Statistics on protein trees

The protein tree pipeline is described at the following page.

• Overview
• Gene tree coverage and Gene QC for each species
• Size of gene trees (split by their root taxon)
• Gene tree nodes, and the inference of speciation / duplication events

Overall Summary

Legend
Internal nodes (ancestral taxa)	Node types	Speciations	Duplications	Dubious nodes
Leaves (extant species)	Gene tree coverage	Genes in multi-species trees	Genes in single-species trees	Orphaned genes
	Gene QC	Validated genes	Short genes	Long genes	Split genes

Galdieria sulphuraria (Galdieria sulphuraria strain 074W)

Cyanidioschyzon merolae (Cyanidioschyzon merolae strain 10D)

Chondrus crispus (Chondrus crispus strain Stackhouse)

Caenorhabditis elegans (Nematode, N2) (Caenorhabditis elegans strain N2)

Drosophila melanogaster (Fruit fly) (Drosophila melanogaster)

C.savignyi (Ciona savignyi)

Human (Homo sapiens)

Saccharomyces cerevisiae (Saccharomyces cerevisiae S288C)

Ostreococcus lucimarinus (Ostreococcus lucimarinus CCE9901)

Chlamydomonas reinhardtii (Chlamydomonas reinhardtii strain CC-503 cw92 mt+)

Eragrostis tef (Eragrostis tef cultivar Dabbi)

Eragrostis curvula (Eragrostis curvula strain Tanganyika)

Oryza sativa Indica Group (Oryza sativa Indica Group strain 93-11)

Oryza nivara (Oryza nivara cultivar IRGC:100897)

Oryza rufipogon (Oryza rufipogon cultivar W1943)

Oryza sativa Japonica Group (Oryza sativa Japonica Group reference (Nipponbare) cultivar)

Oryza glaberrima (Oryza glaberrima cultivar CG14)

Oryza barthii (Oryza barthii cultivar IRGC:105608)

Oryza meridionalis (Oryza meridionalis cultivar OR44 (W2112))

Oryza glumipatula (Oryza glumipatula)

Oryza longistaminata (Oryza longistaminata)

Oryza punctata (Oryza punctata cultivar IRGC:105690)

Oryza brachyantha (Oryza brachyantha cultivar IRGC:101232)

Leersia perrieri (Leersia perrieri cultivar IRGC:105164)

Avena sativa OT3098 (Avena sativa strain OT3098)

Avena sativa Sang (Avena sativa strain sang)

Triticum aestivum (component A) (Triticum aestivum reference (Chinese spring) cultivar (component A))

Triticum timopheevii (component A) (Triticum timopheevii (component A))

Triticum spelta (component A) (Triticum spelta cultivar Spelta (component A))

Triticum turgidum (component A) (Triticum turgidum subsp. durum strain svevo (component A))

Triticum dicoccoides (component A) (Triticum dicoccoides strain Zavitan (Atlit2015) (component A))

Triticum urartu (Triticum urartu strain G1812 (PI428198))

Triticum turgidum (component U) (Triticum turgidum subsp. durum strain svevo (component U))

Triticum aestivum (component U) (Triticum aestivum reference (Chinese spring) cultivar (component U))

Triticum spelta (component D) (Triticum spelta cultivar Spelta (component D))

Aegilops tauschii (Aegilops tauschii subsp. strangulata strain AL8/78)

Triticum aestivum (component D) (Triticum aestivum reference (Chinese spring) cultivar (component D))

Triticum aestivum (component B) (Triticum aestivum reference (Chinese spring) cultivar (component B))

Triticum spelta (component B) (Triticum spelta cultivar Spelta (component B))

Triticum turgidum (component B) (Triticum turgidum subsp. durum strain svevo (component B))

Triticum dicoccoides (component B) (Triticum dicoccoides strain Zavitan (Atlit2015) (component B))

Triticum timopheevii (component B) (Triticum timopheevii (component B))

Hordeum vulgare (Hordeum vulgare subsp. vulgare cultivar Morex)

Secale cereale (Secale cereale)

Lolium perenne (Lolium perenne reference strain)

Brachypodium distachyon (Brachypodium distachyon strain Bd21)

Sorghum bicolor (Sorghum bicolor strain BTx623)

Zea mays (Zea mays strain B73)

Saccharum spontaneum (component B) (Saccharum spontaneum strain AP85-441 (component B))

Saccharum spontaneum (component A) (Saccharum spontaneum strain AP85-441 (component A))

Saccharum spontaneum (component D) (Saccharum spontaneum strain AP85-441 (component D))

Saccharum spontaneum (component C) (Saccharum spontaneum strain AP85-441 (component C))

Digitaria exilis (Digitaria exilis strain digitaria_exilis)

Setaria viridis (Setaria viridis strain A10)

Setaria italica (Setaria italica strain Yugu1)

Echinochloa crus-galli (Echinochloa crus-galli reference strain)

Panicum hallii HAL2 (Panicum hallii var. hallii reference (HAL2) ecotype)

Musa acuminata (Musa acuminata subsp. malaccensis cultivar Doubled-haploid Pahang (DH-Pahang))

Dioscorea rotundata (Dioscorea cayenensis subsp. rotundata)

