2011;43:109–16.

Ideses

b Among these, 75 are shared by three E. albertii strains. Genome size diversity and evolution in land plants. Here, we sequenced the genome of 29 E. albertii strains (3 complete and 26 draft sequences) isolated from multiple sources and performed intraspecies and intragenus genomic comparisons. Huys statement and CAS Article Google Scholar Kenan-Eichler M, Leshkowitz D, Tal L, Noor E, Melamed-Bessudo C, Feldman M, et al. 2 ). Contigs or scaffolds that contained locus of enterocyte effacement (LEE) core regions were extracted from each of the 30 E. albertii draft genome sequences and genes in the LEE core region were manually annotated using the IMC-GE software.

2015;32:1063–71. 2012 ; Murakami et al.

Brief Funct Genomics.

However, most changes in PHAS loci are likely to be spontaneous events, independent of polyploidy events. Leitch IJ, Leitch AR. TM-1) provides a resource for fiber improvement. .

Chalhoub B, Denoeud F, Liu S, Parkin IA, Tang H, Wang X, et al.

Ancestral polyploidy in seed plants and angiosperms. In these strains, eivJ has not been disrupted ( fig. These banks contain domesticated crop relatives that are adapted to grow under varied environmental conditions and that harbor untapped reservoirs of traits that can be used for crop improvement. The discovery of a three‐line hybrid breeding system was successful in breaking the longstanding yield barrier.

Reference genomes can now be used by germplasm banks worldwide. PubMed  This fundamental genomic understanding is likely to be valuable for crop improvement.

Gao D, Li Y, Kim KD, Abernathy B, Jackson SA. Woodhouse MR, Cheng F, Pires JC, Lisch D, Freeling M, Wang X. G 2014;19:91–8.

L

Koh J, Chen S, Zhu N, Yu F, Soltis PS, Soltis DE. 2010;28:951–6.

Maeda Additionally, ANI values between the three E. albertii and the strains of Escherichia cryptic clades (C-I, C-III, C-IV, and C-V) were 89.2–89.4%, 89.4–89.7%, 89.5–89.7%, and 89.0–89.5%, respectively. Berlin: Springer; 2012. 1994;137:891–4. This perspective might be fundamental to much of plant biology, as many different processes, be they metabolic, physiological or ecological, are specified by the size and functional diversification of contemporary multigene family structures, gene expression patterns and the systems biology context of various genomic elements.

Shiga toxin-producing strains have also been identified.

2011;473:97–100. Albert VA, Barbazuk WB, Der JP, Leebens-Mack J, Ma H, Palmer JD, et al.

2013;342:1241089. Polashock J, Zelzion E, Fajardo D, Zalapa J, Georgi L, Bhattacharya D, et al. Pigeonpea is an important pulse crop of the semi‐arid tropics. 2014 ), the genomic features, repertoire of virulence factors, and virulence mechanisms of E. albertii have not yet been characterized. Rapid DNA loss as a counterbalance to genome expansion through retrotransposon proliferation in plants.

2004;101:12404–10.

PT However, the quality of these genome assemblies varies considerably, reflecting a transition from map-based Sanger sequencing (e.g., [35, 51]) to second-generation, low-cost, short-read, whole-genome shotgun sequencing that generally yields ‘gene space’ assemblies. The answer to this question lies in the surprisingly varied spectrum of genomic responses to polyploidy [11–19], which range in timing from those accompanying the initial genome merging and doubling, to others operating over millions of years. In: Pontes O, Jin H, editors. Hayashi Mayer KF, Rogers J, Doležel J, Pozniak C, Eversole K, Feuillet C, et al.

After incubating for 20 h at the same temperature used for precultivation, the motilities of each strain were examined. Hirakawa H, Shirasawa K, Miyatake K, Nunome T, Negoro S, Ohyama A, et al.

Google Scholar. ETT2 is a cryptic second T3SS in the E. coli / Shigella lineage ( Hayashi et al. Moreover, the effect of TEs on presence–absence variation and on the evolution of new genes (with Pack-MULE [57] or TRIM [58] TEs being examples of the latter effect) within a genus or species might not be captured in a single genome sequence. 2001;19:636–9. 2012; 15 (2): 122–130. Conant GC, Birchler JA, Pires JC. D

The genome of the pear (Pyrus bretschneideri Rehd.). Hirsch CN, Foerster JM, Johnson JM, Sekhon RS, Muttoni G, Vaillancourt B, et al. Among these clusters, 1,345 were highly conserved in all Escherichia strains analyzed, and thus likely represent the core CDSs of the genus Escherichia .

Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. We also identified 95 CDSs that were conserved in 44 E. coli strains but not in any E. albertii strains ( supplementary table S6 , Supplementary Material online). Plant Mol Biol. Plant Cell. 2010;42:1027–30.

S1 B , Supplementary Material online) as recently reported by Luo et al. Transposable elements: powerful contributors to angiosperm evolution and diversity. Several recent reviews have highlighted the diversity of small RNAs and their ability to function in trans to direct or communicate their silencing effects across members of gene or TE families [66, 67]. E A model of a hypothetical allopolyploid genome derived from two progenitor diploid genomes (A and B) is shown in the figure. . 3A ). Nikaido Nat Genet. 2010;42:833–9. Wu J, Wang Z, Shi Z, Zhang S, Ming R, Zhu S, et al. Wendel JF, Doyle JJ. Mol Ecol. Soltis DE, Albert VA, Leebens-Mack J, Bell CD, Paterson AH, Zheng C, et al. Gene organizations of genomic loci encoding flagellar biosynthesis- and chemotaxis-related genes are shown. Leach An exciting area for future research is the exploration of the connections between the short-term and long-term responses to WGD and the interconnections of these responses with TE proliferation and small RNA evolution, both in terms of molecular mechanisms and implications for natural selection. Although this pattern is now known, the underlying causes of TE proliferation are far less well understood. 2010 ). Plant Cell. Kawakami T, Strakosh SC, Zhen Y, Ungerer MC. This exclusion is an important consideration not just for the sake of genome completeness per se, but also because many of these repeats are the primary targets of epigenetic/chromatin remodeling pathways that often affect the expression or structure of genes [39, 52]. 2013;22:1503–17. Article  The LEE pathogenicity island (∼35 kb in length) encodes a T3SS machinery, chaperones, and several effectors ( Wong et al.

2009 ; Darmon and Leach 2014 ), the relatively small number of pseudogenes (41–45 genes) in the three E. albertii strains may be partly attributable to the small number of IS elements. 2012 ). 3B ). Curr Opin Plant Biol. Google Scholar. Fractionation mutagenesis and similar consequences of mechanisms removing dispensable or less-expressed DNA in plants. Analyses of LTR-retrotransposon structures reveal recent and rapid genomic DNA loss in rice. DH The implications of this relaxed selection vary among genes and TEs, and among the types of small RNAs that have regulatory roles. 2006;28:240–52. Oliver et al. In our preliminary analysis using strains CB9786 and NIAH_Bird_3, ETT2 gene expression ( eivF and eprH ) was detected by RT-PCR ( supplementary fig. Reference genomes have become highly useful as templates for ‘mapping’ resequencing data from additional accessions, which has led to insights into the structure and history of genetic variation within a crop plant or other species [55].