1kp data analysis working group

In November 2009 a NESCent/iPlant-sponsored 1KP analysis workshop held in Phoenix to bring together members of the iPlant tree of life's (iPToL) Tree Reconciliation working group, the 1KP project and experts in phylogeny estimation using large, multi-gene data sets. The 1000 Plant Transcriptome Sequencing Initiative (www.onekp.com) aims to resolve relationships across the green plant phylogeny in order to elucidate processes contributing to diversification and biological innovations including origins in multi-cellularity, colonization of land, the evolution of vascular systems and the origins of seeds and flowers. In pursuit of these goals, the project is generating an unparalleled plant sequence database for investigating the evolution of gene families, regulatory networks and biosynthetic pathways. In collaboration with iPlant, the 1KP project plans to make all transcriptome sequences, gene trees, species trees and tree reconciliations available to the plant science community through an iPlant Discovery Environment.

As part of the iPlant Assembling the Tree of Life (iPToL) grand challenge project, the Tree Reconciliation Working Group and collaborators are developing pipelines for analysis of gene families within the context of organismal phylogenies. The working group will first analyze a pilot set of strategically placed streptophytic algae and land plant trascriptomes (see table) being generated by the 1KP project as a focal point for developing workflows aimed at circumscribing gene families, and estimating gene trees and species trees. Results will be shared with the larger community of iPToL and 1KP collaborators and prepared for publication.

Major systematics questions to be addressed in pilot project:

Which algal lineage(s) are sister to the land plants?
Do mosses, hornworts and liverworts form a clade?
To what degree is the timing of gene duplication events correlated across gene families?
- Do we see diversification of gene families and/or functional groups associated with the origin of land plants, vascular plants, seed plants and/or flowering plants?
Are gene trees affected by sparse taxon sampling?
Given computational limitations (see below), is it feasible to go even further back in time to resolve the earliest branching events in history of green algae?

Some of the major computational questions include:

Given existing tools, how can we best infer species trees from reconciliation of unrooted and often poorly resolved (very deeply branching) gene trees?
What are the limits of the power of currently available gene tree/ species tree reconciliation methods?
How do we summarize the uncertainty in the gene tree reconciliation in a way that captures uncertainty in the species & gene tree topologies as well as the rooting of both?
How do we visualize the results of gene tree/ species tree reconciliations?
Where are the computational bottlenecks and how do we scale these analyses up?

Our experience with the pilot analysis will form the foundation for much larger analyses of the full 1000 transcriptome data set to be generated over the next 24 months. Most importantly, we will aim to address the computation challenges anticipated with analyses of the complete 1KP data set.

