Jan Dvorak (As Quickly Written Down by a Person with Poor Hearing…Me)

Home , Aphelia (plant), Aristida, Aristida stricta, Centrolepis, Ecdeiocolea, Ecdeiocolea monostachya

1/22/2018

The Impact of Polyploidy on Genome Evolution in Poales and Other Monocots “I don’t have to emphasize that gene duplications are the fabric of evolution in plants.”

-Jan Dvorak (as quickly written down by a person with poor hearing…me)

Michael R. McKain The University of Alabama @mrmckain @mrmckain

Poales Diversity Grass genomes: the choose your own adventure of genome evolution • ~22,800 species • ~11,088 species in Poaceae • Transposons (McClintock, Wessler) • GC content bias (Carels and Bernardi 2000) • Three WGD events

0 • rho (Peterson et al. 2004) 3

• 0

sigma (Tang et al. 2010) 0

• tau (Tang et al. 2010, Jiao et al. 2014) 0 %GC

Givnish et al. 2010 @mrmckain Schnable et al., 2009

Zeroing in on WGD placement

Banana genome Pineapple genome

How has ancient polyploidy altered the genomic landscape in grasses and other Poales?

D’Hont et al. 2012 Ming, VanBuren et al. 2015

Recovered sigma after grass divergence from commelinids Recovered sigma after grass+pineapple divergence from commelinids @mrmckain @mrmckain

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Phylotranscriptomic approach Coalescence-based Phylogeny of 234 Single-copy genes

• Sampling 27 transcriptomes and 7 genomes • Phylogeny consistent with previous • Representation for all families (except Thurniaceae) in nuclear gene results Poales • Conflicting topology with • RNA from young leaf or apical meristem, a combination of chloroplast genome tree: Moncot Tree of Life and 1KP • Ecdeiocolea/Joinvillea sister instead of • General steps: a grade • Trinity assembly • Typha sister to Poales, not • Orthogroup circumscription using a curated 22-genome dataset Bromeliaceae • Aligned amino acids with MUSCLE and created codon alignments with PAL2NAL • Gene tree reconstruction using RAxML

Streptochaeta angustifolia Picture by: Jerry Davis @mrmckain @mrmckain Astral v.4.7.6

Placement of WGD Using PUG How we identify putative paralogs matters

• PUG (Phylogenetic Placement of Polyploidy Using Genomes)

Ecdeiocolea

Streptochaeta’

Streptochaeta

Sorghum’

Sorghum Sorghum

Sorghum’

Oryza’ Oryza • https://github.com/mrmckain/PUG Oryza • Queries a gene tree against a species tree using a focal putative paralog pair

Ecdeiocolea SyntenyAnalysis Tang et al. 2010 Multilabeled Gene Trees

Streptochaeta’

Streptochaeta Streptochaeta

Sorghum’

Sorghum Sorghum

Sorghum’

Oryza’

Oryza Oryza Oryza’

VS.

Testing for Poaceae Origin Hypothesis @mrmckain @mrmckain Ks Frequency Plots

Synteny-derived Paralogs Ks frequency plot-derived Paralogs

Sorghum bicolor Aristida stricta • Synteny from rice and sorghum genomes Total LCAs Dendrocalamus latiflorus r Brachypodium distachyon • Identification of 0 209 417 Oryza sativa Ecdeiocolea Streptochaeta Other Grasses Streptochaeta angustifolia • 8,267 putative rho paralog pairs Ecdeiocolea monostachya Joinvillea ascendens • 3,680 putative sigma + tau paralog pairs Flagellaria indica Chondropetalum tectorum Elegia fenestrata • Included 2,248 putative tau paralog pairs from Centrolepis monogyna Jiao et al. 2014 Lachnocaulon anceps Xyris jupicai Mayaca Lepidosperma gibsonii Cyperus papyrus • After filtering for outgroups, the PUG species tree Mapania palustris Juncus topology, and bootstrap values (80 cutoff) Stegolepis ferruginea s Neoregalia carolinae Typha Brocchina Other Poales Brocchinia reducta Typha latifolia Zingiber officinale • 411 rho LCA nodes Musa acuminata t Elaies guineensis • 26 sigma LCA nodes Phoenix dactylifera Hosta venusta • Yucca filamentosa 50 tau LCA nodes Vitis vinifera Amborella trichopoda

@mrmckain @mrmckain

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Ks frequency plot-derived Paralogs Gene tree-derived Paralogs

