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1.
A unique set of 11,008 onion expressed sequence tags reveals expressed sequence and genomic differences between the monocot orders Asparagales and Poales
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Kuhl JC Cheung F Yuan Q Martin W Zewdie Y McCallum J Catanach A Rutherford P Sink KC Jenderek M Prince JP Town CD Havey MJ 《The Plant cell》2004,16(1):114-125
Enormous genomic resources have been developed for plants in the monocot order Poales; however, it is not clear how representative the Poales are for the monocots as a whole. The Asparagales are a monophyletic order sister to the lineage carrying the Poales and possess economically important plants such as asparagus, garlic, and onion. To assess the genomic differences between the Asparagales and Poales, we generated 11,008 unique ESTs from a normalized cDNA library of onion. Sequence analyses of these ESTs revealed microsatellite markers, single nucleotide polymorphisms, and homologs of transposable elements. Mean nucleotide similarity between rice and the Asparagales was 78% across coding regions. Expressed sequence and genomic comparisons revealed strong differences between the Asparagales and Poales for codon usage and mean GC content, GC distribution, and relative GC content at each codon position, indicating that genomic characteristics are not uniform across the monocots. The Asparagales were more similar to eudicots than to the Poales for these genomic characteristics. 相似文献
2.
Martin WJ McCallum J Shigyo M Jakse J Kuhl JC Yamane N Pither-Joyce M Gokce AF Sink KC Town CD Havey MJ 《Molecular genetics and genomics : MGG》2005,274(3):197-204
The Poales (which include the grasses) and Asparagales [which include onion (Allium cepa L.) and other Allium species] are the two most economically important monocot orders. Enormous genomic resources have been developed for the grasses;
however, their applicability to other major monocot groups, such as the Asparagales, is unclear. Expressed sequence tags (ESTs)
from onion that showed significant similarities (80% similarity over at least 70% of the sequence) to single positions in
the rice genome were selected. One hundred new genetic markers developed from these ESTs were added to the intraspecific map
derived from the BYG15-23×AC43 segregating family, producing 14 linkage groups encompassing 1,907 cM at LOD 4. Onion linkage
groups were assigned to chromosomes using alien addition lines of Allium fistulosum L. carrying single onion chromosomes. Visual comparisons of genetic linkage in onion with physical linkage in rice revealed
scant colinearity; however, short regions of colinearity could be identified. Our results demonstrate that the grasses may
not be appropriate genomic models for other major monocot groups such as the Asparagales; this will make it necessary to develop
genomic resources for these important plants.
Electronic Supplementary Material Supplementary material is available for this article at 相似文献
3.
Joseph C Kuhl Michael J Havey William J Martin Foo Cheung Qiaoping Yuan Lena Landherr Yi Hu James Leebens-Mack Christopher D Town Kenneth C Sink 《Génome》2005,48(6):1052-1060
Garden asparagus (Asparagus officinalis L.) belongs to the monocot family Asparagaceae in the order Asparagales. Onion (Allium cepa L.) and Asparagus officinalis are 2 of the most economically important plants of the core Asparagales, a well supported monophyletic group within the Asparagales. Coding regions in onion have lower GC contents than the grasses. We compared the GC content of 3374 unique expressed sequence tags (ESTs) from A. officinalis with Lycoris longituba and onion (both members of the core Asparagales), Acorus americanus (sister to all other monocots), the grasses, and Arabidopsis. Although ESTs in A. officinalis and Acorus had a higher average GC content than Arabidopsis, Lycoris, and onion, all were clearly lower than the grasses. The Asparagaceae have the smallest nuclear genomes among all plants in the core Asparagales, which typically have huge genomes. Within the Asparagaceae, European Asparagus species have approximately twice the nuclear DNA of that of southern African Asparagus species. We cloned and sequenced 20 genomic amplicons from European A. officinalis and the southern African species Asparagus plumosus and observed no clear evidence for a recent genome doubling in A. officinalis relative to A. plumosus. These results indicate that members of the genus Asparagus with smaller genomes may be useful genomic models for plants in the core Asparagales. 相似文献
4.
