Syntenic Relationships between Medicago truncatulaand Arabidopsis Reveal Extensive Divergence of Genome Organization,

Abstract

Arabidopsis and Medicago truncatula represent sister clades within the dicot subclass Rosidae. We used genetic map-based and bacterial artificial chromosome sequence-based approaches to estimate the level of synteny between the genomes of these model plant species. Mapping of 82 tentative orthologous gene pairs reveals a lack of extended macrosynteny between the two genomes, although marker collinearity is frequently observed over small genetic intervals. Divergence estimates based on non-synonymous nucleotide substitutions suggest that a majority of the genes under analysis have experienced duplication in Arabidopsis subsequent to divergence of the two genomes, potentially confounding synteny analysis. Moreover, in cases of localized synteny, genetically linked loci in M. truncatula often share multiple points of synteny with Arabidopsis; this latter observation is consistent with the large number of segmental duplications that compose the Arabidopsis genome. More detailed analysis, based on complete sequencing and annotation of three M. truncatula bacterial artificial chromosome contigs suggests that the two genomes are related by networks of microsynteny that are often highly degenerate. In some cases, the erosion of microsynteny could be ascribed to the selective gene loss from duplicated loci, whereas in other cases, it is due to the absence of close homologs of M. truncatula genes in Arabidopsis.Comparative genetic mapping has revealed a high degree of conservation in genome structure among closely related plant species, in terms of gene content, order, and function (Paterson et al., 1995(Paterson et al., , 2000Gale and Devos, 1998; Bennetzen, 2000). The bestdocumented cases of genome conservation are from the grass family (Poaceae), where rice (Oryza sativa) with its small genome has been selected as a nodal species to study the economically important cereal crops including corn (Zea mays), sorghum (Sorghum bicolor), wheat (Triticum aestivum), and barley (Hordeum vulgare;Devos and Gale, 2000). Extensive macrosynteny has also been observed within the Solanaceae (Tanksley et al., 1992), the Brassicaceae (Kowalski et al., 1994;Lagercrantz and Lydiate, 1996;Lagercrantz, 1998 In contrast to within-family comparisons, genome structure appears to be less conserved between distantly related species, where collinearity may only be apparent over small chromosomal intervals (Paterson et al., 1996(Paterson et al., , 2000. Paterson and colleagues have suggested that deciphering such relationships will require a very high density of genetic markers for comparison (Paterson et al., 2000). More recent analyses, however, reveal that plant genomes possess a dynamic microstructure (Ku et al., 2000;Vision et al., 2000) that may preclude establishing global relationships between distantly related plant species based on genetic map data alone. In lieu of whole-genome sequence data, an intermediate strategy involving complete sequencing and annotation of bacterial artificial chromosome (BAC)-size clones has been adopted by seve...

Estimating genome conservation between crop and model legume species

“…Factors contributing to this situation are chromosomal rearrangements that result in the progressive fractionation of the genome into increasingly smaller conserved segments and the high frequency of gene loss from within-genome segmental duplications (e.g., refs. 23,24,32,33). The present analysis suggests that the same factors that contribute to divergence between other plant families are also operative within the legumes.…”

Bridging Model and Crop Legumes through Comparative Genomics

“…Grant et al (2000) reported substantial macrosynteny between soybean and Arabidopsis, while comparison between M. truncatula and Arabidopsis revealed a lack of extended macrosynteny between the two genomes (Zhu et al, 2003). Nevertheless, it is obvious that synteny is frequently maintained over small chromosomal segments.…”

“…And recently, segmental duplications within the soybean genome were visualized by fluorescence in situ hybridization of BACs (Pagel et al, 2004). Segmental duplications also were identified in the M. truncatula and L. japonicus genomes through high-throughput genome sequencing (Zhu et al, 2003;N. Young, personal communication).…”

Sequencing and Comparative Analysis of a Conserved Syntenic Segment in the Solanaceae

“…Comparative genomic analyses of sequenced clades have, among other things, allowed for the identification of new genes, regulatory elements, noncoding RNAs, and conserved sequences of unknown function (e.g., Guigó et al 2003;Kellis et al 2003;Bejerano et al 2004;Siepel et al 2007;Stark et al 2007 scrambled with respect to the others by millions of years of rearrangement, duplication, insertion, and deletion, further complicating comparative analyses. Consequently, with a few exceptions (Inada et al 2003;Ma and Bennetzen 2004;Haberer et al 2006;Freeling et al 2007;Thomas et al 2007), comparative genomic studies of plants have largely focused on content of proteincoding genes and repetitive elements (Ku et al 2000;Quiros et al 2001;Song et al 2002;Ilic et al 2003), rather than on the kind of detailed analysis of orthologous functional elements that has been possible in animals.Moreover, comparative studies of plant genomes so far have largely dealt with species that have experienced recent whole-genome duplications (WGDs) (Ku et al 2000;Quiros et al 2001;Song et al 2002;Ilic et al 2003;Zhu et al 2003). These studies have revealed striking differences between species in genome organization, perhaps induced by the massive genetic redundancy created by WGD ( .…”