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

Vigna angularis (Vigna angularis strain Jingnong 6)

Vigna radiata (Vigna radiata var. radiata strain VC1973A)

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

Glycine max (Glycine max strain Williams 82)

Glycine soja (Wild soybean) (Glycine soja)

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

Phaseolus vulgaris (Phaseolus vulgaris strain G19833)

Sphenostylis stenocarpa (Sphenostylis stenocarpa)

Lathyrus sativus (Lathyrus sativus)

Pisum sativum (Pisum sativum cultivar Cameor)

Vicia faba (Vicia faba)

Medicago truncatula (Medicago truncatula)

Trifolium pratense (Trifolium pratense strain Milvus B)

Arachis hypogaea (Arachis hypogaea)

Lupinus angustifolius (Lupinus angustifolius strain Tanjil)

Prunus avium (Prunus avium strain Satonishiki)

Prunus dulcis (Prunus dulcis strain Texas)

Prunus persica (Prunus persica strain Lovell)

Malus domestica Golden (Malus domestica strain Golden Delicious)

Cannabis sativa female (Cannabis sativa)

Ficus carica (Ficus carica cultivar Dottato)

Rosa chinensis (Rosa chinensis)

Corylus avellana (Corylus avellana cultivar Tombul)

Juglans regia (Juglans regia cultivar Chandler)

Quercus lobata (Quercus lobata)

Quercus suber (Quercus suber reference strain)

Citrullus lanatus (Citrullus lanatus strain 97103)

Cucumis melo (Cucumis melo)

Cucumis sativus (Cucumis sativus strain 9930)

Manihot esculenta (Manihot esculenta)

Populus trichocarpa (Populus trichocarpa)

Brassica juncea (Brassica juncea cultivar Sichuan Huangzi)

Brassica napus (Brassica napus strain Darmor-bzh)

Brassica oleracea (Brassica oleracea var. oleracea strain TO1000)

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

Arabidopsis halleri (Arabidopsis halleri subsp. gemmifera strain W302)

Arabidopsis lyrata (Arabidopsis lyrata subsp. lyrata strain MN47)

Arabidopsis thaliana (Arabidopsis thaliana strain Columbia)

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

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

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

Arabis alpina (Arabis alpina)

Eutrema salsugineum (Eutrema salsugineum)

Corchorus capsularis (Corchorus capsularis strain CVL-1)

Gossypium raimondii (Gossypium raimondii)

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

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

Eucalyptus grandis (Eucalyptus grandis strain BRASUZ1)

Citrus clementina (Citrus x clementina strain Clemenules)

Pistacia vera (Pistacia vera strain Batoury)

Vitis vinifera (Vitis vinifera)

Solanum lycopersicum (Solanum lycopersicum strain Heinz 1706)

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

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)

Fraxinus excelsior (Fraxinus excelsior reference strain)

Olea europaea (Olea europaea subsp. europaea variety Farga)

Actinidia chinensis (Actinidia chinensis var. chinensis strain Red5)

Coffea canephora (Coffea canephora strain DH200-94)

Daucus carota (Daucus carota subsp. sativus strain DH1)

Ipomoea triloba (Ipomoea triloba strain NCNSP0323)

Sesamum indicum (Sesamum indicum strain Zhongzhi No. 13)

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

Chenopodium quinoa (Chenopodium quinoa strain PI614886)

Kalanchoe fedtschenkoi (Kalanchoe fedtschenkoi)

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

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

Triticum spelta (component A) (Triticum spelta cultivar Spelta (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 B) (Triticum aestivum reference (Chinese spring) cultivar (component B))

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

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

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

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

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

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

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

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

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

Avena sativa OT3098 (Avena sativa strain OT3098)

Avena sativa Sang (Avena sativa strain sang)

Hordeum vulgare (Hordeum vulgare subsp. vulgare cultivar Morex)

Lolium perenne (Lolium perenne reference strain)

Secale cereale (Secale cereale)

Brachypodium distachyon (Brachypodium distachyon strain Bd21)

Oryza nivara (Oryza nivara cultivar IRGC:100897)

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

Oryza rufipogon (Oryza rufipogon cultivar W1943)

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

Oryza barthii (Oryza barthii cultivar IRGC:105608)

Oryza glaberrima (Oryza glaberrima cultivar CG14)

Oryza glumipatula (Oryza glumipatula)

Oryza longistaminata (Oryza longistaminata)

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)

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

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

Sorghum bicolor (Sorghum bicolor strain BTx623)

Zea mays (Zea mays strain B73)

Digitaria exilis (Digitaria exilis strain digitaria_exilis)

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

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

Setaria italica (Setaria italica strain Yugu1)

Setaria viridis (Setaria viridis strain A10)

Eragrostis curvula (Eragrostis curvula strain Tanganyika)

Eragrostis tef (Eragrostis tef cultivar Dabbi)

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)

Amborella trichopoda (Amborella trichopoda)

Nymphaea colorata (Nymphaea colorata strain Beijing-Zhang1983)

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

Selaginella moellendorffii (Selaginella moellendorffii)

Marchantia polymorpha (Marchantia polymorpha)

Physcomitrium patens (Physcomitrium patens strain Gransden 2004)

Chara braunii (Chara braunii strain S276)

C.savignyi (Ciona savignyi)

Human (Homo sapiens)

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

Drosophila melanogaster (Fruit fly) - GCA_000001215.4 [FlyBase annotation] (Drosophila melanogaster)

Saccharomyces cerevisiae (Saccharomyces cerevisiae S288C)

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

Ostreococcus lucimarinus (Ostreococcus lucimarinus CCE9901)

Cyanidioschyzon merolae (Cyanidioschyzon merolae strain 10D)

Galdieria sulphuraria (Galdieria sulphuraria strain 074W)

Chondrus crispus (Chondrus crispus strain Stackhouse)