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Signatures of Selection Among de novo Assembled Transcriptomes of Four White Pine Species
U. Uzay Sezen University of Connecticut Department of Ecology & Evolutionary Biology Ethan A. G. Baker,Taylor Falk, Patricia Maloney, Detlev Vogler, Annette Delfino-Mix, Camille Jensen, Jeffry Mitton, Jessica Wright, Brian Knaus, Richard Cronn, Hardeep Rai, Daniel Gonzalez-Ibeas, Hans Vasquez-Gross, Randi Famula, Steven Salzberg, Charles Langley, Kristian Stevens, Daniela Puiu, Aleksey Zimin, James Yorke, Marc Crepeau, Carol Loopstra, Jeffrey Puryear, Jun-Jun Liu, Lara Kueppers, David B. Neale, Jill L. Wegrzyn International Plant Animal Genomes Meeting, W740, Jan 9-13, 2015, PAG XXIV , San Diego, California
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(WBP) (LP) (SP) White bark pine (WBP) Limber pine (LP) Sugar pine (SP) Western white pine (WWP) (WWP)
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Eukaryote Non-Model Transcriptome Annotation Pipeline
Source J-J Liu Patricia Maloney Detlev Volger Jessica Wright Richard Cronn Jeffry Mitton Lara Kueppers Library WWP WBP SP LP Tissue Needle Technology Illumina GA IIx Illumina HiSeq Reads PE, 76bp PE, 100bp SE, 80bp Total Reads 398,534,772 1,257,388,110 91,223,401 669,904,522 Total Reads (QC) 208,059,003 839,389,034 66,894,169 374,191,816 Transcripts 23,862 10,494 14,238 9,362 57,956 Sickle > Trinity de novo assembly > Transdecoder > Usearch/Ublast + enTAP Eukaryote Non-Model Transcriptome Annotation Pipeline enTAP
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Transcriptome Assembly
X Trinity de novo assembly > Transdecoder Reference Genome
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Transcriptome Annotation
100 Unknown Uninformative Informative % Transcripts Annotated Eukaryote Non-Model Transcriptome Annotation Pipeline enTAP LP SP WBP WWP
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Functional Annotation by Species Homology (Usearch)
6000 Citrus clementina Citrus sinensis Cucumis sativus Fragaria vesca Glycine max Prunus persica Ricinus communis Theobroma cacao Vitis vinifera LP SP WBP WWP LP SP WBP WWP NCBI full-length plant protein NCBI RefSeq
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90% identity 98% identity 95% coverage Gmap Pine Refseq LP SP WBP WWP
Loblolly Pine (Pinus taeda) Sugar Pine (Pinus lambertiana) Pine Refseq
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408 signatures of selection
Tribe-MCL clustering Muscle alignment codeml (PAML, v.4.6) 408 signatures of selection over 58,000 translated transcripts, implemented through Tribe-MCL, estimated the shared and unique gene space among the four species. This revealed 2025 conserved gene families, of which 408 were aligned to estimate levels of divergence and reveal patterns of selection.
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39 dN/dS > 1 positive selection 9 dN/dS = 1 neutral evolution
The synonymous/nonsynonymous ratio (dN/dS) is an estimate of natural selection acting on the genes: dN/dS < 1 indicates negative purifying selection, dN/dS = 1 indicates neutral evolution, and dN/dS > 1, indicates positive selection. Alignments with dS values < 0.01 and dS or dN > 2 were discarded. Very high dN/dS (> 10) were also removed as they indicate bias. 39 dN/dS > 1 positive selection 9 dN/dS = 1 neutral evolution 360 dN/dS < 1 negative purifying selection dS values < 0.01 and dS or dN > 2 were discarded. dN/dS (>>> 10) were removed to avoid bias. 408
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[1] formyltetrahydrofolate deformylase mitochondrial isoform x1
[2] f-box kelch-repeat protein skip6-like protein degradation tagging activity [3] low quality protein: nitrate reductase [4] arogenate dehydrogenase chloroplastic [5] carrier protein chloroplastic [6] flowering time control protein fpa [7] transcription initiation factor tfiid subunit partial [8] e3 ubiquitin-protein ligase keg isoform x2 protein degradation tagging activity [9] PREDICTED: uncharacterized protein LOC [10] two-component response regulator-like prr37 [11] isoamylase chloroplastic [12] probable u3 small nucleolar rna-associated protein 7 [13] PREDICTED: uncharacterized protein LOC [14] calcium-transporting atpase plasma membrane-type-like isoform x1 [15] protein notum homolog [16] PREDICTED: uncharacterized protein LOC [17] clathrin assembly protein at5g35200 [18] PREDICTED: kanadaptin [19] family 18 glycoside hydrolase [20] dead-box atp-dependent rna helicase 13 [21] probable inactive purple acid phosphatase 27 [22] arginine decarboxylase carboxy-lyase