Background and Aims
Although monocotyledonous plants comprise one of the two major groups of angiosperms and include >65 000 species, comprehensive genome analysis has been focused mainly on the Poaceae (grass) family. Due to this bias, most of the conclusions that have been drawn for monocot genome evolution are based on grasses. It is not known whether these conclusions apply to many other monocots.Methods
To extend our understanding of genome evolution in the monocots, Asparagales genomic sequence data were acquired and the structural properties of asparagus and onion genomes were analysed. Specifically, several available onion and asparagus bacterial artificial chromosomes (BACs) with contig sizes >35 kb were annotated and analysed, with a particular focus on the characterization of long terminal repeat (LTR) retrotransposons.Key Results
The results reveal that LTR retrotransposons are the major components of the onion and garden asparagus genomes. These elements are mostly intact (i.e. with two LTRs), have mainly inserted within the past 6 million years and are piled up into nested structures. Analysis of shotgun genomic sequence data and the observation of two copies for some transposable elements (TEs) in annotated BACs indicates that some families have become particularly abundant, as high as 4–5 % (asparagus) or 3–4 % (onion) of the genome for the most abundant families, as also seen in large grass genomes such as wheat and maize.Conclusions
Although previous annotations of contiguous genomic sequences have suggested that LTR retrotransposons were highly fragmented in these two Asparagales genomes, the results presented here show that this was largely due to the methodology used. In contrast, this current work indicates an ensemble of genomic features similar to those observed in the Poaceae. 相似文献5.
Suzuki G Ogaki Y Hokimoto N Xiao L Kikuchi-Taura A Harada C Okayama R Tsuru A Onishi M Saito N Do GS Lee SH Ito T Kanno A Yamamoto M Mukai Y 《Plant cell reports》2012,31(4):621-628
BAC FISH (fluorescence in situ hybridization using bacterial artificial chromosome probes) is a useful cytogenetic technique for physical mapping, chromosome marker screening, and comparative genomics. As a large genomic fragment with repetitive sequences is inserted in each BAC clone, random BAC FISH without adding competitive DNA can unveil complex chromosome organization of the repetitive elements in plants. Here we performed the comparative analysis of the random BAC FISH in monocot plants including species having small chromosomes (rice and asparagus) and those having large chromosomes (hexaploid wheat, onion, and spider lily) in order to understand a whole view of the repetitive element organization in Poales and Asparagales monocots. More unique and less dense dispersed signals of BAC FISH were observed in species with smaller chromosomes in both the Poales and Asparagales species. In the case of large-chromosome species, 75-85% of the BAC clones were detected as dispersed repetitive FISH signals along entire chromosomes. The BAC FISH of Lycoris did not even show localized repetitive patterns (e.g., centromeric localization) of signals. 相似文献
6.
Background
Spirodela polyrhiza is a species of the order Alismatales, which represent the basal lineage of monocots with more ancestral features than the Poales. Its complete sequence of the mitochondrial (mt) genome could provide clues for the understanding of the evolution of mt genomes in plant.Methods
Spirodela polyrhiza mt genome was sequenced from total genomic DNA without physical separation of chloroplast and nuclear DNA using the SOLiD platform. Using a genome copy number sensitive assembly algorithm, the mt genome was successfully assembled. Gap closure and accuracy was determined with PCR products sequenced with the dideoxy method.Conclusions
This is the most compact monocot mitochondrial genome with 228,493 bp. A total of 57 genes encode 35 known proteins, 3 ribosomal RNAs, and 19 tRNAs that recognize 15 amino acids. There are about 600 RNA editing sites predicted and three lineage specific protein-coding-gene losses. The mitochondrial genes, pseudogenes, and other hypothetical genes (ORFs) cover 71,783 bp (31.0%) of the genome. Imported plastid DNA accounts for an additional 9,295 bp (4.1%) of the mitochondrial DNA. Absence of transposable element sequences suggests that very few nuclear sequences have migrated into Spirodela mtDNA. Phylogenetic analysis of conserved protein-coding genes suggests that Spirodela shares the common ancestor with other monocots, but there is no obvious synteny between Spirodela and rice mtDNAs. After eliminating genes, introns, ORFs, and plastid-derived DNA, nearly four-fifths of the Spirodela mitochondrial genome is of unknown origin and function. Although it contains a similar chloroplast DNA content and range of RNA editing as other monocots, it is void of nuclear insertions, active gene loss, and comprises large regions of sequences of unknown origin in non-coding regions. Moreover, the lack of synteny with known mitochondrial genomic sequences shed new light on the early evolution of monocot mitochondrial genomes. 相似文献7.
