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 C. Majure, Urs Eggli, Stephen A. Smith

Research output: Contribution to journalArticle

2 Citations (Scopus)

Abstract

Several plant lineages have evolved adaptations that allow survival in extreme and harsh environments including many families within the plant clade Portulacineae (Caryophyllales) such as the Cactaceae, Didiereaceae, and Montiaceae. Here, using newly generated transcriptomic data, we reconstructed the phylogeny of Portulacineae and examined potential correlates between molecular evolution and adaptation to harsh environments. Our phylogenetic results were largely congruent with previous analyses, but we identified several early diverging nodes characterized by extensive gene tree conflict. For particularly contentious nodes, we present detailed information about the phylogenetic signal for alternative relationships. We also analyzed the frequency of gene duplications, confirmed previously identified whole genome duplications (WGD), and proposed a previously unidentified WGD event within the Didiereaceae. We found that the WGD events were typically associated with shifts in climatic niche but did not find a direct association with WGDs and diversification rate shifts. Diversification shifts occurred within the Portulacaceae, Cactaceae, and Anacampserotaceae, and whereas these did not experience WGDs, the Cactaceae experienced extensive gene duplications. We examined gene family expansion and molecular evolutionary patterns with a focus on genes associated with environmental stress responses and found evidence for significant gene family expansion in genes with stress adaptation and clades found in extreme environments. These results provide important directions for further and deeper examination of the potential links between molecular evolutionary patterns and adaptation to harsh environments.

Original languageEnglish (US)
Pages (from-to)112-126
Number of pages15
JournalMolecular biology and evolution
Volume36
Issue number1
DOIs
StatePublished - Jan 1 2019

Fingerprint

Family Conflict
Cactaceae
Didiereaceae
gene
Gene Duplication
Genes
Genome
gene duplication
Anacampserotaceae
genes
Portulacaceae
Montiaceae
genome
phylogeny
Caryophyllales
Molecular Evolution
Phylogeny
transcriptomics
phylogenetics
stress response

Keywords

  • Portulacineae
  • gene duplication
  • gene tree conflict
  • molecular evolution
  • paleopolyploidy
  • stress adaptation

PubMed: MeSH publication types

  • Journal Article
  • Research Support, U.S. Gov't, Non-P.H.S.

Cite this

Evolution of Portulacineae Marked by Gene Tree Conflict and Gene Family Expansion Associated with Adaptation to Harsh Environments. / Wang, Ning; Yang, Ya; Moore, Michael J.; Brockington, Samuel F.; Walker, Joseph F.; Brown, Joseph W.; Liang, Bin; Feng, Tao; Edwards, Caroline; Mikenas, Jessica; Olivieri, Julia; Hutchison, Vera; Timoneda, Alfonso; Stoughton, Tommy; Puente, Raúl; Majure, Lucas C.; Eggli, Urs; Smith, Stephen A.

In: Molecular biology and evolution, Vol. 36, No. 1, 01.01.2019, p. 112-126.

Research output: Contribution to journalArticle

Wang, N, Yang, Y, Moore, MJ, Brockington, SF, Walker, JF, Brown, JW, Liang, B, Feng, T, Edwards, C, Mikenas, J, Olivieri, J, Hutchison, V, Timoneda, A, Stoughton, T, Puente, R, Majure, LC, Eggli, U & Smith, SA 2019, 'Evolution of Portulacineae Marked by Gene Tree Conflict and Gene Family Expansion Associated with Adaptation to Harsh Environments', Molecular biology and evolution, vol. 36, no. 1, pp. 112-126. https://doi.org/10.1093/molbev/msy200
Wang, Ning ; Yang, Ya ; Moore, Michael J. ; Brockington, Samuel F. ; Walker, Joseph F. ; Brown, Joseph W. ; Liang, Bin ; Feng, Tao ; Edwards, Caroline ; Mikenas, Jessica ; Olivieri, Julia ; Hutchison, Vera ; Timoneda, Alfonso ; Stoughton, Tommy ; Puente, Raúl ; Majure, Lucas C. ; Eggli, Urs ; Smith, Stephen A. / Evolution of Portulacineae Marked by Gene Tree Conflict and Gene Family Expansion Associated with Adaptation to Harsh Environments. In: Molecular biology and evolution. 2019 ; Vol. 36, No. 1. pp. 112-126.
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