Additional file 1 –Primer symbol, primer sequences, and annealing temperatures of the sod genes




Дата канвертавання24.04.2016
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Additional files

Additional file 1 –Primer symbol, primer sequences, and annealing temperatures of the SOD genes


Symbol

Primer sequences(5'-3')

Temperature

(℃)


copper/zinc- superoxide dismutase

(CSD1a)


CSD1a-F:A(C/G)CCAGGAAG(A/G)ATGGTCCAAC

48

CSD1a-R: CCAGCATTTCCAGTGGTTTTGCT

CSD1a-3'RACE1:GGCTGCATGTCAACTGGACCCAT

51

CSD1a-3'RACE2:GGTGATGATGGCACTGTCAGCT

54.6

CSD1a-5'RACE1:GTCAAGTCACTCTCAAGCATACGGAC

53

CSD1a-5'RACE2:GACAATTGTA AAGCTGACAGTGCCAT

56

CSD1a-Cell-F: ACTCTCTCACTGCCACTCTCT

58

CSD1a -Cell-R: ATACTAGTAGCTTGGAGACCAATGACACC

CSD1a-SP1:TGGCAGCAGGATTGAAATGTGGTC

66

CSD1a -SP2: AATCCATGAAGACCAGGCTTGAGG

66

CSD1a -SP3: CCACAAAGGCTTCCAGTTACGGTAG

67

copper/zinc-

superoxide dismutase

(CSD1b)


CSD1b-F:GACAACGTCAAAGGCTCTCTTC

56

CSD1b -R:CAGATGATTGAAGCCCAATGATAC 

CSD1b -F:GACAACGTCAAAGGCTCTCTTC

55.6

CSD1b -3'RACE1:GAGTGACACATGTGAAAGGGACC

52.7

CSD1b -3'RACE2:GGCAGATTCCTTTGAGTGGGCAAC

53

CSD1b -5'RACE1:GTTGCCCACTCAAAGGAATCTGCC

54

CSD1b -5'RACE2:AGCATGCCGCTCTGTATCGCTG 

58

CSD1b-34237-F: AACAAGTGGC GCTCTGGTTTTCT

55

CSD1b-57061-R: TGCACATTGG TCTTTGTAGTTAGCG

CSD1b-Cell-F:ATCAGATCTA TGGAGAGTGGAAAGAG

55

CSD1b-Cell-R:CACTAGTTACAGAGGACTGA AGCC 

copper/zinc-

superoxide dismutase (CSD2a)



CSD2a-F1:GCTGCTACAAGAAAGCTGTCGCTGT

55

CSD2a-R: TTATACCGGA GTCAAGCCAA CAACAC  

CSD2a-F1:GCTGCTACAAGAAAGCTGTCGCTGT

55

CSD2a-3'RACE2:CTACAACCGTGAATGTTCGTATCAC

52.4

CSD2a-5’RACE1:CTTTCCAAGGTCATCCTCAAGCTC

55.4

CSD2a-5’RACE2:ACAGCGACAGCTTTCTTGTAGCAGC

55.4

CSD2a-Cell-F: ATCAGATCTA TGCAAGCTGCAATAGC

55

CSD2a-Cell-R: CACTAGT CACTGGAGTCAAGCCAA

CSD2a-IP-F1: CTAATGGACCGGATTTAGAGCATGG

55


CSD2a-SP1 :CCACAGCAGT GAGAGTGAAGGT

CSD2a-IP-F2: CCTTCTCAGTTTGGGCACTAGGAC

55

CSD2a-SP2: CCCGGATGTTGAAGACGATTTGATG

iron superoxide dismutase(FSD1a)

FSD1a -F :CACTGGGGGAA(G/A)CA(T/C)CAC(A/C)G

50

FSD1a-R : AGCCAAGCCCAACCAGA(A/G)CCAAAT

FSD1a -3'RACE1:GGAACAGAGCTAGATGGAATGTCACTG

55.1

FSD1a-3'RACE2:CAATGCTGCACAAGCCTGGAACCATG

57.9

FSD1a-5'RACE1:CTTGTTTCCTTATCTCTTCTTCCAC

---

FSD1a-5'RACE2:TCATCAGATGGAAGAGGATTTATGG

53

FSD1a-5'RACE3:GGATTTATGGCATTGTCAACATCAAGTC

55

FSD1a-F1: GGAGACCAAATTACATAGACTCGC

58

FSD1a-R1:GAATTCAAGTCAGCTGCAGCC

FSD1a-R2: TGCCACCGATACAACAAACCCTGA

FSD-SP1: TCTTGTACATCTTCTCTGCACCATCTG

65

FSD-SP2: AGCAGACTAGACCTCTTTGTTTCCC

65

FSD-SP3: AGAATTGGTATACCTTGGCATGGAAAG

65

 iron superoxide dismutase (FSD1b)

