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)

Ostreococcus lucimarinus (Ostreococcus lucimarinus CCE9901)

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

Drosophila melanogaster (Fruit fly) (Drosophila melanogaster)

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

Human (Homo sapiens)

C.savignyi (Ciona savignyi)

Saccharomyces cerevisiae (Saccharomyces cerevisiae S288C)

Oryza rufipogon (Oryza rufipogon cultivar W1943)

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

Oryza nivara (Oryza nivara cultivar IRGC:100897)

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

Oryza barthii (Oryza barthii cultivar IRGC:105608)

Oryza glaberrima (Oryza glaberrima cultivar CG14)

Oryza longistaminata (Oryza longistaminata)

Oryza glumipatula (Oryza glumipatula)

Oryza meridionalis (Oryza meridionalis cultivar OR44 (W2112))

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

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

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

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

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

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

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

Triticum urartu (Triticum urartu strain G1812 (PI428198))

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

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

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

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

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

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

Secale cereale (Secale cereale)

Lolium perenne (Lolium perenne reference strain)

Hordeum vulgare (Hordeum vulgare subsp. vulgare cultivar Morex)

Brachypodium distachyon (Brachypodium distachyon strain Bd21)

Eragrostis curvula (Eragrostis curvula strain Tanganyika)

Eragrostis tef (Eragrostis tef cultivar Dabbi)

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

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)

Setaria italica (Setaria italica strain Yugu1)

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

Digitaria exilis (Digitaria exilis strain digitaria_exilis)

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

Ananas comosus (Ananas comosus strain F153)

Dioscorea rotundata (Dioscorea cayenensis subsp. rotundata)

Asparagus officinalis (Asparagus officinalis strain DH00/086)

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

Chenopodium quinoa (Chenopodium quinoa strain PI614886)

Eucalyptus grandis (Eucalyptus grandis strain BRASUZ1)

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

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

Gossypium raimondii (Gossypium raimondii)

Corchorus capsularis (Corchorus capsularis strain CVL-1)

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

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

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)

Arabis alpina (Arabis alpina)

Eutrema salsugineum (Eutrema salsugineum)

Citrus clementina (Citrus clementina strain Clemenules)

Pistacia vera (Pistacia vera strain Batoury)

Populus trichocarpa (Populus trichocarpa)

Manihot esculenta (Manihot esculenta)

Cucumis melo (Cucumis melo)

Citrullus lanatus (Citrullus lanatus strain 97103)

Cucumis sativus (Cucumis sativus strain 9930)

Prunus persica (Prunus persica strain Lovell)

Prunus dulcis (Prunus dulcis strain Texas)

Prunus avium (Prunus avium strain Satonishiki)

Malus domestica Golden (Malus domestica strain Golden Delicious)

Ficus carica (Ficus carica cultivar Dottato)

Cannabis sativa female (Cannabis sativa)

Rosa chinensis (Rosa chinensis)

Corylus avellana (Corylus avellana cultivar Tombul)

Quercus lobata (Quercus lobata)

Quercus suber (Quercus suber reference strain)

Juglans regia (Juglans regia cultivar Chandler)

Medicago truncatula (Medicago truncatula)

Trifolium pratense (Trifolium pratense strain Milvus B)

Lathyrus sativus (Lathyrus sativus)

Vicia faba (Vicia faba)

Pisum sativum (Pisum sativum cultivar Cameor)

Glycine soja (Wild soybean) (Glycine soja)

Glycine max (Glycine max strain Williams 82)

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

Vigna angularis (Vigna angularis strain Jingnong 6)

Vigna radiata (Vigna radiata var. radiata strain VC1973A)

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

Phaseolus vulgaris (Phaseolus vulgaris strain G19833)

Arachis hypogaea (Arachis hypogaea)

Lupinus angustifolius (Lupinus angustifolius strain Tanjil)

Vitis vinifera (Vitis vinifera strain PN40024)

Fraxinus excelsior (Fraxinus excelsior reference strain)

Olea europaea (Olea europaea subsp. europaea variety Farga)

Cynara cardunculus (Cynara cardunculus var. scolymus)

Helianthus annuus (Helianthus annuus cultivar XRQ/B)

Lactuca sativa (Lactuca sativa cultivar Salinas)

Solanum lycopersicum (Solanum lycopersicum strain Heinz 1706)

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

Nicotiana attenuata (Nicotiana attenuata strain UT)

Capsicum annuum (Capsicum annuum strain Criollo de Morelos 334)

Sesamum indicum (Sesamum indicum strain Zhongzhi No. 13)

Coffea canephora (Coffea canephora strain DH200-94)

Daucus carota (Daucus carota subsp. sativus strain DH1)

Ipomoea triloba (Ipomoea triloba strain NCNSP0323)

Actinidia chinensis (Actinidia chinensis var. chinensis strain Red5)

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)

Physcomitrium patens (Physcomitrium patens strain Gransden 2004)

Marchantia polymorpha (Marchantia polymorpha)

Chara braunii (Chara braunii strain S276)