Presentation is loading. Please wait.

Presentation is loading. Please wait.

U. Uzay Sezen University of Connecticut

Published byEvangeline Wilson Modified over 7 years ago

Similar presentations

Presentation on theme: "U. Uzay Sezen University of Connecticut"— Presentation transcript:

1 A Reference Draft Genome Sequence for Douglas-Fir (Pseudotsuga menziesii (Mirb.) Franco)
U. Uzay Sezen University of Connecticut Department of Ecology & Evolutionary Biology D.B. Neale, P.E. McGuire, N.C. Wheeler, K.A. Stevens, M.W. Crepeau, C. Cardeno, A.V. Zimin, D. Puiu, G.M. Pertea, G. Sablok, C. Casola, T.E. Koralewski, R. Paul, D. Gonzalez, S. Zaman, R. Cronn, M. Yandell, C. Holt, C.H. Langley, J.A. Yorke, S.L. Salzberg, J.L. Wegrzyn International Plant Animal Genomes Meeting, W352, Jan 14-18, 2017, PAG XXV , San Diego, California

2 Image: westernwoodstructures.com

3 Hōkūleʻa (1976) Hawaiian Double Hulled Canoe

4 Pine RefSEQ Project n=12 Genome = 22 Gb n=12 Genome = 33,5 Gb n=13
Loblolly pine (Pinus taeda) Sugar pine (Pinus lambertiana) Douglas fir (Pseudotsuga menziesii) USDA funded project – 5 years – final year Original proposal was for loblolly pine, 2 other species selected to include Individuals were selected to sequence based on mapping populations n=12 Genome = 22 Gb n=12 Genome = 33,5 Gb n=13 Genome = 18,7 Gb Pine RefSEQ Project

5 Challenges to Sequencing a Conifer Genome
Genomes are large! Highly repetitive, large expanded gene families and psuedogenes Seem to lack whole genome duplications

6

7 Sequencing 16Gb Douglas-fir genome from a single megagametophyte/needle 61x coverage via 26 short-fragment libraries [ bp] 3,718,542,883 pairs of reads 11x coverage via 17 long-fragment libraries [ kbp] 700,151,824 pairs of reads Assembly MaSuRCA (Zimin et al. 2013) SOAPdenovo2 (Luo et al. 2012) N50 scaffold 340,704 bp (246,600 bp P. lambertiana)

8 Repeat Annotation 3785 unique Douglas-fir interspersed repeats
Tandem Repeat Finder Repeat Modeler (RECON + RepeatScout) TEclass, CENSOR Repeat Masker v Repbase Library 3785 unique Douglas-fir interspersed repeats

9 Repeat Annotation Tandem Repeat Finder Repeat Modeler
(RECON + RepeatScout) TEclass, CENSOR Repeat Masker v Repbase Library

10 Genome Annotation MAKER-P / Evidence Modeler 54,380 gene models (avg. exon size 200bp max 8000 bp) 17,411 multi-exonic (needle RNA-Seq support) 34,239 High-Quality multi-exonic genes 20,616 multi-exonic full-length) mono-exonic full-length 22,257 High-Quality full-length 35,880 High-Quality with partials Douglas-fir (22,257 HQ and 54,830 total), Loblolly pine (4,690 HQ and 8,775 total), Sugar pine (8,775 HQ and 13,936 total), Norway Spruce (26,437 HQ and 32,150 MQ)

11 Genome, Proteome and Gene Space Completion
BUSCO (950 reference orthologs) CEGMA (248 core eukaryotic genes) DOGMA (965 conserved single domain) (1065 conserved multi-domain) Orthology and Evolutionary Analysis OrthoFinder v.040 Mcl v14-137 Gene Family Evolution Functional Gene Annotation CAFÉ v3.1 enTAP eukaryotic non-model transcriptome analysis pipeline / Wegrzyn Lab Gene Family Expansion/Contraction Agri GO/SEA Plant GO slim db STRING

12 CAFÉ Analysis 16 land plants 6459 gene families 230,055 genes P0583
Casola & Claudio 1.35 – 1.64 x higher

13 2698 1581 P. abies 559 P. glauca 362 P. sitchensis 442 P. taeda bHLH
MYB

14 Secretome Analysis of Douglas-fir

15 Why Douglas-fir is (notoriously) shade intolerant?

16 Light Harvesting Complex (LHC)

17

18 LHCb2 LHCb3 LHCb1 LHCa5 LHCb5 LHCb6 LHCb4

19 LHCb2 intolerant tolerant LHCb5 trimer motif Pinus LHCb4 Picea LHCa5 LHCb3 LHCb6

20 LHCb2 LHCb3 LHCa5 LHCb5 Picea LHCb6 LHCb4 Pinus Phytochrome
Cryptochrome Phototropin D1/D2 VDE STN7/8 PSAH1 PsBs LHCa5 LHCb5 Picea LHCb6 LHCb4 Pinus

