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Table 4 Comparison of Drosophila melanogaster protein recovery for genes in THO complex

From: SAUTE: sequence assembly using target enrichment

Gene and isoform

Method/Reads

SRR10541157

SRR10541159

SRR10541107

SRR10541200

SRR10541164

Read bases (Gb)

2.51

2.78

2.95

3.47

4.49

tho2 isoform A

SAUTE w/ D. mel

1..1527, 100%

Full, 100%

Full, 100%

Full, 100%

Full, 100%

SAUTE w/ D. inn

1..1527, 100%

Full, 100%

Full, 100%

Full, 100%

Full, 100%

rnaSPAdes

Not found

Not found

Not found

Not found

Not found

Trinity

Not found

Full, 100%

Not found

Not found

Not found

Clust w/ D. mel

Not found

Not found

Not found

Not found

Full, 100%

Clust w/ D. inn

Not found

Not found

Not found

Not found

Not found

tho2 isoform B

SAUTE w/ D. mel

Full, 100%

Full, 100%

Full, 100%

Full, 100%

Full, 100%

SAUTE w/ D. inn

Full, 100%

Full, 100%

Full, 100%

Full, 100%

Full, 100%

rnaSPAdes

Full, 100%

Full, 100%

Full, 100%

Full, 100%

Full, 100%

Trinity

Full, 100%

1..1528, 100%

Full, 100%

Full, 100%

Full, 100%

Clust w/ D. mel

Full, 100%

Full, 100%

Full, 100%

Full, 100%

Not found

Clust w/ D. inn

Not found

Not found

Not found

Not found

Not found

tho2 isoform C

SAUTE w/ D. mel

Not found

Not found

Not found

Not found

1..1539, 100%

SAUTE w/ D. inn

Not found

Not found

Not found

Not found

1..1539, 100%

rnaSPAdes

Not found

Not found

Not found

Not found

Not found

Trinity

Not found

Not found

Not found

Not found

Not found

Clust w/ D. mel

Not found

Not found

Not found

Not found

Not found

Clust w/ D. inn

Not found

Not found

Not found

Not found

Not found

thoc5

SAUTE w/ D. mel

Full, 100%

Full, 100%

Full, 100%

Full, 99.5%

Full, 100%

SAUTE w/ D. inn

Full, 100%

Full, 100%

Full, 100%

Full, 99.5%

Full, 100%

rnaSPAdes

Full, 99.8%

Full, 100%

Full, 100%

Full, 99.5%

Full, 99.7%

Trinity

Full, 99.8%

Full, 100%

Full, 100%

Full, 99.5%

Full, 99.7%

Clust w/ D. mel

Full, 100%

Full, 100%

Full, 100%

Full, 99.5%

Full, 99.7%

Clust w/ D. inn

Full, 100%

Full, 99.8%

Full, 100%

Full, 99.5%

Full, 100%

thoc6

SAUTE w/ D. mel

Full, 99.7%

Full, 99.7%

Full, 100%

Full, 99.7%

Full, 99.7%

SAUTE w/ D. inn

Full, 99.7%

Full, 99.7%

Full, 100%

Full, 99.7%

Full, 99.7%

rnaSPAdes

Full, 99.7%

Full, 99.7%

Full, 99.7%

Full, 99.7%

Full, 99.7%

Trinity

Full, 99.7%

Full, 99.7%

Full, 99.7%

Full, 99.7%

Full, 99.7%

Clust w/ D. mel

Full, 99.7%

Full, 99.7%

Full, 99.7%

Full, 99.7%

Full, 99.7%

Clust w/ D. inn

Full, 99.7%

Full, 99.7%

Full, 99.7%

Full, 99.7%

Full, 99.7%

Hpr 1

SAUTE w/ D. mel

Full, 100%

Full, 100%

Full, 100%

Full, 100%

Full, 100%

SAUTE w/ D. inn

Full, 100%

Full, 100%

Full, 100%

Full, 100%

Full, 100%

rnaSPAdes

Full, 100%

Full, 100%

Full, 100%

Full, 100%

Full, 100%

Trinity

Full, 100%

Full, 100%

Full, 100%

Full, 100%

Full, 100%

Clust w/ D. mel

Full, 100%

Full, 100%

Full, 100%

Full, 100%

Full, 100%

Clust w/ D. inn

Full, 100%

Full, 100%

Full, 100%

Full, 100%

Full, 100%

thoc7 isoform A

SAUTE w/ D. mel

Not found

Not found

24..288, 100%

10..288, 100%

Not found

SAUTE w/ D. inn

Not found

Not found

24..288, 100%

10..288, 100%

Not found

rnaSPAdes

Not found

Not found

Full, 99.7%

10..288, 100%

Not found

Trinity

Not found

Not found

Full, 99.7%

10..288, 100%

Not found

Clust w/ D. mel

Not found

Not found

Full, 99.7%

10..288, 100%

Not found

Clust w/ D. inn

Not found

Full, 99.7%

12..288, 99.6%

10..288, 100%

Not found

thoc7 isoform B

SAUTE w/ D. mel

Not found

Not found

Not found

10..287, 100%

Not found

SAUTE w/ D. inn

Not found

Not found

Not found

Not found

Not found

rnaSPAdes

Not found

Not found

Not found

Not found

Not found

Trinity

Not found

Not found

Not found

Not found

Not found

Clust w/ D. mel

Not found

Not found

Not found

Not found

Not found

Clust w/ D. inn

Not found

Not found

Not found

Not found

Not found

  1. SAUTE_PROT low (SAUTE) and CLUSTER (Clust) used proteins in Table 3 for Drosophila melanogaster (D. mel) and Drosophila innubila (D. inn) as targets. Cells in bold and highlighted in yellow show cases where the D. mel protein is recovered perfectly and there is at least one method that does not recover it perfectly. Proteins recovered as full length are marked as ’Full’; otherwise, coordinates on D. mel protein recovered are provided