title: Solanum lycopersicum cv. Heinz 1706 chromosome 6: distribution and abundance of genes and retrotransposable elements.
abstract: 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).
authors.affiliation: Wageningen University Centre for Biosystems Genomics, Droevendaalsesteeg 1 6708 PB Wageningen, The Netherlands. sander.peters@wur.nl
authors.forename: Sander A
authors.initials: SA
authors.lastname: Peters
authors.forename: Erwin
authors.initials: E
authors.lastname: Datema
authors.forename: Dóra
authors.initials: D
authors.lastname: Szinay
authors.forename: Marjo J
authors.initials: MJ
authors.lastname: van Staveren
authors.forename: Elio G W M
authors.initials: EG
authors.lastname: Schijlen
authors.forename: Jan C
authors.initials: JC
authors.lastname: van Haarst
authors.forename: Thamara
authors.initials: T
authors.lastname: Hesselink
authors.forename: Marleen H C
authors.initials: MH
authors.lastname: Abma-Henkens
authors.forename: Yuling
authors.initials: Y
authors.lastname: Bai
authors.forename: Hans
authors.initials: H
authors.lastname: de Jong
authors.forename: Willem J
authors.initials: WJ
authors.lastname: Stiekema
authors.forename: René M
authors.initials: RM
authors.lastname: Klein Lankhorst
authors.forename: Roeland C H J
authors.initials: RC
authors.lastname: van Ham
mesh_terms: D016386:Chromosome Walking; D022202:Chromosomes, Artificial, Bacterial; D032461:Chromosomes, Plant / Q000235:genetics*; D020451:Contig Mapping; D016172:DNA Fingerprinting; D018744:DNA, Plant / Q000235:genetics; D022041:Euchromatin; D017343:Genes, Plant; D006570:Heterochromatin; D017404:In Situ Hybridization, Fluorescence; D018551:Solanum lycopersicum / Q000235:genetics*; D018626:Retroelements; D017422:Sequence Analysis, DNA
chemical_list: D018744:DNA, Plant; D022041:Euchromatin; D006570:Heterochromatin; D018626:Retroelements