A transcriptional blueprint for a spiral-cleaving embryo

BMC Genomics

Table 1 The BLASTN alignment of curated wnt genes

Wnt genes	FPKM^a	Length (bp)	% Identity	Aligned Length (bp)	% Coverage
pdum_wnt1	0	1473	0	0	0.0
pdum_wnt2	0.1 (6 h)	1366	98.02	757	55.4
pdum_wnt4	9.0 (10 h)	2503	97.91	2344	93.6
pdum_wnt5_A^b	15.7 (12 h)	2911	98.25	2906	99.8
pdum_wnt5_B^b	3.8 (14 h)	2190	97.8	1317	60.1
pdum_wnt6	0.1 (8 h)	1475	94.46	992	67.3
pdum_wnt7	0.2 (6 h)	2312	97.1	1309	56.6
pdum_wnt8	3.5 (10 h)	2139	99.58	1908	89.2
pdum_wnt9	0.2 (10 h)	1169	98.95	382	32.7
pdum_wnt10	0.1 (14 h)	1523	95.1	469	30.8
pdum_wnt11	2.3 (14 h)	1835	97.71	1837	100.0
pdum_wnt16	0.2 (10 h)	1903	96.69	1512	79.5
pdum_wntA	12.7 (8 h)	1840	98.42	1832	99.6

^astage with highest FPKM shown
^bwnt 5a and wnt 5b are different splice variants of the same gene.
We evaluate the quality of our assembly by examining curated wnt sequences in Platynereis dumerilii. We used BLASTN to compare the similarity between these sequences with our assembly. The coverage refers to the proportion of the curated genes covered by our assembly. Out of 12 wnt genes, we successfully reconstructed wnt4, wnt5, wnt8, wnt11, wnt16 and wntA with at least 75 % coverage. wnt2, wnt6, wnt7, wnt9, and wnt10 were partially assembled due to the low expression level (<1 FPKM) during early developmental stages

ISSN: 1471-2164