The genome sequence of the wisent (Bison bonasus)

This work was supported by the Youth Science and Technology Innovation Team of Sichuan Province (2014TD003), Shenzhen Industrial Designation Services Cloud Platform (GGJS20150429172906635), International Collaboration 111 Projects of China, Fundamental Research Funds for the Central Universities, 985 and 211 Projects of Sichuan University.The wisent, also known as the European bison, was rescued from extinction approximately 80 years ago through the conservation of 12 individuals. Here, we present the draft genome sequence of a male wisent individual descended from this founding stock. A total of 366 billion base pairs (Gb) of raw reads from whole-genome sequencing of this wisent were generated using the Illumina HiSeq2000 platform. The final genome assembly (2.58 Gb) is composed of 29,074 scaffolds with an N50 of 4.7 Mb. 47.3% of the genome is composed of repetitive elements. We identified 21,542 genes and 58,385 non-coding RNAs. A phylogenetic tree based on nuclear genomes indicated sister relationships between bison and wisent and between the wisent-bison clade and yak. For 75 genes we obtained evidence of positive evolution in the wisent lineage. We provide the first genome sequence and gene annotation for the wisent. The availability of these resources will be of value for the future conservation of this endangered large mammal and for reconstructing the evolutionary history of the Bovini tribe.Publisher PDFPeer reviewe

Generation of ESTs for Flowering Gene Discovery and SSR Marker Development in Upland Cotton

BACKGROUND: Upland cotton, Gossypium hirsutum L., is one of the world's most important economic crops. In the absence of the entire genomic sequence, a large number of expressed sequence tag (EST) resources of upland cotton have been generated and used in several studies. However, information about the flower development of this species is rare. METHODOLOGY/PRINCIPAL FINDINGS: To clarify the molecular mechanism of flower development in upland cotton, 22,915 high-quality ESTs were generated and assembled into 14,373 unique sequences consisting of 4,563 contigs and 9,810 singletons from a normalized and full-length cDNA library constructed from pooled RNA isolated from shoot apexes, squares, and flowers. Comparative analysis indicated that 5,352 unique sequences had no high-degree matches to the cotton public database. Functional annotation showed that several upland cotton homologs with flowering-related genes were identified in our library. The majority of these genes were specifically expressed in flowering-related tissues. Three GhSEP (G. hirsutum L. SEPALLATA) genes determining floral organ development were cloned, and quantitative real-time PCR (qRT-PCR) revealed that these genes were expressed preferentially in squares or flowers. Furthermore, 670 new putative microsatellites with flanking sequences sufficient for primer design were identified from the 645 unigenes. Twenty-five EST-simple sequence repeats were randomly selected for validation and transferability testing in 17 Gossypium species. Of these, 23 were identified as true-to-type simple sequence repeat loci and were highly transferable among Gossypium species. CONCLUSIONS/SIGNIFICANCE: A high-quality, normalized, full-length cDNA library with a total of 14,373 unique ESTs was generated to provide sequence information for gene discovery and marker development related to upland cotton flower development. These EST resources form a valuable foundation for gene expression profiling analysis, functional analysis of newly discovered genes, genetic linkage, and quantitative trait loci analysis

Generation and Analysis of a Large-Scale Expressed Sequence Tag Database from a Full-Length Enriched cDNA Library of Developing Leaves of <i>Gossypium hirsutum</i> L

<div><p>Background</p><p>Cotton (<i>Gossypium hirsutum</i> L.) is one of the world’s most economically-important crops. However, its entire genome has not been sequenced, and limited resources are available in GenBank for understanding the molecular mechanisms underlying leaf development and senescence.</p><p>Methodology/Principal Findings</p><p>In this study, 9,874 high-quality ESTs were generated from a normalized, full-length cDNA library derived from pooled RNA isolated from throughout leaf development during the plant blooming stage. After clustering and assembly of these ESTs, 5,191 unique sequences, representative 1,652 contigs and 3,539 singletons, were obtained. The average unique sequence length was 682 bp. Annotation of these unique sequences revealed that 84.4% showed significant homology to sequences in the NCBI non-redundant protein database, and 57.3% had significant hits to known proteins in the Swiss-Prot database. Comparative analysis indicated that our library added 2,400 ESTs and 991 unique sequences to those known for cotton. The unigenes were functionally characterized by gene ontology annotation. We identified 1,339 and 200 unigenes as potential leaf senescence-related genes and transcription factors, respectively. Moreover, nine genes related to leaf senescence and eleven MYB transcription factors were randomly selected for quantitative real-time PCR (qRT-PCR), which revealed that these genes were regulated differentially during senescence. The qRT-PCR for three <i>GhYLSs</i> revealed that these genes express express preferentially in senescent leaves.</p><p>Conclusions/Significance</p><p>These EST resources will provide valuable sequence information for gene expression profiling analyses and functional genomics studies to elucidate their roles, as well as for studying the mechanisms of leaf development and senescence in cotton and discovering candidate genes related to important agronomic traits of cotton. These data will also facilitate future whole-genome sequence assembly and annotation in <i>G. hirsutum</i> and comparative genomics among <i>Gossypium</i> species.</p></div

Sequence length distribution of upland cotton ESTs after assembly.

<p>Sequence length distribution of upland cotton ESTs after assembly.</p

Phylogeny analysis of putative MYB transcription factors.

<p>Twenty-two putative cotton MYB transcription factors and thirty-one putative MYB transcription factors from other plant species were aligned and analyzed by neighbor-joining in MEGA4.</p

Frequency and distribution of ESTs among assembled contigs.

<p>Frequency and distribution of ESTs among assembled contigs.</p

The most abundant ESTs detected in the <i>Gossypium hirsutum</i> leaf library.

<p>The most abundant ESTs detected in the <i>Gossypium hirsutum</i> leaf library.</p

Analysis of GhYLS8 relationships.

<p>(a) Multiple sequence alignment of GhYLS8 and other homologous proteins in plants: <i>Arabidopsis thaliana</i> YLS8 (AB047811), <i>Hevea brasiliensis</i> YLS8 (XP_004148041), <i>Cucumis sativus</i> TRX4A (XP_004163626), <i>Medicago truncatula</i> TRX4A (XP_003590204), <i>A. thaliana</i> TRXU5(AED91278) and <i>Vitis vinifera</i> TRX4A (XP_002310072). (b)Phylogenetic tree of these plant proteins constructed with MEGA 4 (c) Changes in the transcript levels of GhYLS8 genes at each leaf development stage.</p

Analysis of GhYLS9 relationships.

<p>(a) Multiple sequence alignment of GhYLS9 and other homologous proteins in plants: <i>Arabidopsis thaliana</i> YLS9 (AB047812), <i>Casuarina glauca</i> HIN1 (ABZ80409), <i>Nicotiana tabacum</i> HIN1 (BAD22533), <i>Ricinus communis</i> SYP(XP_002532540), <i>Cucumis sativus</i> SYP24 (XP_004136508) and <i>Glycine max</i> SYP24 (XP_003554459). (b) Phylogenetic tree of these plant proteins constructed with MEGA 4 (c) Changes in transcript levels of GhYLS9 genes at each leaf development stage.</p