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Table 1 Read set information and transcriptome assembly metrics

From: Signal, bias, and the role of transcriptome assembly quality in phylogenomic inference

Species Accession Read length NUMBER of reads High-quality dataset Low-quality dataset
assembler Number of Transcripts BUSCO complete TransRate score Orthogroups Species-specific orthogroups Assembler Number of Transcripts BUSCO complete TransRate score Orthogroups Species-specific orthogroups
Alligator mississippiensis SRR629636 100 36,130,137 ORP 287,695 91.1 0.50848 12,004 32 SPAdes75 466,618 80.2 0.16986 10,737 20
Ambystoma mexicanum SRR5341572 101 46,417,978 ORP 209,702 98.7 0.57581 11,350 59 SPAdes75 528,158 97.4 0.09216 10,832 61
Anas platyrhynchos SRR7127376 101 20,486,658 ORP 142,201 91.1 0.65376 9813 8 SPAdes75 244,848 86.8 0.2212 9129 11
Anolis carolinensis SRR391653 101 17,152,427 Trans-ABySS 40,327 86.2 0.33263 8729 9 Trinity 56,207 90.1 0.18273 9093 9
Astyanax mexicanus SRR2045431 100 32,893,691 ORP 110,132 98.7 0.55641 9902 44 SPAdes75 180,139 97 0.21902 9187 36
Balaenoptera acutotostrata SRR919296 100 23,923,194 ORP 200,511 89.2 0.53496 11,048 10 SPAdes75 364,918 86.1 0.15086 9729 14
Bufo bufo ERR1331718 126 37,410,097 Trans-ABySS 135,770 94 0.33512 11,671 57 SPAdes75 413,473 94.4 0.10086 11,968 34
Caecilia tentaculata SRR5591453 101 28,784,422 ORP 107,413 81.8 0.56427 8737 35 SPAdes75 196,546 77.9 0.15651 7993 29
Caiman crocodilus ERR2198478 variable 31,864,053 Trans-ABySS 163,595 85.8 0.28529 11,113 3 SPAdes75 436,573 81.5 0.20671 11,475 6
Calidris pugnax ERR1018151 150 13,725,659 Trinity 78,074 85.5 0.46221 8239 10 SPAdes75 83,535 77.9 0.24439 7880 2
Callorhinchus milii SRR513760 76 35,000,000 ORP 124,415 67.3 0.32314 8418 17 SPAdes75 95,463 7.2 0.15425 2232 13
Canis lupus familiaris ERR1331673 100 36,371,999 ORP 437,158 83.8 0.58601 10,633 3 SPAdes75 819,785 86.5 0.1697 9826 10
Dasypus novemcinctus SRR494766 101 31,705,473 Trans-ABySS 55,634 79.2 0.33783 8868 7 SPAdes75 192,657 66 0.12049 7478 6
Felis catus ERR1331679 100 40,228,662 ORP 516,209 79.5 0.51854 10,659 8 SPAdes75 945,952 85.2 0.20215 9790 4
Gadhus morhua SRR2045420 100 18,943,673 ORP 85,927 74 0.46787 8082 29 SPAdes75 131,171 64.3 0.21936 6919 15
Gallus gallus ERR1298598 100 14,955,711 ORP 272,485 72.3 0.48137 9069 8 SPAdes75 444,042 62.1 0.15068 7562 9
Haplochromis burtoni SRR387451 101 16,142,312 Trans-ABySS 40,240 69.3 0.34653 7981 14 SPAdes75 60,824 54.5 0.19438 6379 48
Homo sapiens SRR5576267 101 20,633,201 ORP 171,048 72.6 0.48352 9971 5 SPAdes75 317,048 74.2 0.16465 9271 8
Ictalurus punctatus SRR917955 100 28,319,586 ORP 99,232 83.8 0.49223 8645 32 SPAdes75 159,608 73 0.25281 7538 34
