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PubMed2000

Rare etiology of autosomal recessive disease in a child with noncarrier parents.

A child with maple syrup urine disease type 2 (MSUD2) was found to be homozygous for a 10-bp MSUD2-gene deletion on chromosome 1. Both purported parents were tested, and neither carries the gene deletion. Polymorphic simple-sequence repeat analyses at 15 loci on chromosome 1 and at 16 loci on other chromosomes confirmed parentage and revealed that a de novo mutation prior to maternal meiosis I, followed by nondisjunction in maternal meiosis II, resulted in an oocyte with two copies of the de novo mutant allele. Fertilization by a sperm that did not carry a paternal chromosome 1 or subsequent mitotic loss of the paternal chromosome 1 resulted in the propositus inheriting two mutant MSUD2 alleles on two maternal number 1 chromosomes.

Alleles↗

PubMed2000

Genetic and physical mapping of the locus for autosomal dominant renal Fanconi syndrome, on chromosome 15q15.3.

Autosomal dominant renal Fanconi syndrome is a genetic model for the study of proximal renal tubular transport pathology. We were able to map the locus for this disease to human chromosome 15q15.3 by genotyping a central Wisconsin pedigree with 10 affected individuals. After a whole-genome scan with highly polymorphic simple sequence repeat markers, a maximum LOD score of 3.01 was calculated for marker D15S659 on chromosome 15q15.3. Linkage and haplotype analysis for an additional 24 markers flanking D15S659 narrowed the interval to approximately 3 cM, with the two highest single-point LOD scores observed being 4.44 and 4.68 (for D15S182 and D15S537, respectively). Subsequently, a complete bacterial artificial chromosome contig was constructed, from the High Throughput Genomic Sequence Database, for the region bounded by D15S182 and D15S143. The identification of the gene and gene product altered in autosomal dominant renal Fanconi syndrome will allow the study of the physiology of proximal renal tubular transport.

Chromosome Mapping↗

PubMed2026

Molecular investigation of the progenitors, origin and domestication patterns of diploid Chinese old garden roses.

BACKGROUND AND AIMS: Chinese old garden roses are major contributors to the genetic development of modern roses. The RoKSN gene is associated with continuous flowering in roses and is proposed to have originated from Chinese wild roses. However, the wild roses that are implicated in the breeding of Chinese old garden roses and the origin of the RoKSN locus remain unidentified. We collected 25 of the most renowned and classic diploid Chinese old garden roses along with all related wild roses from East Asia. These roses were analysed with the aim of identifying the wild species that contributed to the genetic composition of Chinese old garden roses. In addition, we aimed to infer the geographical origin of the RoKSN gene and to develop a schematic overview of hybrid domestication of Chinese old garden roses. METHODS: We compared the haplotypes of internal transcribed spacers (nrITS), six nuclear single-copy genes and three chloroplast genes between Chinese old garden roses and wild roses. Additionally, we assessed genetic organization using 21 expressed sequence tag-simple sequence repeats to identify potential donor species that contributed to the emergence of these cultivars. Primers were designed for RoKSN to allow comparison of the gene across the entire distribution range of Rosa sect. Chinenses. KEY RESULTS: Our findings confirmed that the majority of rose cultivars are descendants of early hybridization events. Rosa chinensis var. spontanea, R. odorata var. gigantea and R. multiflora var. cathayensis were the primary donors for the 25 cultivar roses. Chinese old garden roses were categorized into four groups. Ten cultivars were hybrids between R. chinensis var. spontanea and R. multiflora var. cathayensis, thereby forming the 'Old Blush' group. Five cultivars were hybrids between 'Old Blush' and the R. kwangtungensis species complex, thereby forming the 'Slater's crimson' group. Six cultivars were hybrids between 'Old Blush' and R. odorata var. gigantea, thereby forming the 'Tea Rose' group, and three cultivars were hybrids that evolved from more than three donors. Moreover, we observed relatively close genetic proximity among Chinese old garden roses with an identical RoKSN-copia gene that is responsible for continuous flowering, which indicates a single origin for this retrotransposon-containing allele. Additionally, we determined that the haplotypes of the RoKSN-copia gene predominantly occurred in the Sichuan Basin region. In contrast, R. chinensis cultivated in the Ya'an region showed no markers of hybridization and displayed a genetic composition that was close to that of the wild species R. chinensis var. spontanea. This cultivar may represent the earliest mutated individual that bears the RoKSN-copia gene and may have served as a bridge from wild species to continuous-flowering old rose cultivars. CONCLUSIONS: The study provides crucial evidence that elucidates the origin of cultivated roses and lays the groundwork for further analysis of the breeding history of Chinese old garden roses using genomic data.

