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Table 1 Information on the species and sequences used in the analysis. Sampling locality is shown for newly sequenced taxa, citations for data obtained from the literature. For deep-sea specimens, sampling depth is also reported

From: A phylogenomic resolution of the sea urchin tree of life

Clade Species Data typea Sampling locality (depth)/Source Voucher number SRA/Genome numbers
Arbacioida Gregory, 1900 Arbacia punctulata (Lamarck, 1816) T [43] SIO-BIC E6740 SRR2843235
Camarodonta Jackson, 1912 Colobocentrotus atratus (Linnaeus, 1758) T Kailua Kona, Hawaii Island SIO-BIC E7012 SRR7513588
  Echinometra mathaei (Blainville, 1825) T Al-Fahal Reef, Red Sea, Makkah, Saudi Arabia SIO-BIC E6896 SRR7513581
  Evechinus chloroticus (Valenciennes, 1846) T [131] SRR1014619
  Heliocidaris erythrogramma (Valenciennes, 1846) T [132] SRR1211283
  Lytechinus variegatus (Lamarck, 1816) T [5] SRR1139214
  Mesocentrotus nudus (A. Agassiz, 1864) T [133] SRR5017175
  Paracentrotus lividus (Lamarck, 1816) T [134] SRR1735501
  Sphaerechinus granularis (Lamarck, 1816) T [5] SRR1139199
  Strongylocentrotus purpuratus (Stimpson, 1857) G [45]; Spur_4.2 GCF 000002235.4
Cidaroida Claus, 1880 Eucidaris tribuloides (Lamarck, 1816) T [43] SIO-BIC E6742 SRR2844625
  Prionocidaris baculosa (Lamarck, 1816) T Al-Fahal Reef, Red Sea, Makkah, Saudi Arabia SIO-BIC E6897 SRR7513584
Clypeasteroida sensu A. Agassiz, 1872-1874 Clypeaster rosaceus (Linnaeus, 1758) T Bocas del Toro, Panama SRR7513591
  Clypeaster subdepressus (Gray, 1825) T Bocas del Toro, Panama SRR7513586
  Dendraster excentricus (Eschscholtz, 1831) T [43] SIO-BIC E5640 SRR2844623
  Echinarachnius parma (Lamarck, 1816) T [5] SRR1139193
  Echinocyamus crispus Mazetti, 1893 T Al-Fahal Reef, Red Sea, Makkah, Saudi Arabia SIO-BIC E6903 SRR7513576
  Mellita tenuis H.L. Clark, 1940 T Apalachee Bay, Wakulla County, Florida SIO-BIC E7015 SRR7513583
Diadematoida Duncan, 1889 Diadema setosum (Leske, 1778) T Al-Fahal Reef, Red Sea, Makkah, Saudi Arabia SIO-BIC E6905 SRR7513577
  Lissodiadema lorioli Mortensen, 1903 T Kaneohe Bay, Honolulu, Hawaii Island UF Echino 18893 SRR7513580
Echinolampadoida Kroh & Smith, 2010 Conolampas sigsbei (A. Agassiz, 1878) T Willemstad, Curaçao (233–300 m) SRR7513579
Echinothurioida Claus, 1880 Araeosoma leptaleum A. Agassiz & H.L. Clark, 1909 T Mount Quepos, Pacific Ocean, Costa Rica (1097 m) SIO-BIC E7021 SRR7513578
  Asthenosoma varium Grube, 1868 T Momi Bay, Viti Levu, Fiji SRR7513575
Holasteroida Durham & Melville, 1957 Pilematechinus sp. T Axial Seamount, Juan de Fuca Ridge (1550 m) SIO-BIC E6947 SRR7513585
Pedinoida Mortensen, 1939 Caenopedina hawaiiensis H.L. Clark, 1912 T Mount Quepos, Pacific Ocean, Costa Rica (1908 m) SIO-BIC E7020 SRR7513589
Spatangoida L. Agassiz, 1840 Brissus obesus Verrill, 1867 T San Clemente Island, California SIO-BIC E7018 SRR7513590
  Meoma ventricosa (Lamarck, 1816) T Bocas del Toro, Panama SRR7513582
Stomopneustoida Kroh & Smith, 2010 Stomopneustes variolaris (Lamarck, 1816) T Sohoa, Mayotte SIO-BIC E7014 SRR7513587
Holothuroidea de Blainville, 1834 Holothuria forskali Delle Chiaje, 1823 T [135] SRR5109955
Asteroidea de Blainville, 1830 Acanthaster planci (Linnaeus, 1758) G [136]; OKI-Apl_1.0 GCA 001949145.1
  Patiria miniata (Brandt, 1835) G [44]; Pmin_1.0 GCA 000285935.1
Hemichordata Bateson, 1885 Saccoglossus kowalevskii A. Agassiz 1873 G [137]; Skow_1.1 GCA 000003605.1
  1. aT transcriptome, G genome