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At least 757 records · Page 42Linked to original sources
PubMed2001

Comparative sequence analysis reveals extensive microcolinearity in the lateral suppressor regions of the tomato, Arabidopsis, and Capsella genomes.

A 57-kb region of tomato chromosome 7 harboring five different genes was compared with the sequence of the Arabidopsis genome to search for microsynteny between the genomes of these two species. For all five genes, homologous sequences could be identified in a 30-kb region located on Arabidopsis chromosome 1. Only two inversion events distinguish the arrangement of the five genes in tomato from that in Arabidopsis. Inversions were not detected when the arrangement of the five Arabidopsis genes was compared with the arrangement in the orthologous region of Capsella, a plant closely related to Arabidopsis. These results provide evidence for microcolinearity between closely and distantly related dicotyledonous species. The degree of microcolinearity found can be exploited to localize orthologous genes in Arabidopsis and tomato in an unambiguous way.

Brassicaceae↗
PubMed2004

Candidate genes for recessive non-syndromic mental retardation on chromosome 3p (MRT2A).

A mild type of autosomal recessive, non-syndromic mental retardation (NSMR) is linked to loci on chromosome 3p. This report delimits the MRT2A minimal critical region to 4.2 Mb between loci D3S3630 and D3S1304. This interval contains nine genes (IL5RA, TRNT1, LRRN1, SETMAR, SUMF1, ITPR1, BHLHB2, EDEM, and MRPS36P1). The results suggest that a mutation does not exist in these genes and that an unknown transcript in the region contributes to the cognitive deficits in NSMR.

Chromosomes, Human, Pair 3↗
PubMed2004

Conservation of the microstructure of genome segments in Brassica napus and its diploid relatives.

The cultivated Brassica species are the group of crops most closely related to Arabidopsis thaliana (Arabidopsis). They represent models for the application in crops of genomic information gained in Arabidopsis and provide an opportunity for the investigation of polyploid genome formation and evolution. The scientific literature contains contradictory evidence for the dynamics of the evolution of polyploid genomes. We aimed at overcoming the inherent complexity of Brassica genomes and clarify the effects of polyploidy on the evolution of genome microstructure in specific segments of the genome. To do this, we have constructed bacterial artificial chromosome (BAC) libraries from genomic DNA of B. rapa subspecies trilocularis (JBr) and B. napus var Tapidor (JBnB) to supplement an existing BAC library from B. oleracea. These allowed us to analyse both recent polyploidization (under 10,000 years in B. napus) and more ancient polyploidization events (ca. 20 Myr for B. rapa and B. oleracea relative to Arabidopsis), with an analysis of the events occurring on an intermediate time scale (over the ca. 4 Myr since the divergence of the B. rapa and B. oleracea lineages). Using the Arabidopsis genome sequence and clones from the JBr library, we have analysed aspects of gene conservation and microsynteny between six regions of the genome of B. rapa with the homoeologous regions of the genomes of B. oleracea and Arabidopsis. Extensive divergence of gene content was observed between the B. rapa paralogous segments and their homoeologous segments within the genome of Arabidopsis. A pattern of interspersed gene loss was identified that is similar, but not identical, to that observed in B. oleracea. The conserved genes show highly conserved collinearity with their orthologues across genomes, but a small number of species-specific rearrangements were identified. Thus the evolution of genome microstructure is an ongoing process. Brassica napus is a recently formed polyploid resulting from the hybridization of B. rapa (containing the Brassica A genome) and B. oleracea (containing the Brassica C genome). Using clones from the JBnB library, we have analysed the microstructure of the corresponding segments of the B. napus genome. The results show that there has been little or no change to the microstructure of the analysed segments of the Brassica A and C genomes as a consequence of the hybridization event forming natural B. napus. The observations indicate that, upon polyploid formation, these segments of the genome did not undergo a burst of evolution discernible at the scale of microstructure.

Brassica↗
PubMed2005

A detailed look at 7 million years of genome evolution in a 439 kb contiguous sequence at the barley Hv-eIF4E locus: recombination, rearrangements and repeats.

