Sequencing of 15,622 gene-bearing BACs reveals new features of the barley genome

Barley (Hordeum vulgareL.) possesses a large and highly repetitive genome of 5.1 Gb that has hindered the development of a complete sequence. In 2012, the International Barley Sequencing Consortium released a resource integrating whole-genome shotgun sequences with a physical and genetic framework. However, since only 6,278 BACs in the physical map were sequenced, detailed fine structure was limited. To gain access to the gene-containing portion of the barley genome at high resolution, we identified and sequenced 15,622 BACs representing the minimal tiling path of 72,052 physical mapped gene-bearing BACs. This generated about 1.7 Gb of genomic sequence containing 17,386 annotated barley genes. Exploration of the sequenced BACs revealed that although distal ends of chromosomes contain most of the gene-enriched BACs and are characterized by high rates of recombination, there are also gene-dense regions with suppressed recombination. Knowledge of these deviant regions is relevant to trait introgression, genome-wide association studies, genomic selection model development and map-based cloning strategies. Sequences and their gene and SNP annotations can be accessed and exported via http://harvest-web.org/hweb/utilmenu.wc or through the software HarvEST:Barley (download from harvest.ucr.edu). In the latter, we have implemented a synteny viewer between barley andAegilops tauschiito aid in comparative genome analysis.

Developing the Performance of Tiling Arrays

Genomic tiling arrays are able to inspect the genome of haphazard species for which the sequence is known. The plan of proper oligonucleotide probes for such arrays is computationally difficult if features such as oligonucleotide quality and recurring regions are considered. Prior works have developed the minimal tiling path problem for the choice of oligonucleotides using Dijkstra’s shortest path algorithm to compute universal finest tiling paths from millions of candidate oligonucleotides on computers. Although Dijkstra’s algorithm works well, it is complicated and may take a long time for routers to process it and the efficiency of the network fails. In this paper, the author discusses a search approach that can decrease the average complexity time of tilling arrays. This aspiration is realized by searching for the shortest path to the probes using a faster algorithm. This paper enhances A* Algorithm and exploits the enhanced version, called A**, instead of Dijkstra’s algorithm. The enhanced version is more efficient and can decrease the average time complexity, thus increasing the performance of tiling array.

Developing the Performance of Tiling Arrays

Genomic tiling arrays are able to inspect the genome of haphazard species for which the sequence is known. The plan of proper oligonucleotide probes for such arrays is computationally difficult if features such as oligonucleotide quality and recurring regions are considered. Prior works have developed the minimal tiling path problem for the choice of oligonucleotides using Dijkstra’s shortest path algorithm to compute universal finest tiling paths from millions of candidate oligonucleotides on computers. Although Dijkstra’s algorithm works well, it is complicated and may take a long time for routers to process it and the efficiency of the network fails. In this paper, the author discusses a search approach that can decrease the average complexity time of tilling arrays. This aspiration is realized by searching for the shortest path to the probes using a faster algorithm. This paper enhances A* Algorithm and exploits the enhanced version, called A**, instead of Dijkstra’s algorithm. The enhanced version is more efficient and can decrease the average time complexity, thus increasing the performance of tiling array.

A Comparative BAC Map for the Gilthead Sea Bream (Sparus aurataL.)

This study presents the first comparative BAC map of the gilthead sea bream (Sparus aurata), a highly valuated marine aquaculture fish species in the Mediterranean. High-throughput end sequencing of a BAC library yielded 92,468 reads (60.6 Mbp). Comparative mapping was achieved by anchoring BAC end sequences to the three-spined stickleback (Gasterosteus aculeatus) genome. BACs that were consistently ordered along the stickleback chromosomes accounted for 14,265 clones. A fraction of 5,249 BACs constituted a minimal tiling path that covers 73.5% of the stickleback chromosomes and 70.2% of the genes that have been annotated. The N50 size of 1,485 “BACtigs” consisting of redundant BACs is 337,253 bp. The largest BACtig covers 2.15 Mbp in the stickleback genome. According to the insert size distribution of mapped BACs the sea bream genome is 1.71-fold larger than the stickleback genome. These results represent a valuable tool to researchers in the field and may support future projects to elucidate the whole sea bream genome.

Swine Genome Sequencing Consortium (SGSC): A Strategic Roadmap for Sequencing The Pig Genome

The Swine Genome Sequencing Consortium (SGSC) was formed in September 2003 by academic, government and industry representatives to provide international coordination for sequencing the pig genome. The SGSC’s mission is to advance biomedical research for animal production and health by the development of DNAbased tools and products resulting from the sequencing of the swine genome. During the past 2 years, the SGSC has met bi-annually to develop a strategic roadmap for creating the required scientific resources, to integrate existing physical maps, and to create a sequencing strategy that captured international participation and a broad funding base. During the past year, SGSC members have integrated their respective physical mapping data with the goal of creating a minimal tiling path (MTP) that will be used as the sequencing template. During the recent Plant and Animal Genome meeting (January 16, 2005 San Diego, CA), presentations demonstrated that a human–pig comparative map has been completed, BAC fingerprint contigs (FPC) for each of the autosomes and X chromosome have been constructed and that BAC end-sequencing has permitted, through BLAST analysis and RH-mapping, anchoring of the contigs. Thus, significant progress has been made towards the creation of a MTP. In addition, whole-genome (WG) shotgun libraries have been constructed and are currently being sequenced in various laboratories around the globe. Thus, a hybrid sequencing approach in which 3x coverage of BACs comprising the MTP and 3x of the WG-shotgun libraries will be used to develop a draft 6x coverage of the pig genome.