Ananas comosus (Ananas comosus strain F153)

Asparagus officinalis (Asparagus officinalis strain DH00/086)

Beta vulgaris (Beta vulgaris subsp. vulgaris strain KWS2320 DH)

Chenopodium quinoa (Chenopodium quinoa strain PI614886)

Corymbia citriodora (Corymbia citriodora subsp. variegata genotype CCV2-018)

Eucalyptus grandis (Eucalyptus grandis strain BRASUZ1)

Theobroma cacao Matina 1-6 (Theobroma cacao reference (Matina) cultivar)

Corchorus capsularis (Corchorus capsularis strain CVL-1)

Gossypium raimondii (Gossypium raimondii)

Camelina sativa (component G1) (Camelina sativa strain dh55 (component G1))

Camelina sativa (component G3) (Camelina sativa strain dh55 (component G3))

Camelina sativa (component G2) (Camelina sativa strain dh55 (component G2))

Arabidopsis halleri (Arabidopsis halleri subsp. gemmifera strain W302)

Arabidopsis lyrata (Arabidopsis lyrata subsp. lyrata strain MN47)

Arabidopsis thaliana (Arabidopsis thaliana strain Columbia)

Brassica juncea (Brassica juncea cultivar Sichuan Huangzi)

Brassica oleracea (Brassica oleracea var. oleracea strain TO1000)

Brassica napus (Brassica napus strain Darmor-bzh)

Brassica rapa R-o-18 (Brassica rapa subsp. trilocularis cultivar R-o-18)

Eutrema salsugineum (Eutrema salsugineum)

Arabis alpina (Arabis alpina)

Citrus clementina (Citrus clementina strain Clemenules)

Pistacia vera (Pistacia vera strain Batoury)

Populus trichocarpa (Populus trichocarpa)

Manihot esculenta (Manihot esculenta)

Cucumis sativus (Cucumis sativus strain 9930)

Citrullus lanatus (Citrullus lanatus strain 97103)

Cucumis melo (Cucumis melo)

Prunus dulcis (Prunus dulcis strain Texas)

Prunus persica (Prunus persica strain Lovell)

Prunus avium (Prunus avium strain Satonishiki)

Malus domestica Golden (Malus domestica strain Golden Delicious)

Cannabis sativa female (Cannabis sativa)

Ficus carica (Ficus carica cultivar Dottato)

Rosa chinensis (Rosa chinensis)

Quercus suber (Quercus suber reference strain)

Quercus lobata (Quercus lobata)

Corylus avellana (Corylus avellana cultivar Tombul)

Juglans regia (Juglans regia cultivar Chandler)

Trifolium pratense (Trifolium pratense strain Milvus B)

Medicago truncatula (Medicago truncatula)

Vicia faba (Vicia faba)

Pisum sativum (Pisum sativum cultivar Cameor)

Lathyrus sativus (Lathyrus sativus)

Glycine soja (Wild soybean) (Glycine soja)

Glycine max (Glycine max strain Williams 82)

Vigna angularis (Vigna angularis strain Jingnong 6)

Vigna unguiculata (Vigna unguiculata strain IT97K-499-35)

Vigna radiata (Vigna radiata var. radiata strain VC1973A)

Cajanus cajan (pigeon pea) - GCA_000340665.1 (Cajanus cajan)

Phaseolus vulgaris (Phaseolus vulgaris strain G19833)

Lupinus angustifolius (Lupinus angustifolius strain Tanjil)

Arachis hypogaea (Arachis hypogaea)

Vitis vinifera (Vitis vinifera strain PN40024)

Fraxinus excelsior (Fraxinus excelsior reference strain)

Olea europaea (Olea europaea subsp. europaea variety Farga)

Solanum tuberosum (Solanum tuberosum cultivar DM 1-3 516 R44)

Solanum lycopersicum (Solanum lycopersicum strain Heinz 1706)

Capsicum annuum (Capsicum annuum strain Criollo de Morelos 334)

Nicotiana attenuata (Nicotiana attenuata strain UT)

Cynara cardunculus (Cynara cardunculus var. scolymus)

Helianthus annuus (Helianthus annuus cultivar XRQ/B)

Lactuca sativa (Lactuca sativa cultivar Salinas)

Ipomoea triloba (Ipomoea triloba strain NCNSP0323)

Actinidia chinensis (Actinidia chinensis var. chinensis strain Red5)

Daucus carota (Daucus carota subsp. sativus strain DH1)

Sesamum indicum (Sesamum indicum strain Zhongzhi No. 13)

Coffea canephora (Coffea canephora strain DH200-94)

Kalanchoe fedtschenkoi (Kalanchoe fedtschenkoi)

Amborella trichopoda (Amborella trichopoda)

Papaver somniferum (Papaver somniferum strain High Noscapine 1 (HN1))

Nymphaea colorata (Nymphaea colorata strain Beijing-Zhang1983)

Selaginella moellendorffii (Selaginella moellendorffii)

Marchantia polymorpha (Marchantia polymorpha)

Physcomitrium patens (Physcomitrium patens strain Gransden 2004)

Chara braunii (Chara braunii strain S276)