FSD1b -F:TCTGGAACCTTATATGAGCAAGAGG

53.9

FSD1b -R:TCAAGCAATTGGGATGTTGGGTTC

FSD1b -3'RACE1:GGTGACATGCCTAGATTTGGAC

55.4

FSD1b -3'RACE2:ATCCTGGAATGCGGCAATGTCAC

55.8

FSD1b -5'RACE1:CCAAATAGTGTGAGGGCAGCTTCTA

---

FSD1b-5'RACE2:GAGGGCAGCTTCTATGAAATTCTCT

53.9

FSD1b-5'RACE3:TAGCCATACAGAAGGTCACTCTTCT

50

FSD1b-Cell-F: ATCAGATCTA TGGTGTCTTT GAGTCC

FSD1b-58802-R: TCCATTATTC ATAGCCAATTAGCCAC

55

FSD1b-F1:GGTAATTTTGCGTCTGGTCCAAATC

Manganese superoxide dismutase (MSD)


MSD-F: TCCACCACCAGAAGCACCACCAG

53.7

MSD-R:GCTCCCAGACATCAATACCA AGC

MSD-3'RACE1:CACCTCCACCGTCGTCAAGCTC

51.2

MSD-3'RACE2:GAGTTCATTGGGTTGGGCTATTGAC

52.4

MSD-F1: ATGGCT(C/G)(T/C)TCGAACTCTGTTGACCA

56.6

MSD-R1:GTTGCAACGA AACAATGCTCCAAGC

MSD-Cell-F: ATCAGATCTATGGCTCTCCGCTCTCTTT

58

MSD-Cell-R: ACACTAGTCTGGCATAATTCCAGTTCATGAC

MSD-SP1:GTCAATAGCCCAACCCAATGAACTCT

65

MSD-SP2: GGTTCACATGCCCTGCACATCATAT

67

MSD-SP3: CTTCACGGGGTTGGATAAAGGTATAACT

65

AUAP

GCCACGCGTCGACTAGTAC

----

M13F(-47)

CGCCAGGGTTTTCCCAGTCACGAC

----

M13R(-48)

AGCGGATAACAATTTCACACAGGA

----

GeneRacer™ RNA Oligo Sequence

CGACUGGAGCACGAGGACACUGACAUGGACUGAAGGAGUAGAAA

----

GeneRacer™Oligo

GCTGTCAACGATACGCTACGTAACGGCATGACAGTG(T)24

----

GeneRacer™5′ Primer

CGACTGGAGCACGAGGACACTGA

----

GeneRacer™ 5′ Nested Primer

GGACACTGACATGGACTGAAGGAGTA

----


Additional file 2 Primer sequences, product sizes, PCR efficiencies and Tm of the SOD genes


Gene names

Primer sequences(5'-3')

Amplification

Products(bp)



PCR efficiencies(%)

Tm(℃)