Changes in plant architecture have been central to the domestication of wild species. Tillering or the degree of branching
determines shoot architecture and is a key component of grain yield and/or biomass. Previously, a tiller inhibition mutant with monoculm phenotype was isolated and the mutant gene (tin3) was mapped in the distal region of chromosome arm 3AmL of Triticum monococcum. As a first step towards isolating a candidate gene for tin3, the gene was mapped in relation to physically mapped expressed sequence tags (ESTs) and sequence tag site (STS) markers
developed based on synteny with rice. In addition, we investigated the relationship of the wheat region containing tin3 with the corresponding region in rice by comparative genomic analysis. Wheat ESTs that had been previously mapped to deletion
bins provided a useful framework to identify closely related rice sequences and to establish the most likely syntenous region
in rice for the wheat tin3 region. The tin3 gene was mapped to a 324-kb region spanned by two overlapping bacterial artificial chromosomes (BACs) of rice chromosome
arm 1L. Wheat–rice synteny was exceptionally high at the tin3 region despite being located in the high-recombination, gene-rich region of wheat. Identification of tightly linked flanking
EST and STS markers to the tin3 gene and its localization to highly syntenic rice BACs will assist in the future development of a high-resolution map and
map-based cloning of the tin3 gene.
Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users. 相似文献
8.
The Araceae, a basal-most family of Alismatales that basally diverged subsequent to Acorales in monocot phylogeny, are known
to have diverse modes of endosperm development: nuclear, helobial, and cellular. However, the occurrence of nuclear and helobial
endosperm development has long been debated. Here, we report a (re-)investigation of endosperm development in Lysichiton, Orontium, and Symplocarpus of the Orontioideae (a basal Araceae), in which nuclear endosperm development was recorded more than 100 years ago. The results
show that all three genera exhibit a cellular, rather than nuclear, endosperm development and suggest that the helobial endosperm
development reported as an “unmistakable record” from Ariopsis is likely cellular. Thus the Araceae are very likely characterized by cellular endosperm development alone. An extensive
comparison with other monocots in light of phylogenetic relationships demonstrates that a plesiomorphic cellular endosperm
development is restricted to the three basal monocot orders Acorales, Alismatales, and Petrosaviales, in which evolutionary
changes from cellular to nuclear endosperm development occurred twice as major events, once within Alismatales and once as
a synapomorphy of the eight remaining monocot orders, including Dioscoreales, Liliales, Asparagales, and Poales, and that
helobial endosperm development, which is known for many monocot families, evolved as homoplasy throughout the monocots. 相似文献
9.
Microsporogenesis in Monocotyledons 总被引:5,自引:1,他引:4
This paper critically reviews the distribution of microsporogenesistypes in relation to recent concepts in monocot systematics.Two basic types of microsporogenesis are generally recognized:successive and simultaneous, although intermediates occur. Theseare characterized by differences in tetrad morphology, generallytetragonal or tetrahedral, although other forms occur, particularlyassociated with successive division. Successive microsporogenesisis predominant in monocotyledons, although the simultaneoustype characterizes the lower Asparagales. Simultaneousmicrosporogenesis also occurs inJaponolirion and Petrosavia(unplaced taxa), some Araceae, Aponogeton, Thalassia andTofieldia(Alismatales), Dioscorea, Stenomeris and Tacca (Dioscoreales),and some Commelinanae: Arecaceae (Arecales), and Cyperaceae,Juncaceae and Thurniaceae (Poales). Simultaneous microsporogenesisis of phylogenetic significance within some of these groups,for example, Asparagales, Dioscoreales and Poales. An intermediatetype is recorded in Stemonaceae (Pandanales), Commelinaceae(Commelinales) and in Eriocaulaceae and Flagellariaceae (Poales).There is little direct relationship between microsporogenesistype and pollen aperture type in monocots (except for trichotomosulcateand pantoporate apertures), although trichotomosulcate aperturesin monocot pollen, and equatorial tricolpate and tricolporateapertures in eudicot pollen, are all related to simultaneousmicrosporogenesis. Copyright 1999 Annals of Botany Company Microsporogenesis, monocotyledons, pollen apertures, phylogeny, tetrads, simultaneous, successive, systematics. 相似文献
10.
Genetic and physical maps around the sex-determining <Emphasis Type="Italic">M</Emphasis>-locus of the dioecious plant asparagus 总被引:1,自引:0,他引:1
Telgmann-Rauber A Jamsari A Kinney MS Pires JC Jung C 《Molecular genetics and genomics : MGG》2007,278(3):221-234
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. 相似文献
11.
