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

Cyanidioschyzon merolae (Cyanidioschyzon merolae strain 10D)

Galdieria sulphuraria (Galdieria sulphuraria strain 074W)

Chondrus crispus (Chondrus crispus strain Stackhouse)

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

Ostreococcus lucimarinus (Ostreococcus lucimarinus CCE9901)

Oryza barthii (Oryza barthii strain IRGC:105608)

Oryza glaberrima (Oryza glaberrima strain CG14)

Oryza nivara (Oryza nivara strain IRGC:100897)

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

Oryza rufipogon (Oryza rufipogon strain W1943)

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

Oryza glumipatula (Oryza glumipatula)

Oryza meridionalis (Oryza meridionalis strain OR44 (W2112))

Oryza longistaminata (Oryza longistaminata)

Oryza punctata (Oryza punctata strain IRGC:105690)

Oryza brachyantha (Oryza brachyantha strain IRGC:101232)

Leersia perrieri (Leersia perrieri strain IRGC:105164)

Avena sativa OT3098 (Avena sativa strain OT3098)

Avena sativa Sang (Avena sativa strain sang)

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

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

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

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

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

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

Secale cereale (Secale cereale)

Hordeum vulgare (Hordeum vulgare subsp. vulgare cultivar Morex)

Lolium perenne (Lolium perenne reference strain)

Brachypodium distachyon (Brachypodium distachyon strain Bd21)

Eragrostis tef (Eragrostis tef cultivar Dabbi)

Eragrostis curvula (Eragrostis curvula strain Tanganyika)

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

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

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

Setaria viridis (Setaria viridis strain A10)

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

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

Digitaria exilis (Digitaria exilis strain digitaria_exilis)

Setaria italica (Setaria italica strain Yugu1)

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)

Chenopodium quinoa (Chenopodium quinoa strain PI614886)

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

Manihot esculenta (Manihot esculenta strain AM560-2)

Populus trichocarpa (Populus trichocarpa)

Cucumis melo (Cucumis melo)

Cucumis sativus (Cucumis sativus strain 9930)

Citrullus lanatus (Citrullus lanatus strain 97103)

Quercus suber (Quercus suber reference strain)

Juglans regia (Juglans regia cultivar Chandler)

Quercus lobata (Quercus lobata)

Corylus avellana (Corylus avellana cultivar Tombul)

Trifolium pratense (Trifolium pratense strain Milvus B)

Medicago truncatula (Medicago truncatula strain A17)

Vigna radiata (Vigna radiata var. radiata strain VC1973A)

Vigna angularis (Vigna angularis strain Jingnong 6)

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

Glycine max (Glycine max strain Williams 82)

Phaseolus vulgaris (Phaseolus vulgaris strain G19833)

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

Lupinus angustifolius (Lupinus angustifolius strain Tanjil)

Pisum sativum (Pisum sativum cultivar Cameor)

Prunus persica (Prunus persica strain Lovell)

Prunus avium (Prunus avium strain Satonishiki)

Prunus dulcis (Prunus dulcis strain Texas)

Malus domestica Golden (Malus domestica strain Golden Delicious)

Cannabis sativa female (Cannabis sativa)

Ficus carica (Ficus carica cultivar Dottato)

Rosa chinensis (Rosa chinensis)

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

Eucalyptus grandis (Eucalyptus grandis strain BRASUZ1)

Corchorus capsularis (Corchorus capsularis strain CVL-1)

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

Gossypium raimondii (Gossypium raimondii)

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

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

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

Arabidopsis lyrata (Arabidopsis lyrata subsp. lyrata strain MN47)

Arabidopsis thaliana (Arabidopsis thaliana strain Columbia)

Arabidopsis halleri (Arabidopsis halleri subsp. gemmifera strain W302)

Brassica napus (Brassica napus strain Darmor-bzh)

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

Brassica juncea (Brassica juncea cultivar Sichuan Huangzi)

Brassica oleracea (Brassica oleracea var. oleracea strain TO1000)

Eutrema salsugineum (Eutrema salsugineum)

Arabis alpina (Arabis alpina)

Pistacia vera (Pistacia vera strain Batoury)

Citrus clementina (Citrus clementina strain Clemenules)

Vitis vinifera (Vitis vinifera strain PN40024)

Olea europaea (Olea europaea subsp. europaea variety Farga)

Fraxinus excelsior (Fraxinus excelsior reference strain)

Lactuca sativa (Lactuca sativa cultivar Salinas)

Cynara cardunculus (Cynara cardunculus var. scolymus)

Helianthus annuus (Helianthus annuus cultivar XRQ/B)

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

Solanum lycopersicum (Solanum lycopersicum strain Heinz 1706)

Nicotiana attenuata (Nicotiana attenuata strain UT)

Capsicum annuum (Capsicum annuum strain Criollo de Morelos 334)

Daucus carota (Daucus carota subsp. sativus strain DH1)

Actinidia chinensis (Actinidia chinensis var. chinensis strain Red5)

Ipomoea triloba (Ipomoea triloba strain NCNSP0323)

Sesamum indicum (Sesamum indicum strain Zhongzhi No. 13)

Coffea canephora (Coffea canephora strain DH200-94)

Kalanchoe fedtschenkoi (Kalanchoe fedtschenkoi)

Nymphaea colorata (Nymphaea colorata strain Beijing-Zhang1983)

Amborella trichopoda (Amborella trichopoda)

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

Selaginella moellendorffii (Selaginella moellendorffii)

Marchantia polymorpha (Marchantia polymorpha strain Tak-1)

Physcomitrium patens (Physcomitrium patens strain Gransden 2004)

Chara braunii (Chara braunii strain S276)

C.savignyi (Ciona savignyi)

Human (Homo sapiens)

Caenorhabditis elegans (PRJNA13758) (Caenorhabditis elegans strain N2)

Drosophila melanogaster (Fruit fly) (Drosophila melanogaster)

Saccharomyces cerevisiae (Saccharomyces cerevisiae S288C)