Table : Taxa to be included in pilot dataset from the 1KP project

	Clade	Order	Family	Species	1KP Code	Comments
1	Basalmost angiosperms	Austrobaileyales	Illiciaceae/Schisan.	Amborella trichopoda	URDJ	Combine 1KP and AAGP data; update 1KP assembly
2	Basalmost angiosperms	Austrobaileyales	Illiciaceae/Schisan.	Nuphar advena	WTKZ	Combine 1KP and AAGP data
3	Basalmost angiosperms	Austrobaileyales	Illiciaceae/Schisan.	Kadsura heteroclite	NWMY
4	Magnoliid	Piperales	Piperaceae	Houttuynia cordata	CSSK
5	Magnoliid	Piperales	Aristolochiaceae	Saruma henryi	QDVW	Combine 1KP and FGP data
6	Magnoliid	Magnoliales	Magnoliaceae	Liriodendron tulipifera	-	AAGP data
7	Magnoliid	Magnoliales	Magnoliaceae	Persea americana	-	AAGP data
8	Chloranthales	Chloranthales	Chloranthaceae	Sarcandra glabra	OSHQ
9	Basal Eudicots	Ranunculales	Berberidaceae	Podophyllum pelatum	WFBF
10	Basal Eudicots	Ranunculales	Papaveraceae	Eschscholzia californica	multi-library	Combine 1KP and FGP data; multi-1kp-library assembly in progress
11	Basal Eudicots	Ranunculales	Ranunculaceae	Aquilegia formosa X pubescens	-	ESTs in GenBank
12	Core Eudicots	Caryophyllales	Amaranthaceae	Kochia scoparia	WGET
13	Core Eudicots/Rosids	Brassicales	Brassicaceae	Arabidopsis thaliana	-	Annotated Genome
14	Core Eudicots/Rosids	Brassicales	Brassicaceae	Arabidopsis lyrata	-	Annotated Genome
15	Core Eudicots/Rosids	Brassicales	Caricaceae	Carica papaya	-	Annotated Genome
16	Core Eudicots/Rosids	Malpighiales	Salicaceae	Populus trichocarpa	-	Annotated Genome
17	Core Eudicots/Rosids	Malpighiales	Euphorbiaceae	Ricinus communis	-	Annotated Genome
18	Core Eudicots/Rosids	Malpighiales	Euphorbiaceae	Manihot esculenta	-	Annotated Genome
19	Core Eudicots/Rosids	Fabales	Fabaceae	Medicago truncatula	-	Annotated Genome
20	Core Eudicots/Rosids	Fabales	Fabaceae	Glycine max	-	Annotated Genome
21	Core Eudicots/Rosids	Cucurbitales	Cucurbitaceae	Cucumis sativus	-	Annotated Genome
22	Core Eudicots/Rosids	Vitales	Vitaceae	Vitis vinifera	-	Annotated Genome
23	Core Eudicots/Rosids	Zygophyllales	Zygophyllaceae	Larrea divaricata	UDUT
24	Core Eudicots/Rosids	Rosales	Urticaceae	Boehmeria nivea	ACFP
25	Core Eudicots/Rosids	Malvales	Malvaceae	Hibiscus cannabinus	OLXF
26	Core Eudicots/Asterids	Gentianales	Apocynaceae	Allamanda cathartica	MGVU	awaiting assembly of top-off
27	Core Eudicots/Asterids	Gentianales	Apocynaceae	Catharanthus roseus	UOYN
28	Core Eudicots/Asterids	Lamiales	Lamiaceae	Rosmarinus officinalis	FDMM
29	Core Eudicots/Asterids	Lamiales	Phrymaceae	Mimulus guttatus	-	Annotated Genome
30	Core Eudicots/Asterids	Solanales	Convolvulaceae	Ipomoea purpurea	multi-library	multi-library assembly assembly in progress
31	Core Eudicots/Asterids	Ericales	Ebenaceae	Diospyros malabarica	KVFU
32	Core Eudicots/Asterids	Asterales	Asteraceae	Inula helenium	AFQQ
33	Core Eudicots/Asterids	Asterales	Asteraceae	Tanacetum parthenium	DUQG
34	Monocots	Acorales	Acoraceae	Acorus americanus	-	MonAtol
35	Monocots	Dioscoreales	Dioscoreaceae	Dioscorea villosa	OCWZ
36	Monocots	Liliales	Colchicaceae	Colchicum autumnale	NHIX
37	Monocots	Liliales	Smilacaceae	Smilax bona-nox	MWYQ	Sequencing in progress
38	Monocots	Asparagales	Asparagaceae	Yucca filamentosa	ICNN
39	Monocots/Commelinids	Arecales	Arecaceae	Chamaedorea seifrizii	-	MonAToL
40	Monocots/Commelinids	Poales	Poaceae	Zea Mays	-	Annotated Genome
41	Monocots/Commelinids	Poales	Poaceae	Sorghum bicolor	-	Annotated Genome
42	Monocots/Commelinids	Poales	Poaceae	Brachypodium distachyon	-	Annotated Genome
43	Monocots/Commelinids	Poales	Poaceae	Oryza sativa	-	Annotated Genome
44	Gymnosperms	Pinales	Taxaceae	Taxus baccata	WWSS
45	Gymnosperms	Pinales	Podocarpaceae	Prumnopitys andina	EGLZ
46	Gymnosperms	Pinales	Sciadopityaceae	Sciadopitys verticillata	YFZK
47	Gymnosperms	Pinales	Cupressaceae	Juniperus scopulorum	XMGP
48	Gymnosperms	Pinales	Cupressaceae	Cunninghamia lanceolata	OUOI
49	Gymnosperms	Pinales	Pinaceae	Pinus taeda	-	Dendrome
50	Gymnosperms	Pinales	Pinaceae	Cedrus libani	GGEA
51	Gymnosperms	Gnetales	Gnetaceae	Gnetum montanum	GTHK	combine with NY Consortium data? same species?
