Supplementary Figure 7. Sequence alignment of Eda of channel catfish (channel)

with that of zebrafish. -------------------- *Catfish+ indicates the number of genes found in channel catfish but not from the species under comparison; § Catfish-indicates the number of genes not found in channel catfish but found from the species under comparison. 
channel DGLPYVKVLKHSGVNSSDTQVLTLHNVTEEESGEYICKVSNYIGQANQSAWLTVTKYAST zebrafish DGLPYVRALK-------------------------------------------------
**Zebrafish+ indicates the number of genes found in zebrafish but not from the species under comparison; § § Zebrafish-indicates the number of genes not found in zebrafish but found from the species under comparison; Supplementary Table 10. Genes commonly shared by all sequenced teleost fish species but absent from cartilaginous fish and jawless species, with high levels of expression in the swimbladder. 
The gene expression levels in various tissues were determined in RPKM by RNA-Seq analysis of publicly available datasets: swimbladder (ERR023143 and ERR023148), skin (SRP013931), intestine (SRR1562529), and liver (SRR891504). The mRNA sequences from the total of 26,459 zebrafish genes were used as reference sequences for RNA-Seq analysis using CLC Genomics Workbench with default settings. The mRNA sequences were retrieved from Ensembl database (v78); only the longest transcripts were selected from each of those genes had isoforms. 



  * *:****: ***:***************************************** **********.** *.***:.:.*::* ******************* channel EGVLKNWKTIAMHQRVFKMHSRSGELEVLQDGMYFIYSQVEVYFLNFTDIASYEVMIDKD zebrafish EGVLKNWRMISIHQRVFKMHSRSGELEVLLDGTYFIYSQVEVYYLNFTDIASYEVMVDKT *******: *::***************** ** **********:************:** channel PFLRCTRSIETGQRKFNTCYTAGVCWLRARQRISIRMVYDDTSISMTNHTTFLGSIRLGE zebrafish PFLRCTRSIETGQRKFNTCYTAGVCLLRARQRISIRMVYEDTSISMSNHTTFLGSIRLGD ************************* *************:******:************* *. * ** ***.**: .: **************::***:******.******** channel GYGVKDEDYDCVSCPPGKFSRGKYEICRRHKDCNALYKATVLTPGTRESDAECGACLPGY zebrafish GYGTKDDDYSCVSCPAGKFSKGKYEICRRHKDCDALYRATVLTPGTSDSDAECGHCLPGY ***.**:**.*****.****:************:***:******** :****** ***** channel FILENRLRNIYSMMCHSCQNAPRNTKECMRTTSTSTKHVPGIPSTSTTTFPHAQKDPTGQ zebrafish YIQENRPQNIYGMVCHSCQNAPRNIKECMRSTPPASGRAPSVSSSSTTIFPQPEKDPTGQ :* *** :***.*:********** *****:*..:: :.*.:.*:*** **:.:****** channel GHLATALIIAMSTIFIMAIAIVMIIMFYILKAKTSGQACCSGQIVKTIEAPMNKQEEKKE zebrafish GHLATALIIAMSTIFIMAIAIVMIIMFYILKSKPSGPVCCSGQLIKAVEAQTNMQEEKKE *******************************:*.** .*****::*::** * ****** channel AQENAVIFTEKDEF---KPPPTKAVKSENDASSENEQLLSRSIDSDEEAAQEKQGATDLC zebrafish AQENVVIFQEKDEFDKLKPSSPKTAKSENDASSENEQLLSRSIDSDEEAAQDKQGAADLC ****.*** ***** **...*:.**************************:****:*** channel LLSLVHLTRDKTCSNNTVSTTVNNNNNNCSNNSRTMGIHSRRKKILELYAKACGVAEGVS zebrafish LLSLVHLTRDKXCX----TNTINNNNNHCS---RATGIHSRRKKILDLYTKACSVAEGLS *********** * :.*:*****:** *: **********:**:***.****:* channel PVELPFDCLERTSRMLSTTYSAEKALVRTWRHLAESFGLKRDEIGGMTDGMQLFDRVSTA zebrafish PTELPFDCLERSSXMLSATYSTDKAVVKTWRHLAESFGLKRDEIGGMTDGMQLFDRISTA *.*********:* ***:***::**:*:****************************:.*****:***.*:*** ** ******.***:* .*******:.** *: channel DDDDESSSEETKQSSSQKLLSNSQELSPTAPEWAQPDKMEKKLHAVPASRTVRFRCPSIG zebrafish EDEVDSSSEEAK-------LSNDQNL-PMAPVWAQPDKMEKKLHAVPASKTVKFRCQANG :*: :*****:* ***.*:* * ** *****************:**:*** : * channel NPTPTLKWLKNGKEFKKDQRIGGFKLRESLWAIIMDSVVPSDKGNYTCVVENKYGSINHT zebrafish NPTPTLKWLKNGKEFKRDQRIGGFKVREHMWTIIMESVVPSDRGNYTCLVENRHGSINHT ****************:********:** :*:***:******:*****:***::****** channel YQLDVVERSPHRPILQAGLPANRTAVVGSDVEFECKVFSDPQPHIQWLKHIEVNGSKVGE zebrafish YQLDVVERSPHRPILQAGLPANRTAVVGSDVEFECKVFSDPQPHIQWLKHIEVNGSRYGP ********************************************************: * 