Domestication↗

PubMed2002

Molecular cytogenetic analysis of Podocarpus and comparison with other gymnosperm species.

DNA sequences have been mapped to the chromosomes of Podocarpus species from New Zealand and Australia by fluorescent in situ hybridization. Unlike other conifers, these species show only one pair of major sites of 45S rDNA genes, and two additional minor sites were seen in the Australian P. lawrencei. Unusually, 45S sequences collocalize to the same chromosomal region as the 5S rDNA. The telomere probe (TTTAGGG)n hybridizes to the ends of all chromosomes as well as to a large number of small sites distributed along the length of all chromosomes. Two other simple sequence repeats, (AAC)5 and (GATA)4, show a diffuse pattern of hybridization sites distributed along chromosomes. Southern blots using a variety of probes obtained from the reverse transcriptase of retroelements (gypsy, copia and LINE) from P. totara, P. nivalis and Dacrycarpus dacrydioides show that these retroelements are abundant and widespread in Podocarpaceae and also in others conifers. Some retroelements such as copia pPonty3 and gypsy pPot1li are more abundant in the genome of Picea abies and Ginkgo biloba than in the species from which they were amplified.

Blotting, Southern↗

PubMed2002

Characterization of a genetic resource collection for Miscanthus (Saccharinae, Andropogoneae, Poaceae) using AFLP and ISSR PCR.

Amplified fragment length polymorphism (AFLP) and inter-simple sequence repeat markers were employed to characterize a genetic resource collection of Miscanthus, a grass under trial in Europe as a biomass crop. The 26 polymorphic markers produced by two ISSR fingerprinting primers were able to discriminate taxa and identify putative clones. AFLP fingerprints were fully reproducible and produced a larger number of markers for the three primer pairs tested, of which 998 were polymorphic (representing 79.3% of all bands). AFLP markers distinguished species, infra-specific taxa (varieties and cultivars) and putatively clonal material. They were also used to assess the inter-relationships of the taxa, to investigate the origin of important hybrid plants and to estimate the overall level of genetic variation in the collection. They were useful for assessing the species status of certain taxa such as M. transmorrisonensis, an endemic from Taiwan that was clearly distinct from M. sinensis; whereas other taxa of disputed species status, such as M. condensatus and M. yakushimanum were not genetically distinct from M. sinensis. The AFLP markers detected a high degree of infra-specific variation and allowed subdivisions of the genetic resource collection to be made, particularly within M. sinensis.

DNA Primers↗

PubMed2003

Genetic diversity in Primula obconica (Primulaceae) from central and south-west China as revealed by ISSR markers.

Genetic diversity was investigated in 60 individuals of Primula obconica from four natural populations (from Hubei, central China, and Sichuan, south-west China) and from cultivated material. Inter-simple sequence repeat (ISSR) techniques produced 249 polymorphic bands and identified 60 ISSR genotypes. Based on Shannon's index and Nei's genetic diversity, the genetic diversity detected in all natural populations of P. obconica was much higher than that in the cultivated plants, and that in the three Dalaoling (Hubei) populations was higher than that in the Wawushan (Sichuan) population. UPGMA cluster analysis showed that there was no distinct genetic differentiation between populations from the Mt Dalaoling area and the Mt Wawushan area. This study provides a population-level genetic profile of P. obconica, which was previously poorly known but which is important for Primula breeding and cultivation.

