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Comparative Analysis of Whole Flower Transcriptomes in the Zingiberales

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Comparative Analysis of Whole Flower Transcriptomes in the Zingiberales 1/25/2019 Summary of the talk California State University East Bay Department of Biological Sciences Almeida Lab - Introduction: - The Zingiberales order - Flower morphology in the Zingiberales - Hypothesis Comparative analysis of whole flower transcriptomes in the Zingiberales - Methods: data collection and analysis Ana Almeida; Alma Piñeyro-Nelson; Roxana Yockteng; Chelsea Specht - Results and discussion - OrthoFinder Ana Almeida - Blastn to oil palm - Transcription factors - Concluding remarks January 2019 Diversification of flower morphology The Zingiberales order Marantaceae g inger inger clade Cannaceae Zingiberaceae Costaceae b Lowiaceae anana group Strelitziaceae Heliconiaceae Musaceae (Saas et al. 2016, PeerJ) Flower morphology in the Musaceae The Zingiberales order Musa basjoo Marantaceae g inger inger clade Cannaceae Orchidantha Heliconia Zingiberaceae Costaceae b Lowiaceae anana group Strelitziaceae Musa Bird-of-paradise Heliconiaceae Musaceae 1 cm (Saas et al. 2016, PeerJ) 1 1/25/2019 The Zingiberales order Flower morphology in the Zingiberales Canna Cardamom Reduction to 1 fertile stamen Marantaceae g Petaloid staminodes inger inger clade Cannaceae Fusion of Reduction to ½ staminodes fertile stamen Costus Tumeric Zingiberaceae Costaceae b Lowiaceae anana group Ginger Strelitziaceae Musa basjoo Costus spicatus Canna sp. Calathea Heliconiaceae Musaceae (Saas et al. 2016, PeerJ) (modif from Specht et al. 2012, Bot Rev) Flower morphology in the Zingiberales Working hypothesis Mechanisms of floral Marantaceae g diversification inger inger clade Cannaceae Depp conservation of ? developmental mechanisms (organ identity) Zingiberaceae Distinct lineage-specific Costaceae developmental programs b Lowiaceae anana group Diversification of floral shape Strelitziaceae (Chanderbali et al. 2010, PNAS) Heliconiaceae Musaceae (Saas et al. 2016, PeerJ) Flower morphology in the Zingiberales Working hypothesis Mechanisms of floral ginger clade diversification Depp conservation of Marantaceae developmental mechanisms (organ identity) Cannaceae Distinct lineage-specific developmental programs staminodes stamen petals gyn Diversification of floral shape (Chanderbali et al. 2010, PNAS) Zingiberaceae sepals Costaceae Tinkering of conserved Evolution of lineage- Co-option of non-flower mechanisms specific mechanisms mechanisms 2 1/25/2019 Working hypothesis Results and discussion Mechanisms of floral - Assembly metrics diversification Depp conservation of developmental mechanisms (organ identity) Distinct lineage-specific developmental programs Diversification of floral shape (Chanderbali et al. 2010, PNAS) Tinkering of conserved Evolution of lineage- Co-option of non-flower mechanisms specific mechanisms mechanisms AG-AP1 ? Ab-ad netowork (Almeida et al. 2015, EvoDevo) (Almeida et al. 2014, SciRepots) (Almeida et al 2018, PeerJ) Methods: data collection and analysis Results and discussion - Species used in this study: - Assembly metrics Marantaceae Calathea zebrina Cannaceae Canna sp. Zingiberaceae Zingiber officinale Costaceae Costus spicatus Lowiaceae Orchidantha fimbriata Strelitziaceae Heliconiaceae Musaceae Musa basjoo Outgroup Dichorisandra thyrsiflora (Almeida et al 2018, PeerJ) Methods: data collection and analysis Results and discussion - Protocol Developing flowers*** - OrthoFinder results Total flower RNA extraction 41,557 orthogroups between transcriptome and CDS from sequenced genomes; cDNA libraries for Illumina (HS2000) Adapters Low quality 17,418 orthogroups had counterparts in at least on of the sequenced genomes; Sequence clean-up and trimming Low complexity Duplicates 6,916 orthogroups with representatives of all species studied; De novo assembly with Contaminants Trinity v2.1.0 Of those, only 28 were single copy. Prediction of long ORFs with 11,511 orthogroups had counterparts in Arabidopsis thaliana; TransDecoder v4.1.0 Blastp against Uniprot 142 orthogroups were Arabidopsis specific. Contig filtering (>300bp) HMM search against Pfam Arabidopsis thaliana Orthology between AGAMOUS-like (AGL) genes: ALG6, ALG12. AGL20, AGL26, AGL29, AGL44, AGL58, Musa acuminata