A physical map of the highly heterozygous Populus genome: integration with the genome sequence and genetic map and analysis of haplotype variation

Abstract

As part of a larger project to sequence the Populus genome and generate genomic resources for this emerging model tree, we constructed a physical map of the Populus genome, representing one of the few such maps of an undomesticated, highly heterozygous plant species. The physical map, consisting of 2802 contigs, was constructed from fingerprinted bacterial artificial chromosome (BAC) clones. The map represents approximately 9.4-fold coverage of the Populus genome, which has been estimated from the genome sequence assembly to be 485 +/- 10 Mb in size. BAC ends were sequenced to assist long-range assembly of whole-genome shotgun sequence scaffolds and to anchor the physical map to the genome sequence. Simple sequence repeat-based markers were derived from the end sequences and used to initiate integration of the BAC and genetic maps. A total of 2411 physical map contigs, representing 97% of all clones assigned to contigs, were aligned to the sequence assembly (JGI Populus trichocarpa, version 1.0). These alignments represent a total coverage of 384 Mb (79%) of the entire poplar sequence assembly and 295 Mb (96%) of linkage group sequence assemblies. A striking result of the physical map contig alignments to the sequence assembly was the co-localization of multiple contigs across numerous regions of the 19 linkage groups. Targeted sequencing of BAC clones and genetic analysis in a small number of representative regions showed that these co-aligning contigs represent distinct haplotypes in the heterozygous individual sequenced, and revealed the nature of these haplotype sequence differences.

A physical map of the Chinese chestnut (Castanea mollissima) genome and its integration with the genetic map

“…Consequently, BACs from variable regions of separate parental haplotypes, while often still overlapping enough to assemble into the same contig, would generate extra restriction fragments that appear to not be nonoverlapping and therefore contribute to the expanded size estimate from the physical contig assembly. Similar expansion in physical size estimated from physical maps was also reported from other heterozygous plant species such as grapevine (Moroldo et al 2008) and poplar (Kelleher et al 2007). Results from this physical map appear to indicate a relatively complex heterozygous genome.…”

Genome structure and emerging evidence of an incipient sex chromosome in Populus

“…Four sources of SSR primers were used for map construction in this study: ORNL primers (O_), PMGC primers (P_), WPMS primers (W_) (Smulders et al 2001), and GCPM primers (G_). The majority of the G_ SSR primers were designed based on end-sequences of BAC contigs used for Populus physical map construction (Kelleher et al 2007). The microsatellite locations on scaffold 117 were identified using the Sputnik program (C. Abajian, University of Washington, Seattle).…”

Genetic Biodiversity and Phylogenetic Studies in Poplar by Means of the Metallothionein Multigene Family

“…The position along the Populus genome of the six genes of the MT family may support the indications provided by Brunner and co-worker (2000) regarding the genome duplication event occurred in Populus during the last 60 millions years. Here, it should be noticed that, in contrast to Arabidopsis, the genome of Populus has not been truncated (Kelleher et al, 2007;Tuskan et al, 2006), which means that for most of the genes still two copies are present in poplar genome. Coherently, we confirm that two isoforms (commonly indicated as "a" and "b") are present in the P. trichocarpa genome for each of the three MT types.This observation is very interesting but contributes in complicating the possible evolutionary pattern of this multigene family.…”