Six overlapping BAC clones covering the Hv-eIF4E gene region in barley were sequenced in their entire length, resulting in a 439.7 kb contiguous sequence. The contig contains only two genes, Hv-eIF4E and Hv-MLL, which are located in a small gene island and more than 88% of the sequence is composed of transposable elements. A detailed analysis of the repetitive component revealed that this chromosomal region was affected by multiple major duplication and deletion events as well as the insertion of numerous transposable elements, resulting in a complete reshuffling of genomic DNA. Resolving this highly complex pattern resulted in a model unraveling evolutionary events that shaped this region over an estimated 7 million years. Duplications and deletions caused by illegitimate recombination and unequal crossing over were major driving forces in the evolution of the Hv-eIF4E region, equaling or exceeding the effects of transposable element activities. In addition to a dramatic reshuffling of the repetitive portion of the sequence, we also found evidence for important contributions of illegitimate recombination and transposable elements to the sequence organization of the gene island containing Hv-eIF4E and Hv-MLL.

Base Composition↗
PubMed2005

Cloning and characterization of micro-RNAs from moss.

Micro-RNAs (miRNAs) are one class of endogenous tiny RNAs that play important regulatory roles in plant development and responses to external stimuli. To date, miRNAs have been cloned from higher plants such as Arabidopsis, rice and pumpkin, and there is limited information on their identity in lower plants including Bryophytes. Bryophytes are among the oldest groups of land plants among the earth's flora, and are important for our understanding of the transition to life on land. To identify miRNAs that might have played a role early in land plant evolution, we constructed a library of small RNAs from the juvenile gametophyte (protonema) of the moss Physcomitrella patens. Sequence analysis revealed five higher plant miRNA homologues, including three members of the miR319 family, previously shown to be involved in the regulation of leaf morphogenesis, and miR156, which has been suggested to regulate several members of the SQUAMOSA PROMOTER BINDING-LIKE (SPL) family in Arabidopsis. We have cloned PpSBP3, a moss SPL homologue that contains an miR156 complementary site, and demonstrated that its mRNA is cleaved within that site suggesting that it is an miR156 target in moss. Six additional candidate moss miRNAs were identified and shown to be expressed in the gametophyte, some of which were developmentally regulated or upregulated by auxin. Our observations suggest that miRNAs play important regulatory roles in mosses.

Base Sequence↗
PubMed2001

Construction and characterization of a Xanthomonas oryzae pv. oryzae bacterial artificial chromosome library.

Xanthomonas oryzae pv. oryzae is an important plant pathogen which causes bacterial blight of rice. To facilitate genome studies of this bacterium, we have constructed a bacterial artificial chromosome (BAC) library of strain MAFF 311018. It consisted of 750 clones representing 16 genome equivalents, and had an insert size ranging from 20 to 220 kb with an average size of 107 kb. This library is the first to be constructed from a X. oryzae pv. oryzae strain. The usefulness of this library was demonstrated through polymerase chain reaction screening of 11 genes and the 16S--23S rDNA spacer region in a 192-clone subset, representing five genome equivalents. The results obtained showed an average of 5.9 BAC clones per screening. This result is in good agreement with the estimated size of the test library, indicating that the constructed BAC library can be used to facilitate genome analysis of X. oryzae pv. oryzae.

Bacterial Proteins↗
PubMed2001

Genomic characterization of Helicobacter hepaticus: ordered cosmid library and comparative sequence analysis.

Helicobacter hepaticus is an important pathogen in laboratory mice and induces the development of liver tumors and gastrointestinal disease in susceptible strains of mice. In this study, a miniset of 36 cosmid clones from a genomic library of H. hepaticus was ordered and grouped into four large contigs representing approximately 1 Mb of the H. hepaticus genome using PCR, DNA sequencing, Southern and dot-blot hybridization and pulsed-field gel electrophoresis. From the 200-300 terminal nucleotide sequences of 38 cosmid clones, 56 coding regions were predicted, of which 51 were found to have orthologs in the public databases and five appeared to be unique to H. hepaticus. Of these 51 genes, 36 have orthologs in Helicobacter pylori and 25 display the highest sequence similarity to H. pylori. However, chromosomal positions of these genes are not conserved between these two helicobacters. In addition, 10 H. hepaticus genes had the highest sequence similarity to orthologs in Campylobacter jejuni. The GC content in a randomly selected 21-kb H. hepaticus genomic sequence was 35.8%, which approximates the average between H. pylori (39%) and C. jejuni (30.6%). These results demonstrate that: (1) H. hepaticus is more closely related to H. pylori than C. jejuni; (2) significant genomic alterations exist between H. hepaticus and H. pylori, including gene organization, protein sequences and GC content, probably in part due to specific adaptation to distinct ecological niches.