China↗

PubMed2005

Population genetic structure of Monimopetalum chinense (Celastraceae), an endangered endemic species of eastern China.

BACKGROUND AND AIMS: Monimopetalum chinense (Celastraceae) standing for the monotypic genus is endemic to eastern China. Its conservation status is vulnerable as most populations are small and isolated. Monimopetalum chinense is capable of reproducing both sexually and asexually. The aim of this study was to understand the genetic structure of M. chinense and to suggest conservation strategies. METHODS: One hundred and ninety individuals from ten populations sampled from the entire distribution area of M. chinense were investigated by using inter-simple sequence repeats (ISSR). KEY RESULTS: A total of 110 different ISSR bands were generated using ten primers. Low levels of genetic variation were revealed both at the species level (Isp=0.183) and at the population level (Ipop=0.083). High clonal diversity (D = 0.997) was found, and strong genetic differentiation among populations was detected (49.06 %). CONCLUSIONS: Small population size, possible inbreeding, limited gene flow due to short distances of seed dispersal, fragmentation of the once continuous range and subsequent genetic drift, may have contributed to shaping the population genetic structure of the species.

Analysis of Variance↗

PubMed2005

Genetic diversity and geographic differentiation in endangered Ammopiptanthus (Leguminosae) populations in desert regions of northwest China as revealed by ISSR analysis.

BACKGROUND AND AIMS: The desert legume genus Ammopiptanthus comprises two currently endangered species, A. mongolicus and A. nanus. Genetic variability and genetic differentiation between the two species and within each species were examined. METHODS: Inter-simple sequence repeat (ISSR) marker data were obtained and analysed with respect to genetic diversity, structure and gene flow. KEY RESULTS: Despite the morphological similarity between A. mongolicus and A. nanus, the two species are genetically distinct from each other, indicated by 63 % species-specific bands. Low genetic variability was detected for both population level (Shannon indices of diversity Hpop = 0.106, percentage of polymorphic loci P = 18.55 % for A. mongolicus; Hpop = 0.070, P = 12.24 % for A. nanus) and species level (Hsp = 0.1832, P = 39.39 % for A. mongolicus; Hsp = 0.1026, P = 25.89 % for A. nanus). Moderate genetic differentiation was found based on different measures (AMOVA PhiST and Hickory B) in both A. mongolicus (0.3743-0.3744) and A. nanus (0.2162-0.2369). CONCLUSIONS: The significant genetic difference between the two species might be due to a possible vicariant evolutionary event from a single common ancestor through the fragmentation of their common ancestor's range. Conservation strategies for these two endangered species are proposed.

Analysis of Variance↗

PubMed2005

Genetic variation within and among populations of a dominant desert tree Haloxylon ammodendron (Amaranthaceae) in China.

BACKGROUND AND AIMS: China is one of the countries most severely affected by desertification. Haloxylon ammodendron (Amaranthaceae) is an ecologically important component of the desert ecosystem and is one of the main tree species used for restoration, yet we know little about its genetic structure. METHODS: Genetic variation within and between nine populations of H. ammodendron from two regions of China was investigated using ISSR (inter-simple sequence repeat) markers. KEY RESULTS: Eight primers used in this study amplified 219 reproducible bands of which 184 (84 %) were polymorphic. Analysis of molecular variance (AMOVA) revealed high genetic variation within populations (97.63 %) and low genetic differentiation between regions (0.62 %) and among populations (1.75 %). CONCLUSIONS: It is suggested that the present genetic structure could have arisen by high levels of gene flow. The gene flow among populations observed here is probably mainly attributable to pollen movement. The genetic structure also has important implications in ecological restoration practice.

