De Novo Discovery and Comparison of Transposable Element Families in S. lycopersicum and S. pimpinellifolium

<p>Solanum lycopersicum has fewer high-copy, full-length long terminal repeat (LTR) retrotransposons than Arabidopsis and sorghum, and the average insertion age is older (2.8 vs 0.8 mya). Tandem repeat families, telomeric repeats and other repeats are found in centromeres, telomeres and other heterochromatic regions. Transposable elements (TEs) are found in both heterochromatin and euchromatin. There is a lack of well characterized repeat libraries for Solanaceous species compared to grasses like rice and wheat.</p> <p>The transposable elements in the domesticated tomato genome, S. lycopersicum heinz 1706, will be compared to S. pimpinellifolium (a close wild ancestor to domesticated tomato) as well as other more distant wild relatives and heirloom varieties and characterized by</p> <p>•Copy number</p> <p>•Within-family sequence similarity</p> <p>•Indels in alignments</p> <p>The identified transposable elements will be catalogued and available through the Sol Genomics network (SGN, http://solgenomics.net/), a clade oriented database and a repository for a large and growing number of solanaceae genomes. The collection of genomic data and computational resources of SGN provides the opportunity to study TEs across a phenotypically diverse and economically important plant family.</p

Starvation-Associated Genome Restructuring Can Lead to Reproductive Isolation in Yeast

<div><p>Knowledge of the mechanisms that lead to reproductive isolation is essential for understanding population structure and speciation. While several models have been advanced to explain post-mating reproductive isolation, experimental data supporting most are indirect. Laboratory investigations of this phenomenon are typically carried out under benign conditions, which result in low rates of genetic change unlikely to initiate reproductive isolation. Previously, we described an experimental system using the yeast <i>Saccharomyces cerevisiae</i> where starvation served as a proxy to any stress that decreases reproduction and/or survivorship. We showed that novel lineages with restructured genomes quickly emerged in starved populations, and that these survivors were more fit than their ancestors when re-starved. Here we show that certain yeast lineages that survive starvation have become reproductively isolated from their ancestor. We further demonstrate that reproductive isolation arises from genomic rearrangements, whose frequency in starving yeast is several orders of magnitude greater than an unstarved control. By contrast, the frequency of point mutations is less than 2-fold greater. In a particular case, we observe that a starved lineage becomes reproductively isolated as a direct result of the stress-related accumulation of a single chromosome. We recapitulate this result by demonstrating that introducing an extra copy of one or several chromosomes into naïve, i.e. unstarved, yeast significantly diminishes their fertility. This type of reproductive barrier, whether arising spontaneously or via genetic manipulation, can be removed by making a lineage euploid for the altered chromosomes. Our model provides direct genetic evidence that reproductive isolation can arise frequently in stressed populations via genome restructuring without the precondition of geographic isolation.</p></div

Sporulation frequencies of backcrosses and self-crosses.

<p>Crosses were made using haploid derivatives of starved isolates from four starved cultures. A – unstarved diploid control. Light grey bars are self crosses, dark grey bars are backcrosses. “*” denote significant differences between the corresponding self-cross and backcross sporulation frequencies (Bonferroni-corrected (n = 17), two-tailed Fisher's exact test at 95% confidence). “‡” denotes isolate (75a) whose self-cross lost the ability to sporulate. Sporulation frequencies among unstarved isolates backcrossed to the ancestor were indistinguishable from the diploid ancestor's (data not shown).</p

The sporulation defect of starved isolate 62a and chromosome fragment-containing strains is cured by tetraploidization.

<p><b>A</b>. Light grey: sporulation frequencies of unstarved diploid control (BY4743), selfed starved isolate 62a and the unstarved BY4743 containing a Chromosome fragment of Chromosome I (CF1); dark grey: their tetraploid derivatives. <b>B</b>. Sporulation frequencies of a diploid SK1 derivative strain containing CF1 (MKCF1) and its control euploid (diploid) strain (MK2N). Error bars are 95% Wilson's binomial CI.</p

Array-Comparative Genome Hybridization of starved isolates and their shared ancestor.

<p>aCGH of the ancestral diploid BY4743, four starved isolates displaying lower fertility in backcross (61, 62, 65, 68), two starved isolates with high fertility in backcross (71, 73), and two unstarved isolates (42 and 45). Roman numerals represent chromosome numbers. Grey vertical lines separate chromosomes. Red denotes copy number increase, green copy number decrease. Genes are represented according to their position from left to right on each chromosome. Isolate 62 displays duplicated Chromosome I. The apparent subtelomeric amplifications are artifacts of DNA preparation. Note that BY4743 is a diploid strain, whereas all isolates are haploid.</p

Extra chromosomes decrease (A) sporulation frequency and (B) spore viability, which are cured by tetraploidization to different extents (see text).

