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Evolution of Portulacineae marked by gene tree conflict and gene family expansion associated with adaptation to harsh environments

Ning Wang, Ya Yang, Michael J. Moore, Samuel F. Brockington, Joseph F. Walker, Joseph W Brown, Bin Liang, Tao Feng, Caroline Edwards, Jessica Mikenas, Julia Olivieri, Vera Hutchison, Alfonso Timoneda, Tommy Stoughton, Raúl Puente, Lucas Majure, Urs Eggli, Stephen A. Smith
doi: https://doi.org/10.1101/294546
Ning Wang
1Department of Ecology & Evolutionary Biology, University of Michigan, 830 North University Avenue, Ann Arbor, MI 48109-1048, USA
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Ya Yang
2Department of Plant and Microbial Biology, University of Minnesota-Twin Cities. 1445 Gortner Avenue, St. Paul, MN 55108 USA
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Michael J. Moore
3Department of Biology, Oberlin College, Science Center K111, 119 Woodland St., Oberlin, Ohio 44074 USA
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Samuel F. Brockington
4Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom
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Joseph F. Walker
1Department of Ecology & Evolutionary Biology, University of Michigan, 830 North University Avenue, Ann Arbor, MI 48109-1048, USA
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Joseph W Brown
5Department of Animal and Plant Sciences, University of Sheffield, Western Bank, Sheffield S10 2TN, United Kingdom
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Bin Liang
1Department of Ecology & Evolutionary Biology, University of Michigan, 830 North University Avenue, Ann Arbor, MI 48109-1048, USA
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Tao Feng
4Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom
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Caroline Edwards
3Department of Biology, Oberlin College, Science Center K111, 119 Woodland St., Oberlin, Ohio 44074 USA
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Jessica Mikenas
3Department of Biology, Oberlin College, Science Center K111, 119 Woodland St., Oberlin, Ohio 44074 USA
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Julia Olivieri
3Department of Biology, Oberlin College, Science Center K111, 119 Woodland St., Oberlin, Ohio 44074 USA
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Vera Hutchison
3Department of Biology, Oberlin College, Science Center K111, 119 Woodland St., Oberlin, Ohio 44074 USA
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Alfonso Timoneda
4Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom
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Tommy Stoughton
6Center for the Environment, MSC 63, Plymouth State University, 17 High Street Plymouth, NH 03264 USA
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Raúl Puente
7Department of Research, Conservation and Collections, Desert Botanical Garden, 1201 N. Galvin Pkwy, Phoenix, AZ 85008 USA
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Lucas Majure
7Department of Research, Conservation and Collections, Desert Botanical Garden, 1201 N. Galvin Pkwy, Phoenix, AZ 85008 USA
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Urs Eggli
8Sukkulenten-Sammlung Zürich, Mythenquai 88, CH-8002 Zürich, Switzerland
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Stephen A. Smith
1Department of Ecology & Evolutionary Biology, University of Michigan, 830 North University Avenue, Ann Arbor, MI 48109-1048, USA
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Abstract

Survival in harsh environments is associated with several adaptations in plants. Species in the Portulacineae (Caryophyllales) have adapted to some of the most extreme terrestrial conditions on Earth, including extreme heat, cold, and salinity. Here, we generated 52 new transcriptomes and combined these with 30 previously generated transcriptomes, forming a dataset containing 68 species of Portulacinaeae, seven from its sister clade Molluginaceae, and seven outgroups. We performed a phylotranscriptomic analysis to examine patterns of molecular evolution within the Portulacineae. Our inferred species tree topology was largely congruent with previous analyses. We also identified several nodes that were characterized by excessive gene tree conflict and examined the potential influence of outlying genes. We identified gene duplications throughout the Portulacineae, and found corroborating evidence for previously identified paleopolyploidy events along with one newly identified event associated with the family Didiereaceae. Gene family expansion within Portulacineae was associated with genes previously identified as important for survival in extreme conditions, indicating possible molecular correlates of niche changes that should be explored further. Some of these genes also showed some evidence for positive selection. The correlation between gene function and expansion suggests that gene/genome duplication have likely contributed to the extreme adaptations seen in the Portulacineae.

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Posted April 05, 2018.
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Evolution of Portulacineae marked by gene tree conflict and gene family expansion associated with adaptation to harsh environments
Ning Wang, Ya Yang, Michael J. Moore, Samuel F. Brockington, Joseph F. Walker, Joseph W Brown, Bin Liang, Tao Feng, Caroline Edwards, Jessica Mikenas, Julia Olivieri, Vera Hutchison, Alfonso Timoneda, Tommy Stoughton, Raúl Puente, Lucas Majure, Urs Eggli, Stephen A. Smith
bioRxiv 294546; doi: https://doi.org/10.1101/294546
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Evolution of Portulacineae marked by gene tree conflict and gene family expansion associated with adaptation to harsh environments
Ning Wang, Ya Yang, Michael J. Moore, Samuel F. Brockington, Joseph F. Walker, Joseph W Brown, Bin Liang, Tao Feng, Caroline Edwards, Jessica Mikenas, Julia Olivieri, Vera Hutchison, Alfonso Timoneda, Tommy Stoughton, Raúl Puente, Lucas Majure, Urs Eggli, Stephen A. Smith
bioRxiv 294546; doi: https://doi.org/10.1101/294546

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