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Pinus kesiya var. langbianensis

ABSTRACT: Transcriptome sequencing of Pinus kesiya var. langbianensis

PROVIDER: PRJNA412687 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR7778006_1.fastq.gz	Fastqsanger.gz
	SRR7778006_2.fastq.gz	Fastqsanger.gz
	SRR7778007_1.fastq.gz	Fastqsanger.gz
	SRR7778007_2.fastq.gz	Fastqsanger.gz

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Pinus kesiya var. langbianensis

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Transcriptome sequencing of Pinus kesiya var. langbianensis and comparative analysis in the Pinus phylogeny.

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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Identification and characterization of microsatellite markers in Pinus kesiya var. langbianensis (Pinaceae).

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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