YAC co-ordinates

SCHMIDT renate.schmidt at afrc.ac.uk
Thu Mar 10 07:23:10 EST 1994


Dear Arabidopsis community,
As part of our effort on the generation of YAC contigs on chromosomes 4 and 
5 of Arabidopsis we have identified YAC co-ordinates corresponding to some 
known repeat sequences in the EG and the EW library. 
As probes we used: 
1) rDNA intergenic spacer sequence
2) 2 cosmids containing Arabidopsis chloroplast DNA (representing more than 
80% of the chloroplast DNA)
3) 2 clones representing the HindIII repeat sequences which have been located 
in the paracentromeric heterochromatin (180 and 500bp sequences).
The library screening was done using colony hybridizations, all co-ordinates 
listed in the table have been identified on duplicate filters. In addition, the 
colony hybridization data were confirmed in Southern blot experiments for all 
the EW clones and a subset of the EG co-ordinates.  
This work has been accepted for publication in The Plant Journal (The 
abstract of the paper is included in this message). But we would like to make 
the YAC co-ordinates available to the community now. Hopefully the following 
list will help in the identification of chimaeric YAC clones. These data will 
also be submitted to AAtDB.

Renate Schmidt and Caroline Dean (on behalf of all contributors to this 
project)

Schmidt at afrc.ac.uk
Arabidopsis at afrc.ac.uk


Analysis of clones carrying repeated DNA sequences in two YAC libraries of 
Arabidopsis thaliana DNA
Renate Schmidt, Joanna Putterill, Joanne West, Gerda Cnops, Frances 
Robson, George Coupland and Caroline Dean
Summary
YAC clones carrying repeated DNA sequences from the Arabidopsis thaliana 
(Arabidopsis) genome have been characterized in two widely-used 
Arabidopsis YAC libraries, the EG library (Grill and Somerville, 1991) and 
the EW library (Ward and Jen, 1990). Ribosomal, chloroplast and the 
paracentromeric repeat sequences are differentially represented in the two 
libraries. The co-ordinates of YAC clones hybridizing to these sequences are 
given. A high proportion of EG YAC clones were classified as containing 
chimaeric inserts because individual clones carried unique sequences and 
repetitive sequences originating from different locations in the genome. None 
of the EW YAC clones analyzed were chimaeric in this way. YAC clones 
carrying tandemly-repeated sequences, such as the paracentromeric or rDNA 
sequences, exhibited a high degree of instability. These observations need to 
be taken into account when using these libraries in the development of a 
physical map of the Arabidopsis genome and in chromosome walking 
experiments.

Table 
YAC clones hybridizing to repeated DNA sequences

EW YAC clones containing chloroplast DNA sequences
1B4, 1F6, 1F7, 2B8, 2C11, 2D4, 2E4, 2G11, 3B4, 3C9, 3E4, 3F4, 3F11, 
3G5, 3G10, 3H3, 4A3, 4A4, 4B9, 4C2, 4C6, 4F1, 4F9, 4G5, 4G10, 4H5, 
4H8, 5A5, 5A11, 5B3, 5C3, 5C11, 5E6, 5G8, 5H6, 5H11, 6A4, 6A9, 6C4, 
6D5, 6E8, 6G7, 7A11, 7B12, 7D2, 7D3, 7D5, 7D6, 7F3, 7G1, 7G8, 7G10, 
7H6, 8A4, 8A5, 8E1, 8F1, 8G3, 8G12, 8H6, 9D10, 9E1, 9G11, 9G12, 9H8, 
10B7, 10C11, 10E5, 10H5, 10H10, 10H11, 11D11, 11F3, 11G1, 12B10, 
13A7, 13B2, 13B8, 13D1, 13D6, 13F7, 13H3, 13H6, 14E10, 14F3, 14G12, 
15A5, 15A7, 15B10, 15D9, 15E4, 15E5, 15E7, 15E8, 15F3, 15G2, 15H1, 
15H4, 16A3, 16A8, 16B6, 16D9, 16F6, 17C5, 17C9, 17C12, 17F7, 17H4, 
18C2, 18C6, 18C12, 18D5, 18E5, 18G2, 18H8, 18H9, 18H10, 18H11, 
19A7, 19A8, 19D1, 19G4, 19H8, 20A6, 20C5, 20D5, 20G4, 20G9, 21A3, 
21B3, 21E6, 22A7, 22B2, 22B12, 22C4, 22D5, 22E12, 22G3, 22G10, 
22G12, 22H9, 23B3, 23B8, 23C5, 23C10, 23F7

