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Table 2 Effects of sequence improvement on the annotation of R-genes

From: Interspecific and intraspecific gene variability in a 1-Mb region containing the highest density of NBS-LRR genes found in the melon genome

Gene Id1 Class2 Sequence changes3 Notes
MELO3C004258 TN No 3′-partial
MELO3C004259 TNL (T)14 -- > (T)11 (I)  
(T)10 -- > (T)9 (I)  
MELO3C004260 TN No 3′-partial
MELO3C004262 TNL (T)7 -- > (T)8 (I) Additional a.a.s (gap closed)
(T)4 -- > (T)3 (I)
1 T deleted (I)
20 N - > [559 bp (I + E) + 30 N (in poly(AT), I)]
MELO3C004266 TNL (N)5054 gap closed (E) Additional a.a.s (gap closed)
(CTATAATTG) -- > (CATTG) (E)
(TGTCGTTTA) -- > (T9GCGTTA) (I)
(TTATA9T) -- > (TA9T) (I)
(A6CA5G) -- > (A7CA6G) (I)
MELO3C004288 N No 5′- and 3′-partial
MELO3C004289 TNL (N)767 gap closed (E) Additional a.a.s (gap closed)
(A)20 -- > (A)26 (I)
(A)16 -- > (A)24 (I)
(T)7(A)11 -- > (T)8(A)1o (I)
MELO3C004290 TN (N)20 - > (N)1 (E) 3′-partial
MELO3C004291 TN (N)2153 gap closed (E)  
(CA5CCT12) -- > (CAAT10) (I) 3′-partial
(CTTTTA13) -- > (CTTTA11) (I) Additional a.a.s (gap closed)
(GAAAG) -- > (GAG) (E)  
MELO3C004292 TNL (A)14 -- > (A)7 (I)  
(AA) deleted (I)  
(A)21 -- > (A)15 (I)  
MELO3C004294 TNL (AA) deleted (I)  
MELO3C004301 TNL (N)73 - > (N)28 (I) (N)28 in poly(TA) (intron)
(TACCA28GAAA) -- > (TCCA28GA) (I)
(A10CCAAAG) -- > (A13CCAAAAG) (I)
(AAAAGTTTA6) -- > (AAAAGTTTCA6) (I)
(GAAAGTATA5TCA) -- > (GAAAGTATAAATCA) (I)
(TTA10TTTGAAAA) -- > (A11TGAAAA) (I)
MELO3C004302-4303 4 NL (CTTGAATGAAACTTA) -- > (CTTGAAC) (E) 5′-partial5
(GTGAAACTTA11CATGG) -- > (GTA8CATGG) (I)
(TACAATT) -- > (TACTT) (E)
(CTA11CAT) -- > (CTA8CAT) (E)
MELO3C004309-4310 6 TNL (N)78 gap closed (I)  
(GTTCCGTATTCTAATTAT4ACT3) -- > (GTCCGATCAATAT3ACT) (I)  
(TAT6C) -- > (TATTC) (E)  
MELO3C004311 TN (N)30 gap closed (E) 3′-partial
(GA4TTTACT) -- > (GA5TACT) (I)
MELO3C004312 TN (N)468 gap closed (introns + exons) 3′-partial
Additional a.a.s (gap closed)
MELO3C004313 TN (N)20 gap closed (E) 3′-partial
Additional a.a.s (gap closed)
MELO3C004317 CNL (N)1414 gap closed (E + I) Additional a.a.s (gap closed)
(N)4442 gap closed (exons + introns)
MELO3C004318 CN (N)4962 gap closed (exons + introns) 3′-partial
Additional a.a.s (gap closed)
MELO3C004320 NL (N)4489 -- > (N)2460 (introns + exon) Add. a.a.s (gap partially solved)
MELO3C004321 CNL (N)3747 gap closed (E) Additional a.a.s (gap closed)
MELO3C004323 CN No 3′-partial
MELO3C004324 NL No  
  1. 1MELO3C004261, MELO3C004265, MELO3C004295, MELO3C004304, MELO3C004319 are ORFs that code for, respectively, 141-, 220-, 98-, 109-, and 233-aa peptides with homology to TNL proteins. Due to their short length, they are most probably not R-genes and, therefore, were not considered for further analysis.
  2. 2TN: TIR-NBS; TNL: TIR-NBS-LRR; N: NBS; NL: NBS-LRR; CNL: CC-NBS-LRR; CN: CC-NBS.
  3. 3Sequence changes between assemblies CM3.5 and CM3.6.1 in each R-gene region (start to stop codon, including introns). I, intron; E, exon.
  4. 4Previous MELO3C004302 gene does belong to the MELO3C004303 ORF, as deduced by sequence comparison with other TNL R-proteins.
  5. 5Gene MELO3C004304 codes for a 109-aa peptide with a TIR domain, and may represent a 5′ fragment of gene MELO3C004302-4303.
  6. 6Previous MELO3C004310 gene does belong to the MELO3C004309 ORF, as deduced by sequence comparison with other TNL R-proteins.
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BMC Genomics

ISSN: 1471-2164

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