The free-living flatworm, Macrostomum lignano has an impressive regenerative capacity. Following injury, it can regenerate almost an entirely new organism because of the presence of an abundant somatic stem cell population, the neoblasts. This set of unique properties makes many flatworms attractive organisms for study-ing the evolution of pathways involved in tissue self-renewal, cell-fate specification, and regeneration. The use of these organisms as models, however, is hampered by the lack of a well-assembled and annotated genome sequences, fundamental to modern genetic and molecular studies. Here we report the genomic sequence of
2016
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The free-living flatworm, Macrostomum lignano has an impressive regenerative capacity. Following injury, it can regenerate almost an entirely new organism because of the presence of an abundant somatic stem cell population, the neoblasts. This set of unique properties makes many flatworms attractive organisms for study-ing the evolution of pathways involved in tissue self-renewal, cell-fate specification, and regeneration. The use of these organisms as models, however, is hampered by the lack of a well-assembled and annotated genome sequences, fundamental to modern genetic and molecular studies. Here we report the genomic sequence of
2013
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An overview of our assembly strategy is shown in Figure 1. We started with a SOAPdenovo- based de novo assembly of Illumina sequence data from human HapMap sample NA12878, which had a contig N50 of 11.1 kb and a scaffold N50 of 590 kb after filtering for scaffolds that were at least 3 kb in length (Table 1). To order and orient these scaffolds into longer blocks, we obtained sequence data from libraries generated using the 10XG GemCode platform. In total, 97× barcoded sequence cover-age of NA12878 was obtained and, after filtering as described in the Online Methods, the result consisted of ~480,000 bar-coded pools, each of which contained an average of ~3 Mb of target DNA. Qualitatively, scaffolds that are physically near each other will co-occur in the same barcoded pools more often than expected by chance. By looking at the patterns of co-occurrence of reads from the same pool mapped onto the ends of scaffolds, we could identify and orient linked scaffolds. We used the program f...
2013
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12
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Transposable elements and expression of retrotransposons Long terminal repeat (LTR) retrotransposons were identified using structural criteria10,11. About 44% of the assembly was accounted for by TEs (Supplementary Table 8 ). LTR retrotransposons were the most abundant of these elements, representing 33% of the assembly. We compared the abundance of LTR retrotransposons in the assembly and the raw reads. The most abundant elements in the raw reads were under-represented in the assembly because of an obligate masking step (Supplementary Table 9). The Pusofa family made up 28% of all LTR retrotransposon–related sequences in the raw reads but only accounted
2013
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12
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02
Winter dormancy is a well known mechanism adopted by temperate plants, to mitigate the chilling temperature of winters. However, acquisition of sufficient chilling during winter dor-mancy ensures the normal phenological traits in subsequent growing period. Thus, low tem-perature appears to play crucial roles in growth and development of temperate plants. Apple, being an important temperate fruit crop, also requires sufficient chilling to release winter dormancy and normal phenological traits, which are often associated with yield and quality of fruits. DNA cytosine methylation is one of the important epigenetic modifications which
2013
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12
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Whole genome protein families were classified by InterProScan analysis (Jones et al., 2014). The peptidase families were identified by BLASTP searching against MEROPS peptidase database release 9.12 with a cutoff e-value of 1e-20 (Rawlings et al., 2014). The transporters were classified on the basis of Transport Classification Database (Saier et al., 2014). Carbohydrate-active enzymes were classified by using hmmer 3.0 (Mistry et al., 2013) to search against a library of catalytic and carbohydrate-binding module enzymes acquired from dbCAN (Yin et al., 2012). G-protein-coupled receptors were selected from the best hits with GPCRDB sequences (Horn et al., 2003) and by confirming that they contained seven transmembrane helices with the amino terminus outside and the carboxyl terminus inside the plasma membrane. Homologs of the Pth11-like GPCRs in Magnaporthales (Kulkarni et al., 2005) were identified by local BLASTP analysis with a cutoff e-value of 1e-10. The divergence tim...
2013
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