Research Article

The Draft Genome and Transcriptome of the Atlantic Horseshoe Crab, Limulus polyphemus

Table 4

Reads per kilobase per million mapped reads (RPKM) for common circadian and control genes. The absolute fold change is shown for two conditions, day/night and high/low tide. Gene name, either homologous gene title identified through BLAST or designated name given based on percent identity to similar gene variants; contig ID, contiguous sequence number given to a particular gene during assembly; RPKM values given for four individual animals (begin day high tide, day low tide, day between tides, and night high tide); absolute fold change day/night, the RPKM difference between begin day high tide and begin night high tide; absolute fold change high/low, difference between begin day high tide and begin day low tide.

Gene name Contig ID RPKM valuesAbsolute fold change day/nightAbsolute fold change high/low
Day high tide (0800)Day low tide (1530)Evening low tide (1800)Night high tide (2030)

Circadian, core
Period A1223312.7112.3513.7213.331.01.0
Period B118926.874.495.926.261.11.5
Period C136531.711.761.591.391.21.0
Clock1651510.6510.979.8411.281.11.0
Cryptochrome 139167.266.235.847.081.01.2
Cryptochrome 2282494.926.186.126.341.31.3
Cycle 1412381.840.431.201.751.14.3
Cycle 2442330.400.120.190.133.13.3
Timeless116865.282.853.434.091.31.9

Circadian, accessory
Timeout195001.312.442.501.151.11.9
Double-time126306.566.045.857.211.11.1
Vrille357322.242.171.733.681.61.0
Casein kinase Iα287230.4331.7842.3334.621.11.0
Casein kinase IIα847320.8525.4319.5224.401.21.2
Casein kinase IIβ1428516.2916.8215.3917.241.11.0
Casein kinase Iε287317.7620.0414.6118.691.11.1

Circadian, regulatory
PDHR/CRHR252981.564.681.141.061.53.0

Control
CRP438960.360.380.360.361.01.1
Tubulin1100120.0119.9120.5824.001.21.0
UBQ243407.00408.00335.00407.001.01.0
SDHA3186124.00139.00142.00129.001.01.1
SYN2315113.4113.5313.5313.391.01.0
Actin 1310462.00316.00371.00544.001.21.5
Actin 21424224.00137.00162.00184.001.21.6
Actin 31190460.00317.00265.00527.001.11.5
Actin 41173366.00346.00379.00381.001.01.1
Actin 53341085.00841.001169.001129.001.01.3
Actin 6339682.00426.00635.00829.001.21.6
Actin 712321042.00811.00979.001046.001.01.3