DlCSD1a-0

CSD1a-F0: CTCGACAGACCAACTCACACAC

147

2.02

58

CSD1a-R0: TTCCCTTGACACCCTCACTGC

DlCSD1a-00

CSD1a-qF2: ACAGCACGCT CATTTGAT

151

1.85

55

CSD1a-qR2: GAACCCAGAT GAGATCTCAG

DlCSD1a-1

CSD1a-qF1: AGTCTGTCACTGCCACTCTC

93

2.03

55

CSD1a-qR2: GAACCCAGATGAGATCTCAG

DlCSD1a-4

CSD1a-qF3: GACAACACATTTATGTGAACTGC

88

2.06

57

CSD1a-qR3: CCATTGAGAA CAGCAACTGCT

DlCSD1a-5

CSD1a-qF1: AGTCTGTCACTGCCACTCTC

90

1.98

55

CSD1a-qR1: CGTCTGTGTGATCTCAGAAC

DlCSD1b-1

CSD1b-qF1: AGTGACACATGTGAAAGGGAC

160

2.05

59

CSD1b-qR1: ATGCCGCTCTGTATCGCTG

DlCSD1b-2

CSD1b-qF2: ACAAGTGACGCTCTGGTT

127

1.96

55

CSD1b-qR2: GAGGAGATGACTGCAACAG

DlCSD2a

CSD2a-qF: GTTGAAGGCGTTGTCTCTC

117

2

54

CSD2a-qR: GGTATCACCATACTCATGTAGG

DlFSD1a

FSD1a-qF: GGTCAGATGGTGAAGCCGTAGAG

105

2.07

58

FSD1a-qR: GTCTATGCCACCGATACAACAAACCC

DlFSD1b

FSD1b-qF: AGAGTGACCTTCTGTATGGC

83

2.15

54

FSD1b-qR: GTTGAACTCGGGTAACGG

DlMSD

MSD-qF: GAAACCACTGGAAATCAGGAC

98

1.99

57

MSD-qR: ACTGTAGGTAGTATGCATGCTC


Additional file 3 Characteristics of proteins encoded by longan DlSODs

Protein names

Number of amino

acids /AA



Molecular weight /KD

Theoretical pI

Atomic composition

(Arg + Lys)

(Asp+ Glu)

DlCSD1a

152

15.2729

5.65

C652H1040N196O218S5

10

16

DlCSD1b

161

16.4383

6.86

C709H1136N220O225S3

13

14

DlCSD2a

223

23.130

6.44

C998H1588N302O312S10

12

16

DlFSD1a

310

35.642

5.08

C1594H2422N430O478S12

37

50

DlFSD1b

250

29.0521

5.82

C1326H1989N345O371S11

26

31

DlFSD1b

(JF316733)



242

28.0261

6.09

C1278H1934N334O356S11

27

30

DlMSD

221

23.9903

6.29

C1064H1697N299O320S6

19

22


Additional file 4Multiple alignment of DlCSD genes.



Additional file 5 cDNA and putative amino acid sequences of (A) DlCSD1b-variant1 (JF316735) and (B) DlFSD1b-variant1 (JF316731). Start and stop codons are boxed, and variant sequences are underlined.

A. DlCSD1b-variant1 (JF316735)

1 ATGGAGAGTGGAAAGAGCACAGTGAAAGCTGTTGCAGTCATCTCCTCTGCAGACAACAACGTTAGAGGCTCTCTTCACTTCCTTCAACACCCCAACGGAGTGACACATGTGAAAGGGACC

1 M E S G K S T V K A V A V I S S A D N N V R G S L H F L Q H P N G V T H V K G T

121 ATTTTTGGATTGAAACCAGGTCTTCATGGCTTCCATATTCACGCCCTTGGTGACACCACCAATGGCTGCAACTCTACTGGACCTCATTTCAATCCACTGAAGAAGGATCATGGGGCTCCC

41 I F G L K P G L H G F H I H A L G D T T N G C N S T G P H F N P L K K D H G A P

241 AGCGATACAGAGCGGCATGCTGGCGATTTGGGTAACATCGTTGCAGGCTCTGATGGAGTTGCTGCGGTTTCAATTTCTGACAGGCAGATTCCTTTGAGTGGGCAACATTCCATATTGGGG

81 S D T E R H A G D L G N I V A G S D G V A A V S I S D R Q I P L S G Q H S I L G

361 AGGGCTGTTGTTGTGCATGCTGATCCTGATGATCTTGGAAAAGATGAAGCACAAACGAAGAAGCTCTTTTGCAGTCTTAAAGCCCTTACATGCCTCTAAATCTAATCTGAATACCTCATG

121 R A V V V H A D P D D L G K D E A Q T K K L F C S L K A L T C L *

481 CGTTTCACTTGAGTTTCCACTTCCGTGATCTGGTTGTAAC


B. DlFSD1b-variant1 (JF316731)

1 ATGGTGTCTTTGAGTCCCAGTCTTACTCATCTTCCGGTGACTGAGTGGAAGAGTCCCAAGCTTCCTGATTGGAAGCGACAAACACCACCTCGGAAAGTTGTTGCTTACTATGGCTTAAAG

1 M V S L S P S L T H L P V T E W K S P K L P D W K R Q T P P R K V V A Y Y G L K

121 ACGCCTCCTTATAAACTTGATGCTTTAGAACCATATATGAGTAAGAGGACATTGGAAATGCATTGGGGAGAGCATCATCGTGGGTATGTAGATGGGTTGAATAAACAGCTTGAGAAGAGT

41 T P P Y K L D A L E P Y M S K R T L E M H W G E H H R G Y V D G L N K Q L E K S

241 GACCTTCTGTATGGCTATACTATGGATGAACTTGTTAAAGTAACTTACAATAATGGCAATCCGTTACCCGAGTTCAACAATGCTGCCCAGGTATGGAATCATGACTTCTTTTGGGAGTCC

