Tropical Plant Biology

, Volume 2, Issue 1, pp 51–62 | Cite as

Duplication and Divergence of Grass Genomes: Integrating the Chloridoids

Article

Abstract

Expressed Sequence Tags from a variety of plant species have been useful for comparative genomics. The evolution of the Chloridoideae subfamily, previously lacking sequence data, was clarified by analysis of Bermudagrass (Cynodon dactylon) ESTs generated from a normalized cDNA library. Using EST collections, we generated unigene sets and analyzed them to further elucidate the evolutionary history of grass subfamilies. A total of eight grasses (C. dactylon, Sorghum bicolor, Saccharum officinarum, Zea mays, Oryza sativa, Hordeum vulgare, Festuca arundinacea, and Triticum aestivum) in four subfamilies and five tribes were analyzed using two different approaches—synonymous substitution rates (Ks) and phylogenetic trees. Ks distributions of paralogous genes suggested several duplication events in C. dactylon, S. bicolor, H. vulgare, and T. aestivum. Phylogenetic analysis with the unigene sets indicated that the analyzed grasses diverged from a common ancestor after a shared ancient polyploidization (ca. 50.0 ~ 67.8 million years ago). Ks distributions of orthologous genes suggested that the Chloridoideae and Panicoideae subfamilies diverged about 34.6 ~ 38.5 million years ago. With the evidence described in this study, we found traces of genomic changes in some grass subfamilies after the divergence of the PACC and BEP clades as well as divergence of Chloridoideae subfamily.

Keywords

Cynodon dactylon Bermudagrass Chloridoideae Grass family Synonymous substitution rate Phylogenetic tree Expressed sequence tags 

Supplementary material

12042_2009_9028_MOESM1_ESM.doc (34 kb)
Supplementary Table 1 All possible secondary Ks peaks formed by paralogous pairs for the analyzed grasses. Note that Ks values are converted to time (T = Ks / 2λ) using λ = 6.5 × 10−9 [10]. (DOC 34 kb)
12042_2009_9028_MOESM2_ESM.doc (40 kb)
Supplementary Table 2 Ks values representing speciation events of grass subfamilies by the analysis of orthologous pairs between grasses. Note that Ks values are converted to time (T = Ks / 2λ) using λ = 6.5 × 10−9 [10]. (DOC 40 kb)
12042_2009_9028_MOESM3_ESM.doc (38 kb)
Supplementary Table 3 Comparison of average Ks values for each rice duplication block and its corresponding time in MYA (million years ago). Note that Ks values are converted to time (T = Ks / 2λ) using λ = 6.5 × 10−9 [10]. Ks values with the same letter are not significantly different according to Student-Newman-Keuls (SNK) test (P < 0.01). (DOC 37 kb)
12042_2009_9028_MOESM4_ESM.doc (40 kb)
Supplementary Table 4 Pairwise comparisons of internal tree ratio for all the blocks between each species tested. Each number indicates P-value based on the 99% confidence limit of a binomial distribution (Note that numbers in bold indicate that the frequencies of internal trees for two species are not significantly different at the 99% confident level). (DOC 40 kb)

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Copyright information

© Springer-Verlag 2009

Authors and Affiliations

  • Changsoo Kim
    • 1
  • Haibao Tang
    • 1
  • Andrew H. Paterson
    • 1
  1. 1.Plant Genome Mapping LabaratoryUniversity of GeorgiaAthensUSA

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