Comparative Genomic Analysis of Adaptive and Economic Traits Related Genes in Southern Pines

Four major Southern pines, Pinus echinata Mill., P. elliottii Engelm., P. palustris Mill. and P. taeda L. are evolutionarily young and closely related. They have not been intensely researched except P. taeda. In this study we addressed the questions of exonintron structure, nucleotide variation and neutrality in adaptive and economic traits related genes, and phylogenetic relationships between these pines. Using publically available data in the NCBI databases, we first developed a series of statistical regression models. We defined functional relationships between the parameters that can be easily estimated from a small data sample (e.g. mean exon length and exon/gene ratio), and parameters that are difficult to assess (e.g. number of genes and exons). Second, we examined the effects of selection upon the set of studied genes in the four pines. We collected data from individuals representing all four Southern pines and merged them with previously published data, and applied four neutrality tests: Tajima’s D, McDonald- Kreitman (MK), Hudson-Kreitman-Aguade (HKA), and synonymous-nonsynonymous nucleotide substitutions ratio. Finally, we analyzed phylogenetic relationships between the four Southern pines, and with respect to other selected pine species (P. radiata, P. pinaster and P. sylvestris), for which the nucleotide sequence data orthologous to the sequences newly generated in this study were available in the NCBI GenBank. We applied Maximum Parsimony, Maximum Likelihood and Bayesian Inference approaches. Based on the statistical models we expect about 13-14 thousand genes in an organism with the mean exon length of 334.8 bp (like P. taeda). This number could be higher in plants (20-21 thousand). Furthermore, we identified signatures of selection in some of the studied genes, and demonstrated that different parts of a gene could be under different forms of selection. Therefore, the results of the neutrality tests performed at the entire gene level could be misleading. Finally, using twelve nuclear loci we confirmed very tight phylogenetic relationships within the subsection Australes, but the conclusions were not robust. Using two exclusive sets of three genes led to robust but conflicting results. Therefore, we demonstrated that conclusions about “species” trees based on “gene” trees may be misleading, especially for closely related species

Exome Genotyping, Linkage Disequilibrium and Population Structure in Loblolly Pine (\u3cem\u3ePinus taeda\u3c/em\u3e L.)

Background: Loblolly pine (Pinus taeda L.) is one of the most widely planted and commercially important forest tree species in the USA and worldwide, and is an object of intense genomic research. However, whole genome resequencing in loblolly pine is hampered by its large size and complexity and a lack of a good reference. As a valid and more feasible alternative, entire exome sequencing was hence employed to identify the gene-associated single nucleotide polymorphisms (SNPs) and to genotype the sampled trees. Results: The exons were captured in the ADEPT2 association mapping population of 375 clonally-propagated loblolly pine trees using NimbleGen oligonucleotide hybridization probes, and then exome-enriched genomic DNA fragments were sequenced using the Illumina HiSeq 2500 platform. Oligonucleotide probes were designed based on 199,723 exons (≈49 Mbp) partitioned from the loblolly pine reference genome (PineRefSeq v. 1.01). The probes covered 90.2 % of the target regions. Capture efficiency was high; on average, 67 % of the sequence reads generated for each tree could be mapped to the capture target regions, and more than 70 % of the captured target bases had at least 10X sequencing depth per tree. A total of 972,720 high quality SNPs were identified after filtering. Among them, 53 % were located in coding regions (CDS), 5 % in 5’ or 3’ untranslated regions (UTRs) and 42 % in non-target and non-coding regions, such as introns and adjacent intergenic regions collaterally captured. We found that linkage disequilibrium (LD) decayed very rapidly, with the correlation coefficient (r 2) between pairs of SNPs linked within single scaffolds decaying to half maximum (r 2 = 0.22) within 55 bp, to r 2 = 0.1 within 192 bp, and to r 2 = 0.05 within 451 bp. Population structure analysis using unlinked SNPs demonstrated the presence of two main distinct clusters representing western and eastern parts of the loblolly pine range included in our sample of trees. Conclusions: The obtained results demonstrated the efficiency of exome capture for genotyping species such as loblolly pine with a large and complex genome. The highly diverse genetic variation reported in this study will be a valuable resource for future genetic and genomic research in loblolly pine

Influence of the electric field on the latent heat of the ferroelectric phase transition in KDP