81 D L L Y G Y T M D E L V K V T Y N N G N P L P E F N N A A Q V W N H D F F W E S

361 ATGCAGCCTGGAGGAGGTGACATGCCTAGATTTGGACTTCTTGACCAAATTGAAAAGGATTTTGGTTCCTTTTCAAATTTCAGAGAGAATTTCATAGAAGCTGCCCTCACACTATTTGGT

121 M Q P G G G D M P R F G L L D Q I E K D F G S F S N F R E N F I E A A L T L F G

481 TCTGGCTGGGTTTGGCTTGCTTTAAAGAGAGAAGAGAGACGTCTTGAAGTAATGAAAACATCAAATGCCATCAATCCTCTAGTTTGGGATGATATTCCTATCATCAGTTTGGATATGTGG

161 S G W V W L A L K R E E R R L E V M K T S N A I N P L V W D D I P I I S L D M W

601 GAGGTAAGTTTGGTATATCTCTTTCTTTTTGTGGCTAATTGGCTATGAATAATGGA

201 E V S L V Y L F L F V A N W L *


Alignment of HM773384(upper line) and DlFSD1b-variant2(JF316732)

(lower line)Identity=99.79%(945/947) Gap=8.94%(93/1040)
1 GGTAATTTTGCGTCTGGTCCAAATCAACCTCTGAGGAGAAAAAATATTGACAGGGAAGAG