Unraveling widespread polyploidy events throughout plant evolution is a necessity for
inferring the impacts of whole-genome duplication (WGD) on speciation, functional innovations, and to guide identification of
true orthologs in divergent taxa. Here, we employed an integrated syntenic and
phylogenomic analyses to reveal an ancient WGD that shaped the genomes of all commelinid monocots, including grasses,
bromeliads, bananas (Musa acuminata), ginger, palms, and other
plants of fundamental, agricultural, and/or horticultural interest. First,
comprehensive phylogenomic analyses revealed 1421 putative gene families that
retained ancient duplication shared by Musa (Zingiberales) and grass
(Poales) genomes, indicating an ancient WGD
in monocots. Intergenomic synteny blocks of Musa and
Oryza were investigated, and 30 blocks were shown to be
duplicated before Musa-Oryza divergence an
estimated 120 to 150 million years ago. Synteny comparisons of four monocot (rice
[Oryza sativa], sorghum [Sorghum bicolor],
banana, and oil palm [Elaeis guineensis]) and two eudicot (grape
[Vitis vinifera] and sacred lotus [Nelumbo
nucifera]) genomes also support this additional WGD in monocots, herein called Tau (τ). Integrating
synteny and phylogenomic comparisons achieves better resolution of ancient polyploidy
events than either approach individually, a principle that is exemplified in the
disambiguation of a WGD series of rho
(ρ)-sigma (σ)-tau (τ) in the grass lineages that echoes the
alpha (α)-beta (β)-gamma (γ) series previously revealed in the
Arabidopsis thaliana lineage. 相似文献
12.
Mary M. Guisinger Timothy W. Chumley Jennifer V. Kuehl Jeffrey L. Boore Robert K. Jansen 《Journal of molecular evolution》2010,70(2):149-166
Plastid genomes of the grasses (Poaceae) are unusual in their organization and rates of sequence evolution. There has been
a recent surge in the availability of grass plastid genome sequences, but a comprehensive comparative analysis of genome evolution
has not been performed that includes any related families in the Poales. We report on the plastid genome of Typha latifolia, the first non-grass Poales sequenced to date, and we present comparisons of genome organization and sequence evolution within
Poales. Our results confirm that grass plastid genomes exhibit acceleration in both genomic rearrangements and nucleotide
substitutions. Poaceae have multiple structural rearrangements, including three inversions, three genes losses (accD, ycf1, ycf2), intron losses in two genes (clpP, rpoC1), and expansion of the inverted repeat (IR) into both large and small single-copy regions. These rearrangements are restricted
to the Poaceae, and IR expansion into the small single-copy region correlates with the phylogeny of the family. Comparisons
of 73 protein-coding genes for 47 angiosperms including nine Poaceae genera confirm that the branch leading to Poaceae has
significantly accelerated rates of change relative to other monocots and angiosperms. Furthermore, rates of sequence evolution
within grasses are lower, indicating a deceleration during diversification of the family. Overall there is a strong correlation
between accelerated rates of genomic rearrangements and nucleotide substitutions in Poaceae, a phenomenon that has been noted
recently throughout angiosperms. The cause of the correlation is unknown, but faulty DNA repair has been suggested in other
systems including bacterial and animal mitochondrial genomes. 相似文献
13.
14.
Lohithaswa HC Feltus FA Singh HP Bacon CD Bailey CD Paterson AH 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》2007,115(2):237-243
Common genome anchor points across many taxa greatly facilitate translational and comparative genomics and will improve our
understanding of the Tree of Life. To add to the repertoire of genomic tools applicable to the study of monocotyledonous plants
in general, we aligned Allium and Musa ESTs to Oryza BAC sequences and identified candidate Allium-Oryza and Musa-Oryza conserved intron-scanning primers (CISPs). A random sampling of 96 CISP primer pairs, representing loci from 11 of the 12
chromosomes in rice, were tested on seven members of the order Poales and on representatives of the Arecales, Asparagales,
and Zingiberales monocot orders. The single-copy amplification success rates of Allium (31.3%), Cynodon (31.4%), Hordeum (30.2%), Musa (37.5%), Oryza (61.5%), Pennisetum (33.3%), Sorghum (47.9%), Zea (33.3%), Triticum (30.2%), and representatives of the palm family (32.3%) suggest that subsets of these primers will provide DNA markers suitable
for comparative and translational genomics in orphan crops, as well as for applications in conservation biology, ecology,
invasion biology, population biology, systematic biology, and related fields.
Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.
H. C. Lohithaswa and F. A. Feltus contributed equally to this work. 相似文献
15.
Alignment of the genomes of Brachypodium distachyon and temperate cereals and grasses using bacterial artificial chromosome landing with fluorescence in situ hybridization 总被引:2,自引:0,他引:2
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Hasterok R Marasek A Donnison IS Armstead I Thomas A King IP Wolny E Idziak D Draper J Jenkins G 《Genetics》2006,174(1):349-362
As part of an initiative to develop Brachypodium distachyon as a genomic "bridge" species between rice and the temperate cereals and grasses, a BAC library has been constructed for the two diploid (2n = 2x = 10) genotypes, ABR1 and ABR5. The library consists of 9100 clones, with an approximate average insert size of 88 kb, representing 2.22 genome equivalents. To validate the usefulness of this species for comparative genomics and gene discovery in its larger genome relatives, the library was screened by PCR using primers designed on previously mapped rice and Poaceae sequences. Screening indicated a degree of synteny between these species and B. distachyon, which was confirmed by fluorescent in situ hybridization of the marker-selected BACs (BAC landing) to the 10 chromosome arms of the karyotype, with most of the BACs hybridizing as single loci on known chromosomes. Contiguous BACs colocalized on individual chromosomes, thereby confirming the conservation of genome synteny and proving that B. distachyon has utility as a temperate grass model species alternative to rice. 相似文献
16.