Animals↗
PubMed1999

The mouse major histocompatibility complex: some assembly required.

We have assembled a contig of 81 yeast artificial chromosome clones that spans 8 Mb and contains the entire major histocompatibility complex (Mhc) from mouse strain C57BL/6 (H2b), and we are in the process of assembling an Mhc contig of bacterial artificial chromosome (BAC) clones from strain 129 (H2bc), which differs from C57BL/6 in the H2-Q and H2-T regions. The current BAC contig extends from Tapasin to D17Leh89 with gaps in the class II, H2-Q, and distal H2-M regions. Only four BAC clones were required to link the class I genes of the H2-Q and H2-T regions, and no new class I gene was found in the previous gap. The proximal 1 Mb of the H2-M region has been analyzed in detail and is ready for sequencing; it includes 21 class I genes or fragments, at least 14 olfactory receptor-like genes, and a number of non-class I genes that clearly establish a conserved synteny with the class I regions of the human and rat Mhc.

Animals↗
PubMed2006

Isolation of the Atlantic salmon tyrosinase gene family reveals heterogenous transcripts in a leukocyte cell line.

In ectothermic vertebrates, visceral organs harbor melanin-containing cells. Their ability as pigment producers is nevertheless disputed. To address expression of the key genes for melanogenesis in Atlantic salmon (Salmo salar), a tyrosinase-positive leukocyte cell line (SHK-1) and skin were used to obtain full-length tyrosinase (Tyr), tyrosinase-like protein-1 (Tyrp1), and dopachrome tautomerase (Dct) mRNA transcripts. In the SHK-1 cells, two different Tyrp1 transcripts were identified, one lacking exon 1. However, only the full-length version of Tyrp1 was identified in the skin. Sequencing of Tyrp1 genomic region revealed that the two Tyrp1 transcripts might originate from two different loci, possibly a result of pseudo-tetraploidity of the Atlantic salmon genome. Expression of Tyr, Tyrp1 and Dct was investigated by quantitative real-time reverse transcriptase polymerase cain reaction showing highest expression in the SHK-1 cell line and skin, intermediate in pronephros, and negligible or absent in liver and muscle. Histological approaches were used to demonstrate melanin and revealed presence of melanized cells in skin, kidney and liver, and absence of such cells in muscle. In addition to verify melanin synthesis abilities of visceral-located cells, our results indicate loci-specific transcription differences between populations of melanin-producing cells in Atlantic salmon.

Amino Acid Sequence↗
PubMed2001

Human chromosome 19 and related regions in mouse: conservative and lineage-specific evolution.

To illuminate the function and evolutionary history of both genomes, we sequenced mouse DNA related to human chromosome 19. Comparative sequence alignments yielded confirmatory evidence for hypothetical genes and identified exons, regulatory elements, and candidate genes that were missed by other predictive methods. Chromosome-wide comparisons revealed a difference between single-copy HSA19 genes, which are overwhelmingly conserved in mouse, and genes residing in tandem familial clusters, which differ extensively in number, coding capacity, and organization between the two species. Finally, we sequenced breakpoints of all 15 evolutionary rearrangements, providing a view of the forces that drive chromosome evolution in mammals.

Animals↗
PubMed2002

A draft sequence of the rice genome (Oryza sativa L. ssp. indica).

We have produced a draft sequence of the rice genome for the most widely cultivated subspecies in China, Oryza sativa L. ssp. indica, by whole-genome shotgun sequencing. The genome was 466 megabases in size, with an estimated 46,022 to 55,615 genes. Functional coverage in the assembled sequences was 92.0%. About 42.2% of the genome was in exact 20-nucleotide oligomer repeats, and most of the transposons were in the intergenic regions between genes. Although 80.6% of predicted Arabidopsis thaliana genes had a homolog in rice, only 49.4% of predicted rice genes had a homolog in A. thaliana. The large proportion of rice genes with no recognizable homologs is due to a gradient in the GC content of rice coding sequences.

Arabidopsis↗
PubMed2003

Enrichment of gene-coding sequences in maize by genome filtration.