EG YAC clones containing chloroplast DNA sequences
1A6, 1A9, 1A10, 1A11, 1A12, 1B3, 1B7, 1B10, 1B11, 1C2, 1C8, 1C11, 
1D4, 1E1, 1E2, 1E4, 1F1, 1F2, 1F4, 1F7, 1G5, 1G6, 1H3, 1H8, 1H9, 2A2, 
2A8, 2B4, 2B8, 2B10, 2C4, 2C8, 2D5, 2D6, 2D7, 2E5, 2E7, 2E8, 2F1, 
2F11, 2G1, 2G2, 2G4, 2G6, 2G7, 2H4, 2H5, 2H6, 3A1, 3A3, 3A4, 3A5, 
3A6, 3A7, 3A10, 3A11, 3A12, 3B1, 3B5, 3B10, 3C1, 3C3, 3C7, 3C9, 
3C11, 3D4, 3D5, 3D6, 3D8, 3D9, 3D10, 3E2, 3E3, 3E4, 3E5, 3E6, 3E7, 
3E9, 3E10, 3E12, 3F1, 3F3, 3F4, 3F5, 3F6, 3F7, 3F11, 3G1, 3G8, 3G12, 
3H1, 3H2, 3H5, 3H10, 3H12, 4A5, 4A6, 4A8, 4A9, 4A12, 4B1, 4B2, 4B7, 
4C2, 4C12, 4D1, 4D6, 4D7, 4D12, 4E2, 4E3, 4E6, 4E7, 4E8, 4F5, 4F6, 4F7, 
4F9, 4G4, 4H3, 4H4, 4H9, 5A1, 5A10, 5B3, 5B6, 5B9, 5C1, 5D1, 5D5, 
5D8, 5E1, 5E4, 5E5, 5E12, 5F1, 5F3, 5F12, 5G1, 5G2, 5G3, 5G4, 5G5, 
5G7, 5G10, 5H3, 5H5, 5H9, 5H12, 6A10, 6A11, 6D1, 6D2, 6D3, 6D6, 
6D12, 6E8, 6F6, 6G2, 6G3, 6G4, 6H2, 6H12, 7A9, 7A11, 7B1, 7B6, 7B8, 
7B9, 7B10, 7B11, 7C4, 7C6, 7C9, 7C10, 7D3, 7D5, 7D7, 7D12, 7E1, 7E3, 
7F7, 7F12, 7G2, 7G12, 7H2, 7H4, 7H11, 7H12, 8A2, 8B3, 8B5, 8B6, 8B9, 
8C6, 8C7, 8D2, 8D7, 8F2, 8F3, 8F6, 8F7, 8F9, 8G1, 8G2, 8G4, 8G7, 8G8, 
8G9, 8H1, 9A1, 9A5, 9A6, 9A10, 9A12, 9B4, 9C11, 9D5, 9D8, 9D11, 9E3, 
9E4, 9E5, 9E8, 9E12, 9F1, 9F2, 9F4, 9F10, 9F11, 9G1, 9G2, 9H5, 9H10, 
9H11, 10A7, 10A8, 10C7, 10C8, 10C9, 10C10, 10C12, 10D1, 10D2, 
10D4, 10D6, 10D8, 10E1, 10E6, 10E8, 10E9, 10E11, 10F1, 10F2, 10F3, 
10F4, 10F8, 10F9, 10F12, 10G6, 10G8, 10G9, 10G11, 10H6, 10H9, 11A2, 
11A3, 11A4, 11A7, 11A10, 11A11, 11A12, 11B3, 11B8, 11B9, 11C1, 
11C10, 11D3, 11D5, 11D6, 11D10, 11E2, 11E4, 11E5, 11E7, 11E10, 11F2, 
11F4, 11F8, 11F11, 11G11, 11H1, 11H2, 11H4, 11H5, 11H6, 11H8, 12A4, 
12A6, 12A9, 12A11, 12B4, 12B7, 12C1, 12C3, 12D7, 12D11, 12E1, 12E5, 
12F1, 12F2, 12F3, 12F5, 12F6, 12F7, 12F8, 12G2, 12G4, 12G5, 12G6, 
