Evidence of intense chromosomal shuffling during conifer evolution

Abstract

Although recent advances have been gained on genome evolution in angiosperm lineages, virtually nothing is known about karyotype evolution in the other group of seed plants, the gymnosperms. Here, we used high-density gene-based linkage mapping to compare the karyotype structure of two families of conifers (the most abundant group of gymnosperms) separated around 290 Ma: Pinaceae and Cupressaceae. We propose for the first time a model based on the fusion of 20 ancestral chromosomal blocks that may have shaped the modern karyotpes of Pinaceae (with n = 12) and Cupressaceae (with n = 11). The considerable difference in modern genome organization between these two lineages contrasts strongly with the remarkable level of synteny already reported within the Pinaceae. It also suggests a convergent evolutionary mechanism of chromosomal block shuffling that has shaped the genomes of the spermatophytes.

A high‐resolution reference genetic map positioning 8.8 K genes for the conifer white spruce: structural genomics implications and correspondence with physical distance

“…Inter‐generic synteny between pines and white spruce maps was here supported by 1851 bridges and no significant large‐scale rearrangements were detected in the genome macrostructure (Figure ). The present data confirmed the high level of conservation in genome macrostructure previously reported between pine and spruce (Pavy et al ., ; de Miguel et al ., ) in significantly more detail. The results obtained support the notion that macro‐scale synteny has been maintained in the various spruce and pine taxa since the divergence of the genera ( Picea and Pinus ) well over 100 million years ago (Savard et al ., ).…”

“…The gene sequences of the Pinus spp. composite map (de Miguel et al ., ) were compared to the gene sequences of the P. glauca gene catalogue (Rigault et al ., ). Best pine matches ( tblastx e‐value <10e −40 ) were identified for 2052 genes mapped on P. glauca , which could be used to assess inter‐generic synteny.…”

“…De Miguel et al . () used the gene loci positions from a previous Picea glauca linkage map (Pavy et al ., ) to generate a Pinaceae composite map positioning 6662 gene loci, and identified 513 bridges (orthologous genes based on sequence similarity) between pine and spruce composite maps. We have updated this analysis with a slightly different procedure by comparing their most recent Pinus composite map to the augmented composite map presented herein for white spruce.…”

Linkage and Association Mapping for Two Major Traits Used in the Maritime Pine Breeding Program: Height Growth and Stem Straightness

“…This reference map was produced with the R package LPmerge [49], by de Miguel et al . [28]. For the F2 population, 79% of the 248 mapped SNPs could be localized on the composite map (S1 Table).…”

“…A series of genetic linkage maps have also been produced on the basis of analyses of the cosegregation of these markers in several maritime pine families. A reference genetic map for maritime pine was recently produced, combining information from independent studies [28]. This reference map is a major achievement as it provides a representation of the maritime pine genome, the sequence of which has yet to be published, due to the difficulties involved in generating highly contiguous sequences for conifer genomes [29–31].…”