Transcriptional alterations reveal Bacillus amyloliquefaciens-rice cooperation under salt stress


DEF qRT-PCR LOC_Os03g03810 F-5' CTTCACGCAAGGTGTTCTC 3' R-5' CTTGAACCGGTGGCTCT 3' 125 DHN ,, LOC_Os11g26750 F-5' GCAACAAGGGCAACAAC 3' R-5' GGTGGCGATCTTGGTATC 3' 98 USP ,, LOC_Os05g28740 F-5' GAGCCATGGTTACGGTTTC 3' R-5' CCTCTTGACGACGACGA 3' 97 GSTU6 ,, LOC_Os10g38600 F-5' GCCTACGTCACCAGAGT 3' R-5' AGGAGGTCGCTCTTGTT 3' 92 LEA ,, LOC_Os05g46480 F-5' TTCCTCGGCGAGAAGAC 3' R-5' GGCAGAGTCCTTGGTGTA 3' 105 Myb ,, LOC_Os02g04640 F-5' GTCTGAACAGCTCGGAATTG 3' R-5' GCAAGATGACACTGGAAGAG 3' 106 Myb ,, LOC_Os04g56990 F-5' CAACAGCATCAGGACAGAAT 3' R-5' CTTGAGGTGGAAACGAGTG 3' 97 bZIP ,, LOC_Os06g41770 F-5' CGACGAGTCCGCCATATTTA 3' R-5' GTCGGCGAAGAACTCTACAT 3' 103 HLH ,, LOC_Os03g26210 F-5' GAGAGGGAGAAGCTTAAACG 3' R-5' GGGTGGTGTCAGTTAGTATG 3' 115 Splicing Factor ,, LOC_Os01g03060 F-5' CTCAGACTCAAGCGATGATAC 3' R-5' GATGCTTTCTCCTGTGTGAG 3' 95 Protein kinase ,, LOC_Os09g39650 F-5' ACGATGATGTTCTTGCTGGTGTT 3' R-5'TGACATGCTCCTTGAACCAATG 3' 83 UBQ ,, LOC_Os09g31031 F-5' TCACCACTGCCGCAAGAAG 3' R-5' GCTATCGAAAGCGAGTTGATGAA 3' 81 Ca-EF hand ,, LOC_Os03g14590 F-5' CTGAGCAACATCGCTGAAAGG 3' R-5' GTTCTCGGTGTGTGCGACAA 3' 60 NAM ,, LOC_Os11g03370 F-5' CAGATGCGGAGGTAATCTTG 3' R-5' CATGGCTCGCACTTGTT 3' 103 NAM ,, LOC_Os05g10620 F-5' CACTTCAGCTCAGCTCCTACCAA 3' R-5' AGTGGTGACCCCGATCAACTT 3' 79 Aldo/keto reductase ,, LOC_Os04g27060 F-5' TTCCGCAAGAGCCTACCTAGATT 3' R-5' CCATGGCATTAACCTTCTCGAA 3' 79 GRAM domain ,, LOC_Os03g08860 F-5' CAGGTGGTTTCCGTTGATAA 3' R-5' GAAGTGCTTCCTGCAGATT 3' 88 PB1 ,, LOC_Os11g25780 F-5' CTGTACCACCGTCAGACT 3' R-5' GTTGTGATGCTGCTGCTG 3' 108 Cyt. P450 ,, LOC_Os01g43750 F-5' CCGTAACCTTCACTCGAAAG 3' R-5' TGGGTCATGGTGTATGAGTA 3' 107 Cystein proteinase inhibitor ,, LOC_Os05g41460 F-5' AATAAGCTGTACGAGGCCAAGGT 3' R-5' TGAAATCCTGGAGCTGCTTGA 3' 67 UGE ,, LOC_Os09g35800 F-5'GGAGATTGCACTGAGGTTT 3' R-5' CCTGCACATGTCCTCTATTC 3' 90 POP9 ,, LOC_Os04g47360 F-5' GCTTGTGCAGTCCATGGTGATA 3' R-5' CAAGCTCCTCATCTGCAAGACA 3' 78 NSHB ,, LOC_Os03g12510 F-5' CATTGGACTCCGCTTCTTCTTG 3' R-5' AGTTGCGCAGGAACGAGAAC 3' 77 Metal transporter ,, LOC_Os07g15460 F-5' CTACTTCCTCAGCACAAAGC 3' R-5' TTCCTGAACGTCAGGTAGAT 3' 138 Actin ,, LOC_Os11g06390 F-5' CGGTGTGATGGTTGGTATG 3' R-5' ATGCTCGATCGGGTACTT 3' 97 OsNAM Full length cloning F1-5' GCATGGTGGAGACTAGTACA 3' R1-5' GCACTAGCTATTACGATGAGTC3' F2-5' ATGGTGGAGACTAGTACATCC3' R2-5' GCTATTACGATGAGTCCCATAG 3' 1080 OsGRAM ,, F1 

Fig. S1 :

 S1 Fig. S1: Phenotype of rice seedlings exposed to salt stress in the presence and absence of SN13. 


Fig. S2 :

 S2 Fig. S2: Blast2GO term assignment of the differential expressed genes in different categories of biological process (a), cellular function (b) and molecular component (c) 


Fig. S4 :

 S4 Fig. S4:A heat map showing under and over represented functional classifications among genes which were differentially regulated. This analysis was performed using the PageMan software package. Red boxes indicate that genes in a category were generally down-regulated while blue boxes indicate that genes in a category were generally up-regulated in the corresponding set of samples relative to controls. 




  of Genomic Research (TIGR)-Rice Genome Annotation Project locus ID. 




