Physcraper Examples: the Dothideomycetes

I. Finding a tree to update

With the Open Tree of Life website

Go to the Open Tree of Life website and use the “search for taxon” menu to look up the taxon Dothideomycetes.

Oh no… it seems like the Dothideomycetes are not represented as a clade on the Open Tree of Life synthetic tree (at the middle of year 2020):

Go to the website and look at it [here](https://tree.opentreeoflife.org/opentree/argus/ottol@346120/Dothideomycetes)

Go to the website and look at it here

What is the MRCA of the “broken” Dothideomycetes in the synthetic tree? follow the “View the MRCA of the members of this taxon in the synthetic tree” link.

It is the Ascomycota, which has more than 1.5k species.

It is time now to ask the question, do we want to update an alignment for all the Ascomycota???

Why are the Dothideomycetes “broken”?

go to the “Show this tree’s conflicts in the study curation tool” link.

There is a published tree that is conflicting with the taxonomy.

Let’s get more information about the taxonomy of the Dothideomycetes, follow the “View this taxon in the taxonomy browser” link.

So, it seems like it is a taxon in NCBI. To verify this, go to the section “Taxon details”, and follow the ncbi:147541 link.

Maybe we can just enrich that part of the tree on the updating step.

Let’s verify that on the study curator of OToL.

Studies matching the word ‘dothideomycetes’ on the curator database, at the middle of year 2020. Some of these studies are not actually about this taxon.

Finding a tree to update using the R package rotl

Explain what a focal clade is.

There is a handy function that will search a taxon among the focal clades reported across trees.

doth <- rotl::studies_find_studies(property="ot:focalCladeOTTTaxonName", value="Dothideomycetes")

It seems like the tree tree137 from study pg_254, is not in the Open Tree of Life synthetic tree.

Let’s get it and plot it here:

schoch2009 <- rotl::get_study_tree(study_id = "pg_254", tree_id = "tree137")
ape::plot.phylo(ape::ladderize(schoch2009), type = "phylogram", cex = 0.3, label.offset = 1, edge.width = 0.5)

The alignment is here https://treebase.org/treebase-web/search/study/matrices.html?id=10245.

wget "http://purl.org/phylo/treebase/phylows/matrix/TB2:M4727?format=nexus" mv TB2:M4727?format=nexus data-raw/alignments/T6859-M4727.nex

