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Rye-specific DNA sequences

PAWS5 Primer 5’-AACGAGGGGTTCGAGGCC-3’248

 

PAWS6 Primer5’-GAGTGTCAAACCCAACGA-3’  248

 

ω-secalin gene23 5’-AAC ATGAAGACCTTCCTCATC-3’  354

    Promoter region to

ω-secalin gene 5’-GGATCCAAATTTGCATGCGTA-3’ 354

30oligonucleotide primers BAMRF (5’-ATA GCA CGC ATG CTC ACA AG-3’) and BAMRR (5’-GCG CCA CTG GAT CAA CAG-3’) are ß-amylase1 specifc primers of rye, located on 5RL2.3 386, 392

Nucleotide and deduced amino acid sequence of low-temperature-induced rye gene rlt1412 (424)

1

CAC

AAT

ACC

ATC

TCC

TCA

GTA

CAT

CAG

AGC

CTC

CCA

GTT

AGC

AAT

ATG

GCA

AAG

TGT

CTC

1

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 M

 A

 K

C  

L

61

GCC

 GCC

 GCG

 CTC

 CTG

 CTA

 CTG

 GTG

 GTG

 CTC

 GCG

 TAC

TGC

GAC

 GGG

 AGG

 GAG

 CTG

 AAC

 CAG

6

A

A

A

L

L

L

L

V

V

L

A

Y

C

D

G

R

E

L

N

Q

121

AAG

GAC

CAG

 GCA

 CTA

 GCA

 ACG

 GCA

CGC

GGT

GCC

GGT

GGT

GGC

GTC

GGC

GAG

 GAG

AAG

ATT

26

K

D

Q

A

L

A

T

A

R

G

A

G

G

G

V

G

E

E

K

I

181

TTG

GGG

TTG

CCA

GAG

TTG

CCG

CTT

GTG

GGA

ACC

GTT

ACA

GGG

ACC

AGT

ACC

GTT

ACC

GGC

46

L

G

L

P

E

L

P

L

V

G

T

V

T

G

T

S

T

V

T

G

241

CCT

GTG

GTG

GTG

CTT

CCT

GCC

CTT

CCT

GCA

CTA

CCG

GCA

CAC

CCA

TGA

TCA

TCT

CGA

GAT

66

P

V

V

V

L

P

A

L

P

A

L

P

A

H

P

 

 

 

 

 

301

TAT

GTG

CTG

GCT

TAC

AAG

ATG

AAG

CTG

AAC

TTG

TGG

CTT

CAG

AAT

TCT

AGC

TAG

AAC

CGT

361

CAG

CTC

GGG

AAG

ATA

AAC

ACC

GGC

GTT

TCG

CTC

ATT

AGC

ATG

TTC

CTT

AAT

GAG

CGT

CTG

421

TAT

CAA

CTA

TGC

TAT

CGT

CTG

TAT

TTT

CTT

TCC

GTT

CAT

GTT

CTA

GTA

TTT

CCC

ATT

CAT

481

CTG

TAT

TTT

CTT

TCA

GTT

CAT

GCT

CTA

GTA

TGA

TGT

ATC

GTC

AAC

 

 

 

 

 

Rye seed chitinase-a (RSC-a = rsca); Basic endochitinase A (432, 433, 434, 435, 436)

Complete sequence length = 321 AA

Defense against chitin containing fungal pathogens; binds the hyphal tips, lateral walls and septa of fungi and degrades mature chitin; random hydrolysis of N-acetyl-beta-D-glucosaminide (1->4)-beta-linkages in chitin and chitodextrins; localized in the aleurone cells of the seed endosperm (at protein level); levels increase from 23 to 40 days after flowering, and are maintained until maturation (at protein level); belongs to the glycosyl hydrolase 19 family; chitinase class I subfamily; contains 1 chitin-binding type-1 domain.

http://www.uniprot.org/uniprot/Q9FRV1

Secalin gene

ω-secalin gene family consists of five length members: 1150bp, 1076bp, 1075bp, 1052bp and 1004bp. Different length family members still include sub-members with the following numbers: 9 for 1076bp; 1 for 1150bp; 1 for 1075bp; 2 for 1052bp and 2 for 1004bp. In all the five length family members only two members from 1076bp, one member from 1052bp and one member from 1004bp have transcriptional activities. Through prokaryotic expression the corresponding bands of three different length ω-secalin on seed acid PAGE is determined (458)

beta amylase fragment (481)

responsible for hydrolysis of (1->4)-alpha-D-glucosidic linkages in polysaccharides so as to remove successive maltose units from the non-reducing ends of the chains

        10         20         30          40         50         60

IMSFHQCXXN VADVVNIPIP QWVRDVGATD PDIXYTNRSG TRNIEYLTLG VDDQPLFHGR

        70         80         90        10 0        110        120

TAVQMYADYM ASFRENMKKF LDAGTIVDIE VGLGPAGEMR YPSYPQSQGW XFPGIGEFIC

       130        140        150        160         170        180

YDKYXEADFK AAAAKAGHPE WELPDDAGEY NDTPEKTQFF KENGTYLTEK GKFFLSWYSN

       190        200        210        220

KLIKHGDKIL DEANKVFLGC RVQLAIKVXG IHWWYRVPNH A

1RS sequencing (483)

Annotation of sequence reads reveals at least 3,121 gene loci and at least 1,882 different gene functions on 1RS; excluding the ribosomal and secalin genes 3.36% of all sequence reads (30,118 reads) identified the gene space of 1RS; the quantity of sequence information resulted in 0.436x sequence coverage of the 1RS chromosome arm, permitting the identification of genes with estimated probability of 95%; more than 5% of the 1RS sequence consisted of gene space, identifying at least 3,121 gene loci representing 1,882 different gene functions; epetitive elements comprised about 72% of the 1RS sequence, Gypsy/Sabrina (13.3%) being the most abundant; more than four thousand simple sequence repeat (SSR) sites mostly located in gene related sequence reads were identified; the existence of chloroplast insertions in 1RS has been verified by identifying chimeric chloroplast-genomic sequence reads; synteny analysis of 1RS to the full genomes of Oryza sativa and Brachypodium distachyon revealed that about half of the genes of 1RS correspond to the distal end of the short arm of rice chromosome 5 and the proximal region of the long arm of B. distachyon chromosome 2; comparison of the gene content of 1RS to 1HS barley chromosome arm revealed high conservation of genes related to chromosome 5 of rice.

   Copyright  R. Schlegel   &   V. Korzun    2004 2005 2006 2007 2008  2009  2010 2011 2012 2013 2014 2015  2016