||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||

1 GGTAATTTTGCGTCTGGTCCAAATCAACCTCTGAGGAGAAAAAATATTGACAGGGAAGAG

61 AAACGAAAGGATGGTGTCTTTGAGTCCCAGTCTTACTCATCTTCCGGTGACTGAGTGGAA

||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||

61 AAACGAAAGGATGGTGTCTTTGAGTCCCAGTCTTACTCATCTTCCGGTGACTGAGTGGAA

121 GAGTCCCAAGCTTCCTGATTGGAAGCGACAAACACCACCTCGGAAAGTTGTTGCTTACTA

||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||

121 GAGTCCCAAGCTTCCTGATTGGAAGCGACAAACACCACCTCGGAAAGTTGTTGCTTACTA

181 TGGCTTAAAGACGCCTCCTTATAAACTTGATGCTTTAGAACCATATATGAGTAAGAGGAC

||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||

181 TGGCTTAAAGACGCCTCCTTATAAACTTGATGCTTTAGAACCATATATGAGTAAGAGGAC

241 ATTGGAAATGCATTGGGGAGAGCATCATCGTGGGTATGTAGATGGGTTGAATAAACAGCT

||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||

241 ATTGGAAATGCATTGGGGAGAGCATCATCGTGGGTATGTAGATGGGTTGAATAAACAGCT

301 TGAGAAGAGTGACCTTCTGTATGGCTATACTATGGATGAACTTGTTAAAGTAACTTACAA

||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||

301 TGAGAAGAGTGACCTTCTGTATGGCTATACTATGGATGAACTTGTTAAAGTAACTTACAA

361 TAATGGCAATCCGTTACCCGAGTTCAACAATGCTGCCCAGGTATGGAATCATGACTTCTT

||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||

361 TAATGGCAATCCGTTACCCGAGTTCAACAATGCTGCCCAGGTATGGAATCATGACTTCTT

421 TTGGGAGTCCATGCAGCCTGGAGGAGGTGACATGCCTAGATTTGGACTTCTTGACCAAAT

||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||

421 TTGGGAGTCCATGCAGCCTGGAGGAGGTGACATGCCTAGATTTGGACTTCTTGACCAAAT

481 TGAAAAGGATTTTGGTTCCTTTTCAAATTTCAGAGAGAATTTCATAGAAGCTGCCCTCAC

||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||

481 TGAAAAGGATTTTGGTTCCTTTTCAAATTTCAGAGAGAATTTCATAGAAGCTGCCCTCAC

541 ACTATTTGGTTCTGGCTGGGTTTGGCTTGCTTTAAAGAGAGAAGAGAGACGTCTTGAAGT

||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||

541 ACTATTTGGTTCTGGCTGGGTTTGGCTTGCTTTAAAGAGAGAAGAGAGACGTCTTGAAGT

601 AATGAAAACATCAAATGCCATCAATCCTCTAGTTTGGGATGATATTCCTATCATCAGTTT

||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||

601 AATGAAAACATCAAATGCCATCAATCCTCTAGTTTGGGATGATATTCCTATCATCAGTTT

661 GGATATGTGGGAGCACGCTTACTATTTGGATTACAAC.......................

|||||||||||||||||||||||||||||||||||||

661 GGATATGTGGGAGCACGCTTACTATTTGGATTACAACGTATGTAACTAATAGCTGCCTCC

698 ..........................................................AA

||

721 TCATCTTTTATGCTCCAGCTGAGATGTTTTCTAAAAGTTCTTGTCTATTTCTAAACAGAA



700 TGACAAAGCAAAATACGTGAATGTCTTTATGAACCACCTTGTATCCTGGAATGCGGCAAT

||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||

781 TGACAAAGCAAAATACGTGAATGTCTTTATGAACCACCTTGTATCCTGGAATGCGGCAAT

760 GTCACGTATGGCCCGTGCAGAGGCCTTTGTGAATTTGGGTGAACCCAAAATTCCTATTGC

||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||

841 GTCACGTATGGCCCGTGCAGAGGCCTTTGTGAATTTGGGTGAACCCAAAATTCCTATTGC

820 TTGAAATGCTTCAACACTGAGAGCTGCAGGTGTATGGTGTCAGGAGGCCAATCAGCAACT

||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||

901 TTGAAATGCTTCAACACTGAGAGCTGCAGGTGTATGGTGTCAGGAGGCCAATCAGCAACT

880 ACACACGTGACTCACAAGGTCACAAGGAGACAGGGTATGTCGAAAATGTGAGTAGTGGCT

||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||

961 ACACACGTGACTCACAAGGTCACAAGGAGACAGGGTATGTCGAAAATGTGAGTAGTGGCT

940 AAGAGAAAAAAAAAAAAAAA

|| | |||

1021 AAAAAAAA............


B. Alignment of DlFSD1b-variant3(JF316733).seq(upper line) and DlFSD1b

-variant4(lower line)Identity=99.78%(911/913) Gap=10.67%(109/1022)
1 GGTAATTTTGCGTCTGGTCCAAATCAACCTCTGAGGAGAAAAAATATTGACAGGGAAGA