Latimeria menadoensis SRR576100 109 39,788,120 Trans-ABySS 101,337 73.3 0.34696 8913 69 SPAdes55 258,443 82.2 0.11311 9692 13
Lepidophyma flavimaculatum DRR034613 variable 20,350,517 Trans-ABySS 121,895 91.4 0.28563 10,505 59 SPAdes75 174,935 90.7 0.14923 10,395 37
Lepisosteus oculatus SRR1287992 101 22,992,842 Trans-ABySS 75,239 95.4 0.44361 10,235 55 SPAdes75 195,782 88.5 0.15598 9172 42
Lethenteron camtschaticum SRR3223459 125 29,559,367 Trans-ABySS 125,856 90.4 0.32322 8577 292 SPAdes75 274,262 92.4 0.14484 8431 93
Lissotriton montandoni SRR3299753 100 32,548,205 ORP 195,142 95.4 0.46462 10,934 68 SPAdes75 387,445 91.1 0.12708 9939 56
Notamacropus eugenii DRR013408, DRR013409, DRR013410 100 24,378,361 ORP 198,447 88.5 0.60651 9859 24 SPAdes75 347,172 82.2 0.16235 8917 28
Notechis scutatus SRR519122 90 25,626,764 ORP 168,738 58.7 0.43875 7908 31 SPAdes75 277,137 42.9 0.18596 6254 32
Oophaga sylvatica SRR9120851 100 22,858,029 ORP 166,747 56.1 0.47685 8650 18 SPAdes75 423,029 49.8 0.13789 7690 24
Oryctolagus cuniculus ERR1331669 100 22,037,691 ORP 158,880 84.8 0.5591 9304 4 SPAdes75 349,879 81.8 0.11102 8469 5
Parus major SRR1847228 101 35,000,000 ORP 155,826 95 0.54739 10,349 16 SPAdes75 261,539 91.7 0.20877 9408 18
Pelodiscus sinensis SRR6157006 150 24,740,727 Trinity 274,343 99 0.32231 12,143 40 SPAdes75 367,085 95.4 0.11519 11,332 23
Pelusios castaneus SRR629649 100 45,163,324 ORP 254,815 97.4 0.42891 12,168 31 SPAdes75 419,831 92.4 0.15182 10,728 19
Protopterus sp. ERR2202465 150 18,298,224 SPAdes75 327,343 61.4 0.34033 9036 127 Trinity 141,824 65.7 0.21121 8558 89
Rana pipiens SRR1185245 101 35,791,829 ORP 136,439 82.2 0.52391 9695 36 SPAdes75 238,110 75.4 0.20868 9029 16
Rhinella marina SRR6311453 100 27,446,915 ORP 511,551 67.4 0.48377 11,184 48 SPAdes75 1,056,698 60.4 0.16511 10,330 32
Rhinolophus sinicus SRR2273875 101 30,559,494 ORP 184,384 90.8 0.68372 10,658 14 SPAdes75 392,613 86.2 0.1185 9933 9
Squalus acanthias ERR1525379 Variable 35,000,000 Trans-ABySS 101,153 84.5 0.23542 9582 25 SPAdes75 363,863 83.2 0.12189 9803 79
Takifugu rubripes SRR1005688 76 35,796,911 Trans-ABySS 35,375 59.7 0.44456 6518 13 SPAdes75 48,271 2.7 0.1206 1287 22
Trachemys scripta ERR2198830 150 22,741,770 SPAdes75 210,713 47.8 0.48531 9322 6 Trinity 94,129 47.6 0.16631 8123 3
  1. For each species, we assembled the transcriptomic reads using the Oyster River Protocol. Of the five resulting transcriptome assemblies, we chose the one with the highest overall TransRate score and the one with the lowest overall TransRate score to use in the high- and low-quality datasets, respectively. We also quantified the number of transcripts in each assembly, calculated the complete BUSCO score, and inferred orthogroups using OrthoFinder