Sorghum bicolor Sorghum bicolor Aristida stricta Aristida stricta Total LCAs Dendrocalamus latiflorus Total LCAs Dendrocalamus latiflorus r r Brachypodium distachyon Brachypodium distachyon 235 402 615 0 51 102 Oryza sativa Oryza sativa Streptochaeta angustifolia • Streptochaeta angustifolia • Ecdeiocolea monostachya Ks frequency plots of all taxa Ecdeiocolea monostachya All possible pairs from multilabeled gene Joinvillea ascendens Joinvillea ascendens Flagellaria indica Flagellaria indica trees Chondropetalum tectorum Chondropetalum tectorum Elegia fenestrata Elegia fenestrata Centrolepis monogyna • Identification of 20,900 putative paralog pairs Centrolepis monogyna Lachnocaulon anceps Lachnocaulon anceps Xyris jupicai Xyris jupicai • Identification of 1,870,214 putative paralog Mayaca Mayaca Lepidosperma gibsonii Lepidosperma gibsonii Cyperus papyrus Cyperus papyrus pairs Mapania palustris • After filtering: 667 map to 343 unique LCA Mapania palustris Juncus • Most of these are isoforms/alleles Juncus Stegolepis ferruginea Stegolepis ferruginea nodes s s Neoregalia carolinae Neoregalia carolinae Brocchinia reducta Brocchinia reducta Typha latifolia Typha latifolia Zingiber officinale g Zingiber officinale b a Musa acuminata • After filtering: 36,567 map to 5,455 unique Musa acuminata t Elaies guineensis Elaies guineensis Phoenix dactylifera Phoenix dactylifera LCA nodes Hosta venusta Hosta venusta Yucca filamentosa Yucca filamentosa Vitis vinifera Vitis vinifera Amborella trichopoda Amborella trichopoda

@mrmckain @mrmckain

Summary of Gene Tree Polyploidy Support GC Content Evolution in Grasses

Event Synteny Ks Plots Gene Trees • Bimodal distribution of genic GC content rho (grass) 411 78 610 • 5’  3’ decreasing GC content gradient sigma (Poales) 26 22 235 • Positive correlation with recombination rate tau (monocot) 88 0 410 • Negative correlation with DNA methylation Restionaceae 0 102 499 • GC biased gene conversion Centrolepidaceae 0 0 200 • Recombination driven Restiid 0 15 184 • GC3 bias/codon usage bias Juncus 0 29 423 Cyperus 0 0 463 • Gene length (longer more GC) Zingiberales 0 0 377 • Increased expression Palms 0 0 345 Glémin et al. 2014 Agavoideae 0 0 615

@mrmckain @mrmckain

0.45 0.55 0.65 %GC

GC content across Sorghum_bicolor Aristida_stricta 13,798 orthogroups Dendrocalamus_latiflorus Brachypodium_distachyon Oryza_sativa Poaceae Streptochaeta_angustifolia Ecdeiocolea_monostachya How has ancient polyploidy altered the genomic Joinvillea_ascendens Flagellaria_indica Chondropetalum_tector um Elegia_fenestrata landscape in grasses and other Poales? Aphelia_sp. Aphelia, Centrolepediaceae Centrolepis_monogyna Lachnocaulon_anceps Lachnocaulon, Eriocaulaceae Xyris_jupicai Mayaca_sp. Xyris, Xyridaceae Mayaca_fluviatilis Lepidosperma_gibsonii Is there a connection between polyploidy and the Cyperus_papyrus Cyperus_alternifolius Mapania_palustris Juncus_inflexus grass bimodal GC distribution? Juncus_effusus Stegolepis_ferruginea Stegolepis, Rapateaceae Neoregalia_carolinae Brocchinia_reducta Neoregalia, Bromeliaceae Typha_latifolia Typha_angustifolia Zingiber_officinale Musa_acuminata Elaies_guineensis Phoenix_dactylifera • Position normalized across Hosta_venusta Yucca_filamentosa Vitis_vinifera alignment to 1% alignment Amborella_trichopoda

