An overview of the apple genome through BAC end sequence analysis

The apple, Malus x domestica Borkh., is one of the most important fruit trees grown worldwide. A bacterial artificial chromosome (BAC)-based physical map of the apple genome has been recently constructed. Based on this physical map, a total of approximately 2,100 clones from different contigs (overlapping BAC clones) have been selected and sequenced at both ends, generating 3,744 high-quality BAC end sequences (BESs) including 1,717 BAC end pairs. Approximately 8.5% of BESs contain simple sequence repeats (SSRs), most of which are AT/TA dimer repeats. Potential transposable elements are identified in approximately 21% of BESs, and most of these elements are retrotransposons. About 11% of BESs have homology to the Arabidopsis protein database. The matched proteins cover a broad range of categories. The average GC content of the predicted coding regions of BESs is 42.4%; while, that of the whole BESs is 39%. A small number of BES pairs were mapped to neighboring chromosome regions of A. thaliana and Populus trichocarpa; whereas, no pairs are mapped to the Oryza sativa genome. The apple has a higher degree of synteny with the closely related Populus than with the distantly related Arabidopsis. BAC end sequencing can be used to anchor a small proportion of the apple genome to the Populus and possibly to the Arabidopsis genomes.     

Inflorescence structure in species of Spartina Schreb. (Poaceae: Chloridoideae: Cynodonteae)

The typology developed by Troll was followed to describe inflorescence structures for 15 species of Spartina. In all species here studied, truncation of the terminal spikelet of the main axis and primary paracladium was observed. The truncation can also involve the short paracladia subzone so that the inflorescence is confined to just the long paracladia subzone. A great homogenization of paracladia and maximum ramification degree limited generally to the second order of branching are distinctive characteristics of the genus. Proximal paracladia with third-order branching were found in only three specimens, and in these exceptional cases, the homogenization is partial. Sometimes, in some species, a subzone of long and short paracladia can be distinguished. The absence of trophotagma paracladia in all the species studied was verified. The variation in the structure of the inflorescence among species is due to the differences in the number of short paracladia, long paracladia, total number of primary paracladia and also in the angle of divergence of the long paracladia from the main axis. The latter, in addition to variations in the intercalary growth of the internodes produces modifications in the general appearance of the inflorescences. The systematic and taxonomic value of the inflorescences in Spartina is discussed.     

Uniformity of the nuclear and chloroplast genomes of Spartina maritima (Poaceae), a salt-marsh species in decline along the Western European Coast

Spartina maritima is a salt-marsh species from European and African Atlantic coasts. In the northern range of the species (including north-west France), a rapid decline of the populations has been observed during the 20th century. In this paper, the molecular diversity of 10 populations of S. maritima from France has been investigated using nuclear and chloroplast DNA markers: inter-simple sequence polymorphism (ISSR), randomly amplified polymorphic DNA (RAPD), inter-retrotransposon amplified polymorphism (IRAP), and PCR-RFLP of a 5 kb long portion of chloroplast DNA. The results reveal an extremely low level of genetic variation in this species: only one nuclear marker (out of 98) was polymorphic, with the presence of two genotypes randomly distributed among the populations. The lack of genetic diversity is interpreted in light of the almost exclusive vegetative propagation of the species in its northern range, the colonization history of the populations, and the origin of S. maritima (2n = 60) in the hexaploid lineage of the genus and in the context of the management of S. maritima populations.     

孟仁草的花序发育研究

在光学显微镜和扫描电镜下观察了禾本科(Poaceae)虎尾草属(Chloris Sw.)孟仁草(Chloris barbata Sw.)的花序发育过程,以寻找适于虎尾草群(Chloris group)分支分析的发育性状.结果发现了未见于成熟花序的23个发育性状.阐明盂仁草花序的本质是二级长侧枝包围平截的主轴构成指形花序.该类型花序仅见于单子叶植物和少数高度特化的双子叶植物.涉及花序分枝的分子遗传机制研究亟待开展.     

