Comparative transcriptomics of a complex of four European pine species

Background Pinus sylvestris, P. mugo, P. uliginosa and P. uncinata are closely related but phenotypically and ecologically very distinct European pine species providing an excellent study system for analysis of the genetic basis of adaptive variation and speciation. For comparative genomic analysis...
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Autor*in:	Wachowiak, Witold [verfasserIn] Trivedi, Urmi Perry, Annika Cavers, Stephen

Format:	E-Artikel
Sprache:	Englisch

Erschienen:	2015

Schlagwörter:	Whole transcriptome sequencing Ontology SNPs Nucleotide divergence Species complex

Anmerkung:	© Wachowiak et al. 2015

Übergeordnetes Werk:	Enthalten in: BMC genomics - London : BioMed Central, 2000, 16(2015), 1 vom: 25. März
Übergeordnetes Werk:	volume:16 ; year:2015 ; number:1 ; day:25 ; month:03

Links:	Volltext

DOI / URN:	10.1186/s12864-015-1401-z

Katalog-ID:	SPR027104729

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520			\|a Background Pinus sylvestris, P. mugo, P. uliginosa and P. uncinata are closely related but phenotypically and ecologically very distinct European pine species providing an excellent study system for analysis of the genetic basis of adaptive variation and speciation. For comparative genomic analysis of the species, transcriptome sequence was generated for 17 samples collected across the European distribution range using Illumina paired-end sequencing technology. Results De novo transcriptome assembly of a reference sample of P. sylvestris contained 40968 unigenes, of which fewer than 0.5% were identified as putative retrotransposon sequences. Based on gene annotation approaches, 19659 contigs were identified and assigned to unique genes covering a broad range of gene ontology categories. About 80% of the reads from each sample were successfully mapped to the reference transcriptome of P. sylvestris. Single nucleotide polymorphisms were identified in 22041-24096 of the unigenes providing a set of ~220-262 k SNPs identified for each species. Very similar levels of nucleotide polymorphism were observed across species (π=0.0044-0.0053) and highest pairwise nucleotide divergence (0.006) was found between P. mugo and P. sylvestris at a common set of unigenes. Conclusions The study provides whole transcriptome sequence and a large set of SNPs to advance population and association genetic studies in pines. Our study demonstrates that transcriptome sequencing can be a very useful approach for development of novel genomic resources in species with large and complex genomes.
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650		4	\|a Nucleotide divergence \|7 (dpeaa)DE-He213
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700	1		\|a Perry, Annika \|4 aut
700	1		\|a Cavers, Stephen \|4 aut
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allfields	10.1186/s12864-015-1401-z doi (DE-627)SPR027104729 (SPR)s12864-015-1401-z-e DE-627 ger DE-627 rakwb eng Wachowiak, Witold verfasserin aut Comparative transcriptomics of a complex of four European pine species 2015 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © Wachowiak et al. 2015 Background Pinus sylvestris, P. mugo, P. uliginosa and P. uncinata are closely related but phenotypically and ecologically very distinct European pine species providing an excellent study system for analysis of the genetic basis of adaptive variation and speciation. For comparative genomic analysis of the species, transcriptome sequence was generated for 17 samples collected across the European distribution range using Illumina paired-end sequencing technology. Results De novo transcriptome assembly of a reference sample of P. sylvestris contained 40968 unigenes, of which fewer than 0.5% were identified as putative retrotransposon sequences. Based on gene annotation approaches, 19659 contigs were identified and assigned to unique genes covering a broad range of gene ontology categories. About 80% of the reads from each sample were successfully mapped to the reference transcriptome of P. sylvestris. Single nucleotide polymorphisms were identified in 22041-24096 of the unigenes providing a set of ~220-262 k SNPs identified for each species. Very similar levels of nucleotide polymorphism were observed across species (π=0.0044-0.0053) and highest pairwise nucleotide divergence (0.006) was found between P. mugo and P. sylvestris at a common set of unigenes. Conclusions The study provides whole transcriptome sequence and a large set of SNPs to advance population and association genetic studies in pines. Our study demonstrates that transcriptome sequencing can be a very useful approach for development of novel genomic resources in species with large and complex genomes. Whole transcriptome sequencing (dpeaa)DE-He213 Ontology (dpeaa)DE-He213 SNPs (dpeaa)DE-He213 Nucleotide divergence (dpeaa)DE-He213 Species complex (dpeaa)DE-He213 Trivedi, Urmi aut Perry, Annika aut Cavers, Stephen aut Enthalten in BMC genomics London : BioMed Central, 2000 16(2015), 1 vom: 25. März (DE-627)326644954 (DE-600)2041499-7 1471-2164 nnns volume:16 year:2015 number:1 day:25 month:03 https://dx.doi.org/10.1186/s12864-015-1401-z kostenfrei Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER SSG-OLC-PHA GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_702 GBV_ILN_2001 GBV_ILN_2003 GBV_ILN_2005 GBV_ILN_2006 GBV_ILN_2008 GBV_ILN_2009 GBV_ILN_2010 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2015 GBV_ILN_2020 GBV_ILN_2021 GBV_ILN_2025 GBV_ILN_2031 GBV_ILN_2038 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2050 GBV_ILN_2055 GBV_ILN_2056 GBV_ILN_2057 GBV_ILN_2061 GBV_ILN_2111 GBV_ILN_2113 GBV_ILN_2190 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 16 2015 1 25 03
