Comparative sequence and genetic analyses of asparagus BACs reveal no microsynteny with onion or rice

Jakše, Jernej; Telgmann, Alexa; Jung, Christian; Khar, Anil; Melgar, Sergio; Cheung, Foo; Town, Christopher D.; Havey, Michael J.

doi:10.1007/s00122-006-0407-y

Cited by 13 publications

(9 citation statements)

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“…Previous reports found negligible colinearity between onion (Asparagales) and rice (Poales) [38,39]. The Asparagales include a number of economically important plants, such as asparagus, chives, garlic, leeks, onions, and orchids.…”

Section: Resultsmentioning

confidence: 99%

An overview of the Phalaenopsisorchid genome through BAC end sequence analysis

et al. 2011

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BackgroundPhalaenopsis orchids are popular floral crops, and development of new cultivars is economically important to floricultural industries worldwide. Analysis of orchid genes could facilitate orchid improvement. Bacterial artificial chromosome (BAC) end sequences (BESs) can provide the first glimpses into the sequence composition of a novel genome and can yield molecular markers for use in genetic mapping and breeding.ResultsWe used two BAC libraries (constructed using the BamHI and HindIII restriction enzymes) of Phalaenopsis equestris to generate pair-end sequences from 2,920 BAC clones (71.4% and 28.6% from the BamHI and HindIII libraries, respectively), at a success rate of 95.7%. A total of 5,535 BESs were generated, representing 4.5 Mb, or about 0.3% of the Phalaenopsis genome. The trimmed sequences ranged from 123 to 1,397 base pairs (bp) in size, with an average edited read length of 821 bp. When these BESs were subjected to sequence homology searches, it was found that 641 (11.6%) were predicted to represent protein-encoding regions, whereas 1,272 (23.0%) contained repetitive DNA. Most of the repetitive DNA sequences were gypsy- and copia-like retrotransposons (41.9% and 12.8%, respectively), whereas only 10.8% were DNA transposons. Further, 950 potential simple sequence repeats (SSRs) were discovered. Dinucleotides were the most abundant repeat motifs; AT/TA dimer repeats were the most frequent SSRs, representing 253 (26.6%) of all identified SSRs. Microsynteny analysis revealed that more BESs mapped to the whole-genome sequences of poplar than to those of grape or Arabidopsis, and even fewer mapped to the rice genome. This work will facilitate analysis of the Phalaenopsis genome, and will help clarify similarities and differences in genome composition between orchids and other plant species.ConclusionUsing BES analysis, we obtained an overview of the Phalaenopsis genome in terms of gene abundance, the presence of repetitive DNA and SSR markers, and the extent of microsynteny with other plant species. This work provides a basis for future physical mapping of the Phalaenopsis genome and advances our knowledge thereof.

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Section: Resultsmentioning

confidence: 99%

An overview of the Phalaenopsisorchid genome through BAC end sequence analysis

et al. 2011

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“…The high level of synteny and collinearity among cereal genomes has long been clear, but parallels to other monocots, such as banana (40), onion, and asparagus (41), have been more difficult to discern. The generally low synteny found in these previous studies may improve after redundancies within cereal (and other) genomes are accounted for.…”

Section: Discussionmentioning

confidence: 99%

Angiosperm genome comparisons reveal early polyploidy in the monocot lineage

Tang

Bowers²,

Wang³

et al. 2009

Proc. Natl. Acad. Sci. U.S.A.

