paula Ralph for lab assistance and Yongde Bao (University of Virginia) for Illumina sequencing. We also thank Daniel J. Cosgrove for helpful discussion and encouragement throughout the course of this research. We thank dePamphilis lab members past and present for their assistance with various aspects of this work, and two anonymous reviewers for helpful comments.",

year = "2013",

month = jan,

day = "9",

doi = "10.1186/1471-2229-13-9",

language = "English (US)",

volume = "13",

journal = "BMC Plant Biology",

issn = "1471-2229",

publisher = "BioMed Central",

number = "1",

}

Honaas, LA, Wafula, EK, Yang, Z, Der, JP, Wickett, NJ, Altman, NS, Taylor, CG, Yoder, JI, Timko, MP, Westwood, JH & dePamphilis, CW 2013, 'Functional genomics of a generalist parasitic plant: Laser microdissection of host-parasite interface reveals host-specific patterns of parasite gene expression', BMC Plant Biology, vol. 13, no. 1, 9. https://doi.org/10.1186/1471-2229-13-9

TY - JOUR

T1 - Functional genomics of a generalist parasitic plant

T2 - Laser microdissection of host-parasite interface reveals host-specific patterns of parasite gene expression

AU - Honaas, Loren A.

AU - Wafula, Eric K.

AU - Yang, Zhenzhen

AU - Der, Joshua P.

AU - Wickett, Norman J.

AU - Altman, Naomi S.

AU - Taylor, Christopher G.

AU - Yoder, John I.

AU - Timko, Michael P.

AU - Westwood, James H.

AU - dePamphilis, Claude W.

N1 - Funding Information: The authors gratefully acknowledge partial funding for this project through NSF Plant Genome award DBI-0701748 to Westwood JH, dePamphilis CW, Timko MP, and Yoder JI, NSF award IOS-0821954 and IOS-1104334 to Taylor CG, McIntyre L and Koch, K, and the Intercollege Graduate Program in Plant Biology and Department of Biology of Penn State University. We thank Paula Ralph for lab assistance and Yongde Bao (University of Virginia) for Illumina sequencing. We also thank Daniel J. Cosgrove for helpful discussion and encouragement throughout the course of this research. We thank dePamphilis lab members past and present for their assistance with various aspects of this work, and two anonymous reviewers for helpful comments.

PY - 2013/1/9

Y1 - 2013/1/9

N2 - Background: Orobanchaceae is the only plant family with members representing the full range of parasitic lifestyles plus a free-living lineage sister to all parasitic lineages, Lindenbergia. A generalist member of this family, and an important parasitic plant model, Triphysaria versicolor regularly feeds upon a wide range of host plants. Here, we compare de novo assembled transcriptomes generated from laser micro-dissected tissues at the host-parasite interface to uncover details of the largely uncharacterized interaction between parasitic plants and their hosts.Results: The interaction of Triphysaria with the distantly related hosts Zea mays and Medicago truncatula reveals dramatic host-specific gene expression patterns. Relative to above ground tissues, gene families are disproportionally represented at the interface including enrichment for transcription factors and genes of unknown function. Quantitative Real-Time PCR of a T. versicolor β-expansin shows strong differential (120x) upregulation in response to the monocot host Z. mays; a result that is concordant with our read count estimates. Pathogenesis-related proteins, other cell wall modifying enzymes, and orthologs of genes with unknown function (annotated as such in sequenced plant genomes) are among the parasite genes highly expressed by T. versicolor at the parasite-host interface.Conclusions: Laser capture microdissection makes it possible to sample the small region of cells at the epicenter of parasite host interactions. The results of our analysis suggest that T. versicolor's generalist strategy involves a reliance on overlapping but distinct gene sets, depending upon the host plant it is parasitizing. The massive upregulation of a T. versicolor β-expansin is suggestive of a mechanism for parasite success on grass hosts. In this preliminary study of the interface transcriptomes, we have shown that T. versicolor, and the Orobanchaceae in general, provide excellent opportunities for the characterization of plant genes with unknown functions.

AB - Background: Orobanchaceae is the only plant family with members representing the full range of parasitic lifestyles plus a free-living lineage sister to all parasitic lineages, Lindenbergia. A generalist member of this family, and an important parasitic plant model, Triphysaria versicolor regularly feeds upon a wide range of host plants. Here, we compare de novo assembled transcriptomes generated from laser micro-dissected tissues at the host-parasite interface to uncover details of the largely uncharacterized interaction between parasitic plants and their hosts.Results: The interaction of Triphysaria with the distantly related hosts Zea mays and Medicago truncatula reveals dramatic host-specific gene expression patterns. Relative to above ground tissues, gene families are disproportionally represented at the interface including enrichment for transcription factors and genes of unknown function. Quantitative Real-Time PCR of a T. versicolor β-expansin shows strong differential (120x) upregulation in response to the monocot host Z. mays; a result that is concordant with our read count estimates. Pathogenesis-related proteins, other cell wall modifying enzymes, and orthologs of genes with unknown function (annotated as such in sequenced plant genomes) are among the parasite genes highly expressed by T. versicolor at the parasite-host interface.Conclusions: Laser capture microdissection makes it possible to sample the small region of cells at the epicenter of parasite host interactions. The results of our analysis suggest that T. versicolor's generalist strategy involves a reliance on overlapping but distinct gene sets, depending upon the host plant it is parasitizing. The massive upregulation of a T. versicolor β-expansin is suggestive of a mechanism for parasite success on grass hosts. In this preliminary study of the interface transcriptomes, we have shown that T. versicolor, and the Orobanchaceae in general, provide excellent opportunities for the characterization of plant genes with unknown functions.

KW - Burkholderia

KW - De novo assembly

KW - Expansin

KW - Generalist parasite

KW - Illumina

KW - Laser microdissection

KW - Maize

KW - Medicago

KW - Orobanchaceae

KW - Parasitic plant

KW - RNA-Seq

KW - Transcriptome

KW - Triphysaria

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U2 - 10.1186/1471-2229-13-9

DO - 10.1186/1471-2229-13-9

M3 - Article

C2 - 23302495

AN - SCOPUS:84872013682

SN - 1471-2229

VL - 13

JO - BMC Plant Biology

JF - BMC Plant Biology

IS - 1

M1 - 9

ER -

Functional genomics of a generalist parasitic plant: Laser microdissection of host-parasite interface reveals host-specific patterns of parasite gene expression

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