|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||

1 GGTAATTTTGCGTCTGGTCCAAATCAACCTCTGAGGAGAAAAAATATTGACAGGGAAGA

61 GAAACGAAAGGATGGTGTCTTTGAGTCCCAGTCTTACTCATCTTCCGGTGACTGAGTGGA

||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||

60 GAAACGAAAGGATGGTGTCTTTGAGTCCCAGTCTTACTCATCTTCCGGTGACTGAGTGGA

121 AGAGTCCCAAGCTTCCTGATTGGAAGCGACAAACACCACCTCGGAAAGTTGTTGCTTACT

||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||

120 AGAGTCCCAAGCTTCCTGATTGGAAGCGACAAACACCACCTCGGAAAGTTGTTGCTTACT

181 ATGGCTTAAAGACGCCTCCTTATAAACTTGATGCTTTAGAACCATATATGAGTAAGAGGA

||||||||||||||||||||||||||||| |||||||||||||||||||||

180 ATGGCTTAAAGACGCCTCCTTATAAACTT..........AACCATATATGAGTAAGAGGA

241 CATTGGAAATGCATTGGGGAGAGCATCATCGTGGGTATGTAGATGGGTTGAATAAACAGC

||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||

230 CATTGGAAATGCATTGGGGAGAGCATCATCGTGGGTATGTAGATGGGTTGAATAAACAGC

301 TTGAGAAGAGTGACCTTCTGTATGGCTATACTATGGATGAACTTGTTAAAGTAACTTACA

||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||

290 TTGAGAAGAGTGACCTTCTGTATGGCTATACTATGGATGAACTTGTTAAAGTAACTTACA

361 ATAATGGCAATCCGTTACCCGAGTTCAACAATGCTGCCCAGGTATGGAATCATGACTTCT

||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||

350 ATAATGGCAATCCGTTACCCGAGTTCAACAATGCTGCCCAGGTATGGAATCATGACTTCT

421 TTTGGGAGTCCATGCAGCCTGGAGGAGGTGACATGCCTAGATTTGGACTTCTTGACCAAA

||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||

410 TTTGGGAGTCCATGCAGCCTGGAGGAGGTGACATGCCTAGATTTGGACTTCTTGACCAAA

481 TTGAAAAGGATTTTGGTTCCTTTTCAAATTTCAGAGAGAATTTCATAGAAGCTGCCCTCA

||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||

470 TTGAAAAGGATTTTGGTTCCTTTTCAAATTTCAGAGAGAATTTCATAGAAGCTGCCCTCA

541 CACTATTTGGTTCTGGCTGGGTTTGGCTTGCTTTAAAGAGAGAAGAGAGACGTCTTGAAG

||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||

530 CACTATTTGGTTCTGGCTGGGTTTGGCTTGCTTTAAAGAGAGAAGAGAGACGTCTTGAAG

601 TAATGAAAACATCAAATGCCATCAATCCTCTAGTTTGGGATGATATT.............

|||||||||||||||||||||||||||||||||||||||||||||||

590 TAATGAAAACATCAAATGCCATCAATCCTCTAGTTTGGGATGATATTGTAAGTCAATCTT

648 ..........................................................CC

||

650 TATATTTTTTGCATGAACAGTTGATTTTATCTTAATATTGACCACCTTTCTTGTGCAGCC



650 TATCATCAGTTTGGATATGTGGGAG........................AATGACAAAGC

|||||||||||||||||| |||||| |||||||||||

710 TATCATCAGTTTGGATATATGGGAGCACGCTTACTATTTGGATTACAACAATGACAAAGC

686 AAAATACGTGAATGTCTTTATGAACCACCTTGTATCCTGGAATGCGGCAATGTCACGTAT

||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||

770 AAAATACGTGAATGTCTTTATGAACCACCTTGTATCCTGGAATGCGGCAATGTCACGTAT

746 GGCCCGTGCAGAGGCCTTTGTGAATTTGGGTGAACCCAAAATTCCTATTGCTTGAAATGC

||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||

830 GGCCCGTGCAGAGGCCTTTGTGAATTTGGGTGAACCCAAAATTCCTATTGCTTGAAATGC

806 TTCAACACTGAGAGCTGCAGGTGTATGGTGTCAGGAGGCCAATCAGCAACTACACACGTG

||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||

890 TTCAACACTGAGAGCTGCAGGTGTATGGTGTCAGGAGGCCAATCAGCAACTACACACGTG

866 ACTCACAAGGTCACAAGGAGACAGGGTATGTCGAAAATGTGAGTAGTGGCTAAAAGAAAA

||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||

950 ACTCACAAGGTCACAAGGAGACAGGGTATGTCGAAAATGTGAGTAGTGGCTAAGAGAAA.

926 AA


1009 ..
Additional file 6Alignment of dlFSD variant sequences in longan. The start and stop codons are highlighted, the variant sequences are in boxes.

Additional file 7–Multiple alignment of DlSOD proteins and SOD proteins from other plant species. Signal peptides are boxed and conserved sequences are highlighted. (A) Multiple alignment of deduced protein sequences from longan DlCSD1a, DlCSD1a, and DlCSD2a. CuZn-SOD signature 1 is underlined; CuZn-SOD signature 2 is indicated by a wavy line. (B) Multiple alignment of deduced protein sequences from longan DlFSD1a, DlFSD1b, and DlFSD1b (JF316733). Mn and Fe-SOD signature 1 is underlined. (C) Multiple alignment of deduced amino acid sequences of longan DlMSD proteins with those of Gossypium hirsutum (Gh), Arabidopsis thaliana (At), Populus trichocarpa (Pt), and Oryza sativa (Os). The “WEHAYY” signature is in bold.
A. DlCSDs