Approximately 80% of the maize genome comprises highly repetitive sequences interspersed with single-copy, gene-rich sequences, and standard genome sequencing strategies are not readily adaptable to this type of genome. Methodologies that enrich for genic sequences might more rapidly generate useful results from complex genomes. Equivalent numbers of clones from maize selected by techniques called methylation filtering and High C0t selection were sequenced to generate approximately 200,000 reads (approximately 132 megabases), which were assembled into contigs. Combination of the two techniques resulted in a sixfold reduction in the effective genome size and a fourfold increase in the gene identification rate in comparison to a nonenriched library.

Chromosomes, Plant↗
PubMed2003

Genomics. A dog's breakfast?

The genomes of human, mouse, and rat have been sequenced. Now, as O'Brien and Murphy announce in their Perspective, the genome sequence derby is heating up with the addition of dog to the list (Kirkness et al.). As they explain, even though the coverage of the dog genome (1.5x) is lower than that of mouse (8x), there are many valuable insights to be gained from comparing the sequence of dog with those of mouse and human.

Animals↗
PubMed2003

Maize genome sequencing by methylation filtration.

Gene enrichment strategies offer an alternative to sequencing large and repetitive genomes such as that of maize. We report the generation and analysis of nearly 100,000 undermethylated (or methylation filtration) maize sequences. Comparison with the rice genome reveals that methylation filtration results in a more comprehensive representation of maize genes than those that result from expressed sequence tags or transposon insertion sites sequences. About 7% of the repetitive DNA is unmethylated and thus selected in our libraries, but potentially active transposons and unmethylated organelle genomes can be identified. Reverse transcription polymerase chain reaction can be used to finish the maize transcriptome.

Algorithms↗
PubMed2006

Metagenomic analysis of coastal RNA virus communities.

RNA viruses infect marine organisms from bacteria to whales, but RNA virus communities in the sea remain essentially unknown. Reverse-transcribed whole-genome shotgun sequencing was used to characterize the diversity of uncultivated marine RNA virus assemblages. A diverse assemblage of RNA viruses, including a broad group of marine picorna-like viruses, and distant relatives of viruses infecting arthropods and higher plants were found. Communities were dominated by distinct genotypes with small genome sizes, and we completely assembled the genomes of several hitherto undiscovered viruses. Our results show that the oceans are a reservoir of previously unknown RNA viruses.

Animals↗
PubMed1998

Regulation of polar auxin transport by AtPIN1 in Arabidopsis vascular tissue.

Polar auxin transport controls multiple developmental processes in plants, including the formation of vascular tissue. Mutations affecting the PIN-FORMED (PIN1) gene diminish polar auxin transport in Arabidopsis thaliana inflorescence axes. The AtPIN1gene was found to encode a 67-kilodalton protein with similarity to bacterial and eukaryotic carrier proteins, and the AtPIN1 protein was detected at the basal end of auxin transport-competent cells in vascular tissue. AtPIN1 may act as a transmembrane component of the auxin efflux carrier.

Amino Acid Sequence↗
PubMed2000

A whole-genome assembly of Drosophila.

We report on the quality of a whole-genome assembly of Drosophila melanogaster and the nature of the computer algorithms that accomplished it. Three independent external data sources essentially agree with and support the assembly's sequence and ordering of contigs across the euchromatic portion of the genome. In addition, there are isolated contigs that we believe represent nonrepetitive pockets within the heterochromatin of the centromeres. Comparison with a previously sequenced 2.9- megabase region indicates that sequencing accuracy within nonrepetitive segments is greater than 99. 99% without manual curation. As such, this initial reconstruction of the Drosophila sequence should be of substantial value to the scientific community.

Algorithms↗
PubMed2000

fw2.2: a quantitative trait locus key to the evolution of tomato fruit size.

Domestication of many plants has correlated with dramatic increases in fruit size. In tomato, one quantitative trait locus (QTL), fw2.2, was responsible for a large step in this process. When transformed into large-fruited cultivars, a cosmid derived from the fw2.2 region of a small-fruited wild species reduced fruit size by the predicted amount and had the gene action expected for fw2.2. The cause of the QTL effect is a single gene, ORFX, that is expressed early in floral development, controls carpel cell number, and has a sequence suggesting structural similarity to the human oncogene c-H-ras p21. Alterations in fruit size, imparted by fw2.2 alleles, are most likely due to changes in regulation rather than in the sequence and structure of the encoded protein.

Alleles↗