Transcriptomics of diapause in an isogenic self-fertilizing vertebrate

BMC Genomics

Table 1 Alignment of Kmar RNA-Seq reads against various reference genomes

Reference Genome/Transcriptome	No. of Mapped RNA-Seq Reads:					Percentage:
Reference Genome/Transcriptome	RNA01:pre-Dia	RNA02:Dia-R1	RNA03:Dia-R2	RNA04:Dia-R3	RNA05:post-Dia	RNA01:pre-Dia	RNA02:Dia-R1	RNA03:Dia-R2	RNA04:Dia-R3	RNA05:post-Dia
Kmar de novo Genome (ABySS)^a	31,590,161	39,192,211	31,524,390	32,811,042	30,944,064	97.08	97.42	97.35	97.32	96.98
Kmar de novo Transcriptome (Trans-ABySS)^a	30,584,171	37,850,616	30,651,957	31,942,287	29,994,937	93.99	94.08	94.66	94.74	94.01
Kmar de novo Transcriptome (Trinity)^a	29,039,228	35,715,712	29,057,499	30,264,954	28,112,433	89.24	88.78	89.74	89.77	88.11
Kmar de novo Partial-Genome (ABySS, RADSeq)^b	4,078,090	4,631,901	3,720,990	3,781,213	3,789,332	12.53	11.51	11.49	11.22	11.88
Amazon Molly Genome^c	3,735,199	4,105,696	3,022,398	3,096,027	2,577,109	11.48	10.21	9.33	9.18	8.08
Platyfish Genome^d	3,250,075	3,733,889	2,736,897	2,824,479	2,278,491	9.99	9.28	8.45	8.38	7.14
Medaka Genome^e	3,668,978	3,476,396	2,512,691	2,499,786	2,198,448	11.28	8.64	7.76	7.41	6.89
Zebrafish Genome^f	1,841,434	1,552,206	1,124,437	1,073,152	982,792	5.66	3.86	3.47	3.18	3.08
Fugu Genome^g	1,302,617	1,557,208	1,097,370	1,143,775	1,036,617	4.00	3.87	3.39	3.39	3.25
Mouse Genome^h	1,324,000	998,352	763,984	712,118	639,505	4.07	2.48	2.36	2.11	2.00
Human Genomeⁱ	1,681,163	1,273,803	961,456	899,559	853,593	5.17	3.17	2.97	2.67	2.68

^aThis study;
^b(Mesak, et al. [32]);
^cPoeFor_5.1.2;
^dXipmac4.4.2 (Schartl, et al. [40]);
^eoryLat2, MEDAKA1 (Kasahara, et al. [41]);
^fdanRer7, Zv9 (Howe, et al. [42]);
^gfr3, FUGU4 (Aparicio, et al. [43]);
^hmm10, GRCm38 (Mouse Genome Sequencing, et al. [44]);
ⁱhg38, GRCh38 (Lander, et al. [45]; Venter, et al. [46]);
Reference genome database can be downloaded from http://www.ensembl.org/info/data/ftp/index.html or http://hgdownload.soe.ucsc.edu/downloads.html

ISSN: 1471-2164