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

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

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

Understory upheaval: factors influencing Japanese stiltgrass invasion in forestlands of Tennessee, United States

Abstract Background Invasions by non-native plants contribute to loss of ecosystem biodiversity and productivity, modification of biogeochemical cycles, and inhibition of natural regeneration of native species. Japanese stiltgrass (Microstegium vimineum (Trin.) A. Campus) is one of the most prevalent invasive grasses in the forestlands of Tennessee, United States. We measured the extent of invasion, identified potential factors affecting invasion, and quantified the relative importance of each factor. We analyzed field data collected by the Forest Inventory and Analysis Program of the U.S. Forest Service to measure the extent of invasion from 2005 to 2011 and identified potential factors affecting invasion during this period using boosted regression trees. Results Our results indicated that presence of Japanese stiltgrass on sampled plots increased 50% (from 269 to 404 plots) during the time period. The probability of invasion was correlated with one landscape condition (elevation) (20.5%) and five forest features (including tree species diversity, basal area, stand age, site productivity, and natural regeneration) (79.5%). Boosted regression trees identified the most influential (highly correlated) variables as tree species diversity (30.7%), basal area (22.9%), elevation (20.5%), and stand age (16.7%). Our results suggest that Japanese stiltgrass is likely to continue its invasion in Tennessee forests. Conclusions The present model, in addition to correlating the probability of Japanese stiltgrass invasions with current climatic conditions and landscape attributes, could aid in the on-going development of control strategies for confronting Japanese stiltgrass invasions by identifying vulnerable areas that might emerge as a result of likely changes in climatic conditions and land use patterns

Timber Production to Manage Chinese Tallow Invasions in Southern U

Abstract Economic costs associated with the invasion of nonnative species are of global concern. We estimated expected costs of Chinese tallow (Triadica sebifera (L.) Small) invasions related to timber production in southern U.S. forestlands under different management strategies. Expected costs were confined to the value of timber production losses plus costs for search and control. We simulated management strategies including (1) no control (NC), and control beginning as soon as the percentage of invaded forest land exceeded (2) 60 (Low Control), (3) 25 (Medium Control), or (4) 0 (High Control) using a spatially-explicit, stochastic, bioeconomic model. With NC, simulated invasions spread northward and westward into Arkansas and along the Gulf of Mexico to occupy &lt;1.2 million hectares within 20 years, with associated expected total costs increasing exponentially to &lt;300 million. With LC, MC, and HC, invaded areas reached <275, 34, and 2 thousand hectares after 20 years, respectively, with associated expected costs reaching <400, $230, and$200 million. Complete eradication would not be cost-effective; the minimum expected total cost was achieved when control began as soon as the percentage of invaded land exceeded 5%. These results suggest the importance of early detection and control of Chinese tallow, and emphasize the importance of integrating spread dynamics and economics to manage invasive species

Typical simulated patterns of Chinese tallow invasion with medium intensity control (A–D) and associated expected total costs (E–H) accumulated to the 5^th, 10^th, 15^th, and 20^th year, respectively.

<p>Simulations were initialized with the observed pattern of Chinese tallow invasion in the year 2003 based on the nonnative invasive plant dataset <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0033877#pone.0033877-USDA4" target="_blank">[53]</a> (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0033877#pone-0033877-g002" target="_blank">Fig. 2A</a>). Each time series of patterns is based on one randomly-chosen stochastic simulation.</p

Mean expected total costs including damage, searching, and control costs, accumulated over a 20-year period with different control thresholds.

<p>Mean expected total costs including damage, searching, and control costs, accumulated over a 20-year period with different control thresholds.</p

Typical simulated patterns of Chinese tallow invasion with high intensity control (A–D) and associated expected total costs (E–H) accumulated to the 5^th, 10^th, 15^th, and 20^th year, respectively.

<p>Simulations were initialized with the observed pattern of Chinese tallow invasion in the year 2003 based on the nonnative invasive plant dataset <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0033877#pone.0033877-USDA4" target="_blank">[53]</a> (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0033877#pone-0033877-g002" target="_blank">Fig. 2A</a>). Each time series of patterns is based on one randomly-chosen stochastic simulation.</p