DlCSD1a ----------------------------------------------------------------------MVKAVAVLNGSEG-VKGTVNFTQEGDGPTT 29



DlCSD1b ----------------------------------------------------------------MESGKSTVKAVAVISPADNNVRGSLHFLQHPNGVTH 36

DlCSD2a MQAAIAAMAAHTILTASPPFSHHPLLSTFPSPNTLTRTSSFRGVSLNPTTHHLHSHCCGLQALHCRRCYKKAVAVAVLKGNSN-VEGVVSLTQENDGPTT 99

DlCSD1a VTGSLCGLKPGLHGFHVHALGDTTNGCMSTGPHFNPAAKEHGSPEDENRHAGDLGNVNVGDDGTVSFTIVDKQIPLTGPNSVVGRAVVVHSDPDDLGKGG 129

DlCSD1b VKGTIFGLKPGLHGFHIHALGDTTNGCNSTGPHFNPLKKDHGAPSDTERHAGDLGNIVAGSDGVAEVSISDRQIPLSGQHSILGRAVVVHADPDDLGKGG 136

DlCSD2a VNVRITGLTPGPHGFHLHEYGDTTNGCMSTGAHFNPNSMTHGAPEDEVRHAGDLGNVVANANGVAEAIIVDNQIPLSGPNTVIGRALVVHELEDDLGKGG 199

DlCSD1a HELSKSTGNAGGRLACGVIGLQA-- 152

DlCSD1b HELSKTTGNAGGRIGCGIIGLQSSV 161

DlCSD2a HELSLSTGNAGGRLACGVVGLTPV- 222



B. DlFSDs


DlFSD1a MKMVAAAAKPVWLTFPCQGLGGQNPSLEFLWGN-KEMVQRRCTRKSRPTTLSAKFE LKPPPYPLNALEPHMSRDTLEYHWGKHHRTYVENLNKQTAGTE- 98



DlFSD1b -------------------MVSLSPSLTHLPVTEWKSPKLPDWKRQTPPRKVVAYYGLKTPPYKLDALEPYMSKRTLEMHWGEHHRGYVDGLNKQLEKSDL 82

JF31673 -------------------MVSLSPSLTHLPVTEWKSPKLPDWKRQTPPRKVVAYYGLKTPPYKLDALEPYMSKRTLEMHWGEHHRGYVDGLNKQLEKSDL 82

DlFSD1a LDGMSLEEVVVVSYNRGYFLPSFNNAAQAWNHDFFWESMKPGGGGKPSGELLQMIERDFGSFERFLSEFKSAAATQFGSGWAWLCYKANRLDVDNAINPS 198

DlFSD1b LYGYTMDELVKVTYNNGNPLPEFNNAAQVWNHDFFWESMQPGGGDMPRFGLLDQIEKDFGSFSNFRENFIEAALTLFGSGWVWLALKR------------ 170

JF31673 LYGYTMDELVKVTYNNGNPLPEFNNAAQVWNHDFFWESMQPGGGDMPRFGLLDQIEKDFGSFSNFRENFIEAALTLFGSGWVWLALKR------------ 170

DlFSD1a DEDKKLVVVKSPNAVNPLVWDYSPLLTIDVWEHAYYLDFQNRRPDYISVFMDKLVSWEAVSRRLEIAKARAAEREVEEEIRKQEEEKEQESDGEAVEMYL 298

DlFSD1b -EERRLEVMKTSNAINPLVWDDIPIISLDMWEHAYYLDYNNDKAKYVNVFMNHLVSWNAAMSRMARAEAFVNLGEPNIPIA------------------- 250

JF31673 -EERRLEVMKTSNAINPLVWDDIPIISLDMWE--------NDKAKYVNVFMNHLVSWNAAMSRMARAEAFVNLGEPKIPIA------------------- 242

DlFSD1a DSDADDLERD 310

DlFSD1b ----------

JF31673 ----------



C. MSDs

DlMSD MALRSLFNTRTLA-----RPARTVGLGL--RGIQTVSLPDLQYDYGALEPAISGEIMQLHHQKHHQAYVTNYNKALEQLDQAISKGDTSTVVKLQSAIKF 93

GhMSD MALRSSITRRTLT-----LGLNSTMLLPLSRSLQTFSLPDLPYDYGALEPAISGEIMQLHHQKHHQTYITNYNKALEQLHEAIQKGDSSTVVKLQSAIKF 95

AtMSD MAIRCVASRKTLA-----GLKETSSRLLRIRGIQTFTLPDLPYDYGALEPAISGEIMQIHHQKHHQAYVTNYNNALEQLDQAVNKGDASTVVKLQSAIKF 95

PtMSD MALRSLVSRKTLG-----LG-----LKLQFRGLQTFSLPDLPYDYGALEPAISGEIMQLHHQKHHQTYITNYNKSLEQLHHAMEKGDSSAVVKLQSAIKF 90

OsMSD MALRTLASRKTLAAAALPLA-----AAAAARGVTTVALPDLPYDYGALEPAISGEIMRLHHQKHHATYVANYNKALEQLDAAVAKGDAPAIVHLQSAIKF 95

DlMSD NGGGHVNHSIFWKNLAPANEGGGEPPKSSLGWAIDTHFGSLEALVQKMNADGAALQGSGWVWLGLDKELKRLVVETTGNQDPLVTKGPSLVPLLGIDVLG 193