1 0 0 0 0 0 0 0 0 0 0 length increments

1 2 3 4 5 6 7 8 9 0

1 @mrmckain @mrmckain Normalize Position Across All Orthogroups

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0 4 8 12 Percent Genes

Sorghum_bicolor Aristida_stricta Dendrocalamus_latiflorus Identification of GC bimodality 0 4 8 12 Brachypodium_distachyon Oryza_sativa Percent Genes Streptochaeta_angustifolia GC content across Ecdeiocolea_monostachya Joinvillea_ascendens 13,798 orthogroups Sorghum_bicolorFlagellaria_indica • Reject null hypothesis of Hartigan’s dip test Aristida_strictaChondropetalum_tector um DendrocalamElegia_fus_latiflorenestrus ata for unimodality for seven taxa Brachypodium_distachAphelia_spy.on Oryza_sativaCentrolepis_monogyna Streptochaeta_angustifLachnocaulon_ancepsolia • Kmeans clustering used to identify the high Patterns of GC: Ecdeiocolea_monostachXyris_jupicaiya Joinvillea_ascendensMayaca_sp. and low means for these taxa • Unimodal-tight distribution Flagellaria_indicaMayaca_fluviatilis Chondropetalum_tectorLepidosperma_gibsoniium • Unimodal-broad distribution Elegia_fenestrCyperata us_papyrus • Bimodal Aphelia_sp. Cyperus_alternifolius Centrolepis_monogynaMapania_palustris Lachnocaulon_ancepsJuncus_inflexus Xyris_jupicaiJuncus_effusus Mayaca_sp.Stegolepis_ferruginea Combined GC Kmeans Results: Mayaca_fluviatilisNeoregalia_carolinae Lepidosperma_gibsoniiBrocchinia_reducta Low: 46.7% Cyperus_papTypha_latifyrus olia Cyperus_alterTypha_angustifnifolius olia Mapania_palustrZingiber_officinaleis High: 63.7% Juncus_infleMusa_acuminataxus Juncus_effususElaies_guineensis Stegolepis_fPhoenix_dactyliferruginea era Neoregalia_carolinaeHosta_venusta Brocchinia_reductaYucca_filamentosa Typha_latifoliaVitis_vinifera Typha_angustifAmborella_trolia ichopoda Zingiber_officinale

5 0 5 0 5 0 5 0 5 0 5 0 5 @mrmckain 2 3 3 4 4 5 5 6 6 7 7 Musa_acuminata8 8 @mrmckain Percent GC Elaies_guineensis Phoenix_dactylifera Hosta_venusta Yucca_filamentosa Vitis_vinifera Amborella_trichopoda

5 0 5 0 5 0 5 0 5 0 5 0 5

2 3 3 4 4 5 5 6 6 7 7 8 8 Percent GC

Classification of Orthogroups by GC Content High/Low GC Orthogroup Distributions

2 • High GC—75% or more of transcripts for a given taxon in an 0 0 High GC High GC High GC

Low GC 0 Low GC Low GC

0 orthogroup are clustered as high GC (63.7%) 8

• 3,662 orthogroups 0

y y y

c c c

n n n

e e e

u u u

q q q

e e e

r r r

F F F

• Low GC—75% or more of transcripts for a given taxon in an 1

0 orthogroups are clustered as low GC (46.7%) 0

2 • 6,770 orthogroups 5

0 0 0

0.0 0.2 0.4 0.6 0.8 1.0 0.0 0.2 0.4 0.6 0.8 1.0 0.0 0.2 0.4 0.6 0.8 1.0 • Mixed GC—remaining orthogroups that do not fall into other classes Percent GC Percent GC Percent GC • 2,595 orthogroups All Taxa Juncus effusus Brachypodiumdistachyon 44.8% Mean GC 56.3% Mean GC @mrmckain @mrmckain

Comparison of paralog retention across WGD and high/low GC orthogroups Summary

• Polyploid events likely occurred prior to the diversification of Poaceae (rho) and Poales (sigma) • Gene tree-derived paralogs more abundant and useful in identifying WGD than synteny or Ks frequency plots • Bimodal GC distribution result of high and low GC gene families • Maintenance of high/low GC gene families in Poales regardless of overall GC content • Paralogs more likely to be lost in high GC gene families High %GC orthogroups more likely to lose duplicated genes

@mrmckain @mrmckain

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Co-authors: • Haibao Tang, Center for Genomics and Biotechnology, Fujian Agriculture and • Funding Forestry University, Fuzhou, China – NSF: DEB-0830009 • Joel McNeal, Kennesaw State University, Kennesaw, GA – NSF: DEB-1010905 • Saravanaraj Ayyampalayam, University of Georgia, Athens, GA • Claude W. dePamphilis, The Pennsylvania State University, University • Thanks to: Park, PA • Thomas J Givnish, Department of – Gane Ka-Shu Wong (University Botany. UW-Madison, Madison, WI of Alberta) • J. Chris Pires, Division of Biological Sciences, University of Missouri, Columbia, MO • Dennis Wm. Stevenson, New York Botanical Garden, Bronx, NY • Jim Leebens-Mack, University of @mrmckain Georgia, Athens, GA

Identification of rho, the grass WGD event

Dot-plot of rice genome syntenic regions Timing of grass WGD event

rho event described as predating Poaceae divergence @mrmckain Paterson et al. 2004

Fine-Scale Placement Requires Strategic Taxonomic Sampling Polyploidy is prevalent in flowering plants

• Sampling each lineage off of the backbone • Streptochaeta • First branch in grasses • Typha (cattail corn dog grass) • Contender with pineapple for first branch in Poales

Givnish et al. 2010

@mrmckain CoGepedia

5 1/22/2018

Michael McKain1,2, Haibao Tang3, Joel McNeal4, Saravanaraj Ayyampalayam5, Claude W. dePamphilis6, Thomas J Givnish7, J. Chris Pires8, Dennis Wm. Stevenson9 and Jim Leebens-Mack5