The Draft Genome and Transcriptome of the Atlantic Horseshoe Crab, Limulus polyphemus
Table 3
Top four contigs of day/night and high/low tide conditions from RNA-Seq volcano plot analysis. Contigs chosen were furthest away from the origin while still having an associated gene name in GenBank (Figures 4 and 5). Contig ID, unique identifier for the Limulus transcriptome dataset; top hit ID, accession ID for the top BLAST result for each contig; predicted gene/protein, BLAST result gene or protein description. Top hit -value, -value for top BLAST result; value, probability of statistical significance; absolute fold change, difference in expression between tested conditions; unique gene reads, total depth of reads found for a particular contig within a particular condition; RPKM, reads per kilobase per million mapped reads.
(a) Day versus Night
Contig ID
Top hit ID
Predicted gene/protein
Top hit -value
value
Absolute fold change
Unique gene reads (day)
Unique gene reads (night)
RPKM day
RPKM night
23185
XM_013938347
Protein trapped in endoderm-1-like
427
5
14.78
0.21
999
XM_013933266
DmX-like protein 2
1
703
0.03
25.7
84677
XM_013932736
Aldehyde dehydrogenase family 8 member A1-like
801
2
8.37
0.02
22396
XM_013292029
54S ribosomal protein L23
1
493
0.02
13.37
(b) High versus Low Tide
Contig ID
Top hit ID
Predicted gene/protein
Top hit -value
value
Absolute fold change
Unique gene reads (high)
Unique gene reads (low)
RPKM high
RPKM low
132
XM_013925651
Ovostatin-like
50
3155
0.27
45.69
1065
XM_013933409
Thyroid peroxidase-like
11
1353
0.09
28.16
9027
XM_013936436
3 Beta-hydroxysteroid dehydrogenase/Delta 5->4-isomerase type 1-like