Characterizing the walnut genome through analyses of BAC end sequences

Persian walnut (Juglans regia L.) is an economically important tree for its nut crop and timber. To gain insight into the structure and evolution of the walnut genome, we constructed two bacterial artificial chromosome (BAC) libraries, containing a total of 129,024 clones, from in vitro-grown shoots of J. regia cv. Chandler using the HindIII and MboI cloning sites. A total of 48,218 high-quality BAC end sequences (BESs) were generated, with an accumulated sequence length of 31.2?Mb, representing approximately 5.1% of the walnut genome. Analysis of repeat DNA content in BESs revealed that approximately 15.42% of the genome consists of known repetitive DNA, while walnut-unique repetitive DNA identified in this study constitutes 13.5% of the genome. Among the walnut-unique repetitive DNA, Julia SINE and JrTRIM elements represent the first identified walnut short interspersed element (SINE) and terminal-repeat retrotransposon in miniature (TRIM) element, respectively; both types of elements are abundant in the genome. As in other species, these SINEs and TRIM elements could be exploited for developing repeat DNA-based molecular markers in walnut. Simple sequence repeats (SSR) from BESs were analyzed and found to be more abundant in BESs than in expressed sequence tags. The density of SSR in the walnut genome analyzed was also slightly higher than that in poplar and papaya. Sequence analysis of BESs indicated that approximately 11.5% of the walnut genome represents a coding sequence. This study is an initial characterization of the walnut genome and provides the largest genomic resource currently available; as such, it will be a valuable tool in studies aimed at genetically improving walnut.     

A comparative, BAC end sequence enabled map of the genome of the American mink (Neovison vison)

In this report we present the results of the analysis of approximately 2.7 Mb of genomic information for the American mink (Neovison vison) derived through BAC end sequencing. Our study, which encompasses approximately 1/1000^th of the mink genome, suggests that simple sequence repeats (SSRs) are less common in the mink than in the human genome, whereas the average GC content of the mink genome is slightly higher than that of its human counterpart. The 2.7 Mb mink genomic dataset also contained 2,416 repeat elements (retroids and DNA transposons) occupying almost 31% of the sequence space. Among repeat elements, LINEs were over-represented and endogenous viruses (aka LTRs) under-represented in comparison to the human genome. Finally, we present a virtual map of the mink genome constructed with reference to the human and canine genome assemblies using a comparative genomics approach and incorporating over 200 mink BESs with unique hits to the human genome.     

Genetic evidence for hybridization between the native Spartina maritima and the introduced Spartina alterniflora (Poaceae) in South-West France: Spartina × neyrautii re-examined

 Spartina alterniflora, a perennial grass native to the North American Atlantic coast, was introduced during the 19th century in western Europe (Southern England and western France) where it hybridized with the native Spartina maritima. In England, the sterile hybrid S. × townsendii gave rise by chromosome doubling to the highly fertile allopolyploid Spartina anglica, which has now invaded many salt marshes and estuaries in western Europe, and has been introduced in several continents. In South-West France, another sterile hybrid was discovered in 1892 in the Bidassoa Estuary, and named Spartina × neyrautii. According to their morphology, some authors suggested that S. × neyrautii and S. × townsendii result from reciprocal crosses. During the 20th century, the hybridization site was severely disturbed, and surviving of S. × neyrautii was questioned. In this paper, various Spartina populations are investigated in the Basque region (France and Spain), and compared to the hybrid taxa formed in England (S. × townsendii and S. anglica). The samples were analyzed using molecular fingerprinting (RAPD and ISSR) and Chloroplast DNA sequence (trnL-trnT spacer, trnL intron and trnL-trnF spacer). In the Bidassoa estuary, a hybrid isolated clone has been found, that displays additive species-specific nuclear markers of S. maritima and S. alterniflora, and that is subsequently considered as a surviving clone of S. × neyrautii. The molecular analyses indicate that S. × neyrautii and S. × townsendii share the same maternal (S. alterniflora), and paternal (S. maritima) parental species, but also that the two independent hybridization events have involved different parental (nuclear) genotypes in England and in South-West France. Received July 12, 2002; accepted October 4, 2002 Published online: March 20, 2003     