GhMSD NGGGHVNHSIFWKNLAPIREGGGEPPKASLGWAIDTHFGSLESLIQKMNAEGAGLQGSGWVWVGVNKELKKLVIETTPNQDPLVTKGPHLVPLLGID--- 192

AtMSD NGGGHVNHSIFWKNLAPSSEGGGEPPKGSLGSAIDAHFGSLEGLVKKMSAEGAAVQGSGWVWLGLDKELKKLVVDTTANQDPLVTKGGSLVPLVGID--- 192

PtMSD NGGGHVNHSIFWKNLTPVQEGGGEPPHGRLGWAIDEDFGSLESLIKKMSTEGAAVQGSGWVWLGLDKESKKLVVETTENQDPLVTKGP-LVPLLGVD--- 187

OsMSD NGGGHVNHSIFWNNLKPISEGGGDPPHAKLGWAIDEDFGSFEALVKKMSAEGAALQGSGWVWLALDKEAKKLSVETTANQDPLVTKGANLVPLLGID--- 192

DlMSD ACILPTVQECQTRLSEKHLESHELELCQ---------------- 221

GhMSD ------VWEHAYYLQYKNVRPDYLKNIWKVINWKYASEVYEKECA 231

AtMSD ------VWEHAYYLQYKNVRPEYLKNVWKVINWKYASEVYEKENN 231

PtMSD ------VWEHAYYLQYKNVRPDYLKNIWKVMNWKYAGEVYDKESS 226

OsMSD ------VWEHAYYLQYKNVRPDYLSNIWKVMNWKYAGEVYENATA 231

Additional file 8–The location of different transcription start sites (TSSs) in DlSODs. ATG indicates the start codon. The first nucleotide in each TSS is indicated either in red (A), green (T), pink (C), or yellow (G). Numbers above each nucleotide sequence indicate the numbers of TSSs.


1/14 2/14 1/14

DlCSD1a-3 ACTCTAGAACAAACAAACAGCCGCTCATTTGATGATAATATTGACACCGCTCTATAAGGACACCACCTACAACCACTCTCTCACTGCCAC

2/14 1/14 7/14

DlCSD1a-5 ------------------------------------AATATTGACACCGCTCTATAAGGACACCACCTACAACCACTCTCTCACTGCCAC
DlCSD1a-3 TCTCTCTCGACAGACCAACTCACACACTTGTCTTCTTCTCTCTCTTGAGGGGTGTTCTGAGATCTCATCTGGGTTCTTTTTTGATCAAGA

DlCSD1a-5 TCTCTCTCGACAGACCAACTCACACACTTGTCTTCTTCTCTCTCTTGAGGGGTGTTCTG----------------------------AGA

+196 bp

DlCSD1a-3 TCACACAGAAAAATG

+132 bp

DlCSD1a-5 TCACACAGAAAAATG

***************

1/13 1/13 2/13 9/13 +84 bp

DlCSD1b-6 AACAAGTGGCGCTCT GGTTTTCTTAGAGAT AAGAATACAACCCGG CCTCGGTGAAGAACA TTTGAAACGAAGACA TAAAAAATG

1/15 8/15 3/15

CSD2a AAAATTTTACAACTT TAGGAGGGCGGAGTA AATGCAAGTATAAAA ACTTAGCAAACAGGG AGAGTTAGCCACCAA AGCCTCACTTACATT



1/15 2/15 +129 bp

ATCATCAAATCGTCT TCAACATCCACATTT TGAAAAATG

1/13 1/13 1/13 1/13 2/13 1/13 1/13 2/13 2/13

DlFSD1a GTACAGTCCTAACAT GTGGTACCTTGCCAT AAAAAATGAGTGTCT AATCTATCCAGTGAG TTTGCATTAGGTTTT GAGACCAAATTACAT

1/13 +126 bp

AGACTCGCTTGTTGT TGAATTGAGTTAAAG AAAATG

2/10 1/10 1/10 1/10 1/10 1/10 1/10

DlFSD1b GTAATGATTCAGTAG TGGAATGGTTGGGGG AAAAAACACAATTAA GTTATGATACTCAAT TTAAACAGTACCTGT GACTGTGAGTAACCT

1/10 +182bp

GTTGCGTTTAGGGCC GGTGGGTAATTTTGC GTCTGGTCCAAATCA ACCTCTGAGGAGAAA AAATATTGACAGGGA AGAGAAACGAAAGGATG

2/18 1/18 3/18 3/18 4/18 1/18 1/18 1/18 2/18 +92bp

DlMSD ATCTCCACTCCATCT CCACTACAAGCAACC ACTTCAACACCTCCA CTCTCCGTCTGTCTG TCTCTCTCTCTCTCT CTCAACACTTCTGGATG







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