The specific heat, heat flux (DTA trace) and dielectric constant of KDP ferroelectric crystal have been measured simultaneously for various electric fields with a conduction calorimeter. The specific heat presents a strong anomaly but these simultaneous measurements allow us to evaluate the latent heat accurately. Latent heat decreases with field and the value of critical electric field --that where latent heat disappears-- is estimated to be (0.44\pm0.03) kV/cm. Incidentally, we have measured simultaneously the dielectric permittivity which suggests that latent heat is developed as domains are growing.Comment: 7 pages, 6 figures, ReVTeX, twocolumn format, to appear in J. Phys. Cond. Matte

The Douglas-Fir Genome Sequence Reveals Specialization of the Photosynthetic Apparatus in Pinaceae.

A reference genome sequence for Pseudotsuga menziesii var. menziesii (Mirb.) Franco (Coastal Douglas-fir) is reported, thus providing a reference sequence for a third genus of the family Pinaceae. The contiguity and quality of the genome assembly far exceeds that of other conifer reference genome sequences (contig N50 = 44,136 bp and scaffold N50 = 340,704 bp). Incremental improvements in sequencing and assembly technologies are in part responsible for the higher quality reference genome, but it may also be due to a slightly lower exact repeat content in Douglas-fir vs. pine and spruce. Comparative genome annotation with angiosperm species reveals gene-family expansion and contraction in Douglas-fir and other conifers which may account for some of the major morphological and physiological differences between the two major plant groups. Notable differences in the size of the NDH-complex gene family and genes underlying the functional basis of shade tolerance/intolerance were observed. This reference genome sequence not only provides an important resource for Douglas-fir breeders and geneticists but also sheds additional light on the evolutionary processes that have led to the divergence of modern angiosperms from the more ancient gymnosperms

Oral capecitabine as an alternative to i.v. 5-fluorouracil-based adjuvant therapy for colon cancer: safety results of a randomized, phase III trial

Background: Oral capecitabine achieves a superior response rate with an improved safety profile compared with bolus 5-fluorouracil-leucovorin (5-FU/LV) as first-line treatment for patients with metastatic colorectal cancer. We report here the results of a large phase III trial investigating adjuvant oral capecitabine compared with 5-FU/LV (Mayo Clinic regimen) in Dukes' C colon cancer. Patients and methods: Patients aged 18-75 years with resected Dukes' C colon carcinoma were randomized to receive 24 weeks of treatment with either oral capecitabine 1250 mg/m2 twice daily, days 1-14 every 21 days (n = 993), or i.v. bolus 5-FU 425 mg/m2 with i.v. leucovorin 20 mg/m2 on days 1-5, repeated every 28 days (n = 974). Results: Patients receiving capecitabine experienced significantly (P <0.001) less diarrhea, stomatitis, nausea/vomiting, alopecia and neutropenia, but more hand-foot syndrome than those receiving 5-FU/LV. Fewer patients receiving capecitabine experienced grade 3 or 4 neutropenia, febrile neutropenia/sepsis and stomatitis (P <0.001), although more experienced grade 3 hand-foot syndrome than those treated with 5-FU/LV (P <0.001). Capecitabine demonstrates a similar, favorable safety profile in patients aged <65 years or ≥65 years old. Conclusions: Based on its improved safety profile, capecitabine has the potential to replace 5-FU/LV as standard adjuvant treatment for patients with colon cancer. Efficacy results are expected to be available in 2004. Keywords: Adjuvant treatment, capecitabine, chemotherapy, colorectal cance

Evolution of Exon-Intron Structure and Alternative Splicing

Despite significant advances in high-throughput DNA sequencing, many important species remain understudied at the genome level. In this study we addressed a question of what can be predicted about the genome-wide characteristics of less studied species, based on the genomic data from completely sequenced species. Using NCBI databases we performed a comparative genome-wide analysis of such characteristics as alternative splicing, number of genes, gene products and exons in 36 completely sequenced model species. We created statistical regression models to fit these data and applied them to loblolly pine (Pinus taeda L.), an example of an important species whose genome has not been completely sequenced yet. Using these models, the genome-wide characteristics, such as total number of genes and exons, can be roughly predicted based on parameters estimated from available limited genomic data, e.g. exon length and exon/gene ratio

