The completion of the human genome sequence has made possible genome-wide studies of retroviral DNA integration. Here we report an analysis of 3,127 integration site sequences from human cells. We compared retroviral vectors derived from human immunodeficiency virus (HIV), avian sarcoma-leukosis virus (ASLV), and murine leukemia virus (MLV). Effects of gene activity on integration targeting were assessed by transcriptional profiling of infected cells. Integration by HIV vectors, analyzed in two primary cell types and several cell lines, strongly favored active genes. An analysis of the effects of tissue-specific transcription showed that it resulted in tissue-specific integration targeting by HIV, though the effect was quantitatively modest. Chromosomal regions rich in expressed genes were favored for HIV integration, but these regions were found to be interleaved with unfavorable regions at CpG islands. MLV vectors showed a strong bias in favor of integration near transcription start sites, as reported previously. ASLV vectors showed only a weak preference for active genes and no preference for transcription start regions. Thus, each of the three retroviruses studied showed unique integration site preferences, suggesting that virus-specific binding of integration complexes to chromatin features likely guides site selection.

https://escholarship.org/content/qt4rn2g7hh/qt4rn2g7hh.pdf?t=qalmw2

Retroviral DNA integration: ASLV, HIV, and MLV show distinct target site preferences.

Strategies for assembling large, complex genomes have evolved to include a combination of whole-genome shotgun sequencing and hierarchal map-assisted sequencing. Whole-genome maps of all types can aid genome assemblies, generally starting with low-resolution cytogenetic maps and ending with the highest resolution of sequence. Fingerprint clone maps are based upon complete restriction enzyme digests of clones representative of the target genome, and ultimately comprise a near-contiguous path of clones across the genome. Such clone-based maps are used to validate sequence assembly order, supply long-range linking information for assembled sequences, anchor sequences to the genetic map and provide templates for closing gaps. Fingerprint maps are also a critical resource for subsequent functional genomic studies, because they provide a redundant and ordered sampling of the genome with clones. In an accompanying paper we describe the draft genome sequence of the chicken, Gallus gallus, the first species sequenced that is both a model organism and a global food source. Here we present a clone-based physical map of the chicken genome at 20-fold coverage, containing 260 contigs of overlapping clones. This map represents approximately 91% of the chicken genome and enables identification of chicken clones aligned to positions in other sequenced genomes.

/pdf/a-physical-map-of-the-chicken-genome-xbkde2n105.pdf

A physical map of the chicken genome

The soybean [Glycine max (L.) Merr.] is grown worldwide for its high protein and oil contents. Characterization of soybean seed components lends itself to understanding how soybean production can meet the needs of a growing world population. For this article, literature was reviewed and condensed to create a well-rounded picture of the current understanding of structural, functional, and nutritional properties of soybean components. Natural variation in soybean protein, lipid, and carbohydrate components, as well as the minor constituents phytic acid and isoflavones, are mentioned. Environment- or genetic-induced shifts in natural variation are described with respect to nutrition and functional improvements in soybean.

Current Knowledge in Soybean Composition

Genome research promises to promote continued and enhanced plant genetic improvement. As a world's leading crop and a model system for studies of many biological processes, genomics research of cottons has advanced rapidly in the past few years. This article presents a comprehensive review on the recent advances of cotton genomics research. The reviewed areas include DNA markers, genetic maps, mapped genes and QTLs, ESTs, microarrays, gene expression profiling, BAC and BIBAC libraries, physical mapping, genome sequencing, and applications of genomic tools in cotton breeding. Analysis of the current status of each of the genome research areas suggests that the areas of physical mapping, QTL fine mapping, genome sequencing, nonfiber and nonovule EST development, gene expression profiling, and association studies between gene expression and fiber trait performance should be emphasized currently and in near future to accelerate utilization of the genomics research achievements for enhancing cotton genetic improvement.

/pdf/recent-advances-in-cotton-genomics-q0envaeyoq.pdf

Recent advances in cotton genomics.

Large-insert bacterial artificial chromosome (BAC) libraries, plant-transformation-competent binary BAC (BIBAC) libraries, and simple sequence repeat (SSR) markers are essential for many aspects of genomics research. We constructed a BAC library and a BIBAC library from the nuclear DNA of chickpea, Cicer arietinum L., cv. Hadas, partially digested with HindIII and BamHI, respectively. The BAC library has 14,976 clones, with an average insert size of 121 kb, and the BIBAC library consists of 23,040 clones, with an average insert size of 145 kb. The combined libraries collectively cover ca. 7.0 x genomes of chickpea. We screened the BAC library with eight synthetic SSR oligos, (GA)10, (GAA)7, (AT)10, (TAA)7, (TGA)7, (CA)10, (CAA)7, and (CCA)7. Positive BACs were selected, subcloned, and sequenced for SSR marker development. Two hundred and thirty-three new chickpea SSR markers were developed and characterized by PCR, using chickpea DNA as template. These results have demonstrated that BACs are an excellent source for SSR marker development in chickpea. We also estimated the distribution of the SSR loci in the chickpea genome. The SSR motifs (TAA)n and (GA)n were much more abundant than the others, and the distribution of the SSR loci appeared non-random. The BAC and BIBAC libraries and new SSR markers will provide valuable resources for chickpea genomics research and breeding (the libraries and their filters are available to the public at http://hbz.tamu.edu).