21 Podocarpaceae Biffin et al. (2012) Leaf evolution in Southern Hemisphere conifers tracks the angiosperm ecological radiation. Proc. R. Soc. B. 279,

22 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

23 A Reference Draft Genome Sequence for Douglas-Fir (Pseudotsuga menziesii (Mirb.) Franco)
U. Uzay Sezen University of Connecticut Department of Ecology & Evolutionary Biology D.B. Neale, P.E. McGuire, N.C. Wheeler, K.A. Stevens, M.W. Crepeau, C. Cardeno, A.V. Zimin, D. Puiu, G.M. Pertea, G. Sablok, C. Casola, T.E. Koralewski, R. Paul, D. Gonzalez, S. Zaman, R. Cronn, M. Yandell, C. Holt, C.H. Langley, J.A. Yorke, S.L. Salzberg, J.L. Wegrzyn International Plant Animal Genomes Meeting, W352, Jan 14-18, 2017, PAG XXV , San Diego, California

24

25

26 LHCIIb1 Chl-a Chl-b Carotenoids LHCIIb2 LHCIIb3 PDB 2BHW

27 C2 S2 M2 (L2) LHCb4 (CP29) LHCb6 (CP24) LHCb5 (CP26) PSII supercomplex
M. Ballottari et al. Evolution and functional properties of Photosystem II light harvesting complexes in eukaryotes Biochimica et Biophysica Acta (BBA) - Bioenergetics, Volume 1817, Issue 1, 2012, 143–157

28 Iwai et al. 2008 The Plant Cell 20: p2177-2189

29 X LHCb6 X LHCb3 PSII PSI LHCb[1-6] LHCa[1-5]

30 10 years old 450 years old Martha et al Tree Physiology 22:

31 Norway spruce Arabidopsis Chlamydomonas
Structural assignment of protein subunits of the photosystem II (PSII) supercomplex. (a) PSII supercomplexes from Norway spruce (Picea abies) and its counterparts from (b) Arabidopsis thaliana and (c) Chlamydomonas reinhardtii. Averaged projection maps are shown for the C2S2M2 supercomplexes from Norway spruce and A. thaliana, and C2S2M2N2 from C. reinhardtii (adapted from Drop et al., ). High‐resolution structures were fitted to the projection maps; the PSII core complex (C2, light violet) (Guskov et al., ), trimeric (the S, M and N trimer in blue, red and yellow, respectively) and monomeric (Lhcb4 and Lhcb5 in green, Lhcb6 in cyan) Lhcb proteins (Liu et al., ). IF THIS IMAGE HAS BEEN PROVIDED BY OR IS OWNED BY A THIRD PARTY, AS INDICATED IN THE CAPTION LINE, THEN FURTHER PERMISSION MAY BE NEEDED BEFORE ANY FURTHER USE. PLEASE CONTACT WILEY'S PERMISSIONS DEPARTMENT ON OR USE THE RIGHTSLINK SERVICE BY CLICKING ON THE 'REQUEST PERMISSIONS' LINK ACCOMPANYING THIS ARTICLE. WILEY OR AUTHOR OWNED IMAGES MAY BE USED FOR NON-COMMERCIAL PURPOSES, SUBJECT TO PROPER CITATION OF THE ARTICLE, AUTHOR, AND PUBLISHER. New Phytologist Volume 210, Issue 3, p , 2016

Download ppt "U. Uzay Sezen University of Connecticut"

Similar presentations

PineRefSeq David B. Neale University of California, Davis Pieter J. de Jong Children’s Hospital of Oakland Research Institute.

PineRefSeq David B. Neale University of California, Davis Pieter J. de Jong Children’s Hospital of Oakland Research Institute.
U. Uzay Sezen University of Connecticut

U. Uzay Sezen University of Connecticut
Individualized pain management plan.

Individualized pain management plan.
Isotope‐based Fluvial Organic Carbon (ISOFLOC) Model: Model formulation, sensitivity, and evaluation Reach‐scale conceptual model of the fluvial carbon.

Isotope‐based Fluvial Organic Carbon (ISOFLOC) Model: Model formulation, sensitivity, and evaluation Reach‐scale conceptual model of the fluvial carbon.
Isotope‐based Fluvial Organic Carbon (ISOFLOC) Model: Model formulation, sensitivity, and evaluation Modeling domain for the main stem of the South Elkhorn.

