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

Spillane, Jennifer L.; LaPolice, Troy M.; MacManes, Matthew D.; Plachetzki, David C.

doi:10.1186/s12862-021-01772-2

BMC Ecology and Evolution

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
Species	Accession	Read length	NUMBER of reads	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

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

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ISSN: 2730-7182

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