Hardwood tree genomics

Unlocking woody plant biology

Gerald A. Tuskan, Andrew T. Groover, Jeremy Schmutz, Stephen Paul DiFazio, Alexander Myburg, Dario Grattapaglia, Lawrence B. Smart, Tongming Yin, Jean Marc Aury, Antoine Kremer, Thibault Leroy, Gregoire Le Provost, Christophe Plomion, John Edward Carlson, Jennifer Randall, Jared Westbrook, Jane Grimwood, Wellington Muchero, Daniel Jacobson, Joshua K. Michener

Research output: Contribution to journalShort survey

Abstract

Woody perennial angiosperms (i.e., hardwood trees) are polyphyletic in origin and occur in most angiosperm orders. Despite their independent origins, hardwoods have shared physiological, anatomical, and life history traits distinct from their herbaceous relatives. New high-throughput DNA sequencing platforms have provided access to numerous woody plant genomes beyond the early reference genomes of Populus and Eucalyptus, references that now include willow and oak, with pecan and chestnut soon to follow. Genomic studies within these diverse and undomesticated species have successfully linked genes to ecological, physiological, and developmental traits directly. Moreover, comparative genomic approaches are providing insights into speciation events while large-scale DNA resequencing of native collections is identifying population-level genetic diversity responsible for variation in key woody plant biology across and within species. Current research is focused on developing genomic prediction models for breeding, defining speciation and local adaptation, detecting and characterizing somatic mutations, revealing the mechanisms of gender determination and flowering, and application of systems biology approaches to model complex regulatory networks underlying quantitative traits. Emerging technologies such as single-molecule, long-read sequencing is being employed as additional woody plant species, and genotypes within species, are sequenced, thus enabling a comparative (“evo-devo”) approach to understanding the unique biology of large woody plants. Resource availability, current genomic and genetic applications, new discoveries and predicted future developments are illustrated and discussed for poplar, eucalyptus, willow, oak, chestnut, and pecan.

Original languageEnglish (US)
Article number1799
JournalFrontiers in Plant Science
Volume871
DOIs
StatePublished - Jan 1 2018

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Hardwoods
Genes
DNA
Throughput
Availability
Molecules
Genomics

All Science Journal Classification (ASJC) codes

  • Plant Science

Cite this

Tuskan, G. A., Groover, A. T., Schmutz, J., DiFazio, S. P., Myburg, A., Grattapaglia, D., ... Michener, J. K. (2018). Hardwood tree genomics: Unlocking woody plant biology. Frontiers in Plant Science, 871, [1799]. https://doi.org/10.3389/fpls.2018.01799
Tuskan, Gerald A. ; Groover, Andrew T. ; Schmutz, Jeremy ; DiFazio, Stephen Paul ; Myburg, Alexander ; Grattapaglia, Dario ; Smart, Lawrence B. ; Yin, Tongming ; Aury, Jean Marc ; Kremer, Antoine ; Leroy, Thibault ; Le Provost, Gregoire ; Plomion, Christophe ; Carlson, John Edward ; Randall, Jennifer ; Westbrook, Jared ; Grimwood, Jane ; Muchero, Wellington ; Jacobson, Daniel ; Michener, Joshua K. / Hardwood tree genomics : Unlocking woody plant biology. In: Frontiers in Plant Science. 2018 ; Vol. 871.
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abstract = "Woody perennial angiosperms (i.e., hardwood trees) are polyphyletic in origin and occur in most angiosperm orders. Despite their independent origins, hardwoods have shared physiological, anatomical, and life history traits distinct from their herbaceous relatives. New high-throughput DNA sequencing platforms have provided access to numerous woody plant genomes beyond the early reference genomes of Populus and Eucalyptus, references that now include willow and oak, with pecan and chestnut soon to follow. Genomic studies within these diverse and undomesticated species have successfully linked genes to ecological, physiological, and developmental traits directly. Moreover, comparative genomic approaches are providing insights into speciation events while large-scale DNA resequencing of native collections is identifying population-level genetic diversity responsible for variation in key woody plant biology across and within species. Current research is focused on developing genomic prediction models for breeding, defining speciation and local adaptation, detecting and characterizing somatic mutations, revealing the mechanisms of gender determination and flowering, and application of systems biology approaches to model complex regulatory networks underlying quantitative traits. Emerging technologies such as single-molecule, long-read sequencing is being employed as additional woody plant species, and genotypes within species, are sequenced, thus enabling a comparative (“evo-devo”) approach to understanding the unique biology of large woody plants. Resource availability, current genomic and genetic applications, new discoveries and predicted future developments are illustrated and discussed for poplar, eucalyptus, willow, oak, chestnut, and pecan.",
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Tuskan, GA, Groover, AT, Schmutz, J, DiFazio, SP, Myburg, A, Grattapaglia, D, Smart, LB, Yin, T, Aury, JM, Kremer, A, Leroy, T, Le Provost, G, Plomion, C, Carlson, JE, Randall, J, Westbrook, J, Grimwood, J, Muchero, W, Jacobson, D & Michener, JK 2018, 'Hardwood tree genomics: Unlocking woody plant biology', Frontiers in Plant Science, vol. 871, 1799. https://doi.org/10.3389/fpls.2018.01799