52	Gymnosperms	Gnetales	Welwitschiaceae	Welwitschia mirabilis	-	FGP set
53	Gymnosperms	Ephedrales	Ephedraceae	Ephedra sinica	VDAO	additional reads?
54	Gymnosperms	Cycadales	Cycadaceae	Cycas micholitzii	XZUY	NY Consortium data? same species?
55	Gymnosperms	Cycadales	Zamiaceae	Zamia vazquezii	-	FGP/AAGP data
56	Gymnosperms	Ginkgoales	Ginkgoaceae	Ginkgo biloba	SGTW	Combine with NY Consortium data
57	Moniliformopses	Osmundales	Osmundaceae	Osmunda cinnamonea		No RNA at BGI; Replacement? Barker data?
58	Moniliformopses	Marattiales	Marattiaceae	Angiopteris evecta	NHCM
59	Moniliformopses	Psilotales	Psilotaceae	Psilotum nudum	QVMR
60	Moniliformopses	Filicales	Cyatheaceae	Cyathea (=Alsophila) spinulosa	GANB
61	Moniliformopses	Polypodiales	Pteridaceae	Cryptogramma acrostichoides		No RNA at BGI; Replacement? Barker data?
62	Moniliformopses	Polypodiales	Pteridaceae	Asplenium rhizophyllum	KJZG	update 1KP assembly
63	Moniliformopses	Equisetales	Equisetaceae	Equisetum sp.	CAPN	awaiting assembly of top-off
64	Lycopods	Lycopodiales	Lycopodiaceae	Huperzia squarrosa	GAON
65	Lycopods	Selaginellales	Selaginellaceae	Selaginella moellendorffii	-	Annotated Genome
66	Bryophyta	Polytrichales	Polytrichaceae	Polytrichum commune	SZYG	gametophyte
67	Bryophyta	Sphagnales	Sphagnaceae	Sphagnum lescurii	GOWD
68	Bryophyta	Funariales	Funariaceae	Physcomitrella patens	-	Annotated Genome
69	Marchantiophyta	Marchantiales	Marchantiaceae	Marchantia polymorpha	JPYU
70	Marchantiophyta	Marchantiales	Marchantiaceae	Marchantia emarginata	TFYI
71	Anthocerotophyta	Anthocerotales	Anthocerotaceae	Nothoceros aenigmaticus	DXOU
72	Anthocerotophyta	Anthocerotales	Anthocerotaceae	Anthoceros	IQJU	very few large scaffolds
73	Streptophytic Green Algae		Mesostigmatophyceae	Mesostigma viride	KYIO
74	Streptophytic Green Algae		Mesostigmatophyceae	Chlorokybus atmophyticus	AZZW	update 1KP assembly
75	Streptophytic Green Algae		Mesostigmatophyceae	Spirotaenia minuta	NNHQ
76	Streptophytic Green Algae		Klebsormidiophyceae	Klebsormidium subtile	FQLP
77	Streptophytic Green Algae		Klebsormidiophyceae	Hormidiella sp.		New
78	Streptophytic Green Algae		Charophyceae	Chara vulgaris	MWXT
79	Streptophytic Green Algae		Coleochaetophyceae	Chaetosphaeridium globosum	DRGY
80	Streptophytic Green Algae		Coleochaetophyceae	Coleochaete scutata	VQBJ
81	Streptophytic Green Algae		Coleochaetophyceae	Coleochaete orbicularis	-	Timme & Delwiche paper
82	Streptophytic Green Algae		Zygnematophyceae	Cosmarium broomei	HIDG	awaiting assembly of top-off
83	Streptophytic Green Algae		Zygnematophyceae	Netrium digitus	FFGR
84	Streptophytic Green Algae		Zygnematophyceae	Spirogyra sp.	HAOX
85	Streptophytic Green Algae		Zygnematophyceae	Spirogyra pratensis	-	Timme & Delwiche paper

Analysis Pipeline and Data Access

Analysis of transcriptome sets for individual species - Collaborators have access to web-accessible databases for blast and annotation term searches.

Phylogenomic Analyses - Coding sequences extracted from transcriptome sets passing quality control will be sorted into gene families and used for estimations of gene trees, species trees and tree reconciliations. Collaborators will have access to alignments and trees.

Transcript Annotation

In support of all 1kp subprojects, all transcript assemblies are or will be accessible in the following ways:

Assemblies and reads are available to contributers through download sites at the Universities of Texas (TACC) and Alberta (Westgrid),
The results of prerun BLAST searches will be available through a project website. These results can be searched for annotation terms.
BLAST searches can be performed on assemblies for each taxon through a project website.
As described above, (see * Phylogenomic Analyses * ) assemblies will be sorted into gene families based on similarity to plant genes in the NCBI RefSeq database http://www.ncbi.nlm.nih.gov/RefSeq/ and genes from annotated plant genomes that are not in RefSeq. Sequence alignments and gene trees for each family will be available for all 1kp collaborators for ortholog identification.