The tomato genome has been published in Nature on May 31, 2012, culminating years of work by the Tomato Genome Consortium, a multi-national team of scientists from 14 countries. The Tomato Genome Consortium started its work in 2003, when scientists analyzed the DNA sequence of tomato using the most modern equipment available at the time. Consortium researchers report that tomatoes possess some 35,000 genes arranged on 12 chromosomes and chromosome 0 (all scaffolds that could not be placed on either of the 12 tomato chromosomes by either the genetic or physical maps were placed on an artificial "chromosome 0". The scaffolds on this chromosome are ordered from large to small and unoriented.). Fortunately, with the recent introduction of so-called "next generation sequencing" technologies, the speed of data output increased 500-fold and enabled the project to move on efficiently to its conclusion. Copy of data used in database development and analysis work is available (Downloaded from: ftp://ftp.solgenomics.net/tomato_genome/wgs/assembly/build_2.40/)

All the 12 chromosomes were chopped into manageable range of 50000 bp using PERL script. These fragments were given to MIcroSAtellite identification tool (MISA) to identify and find the location of perfect and compound microsatellites for all the chromosomes of tomato genome. The SSR numbers, motifs, repeat number, length of the repeat, size of the repeat, repeat type, GC content, start and end position of the repeat and SSR sequence has been compiled. Chromosome wise description of the SSRs have been tabulated as well as represented as graphs. The mono, di, tri, tetra, penta and hexa type of microsatellites have been plotted to show the abundance of the type in chromosomes.In addition, facility to locate the SSRs on chromosomes based on the position number is incorporated which may be very useful to the biotechnologists. The tabulation of simple versus compound shows the proportion of the same.

 

Scientific name
Common name
Chr. no.
Genome Size
Estimated No. of Genes
Solanum lycopersicum
Tomato
12
~950 MegaBases
35,000 genes

Table 1. Description of Tomato genome

 

Type
Number
Percentage
Simple

127207

86.77

Compound

19395

13.23

Total
146602
100.00

Table 2. Description of Microsatellite types in Tomato genome

 

Motif Type
Number
Percentage (%)
Mono

73556

57.82

Di

39125

30.76

Tri

12576

9.89

Tetra

1565

1.23

Penta

232

0.18

Hexa

153

0.12

Table 3. Motif wise distribution of Microsatellites in Tomato genome

 

Chromosome
Simple
Compound
Mono
Di
Tri
Tetra
Penta
Hexa
1

8995

4632

1476

194

35

19

2311

2

6401

2746

867

95

15

6

1363

3

6637

3370

1107

150

18

21

1572

4

6332

3268

1076

115

24

13

1499

5

5714

3300

1028

128

17

11

1632

6

5105

2652

861

102

8

9

1219

7

5801

3097

1045

137

22

11

1580

8

5974

3052

966

136

19

11

1556

9

5886

3275

1098

118

20

17

1613

10

5369

3041

910

140

15

12

1417

11

5005

2640

916

91

16

3

1360

12

5365

3034

995

126

20

18

1687

0

972

1018

231

33

3

2

586

Table 4. Motif wise distribution of Microsatellites in Tomato chromosomes

 

3

Figure 1. Distribution of SSR marker type

 

3

 

Figure 2. Distribution of repeat types

 

 

4

Figure 3. Distribution of repeat kinds

 

 

5

Figure 4. Distribution based on GC Content