Amaranthaceae↗

PubMed2005

Genetic fingerprinting of germplasm accessions as an aid for species conservation: a case study with Borderea chouardii (Dioscoreaceae), one of the most critically endangered Iberian plants.

BACKGROUND AND AIMS: Molecular markers have changed previous expectations about germplasm collections of endangered plants, as new perspectives aim at holding a significant representation of all the genetic diversity in the studied species to accomplish further conservation initiatives successfully. Borderea chouardii is a critically endangered allotetraploid dioecious member of Dioscoreaceae, known from a single population in the Iberian pre-Pyrenees. This population was reported to be highly structured into two genetically distinct groups of individuals corresponding to their spatial separation along the vertical cliff where it grows. In 1999, the Spanish Government of Aragón launched the first conservation programme for the ex situ preservation of this species, and since then a seed collection has been conserved at the Germplasm Bank of the Universidad Politécnica de Madrid. However, as some seed samples had not been labelled clearly at the time of collection, their origin was uncertain. METHODS: Genetic variation in germplasm accessions of B. chouardii was investigated using microsatellite (simple sequence repeat; SSR) markers. KEY RESULTS: The 17 primer pairs used detected 62 SSR alleles in the 46 samples analysed from five different germplasm stocks. Eight alleles scored from the wild population were not detected in the germplasm samples analysed. The relatedness of the germplasm samples to the wild subpopulations through neighbour-joining clustering, principal coordinates analysis (PCO) and assignment tests revealed a biased higher representation of the genetic diversity of the lower cliff (43 samples) subpopulation than that of the upper cliff (three samples). CONCLUSIONS: The collection of additional samples from the upper cliff is recommended to achieve a better representation of the genetic diversity of this subpopulation. It is also recommended that these stocks should be managed separately according to their distinct microspatial origin in order to preserve the genetic substructuring of the wild population.

Alleles↗

PubMed2006

Genetic differentiation and relationships of populations in the Cycas balansae complex (Cycadaceae) and its conservation implications.

BACKGROUND AND AIMS: The Cycas balansae complex is arguably a controversial group with regard to species delineation. Some taxonomists recognize a single polymorphic species while others distinguish five narrowly defined ones. The unresolved taxonomy has the potential to bring about significant problems for species conservation. Thus, an investigation to examine the genetic diversity and differentiation in the C. balansae complex was performed to determine the relationship of populations and to test whether the morphologically defined segregations represent genetically distinct units. METHODS: Inter-simple sequence repeat (ISSR) markers were employed to assess the genetic diversity in the C. balansae complex with a sample of 158 individuals from all extant populations in China. KEY RESULTS: ISSR markers revealed low genetic diversity in all populations studied (H(E) and H(O) averaged 0.0639 and 0.0798 at the population level, respectively). Phenetic analysis showed that the C. balansae complex grouped into five clusters closely corresponding to the narrowly defined C. balansae, C. parvula, C. shiwandashanica, C. tanqingii and C. simplicipinna. CONCLUSIONS: ISSR data suggest that the C. balansae complex has evolved into five genetically distinct units. These might be derived from a relatively widespread common ancestor through multiple vicariant events including geographical isolation resulting from the collision of the Indian plate with the Eurasian plate and from Pleistocene glaciations. In conservation, attention should be paid to each genetic unit.

Biological Evolution↗

PubMed2006

Fine-scale genetic structure among genetic individuals of the clone-forming monotypic genus Echinosophora koreensis (Fabaceae).