  ************::******** *********************:*:*** ***** channel YLEVLIYCVGFFLICVMVVIAVLVKMHSSAKKSDFNSQMAVHKLAKSIPLRRQV--SVDS zebrafish YLEVLIYCVGFFLICVMVGTAVLAKMHSSAKKSDFNSQLAVHKLAKSIPLRRQVTVSVDS ****************** ***.**************:*************** **** channel SSSMHSGVMLVRPSRLSSSGSPMLSGVSEYELPQDPRWELPRDKLVLGKPLGEGCFGQVV zebrafish SSSMHSGGMLVRPSRLSSSGSPMLSGVSEYELPQDPRWEVQRDRLVLGKPLGEGCFGQVM ******* *******************************: **:***************: channel MGEVLGMDKDKPNRVTKVAVKMLKSDATEKDLSDLISEMEMMKIIGKHKNIINLLGACTQ zebrafish MAEAMGMDKEKPNRITKVAVKMLKSDATEKDLSDLISEMEMMKIIGKHKNIINLLGACTQ *.*.:****:****:********************************************* channel DGPLYVIVEYASKGNLREYLRARRPPGMEYCYNPDQVPVETVSVKDLVSCAYQVARGMEY zebrafish DGPLYVIVEFAAKGNLREYLRVRRPPGMEYCYNPDQVPVENMSIKDLVSCAYQVARGMEY *********:*:*********.******************.:*:**************** channel LASKKCIHRDLAARNVLVTEDNVMKIADFGLARDIHHIDYYKKTTNGRLPVKWMAPEALF zebrafish LASKKCIHRDLAARNVLVTEDNVMKIADFGLARDIHHIDYYKKTTNGRLPVKWMAPEALF ************************************************************ channel DRIYTHQSDVWSFGVLLWEIFTLGGSPYPGVPVEELFKLLKEGHRMDRPSTCTHELYMMM zebrafish DRIYTHQSDVWSFGVLLWEIFTLGGSPYPGVPVEELFKLLKEGHRMDRPSTCTHELYMMM ************************************************************ channel RDCWHAAPSQRPTFKQLVEDLDRTLSMTSNQEYLDLSVSLDQYSPSFPDTRSSTCSSGED zebrafish RDCWHAVPSQRPTFKQLVEDLDRTLSMTSNQEYLDLSVSLDQFSPNFPDTRSSTCSSGED ******.***********************************:**.**************:*************************:*** ****::*********:*******:* channel TSPN-NSHDAARQSQITPDSYHEKHREHPDDGKLQDLYSKGHAYSGYPSYIMMTNMNNEP zebrafish ISPNSNSHDAARQSQITPDSYHEKHRDHPDDGKLQDLYSKGHPYPSYPGYIMMTNMNNEP *** *********************:***************.*..**.*********** channel YMNNGSLSPPMPRTSNKVPVVQPSHAVHPLTPLITYSDEHFAPGPHSGHHPQDSK----G zebrafish YMNNGSLSPPIPRTSNKVPVVQPSHAVHPLTPLITYSDEHFAPGPHSGHHPQDVNPKQAG **********:****************************************************.********:*******.**************************:* channel PPHETDLMHMKPQHEQRKEQEPKRPHIKKPLNAFMLYMKEMRANVVAECTLKESAAINQI zebrafish --HDTDLMHMKPQHEQRKEQEPKRPHIKKPLNAFMLYMKEMRANVVAECTLKESAAINQI *:******************************************************** channel LGRRWHALSREEQAKYYELARKERQLHMQLYPGWSARDNYGKKKKRKREKLQESASGTAQ zebrafish LGRRWHALSREEQAKYYELARKERQLHMQLYPGWSARDNYGKKKKRKREKIQEPASGTGQ **************************************************:**.****..*:***:******************************************* channel RWHALTREEQAKYYELARKERQLHMQLYPSWSARDNY----GKKKRRKRDKQQDSAT--zebrafish RWHALTREEQAKYYELARKERQLHVQLYPSWSARDNYVSALGKKKRRKRDKQQDSSTGPG ************************:************ **************:* channel - 




  


Table 2 . Improvement of assembly contiguity with PCR-Free PE libraries and gap closing with Illumina and PacBio sequences.

 2 
	-

Table 3 . Scaffolding using BAC end sequences (BES) and full length transcripts.

