Hong-Bin Zhang

Bio: Hong-Bin Zhang is an academic researcher from Texas A&M University. The author has contributed to research in topics: Genome & Bacterial artificial chromosome. The author has an hindex of 44, co-authored 112 publications receiving 7492 citations. Previous affiliations of Hong-Bin Zhang include International Rice Research Institute & Southern Illinois University Carbondale.

Phytophthora Genome Sequences Uncover Evolutionary Origins and Mechanisms of Pathogenesis

Abstract: Draft genome sequences have been determined for the soybean pathogen Phytophthora sojae and the sudden oak death pathogen Phytophthora ramorum. Oomycetes such as these Phytophthora species share the kingdom Stramenopila with photosynthetic algae such as diatoms, and the presence of many Phytophthora genes of probable phototroph origin supports a photosynthetic ancestry for the stramenopiles. Comparison of the two species' genomes reveals a rapid expansion and diversification of many protein families associated with plant infection such as hydrolases, ABC transporters, protein toxins, proteinase inhibitors, and, in particular, a superfamily of 700 proteins with similarity to known oomycete avirulence genes.

Multi-Platform Next-Generation Sequencing of the Domestic Turkey (Meleagris gallopavo): Genome Assembly and Analysis

Abstract: A synergistic combination of two next-generation sequencing platforms with a detailed comparative BAC physical contig map provided a cost-effective assembly of the genome sequence of the domestic turkey (Meleagris gallopavo). Heterozygosity of the sequenced source genome allowed discovery of more than 600,000 high quality single nucleotide variants. Despite this heterozygosity, the current genome assembly (∼1.1 Gb) includes 917 Mb of sequence assigned to specific turkey chromosomes. Annotation identified nearly 16,000 genes, with 15,093 recognized as protein coding and 611 as non-coding RNA genes. Comparative analysis of the turkey, chicken, and zebra finch genomes, and comparing avian to mammalian species, supports the characteristic stability of avian genomes and identifies genes unique to the avian lineage. Clear differences are seen in number and variety of genes of the avian immune system where expansions and novel genes are less frequent than examples of gene loss. The turkey genome sequence provides resources to further understand the evolution of vertebrate genomes and genetic variation underlying economically important quantitative traits in poultry. This integrated approach may be a model for providing both gene and chromosome level assemblies of other species with agricultural, ecological, and evolutionary interest.

The structure of the Aegilops tauschii genepool and the evolution of hexaploid wheat

Abstract: Polymorphism in the lengths of restriction fragments at 53 single-copy loci, the rRNA locus Nor3, and the high-molecular-weight glutenin locus Glu1 was investigated in the D genome of hexaploid Triticum aestivum and that of Aegilops tauschii, the source of the T. aestivum D genome. The distribution of genetic variation in Ae. tauschii suggests gene flow between Ae. tauschii ssp. strangulata and ssp. tauschii in Iran but less in Transcaucasia. The “strangulata” genepool is wider than it appears on the basis of morphology and includes ssp. strangulata in Transcaucasia and southeastern (SE) Caspian Iran and ssp. tauschii in north-central Iran and southwestern (SW) Caspian Iran. In the latter region, Ae. tauschii morphological varieties ‘meyeri’ and ‘typica’ are equidistant to ssp. strangulata in Transcaucasia, and both belong to the “strangulata” genepool. A model of the evolution of Ae. tauschii is presented. On the geographic region basis, the D genomes of all investigated forms of T. aestivum are most closely related to the “strangulata” genepool in Transcaucasia, Armenia in particular, and SW Caspian Iran. It is suggested that the principal area of the origin of T. aestivum is Armenia, but the SW coastal area of the Caspian Sea and a corridor between the two areas may have played a role as well. Little genetic differentiation was found among the D genomes of all investigated free-threshing and hulled forms of T. aestivum, and all appear to share a single D-genome genepool, in spite of the fact that several Ae. tauschii parents were involved in the evolution of T. aestivum.

The evolution of polyploid wheats: identification of the A genome donor species.

Abstract: Cytogenetic work has shown that the tetraploid wheats, Triticum turgidum and T. timopheevii, and the hexaploid wheat T. aestivum have one pair of A genomes, whereas hexaploid T. zhukovskyi has two....

