Supplementary Tables and Figures RNA-seq analysis of overexpressing ovine AANAT gene of melatonin biosynthesis in switchgrass



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  Supplementary Fig.S3Validation of RNA-Seq analysis by reverse transcription-quantitative polymerase chain reaction (RT-qPCR).FPKM (fragments per kilobase of exon per million fragments mapped) values obtained with RNA-Seq and qPCR values in the analysis of selected genes in the three assayed groups: EV: expressing the empty vector only, A: transgenic oAANAT line. Error bars represent the standard error for three independent experimental replicates. 




  




  Supplementary TableS1Oligonucleotide primers used in RT-PCR analysis Summary of the functional annotation of assembled unigenes. 


	Unigenes	84604		25347	14922	10811	135684 716	1243 97207303
	No. P8 Supplementary Table S4 Public database Unigene Forward primer (5'-3') c65591_g1 GACCCAGTTGACCACTCTTTAC Number of Percentage Reverse primer (5'-3') GCAGCCTCAACCAAGTAAGT
	P10	c65662_g1	CCCGAACCACGATGAACTATG unigenes	(%)	GCATCTTCCGCATCAATCTCTA
	P14 Annotated in NR c56332_g2	CCCATCTTTCCCAGATCACAA 56968	TCTGGCGAGATAGAGGTCAT 41.98
	P17 Annotated in NT c49639_g1	ATCAACCAGCTCGGGTACTA 60512	AGCATGCACATCCATCCATAC 44.59
	P19 Annotated in KO c63279_g3	GCGATCCAGGGAGAGTTATTC 19493	GCGATCCAGGGAGAGTTATTC 14.36
	P20 Annotated in SwissProt c50061_g4 ACGGTTCACTCCCTAGTCTC 38266	28.2	GGGATCGTGATGTCCAGAATG
	P21 Annotated in PFAM c48823_g1	GCCATGTTTCAGGTGACTCT 39624	29.2	CATGTCTGGATGAACTGGAAGG
	P26 Annotated in GO c53254_g2	CTGGAGCTTCTCCATGTTGAT 41494	ACACAAGAGAGCCAGAGAGA 30.58
	P29 Annotated in KOG c49628_g1	GACTGAGTGGCACATAGGAAA 19077	CGAGACACAGATGGTGTAGAAC 14.05
	P30 Annotated in all Databases c102099_g1 TGCCATCGTGGTAGTGTTTG 8900	6.55	GCTCCTGACACCAAAGGATAAG
	P34 Annotated in at least one Database 77421 c27561_g1 GAGAGCCGCAACAAGAGAAA	CTGCTTGTCGGTATGAGGTATG 57.05
	P36 Total Unigenes c55261_g4	TCGGTGAGTTTGGAGGTTTG 135684	100	AGCACCCTACTGTTTGTCTTC
	Sample FPKM		Raw	EV		Clean	Clean A	Error(%) Q20(%)	Q30(%)	GC
	Interval 0-0.1	Reads 69928(51.54%) Reads	Bases 71734(52.87%)		Content(%)
	0.1-0.3			10145(7.48%)	9312(6.86%)	
	A_1 0.3-3.57	80430918 76912922 11.54G 29150(21.48%) 28221(20.8%) 0.01		97.57	94.08	59.66
	A_2 3.57-15		94162412 90354046 13.55G 13661(10.07%) 13380(9.86%) 0.01		97.52	93.91	59.57
	A_3 15-60		92073472 88415412 13.26G 9312(6.86%) 9574(7.06%) 0.01		97.68	94.29	59.69
	EV_1 >60		80891154 76976922 11.55G 3488(2.57%) 3463(2.55%) 0.01		97.24	93.14	58.71
	EV_2		87541130 81777632 12.27G	0.01		97.22	93.26	57.87
	EV_3		89891632 84557876 12.68G	0.01		97.18	93.18	55.11
	Supplementary Table S3 Summary of the switchgrass transcriptome.
	Category	Number 200-500	500-1k	1k-2kb	>2kbp	Total	Mean length	N50	Total nucleotides
	bp Transcripts 111059		bp 57802	p 55055	40953	264869 1052	1792 278653546

Supplementary TableS2Summary of Illumina transcriptome sequencing.EV: expressing the empty vector only, A: transgenic oAANAT line.Supplementary TableS5Statistics of genes in different expression-level interval. EV: expressing the empty vector only, A: transgenic oAANAT line.
Shan Yuan, Yanhua Huang, Cong Guan, Sijia Liu, Xin Cui, Danyang Tian, Yunwei Zhang, Fuyu Yang
Supplementary Tables and Figures RNA-seq analysis of overexpressing ovine AANAT gene of melatonin biosynthesis in switchgrass