Pinus densiflora var. zhangwuensis
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA751417 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR15371578_1.fastq.gz | Fastqsanger.gz | |||
| SRR15371579_1.fastq.gz | Fastqsanger.gz | |||
| SRR15371579_2.fastq.gz | Fastqsanger.gz |
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Project description:BackgroundPines are widely distributed in the Northern Hemisphere and have a long evolutionary history. The availability of transcriptome data has facilitated comparative transcriptomics for studying the evolutionary patterns associated with the different geographical distributions of species in the Pinus phylogeny.ResultsThe transcriptome of Pinus kesiya var. langbianensis was sequenced using the Illumina HiSeq 2000 platform, and a total of 68,881 unigenes were assembled by Trinity. Transcriptome sequences of another 12 conifer species were downloaded from public databases. All of the pairwise orthologues were identified by comparative transcriptome analysis in 13 conifer species, from which the rate of diversification was calculated and a phylogenetic tree inferred. All of the fast-evolving positive selection sequences were identified, and some salt-, drought-, and abscisic acid-resistance genes were discovered.ConclusionsmRNA sequences of P. kesiya var. langbianensis were obtained by transcriptome sequencing, and a large number of simple sequence repeat and short nucleotide polymorphism loci were detected. These data can be used in molecular marker-assisted selected in pine breeding. Divergence times were estimated in the 13 conifer species using comparative transcriptomic analysis. A number of positive selection genes were found to be related to environmental factors. Salt- and abscisic acid-related genes exhibited different selection patterns between coastal and inland Pinus. Our findings help elucidate speciation patterns in the Pinus lineage.
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Project description:To better understand the molecular bases of resin production, a major source of terpenes for industry, the transcriptome of adult Pinus elliottii var. elliottii (slash pine) trees under field commercial resinosis was obtained.
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Project description:PREMISE OF THE STUDY:Microsatellite primers were developed in Pinus kesiya var. langbianensis (Pinaceae), a species native to southwestern China, to investigate its genetic diversity and population structure in order to provide information for the conservation and management of this species. METHODS AND RESULTS:Using next-generation sequencing, a total of 2349 putative simple sequence repeat primer pairs were designed. Eighteen polymorphic markers in 60 individuals belonging to four populations of P. kesiya var. langbianensis were identified and characterized with two to 11 alleles per locus. The observed and expected heterozygosity ranged from 0.000 to 0.800 and 0.000 to 0.840, respectively. Each of these loci cross-amplified in the closely related species P. massoniana, P. densata, P. tabuliformis, and P. yunnanensis, with one to seven alleles per locus. CONCLUSIONS:The new markers are promising tools to study the population genetics of P. kesiya var. langbianensis and related species.
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Project description:Tree height growth is sensitive to climate change; therefore, incorporating climate factors into tree height prediction models can improve our understanding of this relationship and provide a scientific basis for plantation management under climate change conditions. Mongolian pine (Pinus sylvestris var. mongolica) is one of the most important afforestation species in Three-North Regions in China. Yet our knowledge on the relationship between height growth and climate for Mongolian pine is limited. Based on survey data for the dominant height of Mongolian pine and climate data from meteorological station, a mixed-effects Chapman-Richards model (including climate factors and random parameters) was used to study the effects of climate factors on the height growth of Mongolian pine in Zhanggutai sandy land, Northeast China. The results showed that precipitation had a delayed effect on the tree height growth. Generally, tree heights increased with increasing mean temperature in May and precipitation from October to April and decreased with increasing precipitation in the previous growing season. The model could effectively predict the dominant height growth of Mongolian pine under varying climate, which could help in further understanding the relationship between climate and height growth of Mongolian pine in semiarid areas of China.
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Project description:Background and aimsTuberculate ectomycorrhizae are a unique form of ectomycorrhiza where densely packed clusters of mycorrhizal root tips are enveloped by a thick hyphal sheath to form a tubercle. The functional significance of such a unique structure has not previously been established. The purpose of the present study was to investigate and measure the potential nitrogenase activity associated with Suillus tomentosus/Pinus contorta tuberculate ectomycorrhizae in two stand ages, young and old, and across a range of nitrogen-poor soil conditions.MethodsShort roots were compared with other mycorrhizae and non-mycorrhizal secondary roots using tuberculate ectomycorrhizae. Assessment of nitrogenase activity was determined and quantitative measurements were taken on tuberculate ectomycorrhizae in situ in a variety of different circumstances, by using an adaptation of the acetylene reduction assay.Key resultsSignificant nitrogenase activity was measured associated with S. tomentosus/P. contorta tuberculate ectomycorrhizae whereas no nitrogenase activity was measured with non-tuberculate mycorrhizae or secondary roots without mycorrhizae. Average nitrogenase activity ranged from undetectable to 5696.7 nmol C2H4 g(-1) tubercle 24 h(-1). Maximum nitrogenase activity was 25,098.8 nmol C2H4 g(-1) tubercle 24 h(-1). Nitrogenase activity was significantly higher in young stands than in old stands of P. contorta. Season or some covariate also seemed to affect nitrogenase activity and there was suggestion of a site effect.ConclusionsSuillus tomentosus/P. contorta tuberculate ectomycorrhizae are sites of significant nitrogenase activity. The nitrogenase activity measured could be an important contribution to the nitrogen budget of P. contorta stands. Season and stand age affect levels of nitrogenase activity.
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Project description:A set of novel expressed sequence tag (EST) microsatellite markers was developed in Pinus sylvestris var. mongolica to promote further genetic studies in this species. • One hundred seventy-five EST-simple sequence repeat (SSR) primers were designed and synthesized for 31,653 isotigs based on P. tabuliformis EST sequences. The primer pairs were used to identify 25 polymorphic loci in 48 individuals. The number of alleles ranged from two to eight with observed and expected heterozygosity values of 0.0435 to 0.8125 and 0.0430 to 0.7820, respectively. • These new polymorphic EST-SSR markers will be useful for assessing genetic diversity, molecular breeding and genetic improvement, and conservation of P. sylvestris var. mongolica.
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Project description:Transcriptome sequencing of Pinus kesiya var. langbianensis
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Project description:Pinus densiflora var. zhangwuensis S.J.Zhang, C.X.Li & X.Y.Yuan, a tree species with promising afforestation potential in northern China. Here, we assembled and annotated the complete chloroplast (cp) genome of P. densiflora var. zhangwuensis using the Oxford Nanopore sequencing technology. The cp genome was 119,725 bp in length, exhibiting a typical quadripartite structure with a large single-copy (LSC: 65,552 bp) and a small single-copy (SSC: 53,183 bp) separated by a pair of inverted repeats regions (IRA and IRB: each of 495 bp) region. The overall GC content is 37.3%. The genome was predicted to encode 112 distinct genes, including 72 protein-coding, 36 tRNA, and four rRNA genes. Maximum-likelihood (ML) phylogenetic for cp genome sequences of 18 Pinaceae species revealed that P. densiflora var. zhangwuensis was closely related to Pinus sylvestris.
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Project description:The paired-end Illumina sequencing of total genomic DNA from Arabidopsis were performed to detect unique breakpoints consistent with rearrangements of chloroplast DNA.
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