12G11, 12H1, 12H3, 12H6, 12H12, 13A1, 13A11, 13B1, 13B3, 13B10, 
13B11, 13C7, 13C11, 13D4, 13D7, 13D9, 13D10, 13D11, 13E3, 13E4, 
13E8, 13F9, 13F10, 13G6, 13G8, 13H6, 14A2, 14A10, 14A11, 14B2, 
14B4, 14B10, 14C3, 14C7, 14C11, 14D2, 14D3, 14D4, 14D7, 14D9, 
14D10, 14E1, 14E8, 14F1, 14F3, 14F9, 14G3, 14G6, 14G7, 14H5, 14H7, 
14H8, 14H10, 15A1, 15A2, 15A12, 15B4, 15B8, 15C2, 15C4, 15C7, 
15C10, 15D1, 15D6, 15D10, 15D12, 15E1, 15E3, 15E9, 15E12, 15F1, 
15F2, 15F3, 15F8, 15G6, 15G9, 15G11, 15H2, 15H3, 15H6, 15H7, 15H10, 
16A1, 16A2, 16A6, 16A12, 16B4, 16B7, 16B12, 16C2, 16C11, 16D1, 
16D7, 16E1, 16E2, 16E5, 16E6, 16E7, 16F3, 16F4, 16F5, 16F7, 16F9, 
16F10, 16G1, 16G3, 16G4, 16G7, 16G9, 16H2, 16H4, 16H11, 17A5, 
17A11, 17B6, 17B7, 17B9, 17C7, 17D5, 17D9, 17E3, 17E5, 17E9, 17E10, 
17F5, 17F6, 17G10, 17H6, 18A2, 18A4, 18A7, 18A12, 18B1, 18B2, 
18B7, 18B9, 18B10, 18B12, 18C2, 18C6, 18D1, 18D2, 18E6, 18E7, 
18E12, 18F1, 18F11, 18F12, 18G1, 18G3, 18G6, 18G8, 18G10, 18H4, 
18H5, 18H6, 18H7, 18H8, 18H10, 19B4, 19C2, 19C3, 19C4, 19C9, 19D12, 
19E5, 19E7, 19E8, 19E9, 19E12, 19F8, 19F9, 19G2, 19G5, 19G8, 19H2, 
19H3, 19H8, 19H9, 20A1, 20A8, 20A11, 20B1, 20B2, 20B12, 20C1, 
20C6, 20C10, 20D2, 20D4, 20D5, 20D7, 20D10, 20D11, 20D12, 20E4, 
20E9, 20F6, 20F9, 20G3, 20G6, 20H12, 21B1, 21B6, 21B10, 21C3, 21C7, 
21C12, 21D4, 21D6, 21E4, 21F4, 21F5, 21G7, 21H1, 22A4, 22A6, 22A9, 
22B5, 22B8, 22B11, 22B12, 22C4, 22D4, 22D8, 22D9, 22D10, 22E1, 
22E2, 22E10, 22E11, 22E12, 22F2, 22F3, 22F10, 22F11, 22G1, 22G2, 
22G3, 22G7, 22G12, 23A3, 23A4, 23A6, 23B2, 23B3, 23B4, 23B7, 23C7, 
23C9, 23D1, 23D4, 23E3, 23E6, 23E9, 23E11, 23E12, 23F12, 23G1, 23G3, 
23G12, 23H2, 23H4, 23H8, 24A8, 24B5, 24B6, 24B7, 24B8, 24B10, 24C1, 
24C5, 24C11, 24D1, 24D2, 24D3, 24D4, 24E1, 24E7, 24E10, 24E11, 24F6, 
24G4, 24G5, 24H3, 24H4