activity [23] PREDICTED: uncharacterized protein LOC [24] erythronate-4-phosphate dehydrogenase-like protein [25] interferon-induced guanylate-binding protein 2-like [26] nf-x1-type zinc finger protein nfxl1 [27] transmembrane protein 87b-like [28] fructokinase-like chloroplastic [29] bel1-like homeodomain protein 1 [30] cbs domain-containing protein cbsx6 [31] duf21 domain-containing protein at4g14240 [32] probable wrky transcription factor 14 [33] myeloid leukemia factor 1-like isoform x2 [34] mannose-1-phosphate guanylyltransferase 1 [35] phytoene synthase chloroplastic [36] unknown [37] PREDICTED: myosin-10-like [38] universal stress protein a-like protein [39] PREDICTED: uncharacterized protein LOC
![[1] formyltetrahydrofolate deformylase mitochondrial isoform x1](http://slideplayer.com./slide/12939881/78/images/10/%5B1%5D+formyltetrahydrofolate+deformylase+mitochondrial+isoform+x1.jpg "[2] f-box kelch-repeat protein skip6-like protein degradation tagging activity. [3] low quality protein: nitrate reductase. [4] arogenate dehydrogenase chloroplastic. [5] carrier protein chloroplastic. [6] flowering time control protein fpa. [7] transcription initiation factor tfiid subunit partial. [8] e3 ubiquitin-protein ligase keg isoform x2 protein degradation tagging activity. [9] PREDICTED: uncharacterized protein LOC [10] two-component response regulator-like prr37. [11] isoamylase chloroplastic. [12] probable u3 small nucleolar rna-associated protein 7. [13] PREDICTED: uncharacterized protein LOC [14] calcium-transporting atpase plasma membrane-type-like isoform x1. [15] protein notum homolog. [16] PREDICTED: uncharacterized protein LOC [17] clathrin assembly protein at5g [18] PREDICTED: kanadaptin. [19] family 18 glycoside hydrolase. [20] dead-box atp-dependent rna helicase 13. [21] probable inactive purple acid phosphatase 27. [22] arginine decarboxylase carboxy-lyase activity. [23] PREDICTED: uncharacterized protein LOC [24] erythronate-4-phosphate dehydrogenase-like protein. [25] interferon-induced guanylate-binding protein 2-like. [26] nf-x1-type zinc finger protein nfxl1. [27] transmembrane protein 87b-like. [28] fructokinase-like chloroplastic. [29] bel1-like homeodomain protein 1. [30] cbs domain-containing protein cbsx6. [31] duf21 domain-containing protein at4g [32] probable wrky transcription factor 14. [33] myeloid leukemia factor 1-like isoform x2. [34] mannose-1-phosphate guanylyltransferase 1. [35] phytoene synthase chloroplastic. [36] unknown. [37] PREDICTED: myosin-10-like. [38] universal stress protein a-like protein. [39] PREDICTED: uncharacterized protein LOC")
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FBK-SKiP6 E3 UBQ-ligase f-box kelch-repeat protein skip6-like
E3 ubiquitin-protein ligase 26S Ubiquitin-proteasome pathway White Pine Blister Rust (Cronartium ribicola) In WWP, 14 genes involved in the 26S Ubiquitin-proteasome pathway were up-regulated in resistant seedlings (Liu et al. 2010). In Arabidopsis, expression of auxin-responsive genes, trigger plant resistance to necrotrophic fungi (Kepinski and Leyser 2005). Auxin binding to the SCF E3-ubiquitin ligase leads to degradation of transcriptional repressors belonging to the AUX/IAA family through the 26S Ubiquitin-proteasome pathway.
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~700 21 F-box SKiP6 10 E3 ubiquitin–protein ligases
Zheng, N. et al. Structure of the Cul1–Rbx1–Skp1–F boxSkp2 SCF ubiquitin ligase complex. Nature 416, 703–709 (2002).
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Signatures of Selection
WWP (P. monticola) WBP (P. albicaulis) SP (P. lambertiana) LP (P. flexilis) Total Reads (QC) 1,488,534,022 Transcripts 57,956 Gene Families 2025 Sezen P1179 Signatures of Selection 408 Positive Selection 39
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Acknowledgements University of Connecticut Ethan Baker Taylor Falk
Daniel Gonzalez-Ibeas Robin Paul Steven Demurjian Jill Wegrzyn University of California, Davis David Neale Patricia Maloney Randi Famula Hans Vasquez-Gross Charles H. Langley Kristian Stevens Marc Crepeau University of Colorado Jeffry Mitton University of California, Merced Lara Kueppers USDA Forest Service Detlev Vogler Camille Jensen Annette Delfino-Mix Jessica Wright Richard Cronn Acknowledgements University of Maryland Aleksey Zimin James A Yorke Texas A&M University Carol Loopstra Jeffrey Puryear Johns Hopkins University, School of Medicine Daniela Puiu Steven L. Salzberg USDA Agricultural Research Service Brian Knaus Utah State University Hardeep Rai
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