Hardwood tree genomics : Unlocking woody plant biology. / Tuskan, Gerald A.; Groover, Andrew T.; Schmutz, Jeremy; DiFazio, Stephen Paul; Myburg, Alexander; Grattapaglia, Dario; Smart, Lawrence B.; Yin, Tongming; Aury, Jean Marc; Kremer, Antoine; Leroy, Thibault; Le Provost, Gregoire; Plomion, Christophe; Carlson, John Edward; Randall, Jennifer; Westbrook, Jared; Grimwood, Jane; Muchero, Wellington; Jacobson, Daniel; Michener, Joshua K.

In: Frontiers in Plant Science, Vol. 871, 1799, 01.01.2018.

Research output: Contribution to journalShort survey

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T2 - Unlocking woody plant biology

AU - Tuskan, Gerald A.

AU - Groover, Andrew T.

AU - Schmutz, Jeremy

AU - DiFazio, Stephen Paul

AU - Myburg, Alexander

AU - Grattapaglia, Dario

AU - Smart, Lawrence B.

AU - Yin, Tongming

AU - Aury, Jean Marc

AU - Kremer, Antoine

AU - Leroy, Thibault

AU - Le Provost, Gregoire

AU - Plomion, Christophe

AU - Carlson, John Edward

AU - Randall, Jennifer

AU - Westbrook, Jared

AU - Grimwood, Jane

AU - Muchero, Wellington

AU - Jacobson, Daniel

AU - Michener, Joshua K.

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N2 - Woody perennial angiosperms (i.e., hardwood trees) are polyphyletic in origin and occur in most angiosperm orders. Despite their independent origins, hardwoods have shared physiological, anatomical, and life history traits distinct from their herbaceous relatives. New high-throughput DNA sequencing platforms have provided access to numerous woody plant genomes beyond the early reference genomes of Populus and Eucalyptus, references that now include willow and oak, with pecan and chestnut soon to follow. Genomic studies within these diverse and undomesticated species have successfully linked genes to ecological, physiological, and developmental traits directly. Moreover, comparative genomic approaches are providing insights into speciation events while large-scale DNA resequencing of native collections is identifying population-level genetic diversity responsible for variation in key woody plant biology across and within species. Current research is focused on developing genomic prediction models for breeding, defining speciation and local adaptation, detecting and characterizing somatic mutations, revealing the mechanisms of gender determination and flowering, and application of systems biology approaches to model complex regulatory networks underlying quantitative traits. Emerging technologies such as single-molecule, long-read sequencing is being employed as additional woody plant species, and genotypes within species, are sequenced, thus enabling a comparative (“evo-devo”) approach to understanding the unique biology of large woody plants. Resource availability, current genomic and genetic applications, new discoveries and predicted future developments are illustrated and discussed for poplar, eucalyptus, willow, oak, chestnut, and pecan.

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Tuskan GA, Groover AT, Schmutz J, DiFazio SP, Myburg A, Grattapaglia D et al. Hardwood tree genomics: Unlocking woody plant biology. Frontiers in Plant Science. 2018 Jan 1;871. 1799. https://doi.org/10.3389/fpls.2018.01799