  


Table S1 :

 S1 List of primers used in 



the study Gene(s) Description Accession no.* Primer Sequence Amplicon Length

  

Table S2 :

 S2 Effect of NBRI-SN13 on the growth parameters of rice cultivars subjected to salt stress. 


	Treatments	Shoot length (cm.)	Root Length (cm.) Fresh weight (mg.) Dry weight (mg.)
	Control	16.25±1.7 b	6.48±1.25 a	116.35±14.9 c	5.55±1.20 a
	SN13	17.45±0.98 b	8.00±0.67 b	223.00±13.8 d	10.53±1.28 b
	Salt	8.58±0.85 a	7.65±0.73 ab	57.23±5.0 a	5.73±0.59 a
	Salt+SN13	9.25±0.47 a	6.43±0.72 a	75.98±9.7 b	7.28±1.40 a

Table S3 :

 S3 A NGSQCTOOL kit result for control, salt, SN13, salt+SN13 samples. 


	File name Minimum read length Maximum read length Average read length Total number of reads Total number of reads with non-Percentage of reads with non-ATGC bases Total number of bases Total number of HQ bases Percentage of HQ bases Total number of non-ATGC bases Percentage of non-ATGC bases File name Minimum read length Average read length Total number of reads Total number of reads with non-ATGC bases Percentage of reads with non-ATGC bases Total number of bases Total number of HQ bases Percentage of HQ bases Total number of non-ATGC bases Percentage of non-ATGC bases File name Minimum read length Maximum read length Average read length Total number of reads Total number of reads with non-ATGC bases Percentage of reads with non-ATGC bases Total number of bases Total number of HQ bases Percentage of HQ bases Total number of non-ATGC bases Percentage of non-ATGC bases File name Minimum read length Maximum read length Average read length Total number of reads Total number of reads with non-ATGC bases Percentage of reads with non-ATGC bases Total number of bases Total number of HQ bases Percentage of HQ bases Total number of non-ATGC bases 24027 ATGC bases Control_1.fq Control_2.fq Control_1.fq_ filtered 100 100 100 100 100 100 100 100 100 16568439 16568439 16568439 24027 2287 0.15% 0.01% 0.15% 1656843900 1656843900 1656843900 1637763602 1633570766 1637763602 98.85% 98.60% 98.85% 24669 3760 24669 0.00% 0.00% 0.00% Salt_1.fq Salt_2.fq Salt_1.fq_ filtered 100 100 100 100 100 100 23387476 23387476 23387476 34117 3333 34117 0.15% 0.01% 0.15% 2338747600 2338747600 2338747600 2312807360 2305168395 2312807360 98.89% 98.56% 98.89% 34958 5374 34958 0.00% 0.00% 0.00% SN13_1.fq SN13_2.fq SN13_1.fq_ filtered 100 100 100 100 100 100 100 100 100 17739411 17739411 17739411 26065 2505 26065 0.15% 0.01% 0.15% 1773941100 1773941100 1773941100 1754884582 1749699923 1754884582 98.93% 98.63% 98.93% 26703 4184 26703 0.00% 0.00% 0.00% SN13+Salt_1.fq SN13+Salt_2.fq SN13+Salt_1.fq_ filtered 100 100 100 100 100 100 100 100 100 24147409 24147409 24147409 35741 3466 35741 0.15% 0.01% 0.15% 2414740900 2414740900 2414740900 2388732530 2382207391 2388732530 98.92% 98.65% 98.92% 36664 5768 36664 Maximum read length 100 100 100 Percentage of non-ATGC bases 0.00% 0.00% 0.00%	Control_2.fq_ filtered 100 100 100 16568439 0.01% 1656843900 1633570766 98.60% 3760 0.00% Salt_2.fq_ filtered 100 100 23387476 3333 0.01% 2338747600 2305168395 98.56% 5374 0.00% SN13_2.fq_ filtered 100 100 100 17739411 2505 0.01% 1773941100 1749699923 98.63% 4184 0.00% SN13+Salt_2.fq_ filtered 100 100 100 24147409 3466 0.01% 2414740900 2382207391 98.65% 5768 100 0.00%

Table S4 :

 S4 TopHat Alignment Summary for control, salt, SN13, salt+SN13 samples. 


	Samples		Left Reads			Right Reads	
		HQ Reads	Aligned Reads	Unaligned Reads HQ Reads Aligned Reads	Unaligned Reads
	Control 16568439	14176033 (85.6%)	2392406 (14.4%)	16568439	14145712 (85.4%)	2422727 (14.6%)
	Salt	23387476	19811116 (84.7%)	3576360 (15.3%)	23387476	19761936 (84.5%)	3625540 (15.5%)
	SN13	17739411 15616276 (88%)	2123135 (11.9%)	17739411	15584732 (87.9%)	2154679 (12.1%)
	SN13+ Salt	24147409	20070035 (83.1%)	4077374 (16.9%)	24147409	20029887 (82.9%)	(17%)
Puneet Singh Chauhan, Charu Lata, Shalini Tiwari, Abhishek Singh Chauhan, Shashank Kumar Mishra, Lalit Agrawal, Debasis Chakrabarty, Dr Chandra Shekhar Nautiyal
Transcriptional alterations reveal Bacillus amyloliquefaciens-rice cooperation under salt stress