The attitudes toward forcible date rape (FDR) scale: Development of a measurement model

Using data from 341 female and 237 male college students that were collected previously (Fischer, G. J., Archives of Sexual Behavior , 15, 457–466, 1986), several true score measurement models were used to describe the variance-covariance structure of a nine-item attitude toward a forcible date rape (FDR) scale. The congeneric true score model fit the data best, but not satisfactorily. By deleting “noncongeneric” items, a six-item, unweighted linear composite variable based on the congeneric true score model was shown to fit the data, and reliabilities and validities based on this model proved satisfactory for females, males, and the total sample. The factor structure of the model for females and for males was not equivalent, but the general patterns were similar. Suggestions for further research included a validation study of the six-item scale on an independent sample and a comparison of 5-and 7-point Likert response scales to see if the lack of model equivalence by gender could be due, in part, to more variability in attitudes toward forcible date rape in men than women.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/44789/1/10862_2005_Article_BF02229064.pd

Conflicting genomic signals affecting phylogenetic inference in four species of North American pines

Текст статьи не публикуется в открытом доступе в соответствии с политикой журнала.Adaptive evolutionary processes in plants may be accompanied by episodes of introgression, parallel evolution and incomplete lineage sorting that pose challenges in untangling species evolutionary history. Genus Pinus (pines) is one of the most abundant and most studied groups among gymnosperms, and a good example of a lineage where these phenomena have been observed. Pines are among the most ecologically and economically important plant species. Some, such as the pines of the southeastern USA (southern pines in subsection Australes), are subjects of intensive breeding programs. Despite numerous published studies, the evolutionary history of Australes remains ambiguous and often controversial. We studied the phylogeny of four major southern pine species: shortleaf (Pinus echinata), slash (P. elliottii), longleaf (P. palustris) and loblolly (P. taeda), using sequences from 11 nuclear loci and maximum likelihood and Bayesian methods. Our analysis encountered resolution difficulties similar to earlier published studies. Although incomplete lineage sorting and introgression are two phenomena presumptively underlying our results, the phylogenetic inferences seem to be also influenced by the genes examined, with certain topologies supported by sets of genes sharing common putative functionalities. For example, genes involved in wood formation supported the clades echinata–taeda, genes linked to plant defence supported the clade echinata–elliottii, whereas genes linked to water management properties supported the clade echinata-palustris. The support for these clades was very high and consistent across methods. We discuss the potential factors that could underlie these observations, including incomplete lineage sorting, hybridization and parallel or adaptive evolution. Our results likely reflect the relatively short evolutionary history of the subsection that is thought to have begun during the middle Miocene and has been influenced by climate fluctuations

Conflicting genomic signals affecting phylogenetic inference in four species of North American pines

Текст статьи не публикуется в открытом доступе в соответствии с политикой журнала.Adaptive evolutionary processes in plants may be accompanied by episodes of introgression, parallel evolution and incomplete lineage sorting that pose challenges in untangling species evolutionary history. Genus Pinus (pines) is one of the most abundant and most studied groups among gymnosperms, and a good example of a lineage where these phenomena have been observed. Pines are among the most ecologically and economically important plant species. Some, such as the pines of the southeastern USA (southern pines in subsection Australes), are subjects of intensive breeding programs. Despite numerous published studies, the evolutionary history of Australes remains ambiguous and often controversial. We studied the phylogeny of four major southern pine species: shortleaf (Pinus echinata), slash (P. elliottii), longleaf (P. palustris) and loblolly (P. taeda), using sequences from 11 nuclear loci and maximum likelihood and Bayesian methods. Our analysis encountered resolution difficulties similar to earlier published studies. Although incomplete lineage sorting and introgression are two phenomena presumptively underlying our results, the phylogenetic inferences seem to be also influenced by the genes examined, with certain topologies supported by sets of genes sharing common putative functionalities. For example, genes involved in wood formation supported the clades echinata–taeda, genes linked to plant defence supported the clade echinata–elliottii, whereas genes linked to water management properties supported the clade echinata-palustris. The support for these clades was very high and consistent across methods. We discuss the potential factors that could underlie these observations, including incomplete lineage sorting, hybridization and parallel or adaptive evolution. Our results likely reflect the relatively short evolutionary history of the subsection that is thought to have begun during the middle Miocene and has been influenced by climate fluctuations