EW YAC clones containing rDNA sequences
1E2, 1E3, 1B8, 3C12, 3D9, 3G6, 4E4, 5D10, 6C9, 6D2, 6F1, 6F11, 6H2, 
8A12, 8F6, 10A3, 10B1, 10C1, 10G7, 10G10, 11B7, 11C8, 11H11, 12A6, 
12A8, 12F9, 13D8, 14C8, 14H11, 15G4, 16A12, 16F3, 17D3, 17E8, 18C4, 
18D6, 18G1, 19H4, 19H12, 20B2, 20G7, 20H9, 21A11, 21D5, 21F7, 22B5, 
22H3, 23A2, 23B11, 23F8, 23H8

EG YAC clones containing rDNA sequences
1A8, 1B3, 1C2, 1C3, 1C12, 1D4, 1E4, 1E7, 1E8, 1E9, 1E10, 1F1, 1F2, 
1F8, 1F9, 1G1, 1G2, 1G6, 1H5, 1H6, 1H7, 2A3, 2A7, 2B4, 2B7, 2C3, 2D2, 
2D5, 2D6, 2E7, 2E8, 2E9, 2E11, 2F5, 2F6, 2F7, 2F9, 2F11, 2G5, 2G8, 2G9, 
2G10, 2H5, 2H12, 3A1, 3A3, 3A6, 3A8, 3B9, 3B10, 3C9, 3D1, 3E1, 3F4, 
3F6, 3F8, 3F12, 3G1, 3G4, 3G9, 3H9, 4A11, 4B1, 4B2, 4B3, 4B4, 4B5, 
4B12, 4C2, 4C6, 4C11, 4D10, 4D11, 4D12, 4F9, 4G2, 4G9, 4H8, 5B2, 5B5, 
5C11, 5D8, 5D11, 5E9, 5F9, 5H12, 6A4, 6A5, 6A7, 6B8, 6B9, 6B11, 
6B12, 6C2, 6D1, 6D3, 6D10, 6E4, 6E6, 6F9, 6G5, 6H7, 6H11, 7B1, 7B8, 
7C9, 7D1, 7D10, 7G2, 7G6, 7G12, 7H2, 7H4, 7H11, 7H12, 8B4, 8B12, 
8C7, 8C9, 8D3, 8E6, 8E7, 8E8, 8F2, 8F7, 8F8, 8F10, 8F12, 8G2, 8H6, 8H7, 
8H9, 8H10, 8H11, 9A7, 9A8, 9B5, 9C12, 9D4, 9E2, 9E4, 9F1, 9G6, 9H6, 
9H11, 10A2, 10A7, 10A8, 10B2, 10C1, 10C2, 10D4, 10D6, 10D7, 10D8, 
10E1, 10E10, 10F2, 10G3, 10G8, 10G9, 10H4, 10H12, 11B3, 11B4, 11B5, 
11B12, 11C2, 11D1, 11D2, 11D4, 11D5, 11D6, 11D7, 11D9, 11E1, 11E5, 
11E6, 11G8, 11H9, 12A4, 12A7, 12A10, 12B4, 12B9, 12C3, 12C7, 12E1, 
12E3, 12F1, 12F4, 12F7, 12G8, 12G12, 13B10, 13D5, 13D6, 13F1, 13F11, 
13H9, 13H11, 13H12, 14A10, 14A11, 14B6, 14B10, 14C3, 14C4, 14C8, 
14F9, 14G2, 14G5, 14G12, 14H8, 15A3, 15A11, 15B1, 15B3, 15B5, 
15B11, 15C2, 15C6, 15C7, 15C10, 15D1, 15E1, 15E3, 15F3, 15F8, 15G6, 
15G7, 15G11, 15H3, 15H7, 16A1, 16B7, 16C2, 16C10, 16D10, 16E1, 
16E7, 16E8, 16E9, 16E12, 16F11, 16F12, 16G2, 16G7, 16H4, 16H11, 
17A3, 17A11, 17B3, 17D3, 17E9, 17G2, 17G10, 17H7, 18A2, 18A12, 
18B2, 18B4, 18B8, 18C2, 18D2, 18D4, 18D5, 18D7, 18D12, 18E2, 18G6, 
18G8, 18H5, 18H6, 18H7, 19A1, 19A5, 19B4, 19C1, 19D12, 19E10, 
19E11, 19G3, 19G5, 19G8, 19H1, 19H3, 20A4, 20B2, 20B4, 20B6, 20B10, 
20C8, 20C9, 20E4, 20F2, 20G6, 20G9, 20G12, 20H9, 20H10, 20H12, 
21A7, 21C2, 21C10, 21C11, 21D6, 21D12, 21E1, 21E9, 21F7, 21G10, 
21H3, 22A1, 22A7, 22B2, 22B11, 22D8, 22E3, 22E11, 22F3, 22F5, 22F6, 
22F10, 22F12, 22H4, 22H5, 22H12, 23A3, 23C4, 23C8, 23D5, 23E6, 
23F4, 23F5, 23F11, 23F12, 23G4, 23G12, 23H10, 24A3, 24B12, 24C1, 
24C12, 24D1, 24D4, 24D8, 24E7, 24E8, 24E10, 24E11, 24F6, 24G1, 24H6