Construction of BAC and BIBAC libraries and their applications for generation of SSR markers for genome analysis of chickpea, Cicer arietinum L.

A genome-wide physical map constructed with bacterial artificial chromosomes (BACs) is an essential component in linking phenotypic traits to the responsible genetic variation in the genomes of plants and animals. We have constructed a physical map of the chicken genome from 57,091 BACs (7.9-fold haploid genome coverage) by restriction fingerprint analysis using high-resolution polyacrylamide gel electrophoresis. The physical map consists of 2331 overlapping BAC contigs and is estimated to span 1510 Mb in physical length. BAC contigs were verified manually and by screening the BACs with 367 DNA markers. A total of 361 of the contigs have been anchored to the existing chicken genetic map. This map represents the first genome-wide, BAC-based physical map of the chicken genome. It provides a powerful platform for many areas of chicken genomics, including targeted marker development, fine mapping of genes and QTL alleles, positional cloning, analysis of avian genome organization and evolution, chicken-mammalian comparative genomics, and large-scale genome sequencing.

/pdf/a-bac-based-physical-map-of-the-chicken-genome-3rvbf312dz.pdf

A BAC-Based Physical Map of the Chicken Genome

We herein report a detailed physical map of the horse Y chromosome. The euchromatic region of the chromosome comprises ≈15 megabases (Mb) of the total 45- to 50-Mb size and lies in the distal one-third of the long arm, where the pseudoautosomal region (PAR) is located terminally. The rest of the chromosome is predominantly heterochromatic. Because of the unusual organization of the chromosome (common to all mammalian Y chromosomes), a number of approaches were used to crossvalidate the results. Analysis of the 5,000-rad horse × hamster radiation hybrid panel produced a map spanning 88 centirays with 8 genes and 15 sequence-tagged site (STS) markers. The map was verified by several fluorescence in situ hybridization approaches. Isolation of bacterial artificial chromosome (BAC) clones for the radiation hybrid-mapped markers, end sequencing of the BACs, STS development, and bidirectional chromosome walking yielded 109 markers (100 STS and 9 genes) contained in 73 BACs. STS content mapping grouped the BACs into seven physically ordered contigs (of which one is predominantly ampliconic) that were verified by metaphase-, interphase-, and fiber-fluorescence in situ hybridization and also BAC fingerprinting. The map spans almost the entire euchromatic region of the chromosome, of which 20–25% (≈4 Mb) is covered by isolated BACs. The map is presently the most informative among Y chromosome maps in domesticated species, third only to the human and mouse maps. The foundation laid through the map will be critical in obtaining complete sequence of the euchromatic region of the horse Y chromosome, with an aim to identify Y specific factors governing male infertility and phenotypic sex variation.

A detailed physical map of the horse Y chromosome

Source/description: Large-insert BAC libraries have been essential components in the physical mapping and sequencing of the human genome and those of other species. Crooijmans et al. constructed a chicken BAC library with a 5.5-fold representation of the chicken genome using HindIII partial digest fragments. However, this is unlikely to provide full coverage by itself, as the use of only a single enzyme will bias against regions of the genome with unusually high or low densities of restriction sites. Kato et al. recently described a HindIII-based library of similar size, but this is not publicly available. This paper describes chicken BAC libraries constructed with three different restriction enzyme-generated inserts (HindIII, BamHI and EcoRI). Together, the three libraries should provide nearly full coverage of the chicken genome, suitable for high-resolution physical mapping and sequence analysis. All three libraries are publicly available, distributed as duplicated libraries, individual BACs and high-density colony filters. A female of the Red Jungle Fowl (Gallus gallus gallus) line UCD001 was the DNA source. A single bird from an inbred line was chosen to minimize heterozygosity that could impede eventual BAC contig assembly using fingerprint analysis. In addition, comparison of the UCD001 sequence to numerous available White Leghorn accessions should generate dense single-nucleotide polymorphism coverage of the genome...

Chengwei Ren

Papers

A BAC-Based Physical Map of the Chicken Genome

A detailed physical map of the horse Y chromosome

Construction and characterization of three BAC libraries for analysis of the chicken genome.

Genomic DNA Libraries and Physical Mapping

Whole-Genome Physical Mapping: An Overview on Methods for DNA Fingerprinting