Ascomycota

asco <- rotl::studies_find_studies(property="ot:focalCladeOTTTaxonName", value="Ascomycota")
datatable(asco, class = 'order-column hover compact row-border', options = list(dom = 't'), rownames = FALSE, editable = FALSE)
knitr::kable(asco, caption = "Studies with the **Ascomycota** as focal clade.")
Studies with the Ascomycota as focal clade.
study_ids n_trees tree_ids candidate study_year title study_doi
pg_1682 5 tree3388, tree3389, tree3391, tree3392, tree5491 tree5491 1999 Molecular phylogeny of the cleistothecial fungi placed in Cephalothecaceae and Pseudeurotiaceae http://dx.doi.org/10.2307/3761537
pg_854 2 tree1646, tree1647 2009 Phylogeny and taxonomy of obscure genera of microfungi http://dx.doi.org/10.3767/003158509X461701
ot_1421 3 tree1, tree2, tree3 2016 ‘Novel fungi from an ancient niche: cercosporoid and related sexual morphs on ferns’ http://dx.doi.org/10.3767/003158516x690934
pg_831 8 tree1597, tree1598, tree1599, tree1600, tree5682, … 2008 Phylogenetic diversity of fungi from the deep-sea sediments of the Central Indian Basin and their growth characteristics http://dx.doi.org/10.1007/s13225-009-0009-5
pg_238 1 tree109 2009 http://dx.doi.org/10.1093/sysbio/syp020
pg_875 1 tree1682 2002 Higher level phylogenetic relationships of Euascomycetes (Pezizomycotina) inferred from a combined analysis of nuclear and mitochondrial sequence data http://dx.doi.org/10.1007/s11557-006-0005-z
pg_845 1 tree1625 2008 Foliicolous microfungi occurring on Encephalartos http://dx.doi.org/10.3767/003158508X380612
pg_1733 1 tree3485 2001 Two pantropical Ascomycetes: Chaetosphaeria cylindrospora sp http://dx.doi.org/10.2307/3761669
pg_2226 2 tree4705, tree4706 2002 New genes for phylogenetic studies of lichenized fungi: glyceraldehyde-3-phosphate dehydrogenase and beta-tubulin genes http://dx.doi.org/10.1006/lich.2002.0390
ot_239 1 Tr6287 2009 Multiple origins of symbioses between ascomycetes and bryophytes suggested by a five-gene phylogeny http://dx.doi.org/10.1111/j.1096-0031.2009.00299.x
pg_1080 1 tree2103 2012 Culture-free survey reveals diverse and distinctive fungal communities associated with developing figs (Ficus spp http://dx.doi.org/10.1007/s00248-012-0079-x
pg_2442 5 tree5182, tree5183, tree5184, tree5185, tree6009 2011 Molecular phylogeny of two coelomycetous genera with star-shaped conidia, Prosthemium and Asterosporium on Fagales tree http://dx.doi.org/10.1139/B10-078
ot_471 5 Tr88710, Tr88708, Tr88709, Tr88706, Tr88707 Tr88706 2015 The Genera of Fungi - fixing the application of the type species of generic names ? G 2: Allantophomopsis, Latorua, Macrodiplodiopsis, Macrohilum, Milospium, Protostegia, Pyricularia, Robillarda, Rotula, Septoriella, Torula, and Wojnowicia http://dx.doi.org/10.5598/imafungus.2015.06.01.11
ot_351 1 Tr53295 Tr53295 2012 Fungal Planet description sheets: 107?127 http://dx.doi.org/10.3767/003158512X652633
pg_2392 2 tree5032, tree5033 2011 Interkingdom gene transfer of a hybrid NPS/PKS from bacteria to filamentous Ascomycota http://dx.doi.org/10.1371/journal.pone.0028231
pg_736 1 tree1330 2001 Phylogenetic analysis of nuclear and mitochondrial rDNA sequences supports that loculoascomycetes are not monophyletic http://dx.doi.org/10.1016/S0953-7562(08)61988-7
pg_1059 2 tree2038, tree5775 2010 Species richness analysis and ITS rDNA phylogeny revealed the majority of cultivable foliar endophytes from beech (Fagus sylvatica L http://dx.doi.org/10.1016/j.funeco.2010.03.001
pg_1196 3 tree2414, tree2415, tree2416 2011 http://dx.doi.org/10.3767/003158511X574532
pg_1198 1 tree2419 2011 Fungal Planet description sheets: 69–91 http://dx.doi.org/10.3767/003158511X581723
pg_2225 2 tree4704, tree5949 2001 The phylogeny of plant and animal pathogens in the Ascomycota http://dx.doi.org/10.1006/pmpp.2001.0355
pg_2224 1 tree4703 2000 "Fungal molecular evolution: gene trees and geologic time
pg_2223 1 tree4702 2000 Evolution of Filamentous Ascomycetes Inferred from LSU rDNA Sequence Data http://dx.doi.org/10.1055/s-2000-7472
pg_1037 1 tree1990 2010 Phylogenetic analysis of ascomycete yeasts that form coenzyme Q-9 and the proposal of the new genera Babjeviella, Meyerozyma, Millerozyma, Priceomyces, and Scheffersomyces http://dx.doi.org/10.1007/s10267-009-0011-5
ot_424 4 Tr75536, Tr68229, Tr68227, Tr68230 Tr68230 2014 ’Fodinomyces uranophilus gen. nov. sp. nov. and Coniochaeta fodinicola sp. nov. http://dx.doi.org/10.3852/14-013
pg_1201 1 tree2423 2012 Fungal Planet description sheets: 107-127 http://dx.doi.org/10.3767/003158512X652633
pg_862 1 tree1657 2010 Coniochaeta (Lecythophora), Collophora gen http://dx.doi.org/10.3767/003158510X500705
pg_863 2 tree1658, tree1659 2010 Microcyclospora and Microcyclosporella: novel genera accommodating epiphytic fungi causing sooty blotch on apple http://dx.doi.org/10.3767/003158510X510560
pg_2245 1 tree4759 2005
ot_1616 1 tree1 2018 ‘Two new classes of Ascomycota: Xylobotryomycetes and Candelariomycetes’ http://dx.doi.org/10.3767/persoonia.2019.42.02

It seems like the tree tree109 from study pg_238, is not in the Open Tree of Life synthetic tree.

Ascomycota alignments here https://treebase.org/treebase-web/search/study/matrices.html?id=2137.

wget "http://purl.org/phylo/treebase/phylows/matrix/TB2:M3939?format=nexus"
mv TB2:M3939?format=nexus data-raw/alignments/Tr5276-M3939.nex

wget "http://purl.org/phylo/treebase/phylows/matrix/TB2:M3938?format=nexus"
mv TB2:M3938?format=nexus data-raw/alignments/Tr5276-M3938.nex

wget "http://purl.org/phylo/treebase/phylows/matrix/TB2:M3802?format=nexus"
mv TB2:M3802?format=nexus data-raw/alignments/Tr5276-M3802.nex

wget "http://purl.org/phylo/treebase/phylows/matrix/TB2:M3956?format=nexus"
mv TB2:M3956?format=nexus data-raw/alignments/Tr5276-M3956.nex

Downloading them with physcraper

physcraper_run.py -s pg_238 -t tree109 -tb -no_est -o ../physcraperex/data/schoch_ascomycota_0_2020.06.06

Current run

physcraper_run.py -s pg_238 -t tree109 -a ../physcraperex/data-raw/alignments/Tr5276-M3939-mod.nex -as nexus  -db /branchinecta/shared/local_blast_db -o ../physcraperex/data/schoch_ascomycota_1_2020.06.06