A biogeographical analysis of Muhlenbergia (Poaceae: Chloridoideae: Cynodonteae: Muhlenbergiinae)

A phylogeny based on the analysis of six DNA sequence markers (ITS, ndhA intron, rpl32-trnL, rps3, rps16 intron, and rps16-trnK) is used to infer ancestral areas and divergence times, and reconstruct the biogeographical history and evolution of 150 of the 183 (82%) species of Muhlenbergia. Our results suggest that the genus originated 9.3 mya in the Sierra Madre (Occidental and Oriental) in Mexico, splitting into six lineages: M. ramulosa diverging 8.2 mya, M. subg. Muhlenbergia at 5.9 mya, M. subg. Pseudosporobolus at 5.9 mya, M. subg. Clomena at 5.4 mya, M. subg. Bealia at 4.3 mya, and M. subg. Trichochloa at 1 mya, each of these with a high probability of Sierra Madrean origin. Our results further suggest that founder-event speciation from Sierra Madre to South America occurred independently multiple times in all five subgenera during the Pleistocene and late Pliocene. One long-distance dispersal event most likely originating from Central or Eastern North America to East and Central Asia occurred 1.6–1 mya in M. subg. Muhlenbergia. In our cladogram, members of M. subg. Trichochloa show little genetic resolution, suggesting very low levels of divergence among the species, and this may be a consequence of rapid radiation.     

禾本科虎尾草亚科细胞学研究分析

总结了虎尾草亚科72属601个分类单位的细胞学资料。虎尾草亚科的染色体基数是10和9,来源于原始染色体基数6经非整倍性减少为5,再经多倍化及非整倍性减少而来。细胞学性状对虎尾草亚科属上类群的分类具有相当重要的价值。推测染色体基数演化的趋势为:x=6→x=5→x=10→x=9。据认为,虎尾草亚科的原始染色体基数为5的二倍体类群在演化早期就灭绝了。     

Reproductive biology of the native forage grass Trichloris crinita (Poaceae,Chloridoideae)

• Trichloris crinita is a perennial forage grass species native to arid regions of the American continent. Due to its extensive area of distribution, good forage quality and resistance to drought and grazing, this species is widely utilised as forage and for revegetation purposes in environments with low water availability. Despite its importance, genetic improvement of T. crinita has been very limited, partly as consequence of the lack of knowledge on its mode of reproduction.
• In the present work, we studied the reproductive biology of T. crinita by means of embryological analyses, flow cytometric seed screen (FCSS), self‐compatibility tests and progeny testing with morphological and molecular markers.
• Cytological analyses revealed embryo sacs with eight nuclei and of Polygonum type for all T. crinita accessions analysed. FCSS histograms exhibited two clear peaks corresponding to 2C and 3C DNA content, indicating embryo sacs of sexual origin. Controlled pollination experiments designed to evaluate seed set (%) demonstrated that T. crinita is self‐compatible, whereas results from morphological and simple sequence repeat (SSR) marker analysis of progeny revealed lack of outcrossing.
• Together, these results indicate that T. crinita reproduces sexually. It is a self‐compatible and autogamous species. It is expected that these data will have a positive impact in the genetics and breeding of this species, and therefore contribute to its proper utilisation in arid regions.