BACKGROUND AND AIMS: For rare endemics or endangered plant species that reproduce both sexually and vegetatively it is critical to understand the extent of clonality because assessment of clonal extent and distribution has important ecological and evolutionary consequences with conservation implications. A survey was undertaken to understand clonal effects on fine-scale genetic structure (FSGS) in two populations (one from a disturbed and the other from an undisturbed locality) of Echinosophora koreensis, an endangered small shrub belonging to a monotypic genus in central Korea that reproduces both sexually and vegetatively via rhizomes. METHODS: Using inter-simple sequence repeats (ISSRs) as genetic markers, the spatial distribution of individuals was evaluated using Ripley's L(d)-statistics and quantified the spatial scale of clonal spread and spatial distribution of ISSR genotypes using spatial autocorrelation analysis techniques (join-count statistics and kinship coefficient, F(ij)) for total samples and samples excluding clones. KEY RESULTS: A high degree of differentiation between populations was observed (phi(ST(g)) = 0.184, P < 0.001). Ripley's L(d)-statistics revealed a near random distribution of individuals in a disturbed population, whereas significant aggregation of individuals was found in an undisturbed site. The join-count statistics revealed that most clones significantly aggregate at < or = 6-m interplant distance. The Sp statistic reflecting patterns of correlograms revealed a strong pattern of FSGS for all four data sets (Sp = 0.072-0.154), but these patterns were not significantly different from each other. At small interplant distances (< or = 2 m), however, jackknifed 95% CIs revealed that the total samples exhibited significantly higher F(ij) values than the same samples excluding clones. CONCLUSION: The strong FSGS from genets is consistent with two biological and ecological traits of E. koreensis: bee-pollination and limited seed dispersal. Furthermore, potential clone mates over repeated generations would contribute to the observed high F(ij) values among genets at short distance. To ensure long-term ex situ genetic variability of the endangered E. koreensis, individuals located at distances of 10-12 m should be collected across entire populations of E. koreensis.

Conservation of Natural Resources↗

PubMed2006

Genetic diversity and geographic differentiation in Tacca chantrieri (Taccaceae): an autonomous selfing plant with showy floral display.

BACKGROUND AND AIMS: Despite considerable investment in elaborate floral displays, Tacca chantrieri populations are predominantly selfing. It is hypothesized that this species might possess considerable spatial or temporal variation in outcrossing rates among populations. To test this hypothesis, genetic variability and genetic differentiation within and among T. chantrieri populations were investigated to find out if they are in agreement with expectations based on a predominantly inbred mating system. METHODS: Genetic diversity was quantified using inter-simple sequence repeats (ISSR) in 303 individuals from 13 populations taken from known locations of T. chantrieri in China, and from one population in Thailand. KEY RESULTS: Of the 113 primers screened, 24 produced highly reproducible ISSR bands. Using these primers, 160 discernible DNA fragments were generated, of which 145 (90.62 %) were polymorphic. This indicated considerable genetic variation at the species level. However, there were relatively low levels of polymorphism at population levels, with percentages of polymorphic bands (PPB) ranging from 8.75 % to 55 %. A high level of genetic differentiation among populations was detected based on different measures (Nei's genetic diversity analysis: G(ST) = 0.5835; AMOVA analysis: F(ST) = 0.6989). Furthermore, based on levels of genetic differentiation, the 14 populations clustered into two distinct groups separated by the Tanaka Line. CONCLUSIONS: High levels of differentiation among populations and low levels of diversity within populations at large spatial scales are consistent with earlier small-scale studies of mating patterns detected by allozymes which showed that T. chantrieri populations are predominantly selfing. However, it appears that T. chantrieri has a mixed-mating system in which self-fertilization predominates, but there is occasional outcrossing. Significant genetic differences between the two distinct regions might be attributed to vicariance along the Tanaka Line. Finally, possible mechanisms of geographic patterns based on genetic differentiation of T. chantrieri are discussed.

Dioscoreaceae↗

PubMed2006

High genetic diversity vs. low genetic differentiation in Nouelia insignis (Asteraceae), a narrowly distributed and endemic species in China, revealed by ISSR fingerprinting.

