The first insight into the Taxus genome via fosmid library construction and end sequencing

Abstract

Taxus mairei is a critically endangered and commercially important cultured medicinal gymnosperm in China and forms an important medicinal resource, but the research of its genome is absent. In this study, we constructed a T. mairei fosmid library and analyzed the fosmid end sequences to provide a preliminary assessment of the genome. The library consists of one million clones with an average insert size of about 39 kb, amounting to 3.9 genome equivalents. Fosmid stability assays indicate that T. mairei DNA was stable during propagation in the fosmid system. End sequencing of both 5 0 and 3 0 ends of 968 individual clones generated 1,923 sequences after trimming, with an average sequence length of 839 bp. BLASTN searches of the nr and EST databases of GenBank and BLASTX searches of the nr database resulted in 560 (29.1%) significant hits (E \ e -5 ). Repetitive sequences analysis revealed that 20.8% of end sequences are repetitive elements, which were composed of retroelements, DNA transposons, satellites, simple repeats, and low complexity sequences. The distribution pattern of various repeat types was found to be more similar to the gymnosperm Pinus and Picea than to the monocot and dicot. The satellites of T. mairei were significantly longer than those of P. taeda and P. glauca. The tetra-nucleotide repeats of T. mairei were much longer than those of P. glauca and P. taeda. The fosmid library and the fosmid end sequences, for the first time, will serve as a useful resource for large-scale genome sequencing, physical mapping, SSR marker development and positional cloning, and provide a better understanding of the Taxus genome.

Transcriptomic Response of Chinese Yew (Taxus chinensis) to Cold Stress

“…Almost twice as many genes (62,654 vs. 36,493) were assembled in the present study as previously reported (Hao et al, 2011). This may be due to the existence of cold activated genes, as overall, 29,783 transcripts up-regulated under cold stressed condition by a factor of 4 (|log 2 FC|> 2).…”

“…The transcriptome of the genus Taxus has been previously reported for gene expression profiles in leaf, stem, and root tissues using Illumina sequencing (Hao et al, 2011) and in needles using 454 pyrosequencing (Wu et al, 2011). However, information on the large-scale regulation of gene expression profiles in response to cold stress is still lacking for this temperature-sensitive genus.…”

Transcriptome Analysis of the Tadpole Shrimp (Triops longicaudatus) by Illumina Paired-End Sequencing: Assembly, Annotation, and Marker Discovery

“…The total number of contigs, as well as the mean length, the N 50 length, and GC% were recorded. The contigs were further assembled into sequences that could not be extended at either end; these are called unigenes (having 94% identity, 30 bp overlap) [34,35]. Such unigenes were subjected to annotation analysis against public protein and nucleotide databases.…”

Advances in BAC-Based Physical Mapping and Map Integration Strategies in Plants

“…As opposed to the high technical skills and costs required to develop large-insert deep-coverage BAC libraries, Fosmid library construction remains quite trivial [33]. The narrower insert range, stable maintenance, and easy production have made Fosmids suitable for a wide range of applications [30, 34]. For instance, Fosmid libraries per se are useful for whole-genome physical mapping [35–37] and refining the BAC/PAC-based physical maps by effective gap filling [26, 30].…”

“…For instance, Fosmid libraries per se are useful for whole-genome physical mapping [35–37] and refining the BAC/PAC-based physical maps by effective gap filling [26, 30]. Furthermore, paired Fosmid end sequences, due to the narrower insert size range of Fosmid clones, are useful for sequence scaffolding in large-scale sequencing projects and studies related to structural variation and organization of the genomes [34, 38–41]. …”