EW YAC clones containing the paracentromeric repeat sequences
1D5, 1D8, 1H3, 2A3, 2A6, 2D9, 2E12, 2F1, 2F12, 3A6, 3B1, 3B5, 3B9, 
3C1, 3D8, 3E2, 3F1, 3F5, 3F6, 3F12, 3G4, 3G8, 3G11, 3H11, 4B2, 4B12, 
4E11, 4H2, 5C2, 5D3, 5F3, 5F4, 5F9, 5H1, 6B4, 6B10, 6C1, 6C6, 6C10, 
6C12, 6E6, 6G1, 6G6, 6G12, 6H12, 7A4, 7B10, 7B4, 7B11, 7D8, 7E11, 
7F6, 8A7, 8B3, 8B11, 8B12, 8C1, 8F3, 8F11, 8G1, 8G4, 8H9, 9A5, 9A7, 
9D1, 9D8, 9D11, 9E6, 9E11, 9G1, 9G9, 9H11, 10B11, 10D12, 10E2, 10E8, 
10H8, 11A3, 11B10, 11D4, 11E11, 11F5, 11H6, 11H7, 12A3, 12A5, 
12A10, 12B6, 12C2, 12D7, 12F7, 12F12, 12G3, 12G8, 12H3, 12H7, 
13A10, 13B5, 13B7, 13B11, 13F10, 13G2, 13G12, 13H1, 13H2, 14A10, 
14B1, 14C1, 14C5, 14C7, 14C10, 14D9, 14E2, 14F7, 15B8, 15C2, 15C5, 
15C9, 16B5, 16D7, 16D9, 16H5, 17A6, 17C4, 17D2, 17D10, 17D11, 17E4, 
17E10, 17F12, 17G1, 17G2, 17H1, 17H10, 18A2, 18B4, 18B9, 18C5, 
18C11, 18D1, 18D9, 18F4, 18F9, 18G4, 18H6, 19A2, 19B4, 19E6, 19F1, 
19G2, 19G8, 19G12, 20A9, 20B2, 20B5, 20C1, 20D10, 20D11, 20E1, 
20E2, 20F5, 21A10, 21B6, 21B8, 21C10, 21D2, 21D3, 21D6, 21E12, 
21F3, 21F6, 21F9, 21G1, 21H5, 22A5, 22B8, 22C1, 22E1, 22H7, 22H10, 
23E3, 23E7, 23G1, 23G5, 23H9, 23H12

EG YAC clones containing the paracentromeric repeat sequences
2A11, 2B6, 2C6, 2D5, 2E6, 5F4, 6A8, 7E10, 8C9, 8F11, 9A4, 9B3, 10D12, 
10F5, 10F10, 10H10, 11B11, 12C9, 12E5, 12G1, 12G6, 12H2, 14A8, 
14G10, 16E6, 17C8, 17C9, 17G2, 18C12, 18D5, 19E6, 20D7, 20E12, 
23A12, 23B2, 23H5, 23H6






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