Penaeid shrimp genome provides insights into benthic adaptation and frequent molting

Abstract: Crustacea, the subphylum of Arthropoda which dominates the aquatic environment, is of major importance in ecology and fisheries. Here we report the genome sequence of the Pacific white shrimp Litopenaeus vannamei, covering ~1.66 Gb (scaffold N50 605.56 Kb) with 25,596 protein-coding genes and a high proportion of simple sequence repeats (>23.93%). The expansion of genes related to vision and locomotion is probably central to its benthic adaptation. Frequent molting of the shrimp may be explained by an intensified ecdysone signal pathway through gene expansion and positive selection. As an important aquaculture organism, L. vannamei has been subjected to high selection pressure during the past 30 years of breeding, and this has had a considerable impact on its genome. Decoding the L. vannamei genome not only provides an insight into the genetic underpinnings of specific biological processes, but also provides valuable information for enhancing crustacean aquaculture. The Pacific white shrimp Litopenaeus vannamei is an important aquaculture species and a promising model for crustacean biology. Here, the authors provide a reference genome assembly, and show that gene expansion is involved in the regulation of frequent molting as well as benthic adaptation of the shrimp.

A fast, lock-free approach for efficient parallel counting of occurrences of k-mers

Abstract: Motivation: Counting the number of occurrences of every k-mer (substring of length k) in a long string is a central subproblem in many applications, including genome assembly, error correction of sequencing reads, fast multiple sequence alignment and repeat detection. Recently, the deep sequence coverage generated by next-generation sequencing technologies has caused the amount of sequence to be processed during a genome project to grow rapidly, and has rendered current k-mer counting tools too slow and memory intensive. At the same time, large multicore computers have become commonplace in research facilities allowing for a new parallel computational paradigm. Results: We propose a new k-mer counting algorithm and associated implementation, called Jellyfish, which is fast and memory efficient. It is based on a multithreaded, lock-free hash table optimized for counting k-mers up to 31 bases in length. Due to their flexibility, suffix arrays have been the data structure of choice for solving many string problems. For the task of k-mer counting, important in many biological applications, Jellyfish offers a much faster and more memory-efficient solution. Availability: The Jellyfish software is written in C++ and is GPL licensed. It is available for download at http://www.cbcb.umd.edu/software/jellyfish. Contact: [email protected] Supplementary information:Supplementary data are available at Bioinformatics online.

The tomato genome sequence provides insights into fleshy fruit evolution

Abstract: Tomato (Solanum lycopersicum) is a major crop plant and a model system for fruit development. Solanum is one of the largest angiosperm genera1 and includes annual and perennial plants from diverse habitats. Here we present a high-quality genome sequence of domesticated tomato, a draft sequence of its closest wild relative, Solanum pimpinellifolium2, and compare them to each other and to the potato genome (Solanum tuberosum). The two tomato genomes show only 0.6% nucleotide divergence and signs of recent admixture, but show more than 8% divergence from potato, with nine large and several smaller inversions. In contrast to Arabidopsis, but similar to soybean, tomato and potato small RNAs map predominantly to gene-rich chromosomal regions, including gene promoters. The Solanum lineage has experienced two consecutive genome triplications: one that is ancient and shared with rosids, and a more recent one. These triplications set the stage for the neofunctionalization of genes controlling fruit characteristics, such as colour and fleshiness.

Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution

Abstract: We present here a draft genome sequence of the red jungle fowl, Gallus gallus. Because the chicken is a modern descendant of the dinosaurs and the first non-mammalian amniote to have its genome sequenced, the draft sequence of its genome--composed of approximately one billion base pairs of sequence and an estimated 20,000-23,000 genes--provides a new perspective on vertebrate genome evolution, while also improving the annotation of mammalian genomes. For example, the evolutionary distance between chicken and human provides high specificity in detecting functional elements, both non-coding and coding. Notably, many conserved non-coding sequences are far from genes and cannot be assigned to defined functional classes. In coding regions the evolutionary dynamics of protein domains and orthologous groups illustrate processes that distinguish the lineages leading to birds and mammals. The distinctive properties of avian microchromosomes, together with the inferred patterns of conserved synteny, provide additional insights into vertebrate chromosome architecture.