 3 
	BES	Total number of BES	63,388
		Number of BES pairs	25,677
		Number of BES uniquely mapped to repeat-masked	7,725
		reference sequence	
		BES uniquely mapped to same scaffolds	7,471
		BES uniquely mapped to different scaffolds	254
		Number of the scaffold pairs with at least two pairs of	39
		BES matches	
		Number of scaffolds reduced by BES	21
	Gene	Number of cDNAs that match ≥2 scaffolds	94
	transcripts	Number of scaffolds reduced by using cDNA	136

Table 4 . Definition of channel catfish chromosomes based on aggregate length of scaffolds in genetic linkage group (LG).

 4 Statistics do not include the inter-scaffold gaps. 


	Chromo-	# of	Physical	# of	LG	Genetic	Average	Average
	some	scaffolds	size	genes	number	size (cM)	kb/cM	gene/Mb
	1		37,506,655	1,233	1	139.5	268.9	32.9
	2		37,241,186	1,295	3	169.7	219.5	34.8
	3		34,901,054	1,091	6	163.3	213.7	31.3
	4		34,498,793	990	4	128.1	269.3	28.7
	5		32,117,789	1,137	11	152.7	210.3	35.4
	6		32,336,212	914	17	138.2	234.0	28.3
	7		32,227,861	1,152	8	117.3	274.7	35.7
	8		30,408,258	966	9	146.9	207.0	31.8
	9		30,148,133	986	16	145.3	207.5	32.7
	10		29,044,225	907	20	126.0	230.5	31.2
	11		28,206,976	801	7	102.1	276.3	28.4
	12		28,144,356	1,007	12	104.8	268.6	35.8
	13		27,389,953	943	5	110.2	248.5	34.4
	14		26,696,778	847	18	114.8	232.6	31.7
	15		26,074,281	932	15	115.7	225.4	35.7
	16		25,964,284	843	25	127.6	203.5	32.5
	17		25,913,994	834	22	68.4	378.9	32.2
	18		24,511,808	911	13	131.1	187.0	37.2
	19		23,654,134	744	23	93.3	253.5	31.5
	20		21,426,798	799	2	116.2	184.4	37.3
	21		20,985,506	713	21	110.3	190.3	34.0
	22		19,855,691	693	26	101.2	196.2	34.9
	23	4	18,814,537	658	19	118.9	158.2	35.0
	24		19,557,860	734	24	106.9	183.0	37.5
	25		19,456,751	679	28	114.1	170.5	34.9
	26		19,063,806	744	10	105.8	180.2	39.0
	27		18,540,812	553	27	113.7	163.1	29.8
	28		18,160,844	750	14	113.8	159.6	41.3
	29		15,253,832	525	29	109.5	139.3	34.4
	Assigned	634	758,103,167 25,381	-	3505.4	218.4	33.8
	Unassigned	9,340	25,091,658	1,280	-	-	-	-
	Total	9,974	783,194,825 26,661				

Table 6 . Assessment of the completeness of the channel catfish reference genome sequence through gene content contained in the sequenced fish genomes.

 6 
	Species	# unique genes Catfish+* Catfish- § Zebrafish+** Zebrafish- § §
	Catfish	26,661	-	-	723	
	Zebrafish	26,415	970	723	-	-
	Cave fish	23,042	1,178	373	791	
	Atlantic cod	20,083	1,805	675	1,204	
	Fugu	18,518	1,923	198	1,375	
	Medaka	19,682	1,812	919	1,330	
	Platyfish	20,379	1,437	384	923	
	Sole	21,485	1,205	533	772	
	Spotted gar	18,341	1,272	463	832	
	Stickleback	20,785	1,719	1,042	1,134	
	Tetraodon	19,595	2,095	358	1,485	
	Tilapia	21,437	1,600	309	1,112	
	Amazon molly	23,614	1,210	463	786	

Supplementary Information Supplementary Figures

Supplementary Figure 1. Estimation of genome size from analysis of k-mers from raw sequence of the Illumina short insert library. Genome size was calculated as total trusted sequence divided by the multiplicity at the mode. Genome size estimate ranged from 1.008-1.013 Gb. MaSuRCA automatically utilized a kmer length of 31 which produced a genome size estimate of 1.008 Gb based on 88.7 Gb of trusted sequence. In comparison, the genome size estimated from 5.1 Gb of trusted 31-mer sequence from the Illumina-corrected PacBio sequence was 1.021 Gb. 

Supplementary


Catfish Zebrafish

Supplementary Tables Supplementary Table 1. Sequence inputs for the channel catfish reference genome assembly. 7. Comparative Analysis for orthologous chromosomes between channel catfish and zebrafish using single copy genes. Z1 to Z25 represent zebrafish chromosomes, C1 to C29 represent catfish chromosomes. 
The number in the cell is the percentage of catfish genes on a chromosome that are homologous to zebrafish genes on the corresponding zebrafish chromosome. Percentages >5% are highlighted in yellow.