PMID- 19207213
OWN - NLM
STAT- MEDLINE
DCOM- 20090902
LR  - 20221207
IS  - 1365-313X (Electronic)
IS  - 0960-7412 (Linking)
VI  - 58
IP  - 5
DP  - 2009 Jun
TI  - Solanum lycopersicum cv. Heinz 1706 chromosome 6: distribution and abundance of 
      genes and retrotransposable elements.
PG  - 857-69
LID - 10.1111/j.1365-313X.2009.03822.x [doi]
AB  - We studied the physical and genetic organization of chromosome 6 of tomato 
      (Solanum lycopersicum) cv. Heinz 1706 by combining bacterial artificial 
      chromosome (BAC) sequence analysis, high-information-content fingerprinting, 
      genetic analysis, and BAC-fluorescent in situ hybridization (FISH) mapping data. 
      The chromosome positions of 81 anchored seed and extension BACs corresponded in 
      most cases with the linear marker order on the high-density EXPEN 2000 linkage 
      map. We assembled 25 BAC contigs and eight singleton BACs spanning 2.0 Mb of the 
      short-arm euchromatin, 1.8 Mb of the pericentromeric heterochromatin and 6.9 Mb 
      of the long-arm euchromatin. Sequence data were combined with their corresponding 
      genetic and pachytene chromosome positions into an integrated map that covers 
      approximately a third of the chromosome 6 euchromatin and a small part of the 
      pericentromeric heterochromatin. We then compared physical length (Mb), genetic 
      (cM) and chromosome distances (microm) for determining gap sizes between contigs, 
      revealing relative hot and cold spots of recombination. Through sequence 
      annotation we identified several clusters of functionally related genes and an 
      uneven distribution of both gene and repeat sequences between heterochromatin and 
      euchromatin domains. Although a greater number of the non-transposon genes were 
      located in the euchromatin, the highly repetitive (22.4%) pericentromeric 
      heterochromatin displayed an unexpectedly high gene content of one gene per 36.7 
      kb. Surprisingly, the short-arm euchromatin was relatively rich in repeats as 
      well, with a repeat content of 13.4%, yet the ratio of Ty3/Gypsy and Ty1/Copia 
      retrotransposable elements across the chromosome clearly distinguished 
      euchromatin (2:3) from heterochromatin (3:2).
FAU - Peters, Sander A
AU  - Peters SA
AD  - Wageningen University Centre for Biosystems Genomics, Droevendaalsesteeg 1 6708 
      PB Wageningen, The Netherlands. sander.peters@wur.nl
FAU - Datema, Erwin
AU  - Datema E
FAU - Szinay, Dora
AU  - Szinay D
FAU - van Staveren, Marjo J
AU  - van Staveren MJ
FAU - Schijlen, Elio G W M
AU  - Schijlen EG
FAU - van Haarst, Jan C
AU  - van Haarst JC
FAU - Hesselink, Thamara
AU  - Hesselink T
FAU - Abma-Henkens, Marleen H C
AU  - Abma-Henkens MH
FAU - Bai, Yuling
AU  - Bai Y
FAU - de Jong, Hans
AU  - de Jong H
FAU - Stiekema, Willem J
AU  - Stiekema WJ
FAU - Klein Lankhorst, Rene M
AU  - Klein Lankhorst RM
FAU - van Ham, Roeland C H J
AU  - van Ham RC
LA  - eng
PT  - Journal Article
PT  - Research Support, Non-U.S. Gov't
DEP - 20090204
PL  - England
TA  - Plant J
JT  - The Plant journal : for cell and molecular biology
JID - 9207397
RN  - 0 (DNA, Plant)
RN  - 0 (Euchromatin)
RN  - 0 (Heterochromatin)
RN  - 0 (Retroelements)
SB  - IM
MH  - Chromosome Walking
MH  - Chromosomes, Artificial, Bacterial
MH  - Chromosomes, Plant/*genetics
MH  - Contig Mapping
MH  - DNA Fingerprinting
MH  - DNA, Plant/genetics
MH  - Euchromatin
MH  - *Genes, Plant
MH  - Heterochromatin
MH  - In Situ Hybridization, Fluorescence
MH  - Solanum lycopersicum/*genetics
MH  - *Retroelements
MH  - Sequence Analysis, DNA
EDAT- 2009/02/12 09:00
MHDA- 2009/09/03 06:00
CRDT- 2009/02/12 09:00
PHST- 2009/02/12 09:00 [entrez]
PHST- 2009/02/12 09:00 [pubmed]
PHST- 2009/09/03 06:00 [medline]
AID - TPJ3822 [pii]
AID - 10.1111/j.1365-313X.2009.03822.x [doi]
PST - ppublish
SO  - Plant J. 2009 Jun;58(5):857-69. doi: 10.1111/j.1365-313X.2009.03822.x. Epub 2009 
      Feb 4.