TEM investigation of sieve-element plastids in three species of Trithuria, the sole genus of the small aquatic family Hydatellaceae, show that P-type plastids are absent from this genus and only starch-accumulating (S-type) sieve-element plastids are present. This discovery is consistent with the recent transfer of Hydatellaceae from the highly derived monocot order Poales (grasses and their allies) to the early-divergent angiosperm order Nymphaeales (waterlilies) based on molecular phylogenetic data. Species of Poales consistently possess P2-subtype plastids, in common with other monocots, but only S-type plastids are present in Nymphaeales. The results confirm that Hydatellaceae do not belong in monocots. Optimisation of the two major types of sieve-element plastid onto a recent phylogeny of early-divergent angiosperms confirms that S-type is the primitive form and indicates that P-type sieve-element plastids have evolved more than once in angiosperms. 相似文献
17.
Chase MW 《American journal of botany》2004,91(10):1645-1655
In 10 years, the monocots have gone from being one of the least studied and most phylogenetically misunderstood groups of the angiosperms to one of the best characterized. Based on analyses of seven genes representing all three genomes, the following clades have high bootstrap support: Acorales (with the single genus Acorus) is sister to the rest of the monocots, followed successively by Alismatales (including Araceae and Tofieldiaceae), Petrosaviales, Dioscoreales/Pandanales, Liliales, Asparagales, and finally a polytomy of Arecales, Commelinales/Zingiberales, Dasypogonaceae, and Poales. Many of these results also have support from at least some morphological data, but some are unique to the trees created from DNA sequence data. Monocots have been shown in molecular clock studies to be at least 140 million years old, and all major clades and most families date to well before the end of the Cretaceous. More data are required to clarify the positions of the remaining unclearly placed orders, Asparagles, Liliales, and Arecales, as well as Dasypogonaceae. More sequences from the nuclear and mitochondrial genomes are also needed to complement those from the plastid genome, which is the most sampled and thus far most pattern-rich. 相似文献
18.
Syntenic relationships between Medicago truncatula and Arabidopsis reveal extensive divergence of genome organization 总被引:4,自引:0,他引:4
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Zhu H Kim DJ Baek JM Choi HK Ellis LC Küester H McCombie WR Peng HM Cook DR 《Plant physiology》2003,131(3):1018-1026
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. 相似文献
19.
Conner JA Goel S Gunawan G Cordonnier-Pratt MM Johnson VE Liang C Wang H Pratt LH Mullet JE DeBarry J Yang L Bennetzen JL Klein PE Ozias-Akins P 《Plant physiology》2008,147(3):1396-1411
Apomixis, asexual reproduction through seed, is widespread among angiosperm families. Gametophytic apomixis in Pennisetum squamulatum and Cenchrus ciliaris is controlled by the apospory-specific genomic region (ASGR), which is highly conserved and macrosyntenic between these species. Thirty-two ASGR bacterial artificial chromosomes (BACs) isolated from both species and one ASGR-recombining BAC from P. squamulatum, which together cover approximately 2.7 Mb of DNA, were used to investigate the genomic structure of this region. Phrap assembly of 4,521 high-quality reads generated 1,341 contiguous sequences (contigs; 730 from the ASGR and 30 from the ASGR-recombining BAC in P. squamulatum, plus 580 from the C. ciliaris ASGR). Contigs containing putative protein-coding regions unrelated to transposable elements were identified based on protein similarity after Basic Local Alignment Search Tool X analysis. These putative coding regions were further analyzed in silico with reference to the rice (Oryza sativa) and sorghum (Sorghum bicolor) genomes using the resources at Gramene (www.gramene.org) and Phytozome (www.phytozome.net) and by hybridization against sorghum BAC filters. The ASGR sequences reveal that the ASGR (1) contains both gene-rich and gene-poor segments, (2) contains several genes that may play a role in apomictic development, (3) has many classes of transposable elements, and (4) does not exhibit large-scale synteny with either rice or sorghum genomes but does contain multiple regions of microsynteny with these species. 相似文献
20.