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-
superoxidedismutase
(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:ATCAGATCTATGGAGAGTGGAAAGAG / 55
CSD1b-Cell-R:CACTAGTTACAGAGGACTGAAGCC
copper/zinc-
superoxide dismutase (CSD2a) / CSD2a-F1:GCTGCTACAAGAAAGCTGTCGCTGT / 55
CSD2a-R:TTATACCGGAGTCAAGCCAACAACAC
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:ATCAGATCTATGCAAGCTGCAATAGC / 55
CSD2a-Cell-R:CACTAGTCACTGGAGTCAAGCCAA
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:GTTGCAACGAAACAATGCTCCAAGC
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') / AmplificationProducts(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 aminoacids /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
1
Additional file 4 –Multiple 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 *
1
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 6 –Alignment 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 1/14DlCSD1a-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
1