Reconstruction of monocotelydoneous proto-chromosomes reveals faster evolution in plants than in animals

Abstract

Paleogenomics seeks to reconstruct ancestral genomes from the genes of today's species. The characterization of paleo-duplications represented by 11,737 orthologs and 4,382 paralogs identified in five species belonging to three of the agronomically most important subfamilies of grasses, that is, Ehrhartoideae (rice) Panicoideae (sorghum, maize), and Pooideae (wheat, barley), permitted us to propose a model for an ancestral genome with a minimal size of 33.6 Mb structured in five proto-chromosomes containing at least 9,138 predicted proto-genes. It appears that only four major evolutionary shuffling events (␣, ␤, ␥, and ␦) explain the divergence of these five cereal genomes during their evolution from a common paleo-ancestor. Comparative analysis of ancestral gene function with rice as a reference indicated that five categories of genes were preferentially modified during evolution. Furthermore, alignments between the five grass proto-chromosomes and the recently identified seven eudicot proto-chromosomes indicated that additional very active episodes of genome rearrangements and gene mobility occurred during angiosperm evolution. If one compares the pace of primate evolution of 90 million years (233 species) to 60 million years of the Poaceae (10,000 species), change in chromosome structure through speciation has accelerated significantly in plants.grasses ͉ paleogenomics P aleogenomics, the study of ancestral genome structures, allows the identification and characterization of mechanisms (e.g., duplications, translocations, and inversions) that have shaped genome species during their evolution and provides a framework to better integrate results from genetics, genomics, and comparative analyses. Studies of fossils and lower taxa organisms [Neanderthal (1), Echinoderms (2), Mammoth (3), Sponge (4), and Moss (5)] have yielded unprecedented information on the evolution of animal species and the relationships between them. When fossil DNA is not available, paleogenomics can be performed through largescale comparative analyses of actual species and through ancestor modeling.In silico colinearity studies and ancestral genome reconstruction in mammals have been facilitated by a generally moderate reshuffling of chromosomal segments since their divergence from a common ancestor Ϸ130 million years ago (mya) (6-9). Recently, Nakatani et al. (10) provided an integrated view of vertebrate paleogenomics with an ancestor of 10 to 13 proto-chromosomes. In contrast to mammals, paleogenomics has been poorly investigated in plants as angiosperm species have undergone serial whole genome or segmental duplications, diploidization, small-scale rearrangements (translocations, gene conversions), and gene copying events that make comparative studies between and within the monocotyledon (mainly grasses) and eudicot families very challenging. For the eudicots, two scenarios based on comparisons between the grape, Arabidopsis thaliana, and poplar genome sequences have been proposed recently. In the first one, the eudicots were proposed t...

The genome of Eucalyptus grandis

“…Genome-wide gene expression profiling was performed using Illumina RNA-seq analysis of seven developing tissues from E. grandis. We identified whole-genome duplications using an approach 45,46 based on paralogue-and orthologue-specific comparisons of the 36,376 predicted protein-coding genes and further refined the estimated age of the lineage-specific WGD event using a phylogenetic dating approach 13 . Genome synteny between E. grandis and P. trichocarpa was evaluated using the VISTA pipeline infrastructure 47,48 .…”

“…Independent intraspecific (that is, paralogue) and interspecific (that is, orthologue) comparisons were necessary to infer gene relationships between Eucalyptus and the other rosid genomes. We applied a robust and direct approach 45,46 allowing the characterization of genome duplications by aligning the available genes (36,376) on themselves with stringent alignment criteria and statistical validation.…”

A high-quality carrot genome assembly provides new insights into carotenoid accumulation and asterid genome evolution

“…This WGD is likely shared with lettuce and may represent a whole-genome triplication (WGT) recently described in lettuce that is basal to Asteraceae 31 . Using methods previously described 32,33 , we reconstructed the carrot paleopolyploidy history. Carrot chromosomal blocks descending from the seven ancestral core eudicot chromosomes were highly fragmented and dispersed along the nine carrot chromosomes (Fig.…”

Genome-Wide Characterization of the HD-ZIP IV Transcription Factor Family in Maize: Preferential Expression in the Epidermis

“…Cereal genome evolution has been marked by two whole genome duplications. The first concerns all cereals and took place approximately 90 million years ago in the common ancestor of rice, sorghum, and maize, while the second occurred approximately 12 million years ago specifically in the lineage leading to maize (Salse et al, 2009). As a consequence of the second duplication event, approximately 25% of the genes in the maize genome possess closely related paralogs (Schnable et al, 2009).…”