BACKGROUND AND AIMS: Nouelia insignis Franch., a monotypic genus of the Asteraceae, is an endangered species endemic in Yunnan and Sichuan Provinces of China. Most of the populations are seriously threatened. Some of them are even at the brink of extinction. In this study, the genetic diversity and differentiation between populations of this species were examined in two drainage areas. METHODS: DNA fingerprinting based on inter-simple sequence repeat polymorphisms was employed to detect the genetic variation and population structure in the species. KEY RESULTS: Genetic diversity at species level was high with P=65.05% (percentage of polymorphic loci) and Ht=0.2248 (total genetic diversity). The coefficient of genetic differentiation among populations, Gst, which was estimated by partitioning the total gene diversity, was 0.2529; whereas, the genetic differentiation between populations in the Jinsha and Nanpan drainage areas was unexpectedly low (Gst=0.0702). CONCLUSIONS: Based on the genetic analyses of the DNA fingerprinting, recent habitat fragmentation may not have led to genetic differentiation or the loss of genetic diversity in the rare species. Spatial apportionment of fingerprinting polymorphisms provides a footprint of historical migration across geographical barriers. The high diversity detected in this study holds promise for conservation and restoration efforts to save the endangered species from extinction.

Asteraceae↗

PubMed2003

Msh2 deficiency enhances somatic Apc and p53 mutations in Apc+/-Msh2-/- mice.

Inactivation of the adenomatous polyposis coli (Apc) gene by loss of the wild-type Apc allele (LOH) is a prerequisite for the development of intestinal adenomas in Msh2 proficient Min (Apc+/-Msh2+/+) mice. In contrast, adenomas from Msh2 deficient Min (Apc+/-Msh2-/-) mice are not usually associated with LOH. Given the role of Msh2 in post-replicative DNA repair, this study investigated whether Msh2 deficiency enhances somatic Apc and p53 mutations in Apc+/-Msh2-/- mice. Somatic Apc mutations (5/sample) were observed in the non-neoplastic intestinal mucosa from Apc+/-Msh2-/- mice but not from Min mice, suggesting that Msh2 deficiency is associated with a hypermutable state in the intestinal mucosa from Apc+/-Msh2-/- mice. Adenomas from Apc+/-Msh2-/- mice had a 2-fold higher rate of somatic Apc mutations (10/adenoma) than the non-neoplastic intestinal mucosa (5/sample), and did not demonstrate LOH. Truncating Apc mutations were observed in 82% of the adenomas from Apc+/-Msh2-/- mice and were not observed at all in the non-neoplastic intestinal mucosa. In contrast, in Min mice, all adenomas demonstrated LOH, had significantly less numbers of somatic Apc mutations (1.8 mutations/adenoma) compared with the adenomas from Apc+/-Msh2-/- mice, and harbored no truncating Apc mutations. These observations suggest that somatic Apc mutations, and not LOH, is a likely mechanism by which the Apc gene is inactivated in the development of adenomas in Apc+/-Msh2-/- mice in contrast to Min mice. Adenomas from Apc+/-Msh2-/- mice, but not from Min mice, also harbored somatic p53 mutations (mutation frequency of 45.5%), reflecting hypermutability associated with Msh2 deficiency. The nature and frequency of somatic Apc and p53 mutations in Apc+/-Msh2-/- mice suggest that many genomic sites, in addition to genes containing simple repeated sequences, are at risk of somatic mutations associated with Msh2 deficiency.

Adenoma↗

PubMed2005

The initiation of colon cancer in a chronic inflammatory setting.