genomes and filtered CDS with AGL61, AGL65, AGL104; Phoenix dactylifera Orthofinder v2.2.3 Elaeis guineensis MADS-box genes: APETALA3 (AP3), PISTALLATA (PI), SEPALLATA3 (SEP3), CAULIFLOWER Blastn to Elaeis guineensis (CAL), SHATTERPROOF2 (SHP2), CRABS CLAW (CRC), various TCP. Transcription factors were identified based on PlantTFDB v4.0 3 1/25/2019 Results and discussion Results and discussion - Blastn against Elaeis guineensis - Blastn against Elaeis guineensis Contigs blasted to 22,959 E. guineensis CDS Contigs blasted to 22,959 E. guineensis CDS - Developmental genes: AP2-like homologs AGL6-like homologs HUA2-like homologs LEUNIG-like homologs KNOTTED1-like homologs GATA-like homologs MYB-like homologs TCP-like homologs CONSTANS-like homologs WUSHEL-like homologs - Stress and pathogen response: (WRKY, NAC) Results and discussion Results and discussion - Blastn against Elaeis guineensis - Blastn against Elaeis guineensis Contigs blasted to 22,959 E. guineensis CDS Paralogues of the same gene/gene family in different floral transcriptomes: Marantaceae LATERAL ORGAN BOUNDARIES LOB18-like (LOB)-domain homologs Cannaceae found in all lineages 47% - enzymes Zingiberaceae LOB4-like 26% - structural proteins Costaceae LOB40-like, 15% - uncharacterized LOB41-like ~12% - regulatory Lowiaceae Strelitziaceae LOB6-like, LOB36-like 508 proteins could be assigned Heliconiaceae to known transcription factor families Musaceae Outgroup LOB15-like Results and discussion Results and discussion - In terms of Transcription Factors - Blastn against Elaeis guineensis Paralogues of the same gene/gene family in different floral transcriptomes: Marantaceae LATERAL ORGAN BOUNDARIES LOB18-like (LOB)-domain homologs Cannaceae found in all lineages Zingiberaceae LOB4-like LOB40-like, LIM domain Bromodomain Bromodomain Costaceae LOB41-like family family (GTE4-like, family (GTE9- (SEUSS-like) GTE6-like), like), YL1 Lowiaceae PUR-A domain domain family NCBI Conserved Domain family (PURA1-like) (SWR1) Strelitziaceae LOB6-like, Dataset Other lineage-specific LOB36-like paralogues: Bromodomain-family (GTE7- Heliconiaceae like), TFIIS-domain family DIVERICATA-like (IWS1-like), SAND-domain Musaceae TGA-like family (ULTRAPETALA1-like) ASIL-like Outgroup LOB15-like 4 1/25/2019 Results and discussion Concluding remarks - Blastn against Elaeis guineensis Mechanisms of floral diversification Lineage-specific regulatory genes: Marantaceae Tinkering of conserved Evolution of lineage- Co-option of non-flower mechanisms mechanisms Cannaceae specific mechanisms A clear, well-established phylogenetic framework is essential - “model clades” Zingiberaceae (Chanderbali et al. 2016); Duplications are a widespread phenomenon; Costaceae Lowiaceae FLORICAULA/LEAFY-like Strelitziaceae ODORANT1-like JUNGBRUNNEN-like Heliconiaceae RAX-like DPB-like Musaceae SOMBRERO-like among others. Outgroup Results and discussion Concluding remarks - Blastn against Elaeis guineensis Mechanisms of floral diversification Lineage-specific regulatory genes: Marantaceae Tinkering of conserved Evolution of lineage- Co-option of non-flower mechanisms Cannaceae specific mechanisms mechanisms A clear, well-established phylogenetic framework is essential - “model clades” Zingiberaceae (Chanderbali et al. 2016); Duplications are a widespread phenomenon; Costaceae The set of Commelinid shared genes (~4,000) - conserved regulators of floral Lowiaceae CCA1-like development in monocots. It is yet unclear what their roles might be in flower FLX2-like development and diversification in the monocots; Strelitziaceae KT112-like Lineage-specific gene sets provide interesting candidate gene lists for further studies; YABBY4-like Heliconiaceae CPC-like Addition of other outgroup species might influence the Zingiberales specific SPATULA-like datasets; Musaceae Expression levels an analysis of the non-coding sequences might provide Outgroup additional layers of developmental regulation. Results and discussion Acknowledgements - Blastn against Elaeis guineensis Lineage-specific regulatory genes: Marantaceae Holly Forbes (UCBG) AS1-like Cannaceae DROOPING LEAF-like CUC2-like EXORDIUM-like Zingiberaceae FAF-like Chelsea Specht Roxana Yockteng Alma Piñeyro SPX-like Cornell U CORPIOCA UAM Costaceae Lowiaceae Strelitziaceae Thank you! Heliconiaceae Musaceae Outgroup 5.
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