     

Lemma micromorphological characters in the Chloridoideae (Poaceae) optimized on a molecular phylogeny

Eight lemma micromorphological characters of 83 taxa representing 61 genera in the Chloridoideae have been investigated using Scanning Electron Microscopy, including long cells, cork cells, stomata, bicellular microhairs, papillae, silica cells, microprickles, and macrohairs. Five new types of lemma micromorphological characters were reported here. Data for 27 taxa representing 19 genera from previous publications were also supplied to access the homology of lemma micromorphological characters for different groups through optimization onto a molecular cladogram. Given the optimization, five characters including long cells, cork cells, stomata, papillae, microprickles are of phylogenetic significance for supra-generic groups. Seven characters including straight outline long cells, crescent-shaped cork cells, absent stomata, absent papillae, dumb-bell-shaped silica cells, c-type microprickles, and papillate-base macrohairs may not be homologous, however, the enneapogonoid-type bicellular microhairs appeared as a synapomorphy for the Chloridoideae.     

A new cleistogamous South American species of Eragrostis (Poaceae: Chloridoideae)

Eragrostis riobrancensis (Poaceae, Chloridoideae), a new species with cleistogamous spikelets from sandy river banks of southern Guyana and adjacent Terr. Roraima, Brazil, is described and illustrated.     

The nuclear genome of Brachypodium distachyon: analysis of BAC end sequences

Due in part to its small genome (~350 Mb), Brachypodium distachyon is emerging as a model system for temperate grasses, including important crops like wheat and barley. We present the analysis of 10.9% of the Brachypodium genome based on 64,696 bacterial artificial chromosome (BAC) end sequences (BES). Analysis of repeat DNA content in BES revealed that approximately 11.0% of the genome consists of known repetitive DNA. The vast majority of the Brachypodium repetitive elements are LTR retrotransposons. While Bare-1 retrotransposons are common to wheat and barley, Brachypodium repetitive element sequence-1 (BRES-1), closely related to Bare-1, is also abundant in Brachypodium. Moreover, unique Brachypodium repetitive element sequences identified constitute approximately 7.4% of its genome. Simple sequence repeats from BES were analyzed, and flanking primer sequences for SSR detection potentially useful for genetic mapping are available at . Sequence analyses of BES indicated that approximately 21.2% of the Brachypodium genome represents coding sequence. Furthermore, Brachypodium BES have more significant matches to ESTs from wheat than rice or maize, although these species have similar sizes of EST collections. A phylogenetic analysis based on 335 sequences shared among seven grass species further revealed a closer relationship between Brachypodium and Triticeae than Brachypodium and rice or maize. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users. N. Huo and G.R. Lazo contributed equally to this work.     

Diversity of inflorescences in the Boutelouinae subtribe (Poaceae: Chloridoideae: Cynodonteae)

The Boutelouinae subtribe is comprised of one monophyletic genus, Bouteloua, with 57 species inhabiting the semi-arid regions of the New World. The inflorescences show significant structural variations, which provides an interesting system to examine their morphological evolution and identify characters and processes that may help to understand the group systematics. The structure of inflorescences was studied in 25 species of Bouteloua. All the species covered under this study have truncated polytelic inflorescences. Structural variations in the inflorescence unit among species may be accounted for by: (1) symmetry of the inflorescence unit, (2) total number of long primary branches, (3) total number of spikelets per branch, (4) number of perfect flowers per spikelet, (5) number of rudimentary flowers, and (6) reproductive system. Homogenization and truncation processes account for the diversity of mature inflorescences that exists in Bouteloua. In this work, we discuss the systematic and taxonomic value of the inflorescence in the Boutelouinae subtribe.     

Characterization of microsatellite loci in Spartina species (Poaceae)

The cordgrasses in the genus Spartina have become model organisms for studying biological invasions from both ecological and genetic perspectives. Here we characterize 11 disomic loci in Spartina alterniflora that show promise for population studies and for studying hybridization events between S. alterniflora and S. foliosa. Comparisons among invasive and native S. alterniflora populations showed that levels of allelic variation are lower in invasive populations. In addition, nearly all loci that amplified in S. foliosa populations and in a swarm of S. alterniflora×foliosa hybrids were polymorphic. We also found that several loci amplified successfully in other Spartina species.