<p>Light grey, 2N – diploid strain and its derivatives containing one or several supernumerary chromosomes, as indicated. Dark grey, 4N – tetraploid derivatives. Error bars are 95% Wilson's binomial CI.</p

Additional file 2: Fig. S1. of The first whole genome and transcriptome of the cinereous vulture reveals adaptation in the gastric and immune defense systems and possible convergent evolution between the Old and New World vultures

Estimation of genome size using 17-mers. Fig. S2 The divergence time of avian species. Fig. S3 Specific amino acid changes in the gastric acid secretion associated genes. Fig. S4 Species distribution of BLASTx top hits of cinereous vulture transcripts. Fig. S5 NR protein database properties for the assembled unigenes. Fig. S6 Gene Ontology classifications of cinereous vulture unigenes. Fig. S7 Amino-acid sequence comparison of toll-like receptor 1 of the Griffon and cinereous vultures. (DOCX 2228 kb

Additional file 1: Table S1. of The first whole genome and transcriptome of the cinereous vulture reveals adaptation in the gastric and immune defense systems and possible convergent evolution between the Old and New World vultures

Sequencing and analysis statistics of the cinereous vulture’s WGS relative to the bald eagle genome. Table S2 17-mer statistics. Table S3 Summary of SNVs and small indel in the cinereous vulture. Table S4 PSGs list of the Accipitrimorphae using a branch-site model. Table S5 PSGs list of the Accipitrimorphae using a branch model. Table S6 Functional annotation chart of PSGs of the Accipitrimorphae. Table S7 PSGs list of the cinereous vulture using a branch-site model. Table S8 PSGs list of the cinereous vulture using a branch model. Table S9 PSGs list of the turkey vulture using a branch-site model. Table S10 PSGs list of the turkey vulture using a branch model. Table S11 Functional annotation chart of PSGs of the cinereous vulture. Table S12 Functional annotation chart of PSGs of the turkey vulture. Table S13 Unique amino acid changes of the turkey vulture. Table S14 Unique amino acid changes of the cinereous vulture Table S15 Unique amino acid changes of the Accipitridae. Table S16 Unique amino acid changes on sites between Accipitridae and Cathartidae of the digestive system-related proteins. Table S17 Unique amino acid changes on sites between Accipitridae and Cathartidae of the gastric acid secretion-related proteins. Table S18 Statistics regarding whole-transcriptome sequences and unigene construction. Table S19 GO analysis for the blood transcriptome of the cinereous vulture. Table S20 KEGG pathway analysis for the blood transcriptome of the cinereous vulture. Table S21 Gene expression in the cinereous vulture compared to the other avian species. Table S22 Immune related genes expression in the cinereous vulture compared to the other avian species. (XLSX 635 kb

NY-ESO-1 expression in DCIS: A new predictor of good prognosis

BACKGROUND: At present, it is difficult to predict which patients with ductal carcinoma-in-situ (DCIS) will subsequently develop frank invasive breast cancer (IDC). A recent survey by our group has shown that NY-ESO-1 and MAGEA are both expressed in DCIS. This study was aimed at determining whether expression of these antigens was related to the later development of IDC. RESULTS: 14 of 42 (33%) of patients developed invasive breast cancer during the follow up period. Only one of those DCIS cases that relapsed was positive for NYESO-1 at diagnosis. In contrast, DCIS samples of 15 of the 28 (54%) of those patients who remained disease-free expressed NY-ESO-1. (Permutation chi square p=0.0033). METHODS: We identified 42 patients with DCIS, and followed them up for more than 10 years. NY-ESO-1 and MAGEA were demonstrated by immunostaining as were CD8+ infiltrates on all sections together with the conventional markers, ER, PR, and HER2. CONCLUSIONS: Expression of NY-ESO-1 may predict those patients who will not subsequently develop invasive breast cancer and could therefore potentially be helpful in defining prognosis in patients with DCIS

Additional file 2: Figure S1. of Comparison of carnivore, omnivore, and herbivore mammalian genomes with a new leopard assembly

Species and sub-species identification for three leopard samples. Figure S2. Distribution of K-mer frequency in the error-corrected reads. Figure S3. GC content distributions. Figure S4. Composition of mammalian orthologous genes. Figure S5. Divergence time estimation of 18 mammals. Figure S6. Contraction of the amylase gene families (AMY1 and AMY2) in carnivores. Figure S7. Frame-shift mutations in Felidae GCKR genes. Figure S8. Felidae-specific amino acid changes in DNA repair system. Figure S9. Felidae-specific amino acid change in MEP1A protein. Figure S10. Felidae-specific amino acid change in ACE2 protein. Figure S11. Felidae-specific amino acid change in PRCP protein. (DOCX 2024 kb