Isotope‐based Fluvial Organic Carbon (ISOFLOC) Model: Model formulation, sensitivity, and evaluation Modeling domain for the main stem of the South Elkhorn.
(a) illuminance measured in the horizontal plane from a typical street light (Phillips Cosmopolis, metal halide lamp). The intensity of light decays rapidly.

(a) illuminance measured in the horizontal plane from a typical street light (Phillips Cosmopolis, metal halide lamp). The intensity of light decays rapidly.
Isotope‐based Fluvial Organic Carbon (ISOFLOC) Model: Model formulation, sensitivity, and evaluation Sensitivity analysis of the ISOFLOC model displays.

Isotope‐based Fluvial Organic Carbon (ISOFLOC) Model: Model formulation, sensitivity, and evaluation Sensitivity analysis of the ISOFLOC model displays.
Isotope‐based Fluvial Organic Carbon (ISOFLOC) Model: Model formulation, sensitivity, and evaluation Model flowchart for ISOFLOC which details inputs,

Isotope‐based Fluvial Organic Carbon (ISOFLOC) Model: Model formulation, sensitivity, and evaluation Model flowchart for ISOFLOC which details inputs,
Evening evapotranspirative cooling in relation to vegetation and urban geometry in the city of Ouagadougou, Burkina Faso Relation between sky view factor.

Evening evapotranspirative cooling in relation to vegetation and urban geometry in the city of Ouagadougou, Burkina Faso Relation between sky view factor.
Matrilin‐2 prevents the TNFα‐induced apoptosis of WB‐F344 cells via suppressing JNK pathway Matrilin‐2 knockdown promotes the apoptosis of WB‐F344 cells.

Matrilin‐2 prevents the TNFα‐induced apoptosis of WB‐F344 cells via suppressing JNK pathway Matrilin‐2 knockdown promotes the apoptosis of WB‐F344 cells.
RNA N6‐methyladenosine methyltransferase‐like 3 promotes liver cancer progression through YTHDF2‐dependent posttranscriptional silencing of SOCS2 Knockdown.

RNA N6‐methyladenosine methyltransferase‐like 3 promotes liver cancer progression through YTHDF2‐dependent posttranscriptional silencing of SOCS2 Knockdown.
Adaptive resistance of melanoma cells to RAF inhibition via reversible induction of a slowly dividing de‐differentiated state Immunohistochemical analysis.

Adaptive resistance of melanoma cells to RAF inhibition via reversible induction of a slowly dividing de‐differentiated state Immunohistochemical analysis.
KLF4 is a key determinant in the development and progression of cerebral cavernous malformations qRT–PCR analysis of Klf4 during disease progression at.

KLF4 is a key determinant in the development and progression of cerebral cavernous malformations qRT–PCR analysis of Klf4 during disease progression at.
Details of the binding sites of tetracycline and edeine

Details of the binding sites of tetracycline and edeine
Co‐immunoprecipitation of Larp with MDI‐myc in transfected S2 cells

Co‐immunoprecipitation of Larp with MDI‐myc in transfected S2 cells
Allelic exchange at the endogenous genomic locus in Plasmodium falciparum proves the role of dihydropteroate synthase in sulfadoxine‐resistant malaria.

Allelic exchange at the endogenous genomic locus in Plasmodium falciparum proves the role of dihydropteroate synthase in sulfadoxine‐resistant malaria.
Global cancer statistics 2018: GLOBOCAN estimates of incidence and mortality worldwide for 36 cancers in 185 countries Global Maps Presenting the Most.

Global cancer statistics 2018: GLOBOCAN estimates of incidence and mortality worldwide for 36 cancers in 185 countries Global Maps Presenting the Most.
Exogenous N‐acyl‐homoserine lactones enhance the expression of flagella of Pseudomonas syringae and activate defence responses in plants Comparisons of.

Exogenous N‐acyl‐homoserine lactones enhance the expression of flagella of Pseudomonas syringae and activate defence responses in plants Comparisons of.
The trimeric coiled‐coil HSBP1 protein promotes WASH complex assembly at centrosomes The stable MDA‐MB‐231 cell line expressing FLAG‐HaloTag‐WASH (FHT‐WASH)

The trimeric coiled‐coil HSBP1 protein promotes WASH complex assembly at centrosomes The stable MDA‐MB‐231 cell line expressing FLAG‐HaloTag‐WASH (FHT‐WASH)
The trimeric coiled‐coil HSBP1 protein promotes WASH complex assembly at centrosomes MDA‐MB‐231 cells expressing HaloTag WASH or CCDC53 were stained with.

The trimeric coiled‐coil HSBP1 protein promotes WASH complex assembly at centrosomes MDA‐MB‐231 cells expressing HaloTag WASH or CCDC53 were stained with.

Similar presentations

Ads by Google