254

230

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Although the timing and extent of a whole-genome duplication occurring in the common lineage of most modern cereals are clear, the existence or extent of more ancient genome duplications in cereals and perhaps other monocots has been hinted at, but remain unclear. We present evidence of additional duplication blocks of deeper hierarchy than the pancereal rho (ρ) duplication, covering at least 20% of the cereal transcriptome. These more ancient duplicated regions, herein called σ, are evident in both intragenomic and intergenomic analyses of rice and sorghum. Resolution of such ancient duplication events improves the understanding of the early evolutionary history of monocots and the origins and expansions of gene families. Comparisons of syntenic blocks reveal clear structural similarities in putatively homologous regions of monocots (rice) and eudicots (grapevine). Although the exact timing of the σ-duplication(s) is unclear because of uncertainties of the molecular clock assumption, our data suggest that it occurred early in the monocot lineage after its divergence from the eudicot clade.collinearity | paleopolyploidy | synteny W hole-genome duplications (WGDs) have occurred in the lineages of plants (1-3), animals (4, 5), and fungi (6), with consequences ranging from the origin of evolutionary novelty (7) to the provision of genetic "buffer capacity" that increases genetic robustness (8-10). Reciprocal gene loss following a WGD can contribute to reproductive isolation through divergent resolution of duplicate copies (11), foreshadowing the diversification of species (12)(13)(14).WGDs are particularly widespread in the phylogeny of flowering plants, giving rise to large gene families and complicating comparative studies (1,(15)(16)(17). Relatively recent WGDs often are readily identified through intragenomic comparisons; however, more ancient WGDs are less tractable and often have been studied through "bottom-up" reconstruction of intermediate orders (1,5), iteratively inferring the state of the ancestral genome before successively more ancient duplications.It is well established that one WGD (hereinafter denoted as ρ) occurred in the cereal lineage an estimated 70 million years ago, preceding the radiation of the major cereal clades by 20 million years or more (2, 18). "Quartet" comparisons of the two resulting paralogous (homeologous) chromosomal regions in rice and sorghum show that 97%-98% of postduplication gene losses are orthologous (19), consistent with the ρ event predating the diversification of major grass lineages (2,20). This suggests that rice-sorghum gene arrangements likely are representative of those of most grass genomes, albeit further modified in some lineages by additional cycles of duplication and gene loss. The ρ duplication is extensive, involving all modern chromosomes of rice and sorghum and covering much of the euchromatin (2, 21). Even a duplication previously thought to be recent and segmental apparently results from ρ with subsequent concerted evolution (19,22).While several studi...

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“…The sequence information was used for microsynteny analysis between asparagus, onion and rice (Jakse et al 2006) as well as a source to gain an insight in the genetic structure of the M region. Based on the presented results, the sex determining region on L5 features as follows:…”

Section: Characteristics Of the Sex Locus Of Asparagusmentioning

confidence: 99%

Genetic and physical maps around the sex-determining M-locus of the dioecious plant asparagus

et al. 2007

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Asparagus officinalis L. is a dioecious plant. A region called the M-locus located on a pair of homomorphic sex chromosomes controls the sexual dimorphism in asparagus. The aim of this work was to clone the region determining sex in asparagus from its position in the genome. The structure of the region encompassing M should be investigated and compared to the sex-determining regions in other dioecious model species. To establish an improved basis for physical mapping, a high-resolution genetic map was enriched with AFLP markers closely linked to the target locus by carrying out a bulked segregant analysis. By screening a BAC library with AFLP- and STS-markers followed by chromosome walking, a physical map with eight contigs could be established. However, the gaps between the contigs could not be closed due to a plethora of repetitive elements. Surprisingly, two of the contigs on one side of the M-locus did not overlap although they have been established with two markers, which mapped in a distance as low as 0.25 cM flanking the sex locus. Thus, the clustering of the markers indicates a reduced recombination frequency within the M-region. On the opposite side of the M-locus, a contig was mapped in a distance of 0.38 cM. Four closely linked BAC clones were partially sequenced and 64 putative ORFs were identified. Interestingly, only 25% of the ORFs showed sequence similarity to known proteins and ESTs. In addition, an accumulation of repetitive sequences and a low gene density was revealed in the sex-determining region of asparagus. Molecular cytogenetic and sequence analysis of BACs flanking the M-locus indicate that the BACs contain highly repetitive sequences that localize to centromeric and pericentromeric locations on all asparagus chromosomes, which hindered the localization of the M-locus to the single pair of sex chromosomes. We speculate that dioecious Silene, papaya and Asparagus species may represent three stages in the evolution of XX, XY sex determination systems. Given that asparagus still rarely produces hermaphroditic flowers and has homomorphic sex chromosomes, this species may be an ideal system to further investigates early sex chromosome evolution and the origins of dioecy.

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Comparative sequence and genetic analyses of asparagus BACs reveal no microsynteny with onion or rice

Cited by 13 publications

References 55 publications

An overview of the Phalaenopsisorchid genome through BAC end sequence analysis

An overview of the Phalaenopsisorchid genome through BAC end sequence analysis

Angiosperm genome comparisons reveal early polyploidy in the monocot lineage

Genetic and physical maps around the sex-determining M-locus of the dioecious plant asparagus

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