Chronic inflammation predisposes to cancer. We used an inflammation-induced human model of tumorigenesis to explore how populations of mutated cells expand and initiate the earliest stages of cancer. Ulcerative colitis (UC) is a chronic inflammatory disease of the colon associated with an increased risk of colorectal cancer mediated through a process of genomic instability. In order to characterize the process of clonal expansion, arbitrary primed (AR) and inter-simple sequence repeat (ISSR) PCR DNA fingerprint mutation profiles of single crypts were compared with the mutational profiles from clusters of crypts and whole biopsies within the same individual. To provide information at the earliest steps of neoplastic progression, we examined histologically negative crypts, as well as dysplastic crypts. Crypts from UC dysplasia/cancer show alterations in 10-20% of DNA fingerprint sites, regardless of (i) whether the crypts were dysplastic or non-dysplastic and (ii) whether the DNA came from one crypt or thousands of crypts. Of the mutational changes in single crypts, almost half are clonally expanded to adjacent crypts and/or to the thousands of crypts in a single biopsy. Using fluorescent in-situ hybridization to examine p53 alterations in individual crypt cells, we demonstrate that the mechanism of clonal expansion can occur through crypt fission. DNA alterations are initiated in colonic crypts and expand to adjacent crypts through crypt fission. Our data suggest that a continuous process of DNA mutations, clonal expansion through crypt fission and clonal succession initiates the development of inflammatory-associated colon cancer; this mutational process is moderated by crypt cell turn-over and cell death. This paradigm may apply to other inflammatory-induced cancers.

Biopsy↗

PubMed2006

Securin induces genetic instability in colorectal cancer by inhibiting double-stranded DNA repair activity.

Genetic instability (GI) is a hallmark feature of tumor development. Securin, also known as pituitary tumor transforming gene (PTTG), is a mitotic checkpoint protein which is highly expressed in numerous cancers, is associated with tumor invasiveness, and induces GI in thyroid cells. We used fluorescence inter-simple sequence repeat PCR to assess GI caused primarily by DNA breakage events in 19 colorectal tumors. GI values ranged significantly, with Dukes' stage C&D colorectal tumors exhibiting greater GI and higher securin expression than Dukes' stage A&B tumors. Consistent with these findings, we observed a dose-dependent increase in GI in HCT116 cells in response to securin overexpression, as well as in non-transformed human fibroblasts. As securin has been implicated in a novel DNA repair pathway in fission yeast, we investigated its potential role in chemotoxic DNA damage response pathways in mammalian cells, using host cell reactivation assays. Securin overexpression in HCT116 cells inhibited etoposide-induced double-stranded DNA damage repair activity, and repressed Ku heterodimer function. Additionally, we observed that securin and Ku70 showed a reciprocal cytosol-nuclear translocation in response to etoposide-induced dsDNA damage. Our data suggest that, by repressing Ku70 activity and inhibiting the non-homologous end-joining dsDNA repair pathway, securin may be a critical gene in the development of GI in colorectal cancer.

Animals↗

PubMed2003

Structural analysis of a Lotus japonicus genome. III. Sequence features and mapping of sixty-two TAC clones which cover the 6.7 Mb regions of the genome.

A total of sixty-two clones were selected from a TAC (transformation-competent artificial chromosome) genomic library of the Lotus japonicus accession MG-20 based on the sequence information of expressed sequence tags (ESTs), cDNA and gene information, and their nucleotide sequences were determined. The length of the sequenced regions in this study is 6,682,189 bp, and the total length of the regions sequenced so far is 18,711,484 bp together with the nucleotide sequences of 121 TAC clones previously reported. By comparison with the sequences in protein and EST databases and analysis with computer programs for gene modeling, a total of 573 potential protein-coding genes with known or predicted functions, 91 gene segments and 272 pseudogenes were identified in the newly sequenced regions. Each of the sequenced clones was localized onto the linkage map of two accessions of L. japonicus, Gifu B-129 and Miyakojima MG-20, using simple sequence repeat length polymorphism (SSLP) or derived cleaved amplified polymorphic sequence (dCAPS) markers generated based on the nucleotide sequences of the clones. The sequence data, gene information and mapping information are available through the World Wide Web at http://www.kazusa.or.jp/lotus/.

Base Sequence↗