spelling	10.1186/s12864-015-1401-z doi (DE-627)SPR027104729 (SPR)s12864-015-1401-z-e DE-627 ger DE-627 rakwb eng Wachowiak, Witold verfasserin aut Comparative transcriptomics of a complex of four European pine species 2015 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © Wachowiak et al. 2015 Background Pinus sylvestris, P. mugo, P. uliginosa and P. uncinata are closely related but phenotypically and ecologically very distinct European pine species providing an excellent study system for analysis of the genetic basis of adaptive variation and speciation. For comparative genomic analysis of the species, transcriptome sequence was generated for 17 samples collected across the European distribution range using Illumina paired-end sequencing technology. Results De novo transcriptome assembly of a reference sample of P. sylvestris contained 40968 unigenes, of which fewer than 0.5% were identified as putative retrotransposon sequences. Based on gene annotation approaches, 19659 contigs were identified and assigned to unique genes covering a broad range of gene ontology categories. About 80% of the reads from each sample were successfully mapped to the reference transcriptome of P. sylvestris. Single nucleotide polymorphisms were identified in 22041-24096 of the unigenes providing a set of ~220-262 k SNPs identified for each species. Very similar levels of nucleotide polymorphism were observed across species (π=0.0044-0.0053) and highest pairwise nucleotide divergence (0.006) was found between P. mugo and P. sylvestris at a common set of unigenes. Conclusions The study provides whole transcriptome sequence and a large set of SNPs to advance population and association genetic studies in pines. Our study demonstrates that transcriptome sequencing can be a very useful approach for development of novel genomic resources in species with large and complex genomes. Whole transcriptome sequencing (dpeaa)DE-He213 Ontology (dpeaa)DE-He213 SNPs (dpeaa)DE-He213 Nucleotide divergence (dpeaa)DE-He213 Species complex (dpeaa)DE-He213 Trivedi, Urmi aut Perry, Annika aut Cavers, Stephen aut Enthalten in BMC genomics London : BioMed Central, 2000 16(2015), 1 vom: 25. März (DE-627)326644954 (DE-600)2041499-7 1471-2164 nnns volume:16 year:2015 number:1 day:25 month:03 https://dx.doi.org/10.1186/s12864-015-1401-z kostenfrei Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER SSG-OLC-PHA GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_702 GBV_ILN_2001 GBV_ILN_2003 GBV_ILN_2005 GBV_ILN_2006 GBV_ILN_2008 GBV_ILN_2009 GBV_ILN_2010 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2015 GBV_ILN_2020 GBV_ILN_2021 GBV_ILN_2025 GBV_ILN_2031 GBV_ILN_2038 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2050 GBV_ILN_2055 GBV_ILN_2056 GBV_ILN_2057 GBV_ILN_2061 GBV_ILN_2111 GBV_ILN_2113 GBV_ILN_2190 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 16 2015 1 25 03
allfields_unstemmed	10.1186/s12864-015-1401-z doi (DE-627)SPR027104729 (SPR)s12864-015-1401-z-e DE-627 ger DE-627 rakwb eng Wachowiak, Witold verfasserin aut Comparative transcriptomics of a complex of four European pine species 2015 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © Wachowiak et al. 2015 Background Pinus sylvestris, P. mugo, P. uliginosa and P. uncinata are closely related but phenotypically and ecologically very distinct European pine species providing an excellent study system for analysis of the genetic basis of adaptive variation and speciation. For comparative genomic analysis of the species, transcriptome sequence was generated for 17 samples collected across the European distribution range using Illumina paired-end sequencing technology. Results De novo transcriptome assembly of a reference sample of P. sylvestris contained 40968 unigenes, of which fewer than 0.5% were identified as putative retrotransposon sequences. Based on gene annotation approaches, 19659 contigs were identified and assigned to unique genes covering a broad range of gene ontology categories. About 80% of the reads from each sample were successfully mapped to the reference transcriptome of P. sylvestris. Single nucleotide polymorphisms were identified in 22041-24096 of the unigenes providing a set of ~220-262 k SNPs identified for each species. Very similar levels of nucleotide polymorphism were observed across species (π=0.0044-0.0053) and highest pairwise nucleotide divergence (0.006) was found between P. mugo and P. sylvestris at a common set of unigenes. Conclusions The study provides whole transcriptome sequence and a large set of SNPs to advance population and association genetic studies in pines. Our study demonstrates that transcriptome sequencing can be a very useful approach for development of novel genomic resources in species with large and complex genomes. Whole transcriptome sequencing (dpeaa)DE-He213 Ontology (dpeaa)DE-He213 SNPs (dpeaa)DE-He213 Nucleotide divergence (dpeaa)DE-He213 Species complex (dpeaa)DE-He213 Trivedi, Urmi aut Perry, Annika aut Cavers, Stephen aut Enthalten in BMC genomics London : BioMed Central, 2000 16(2015), 1 vom: 25. März (DE-627)326644954 (DE-600)2041499-7 1471-2164 nnns volume:16 year:2015 number:1 day:25 month:03 https://dx.doi.org/10.1186/s12864-015-1401-z kostenfrei Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER SSG-OLC-PHA GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_702 GBV_ILN_2001 GBV_ILN_2003 GBV_ILN_2005 GBV_ILN_2006 GBV_ILN_2008 GBV_ILN_2009 GBV_ILN_2010 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2015 GBV_ILN_2020 GBV_ILN_2021 GBV_ILN_2025 GBV_ILN_2031 GBV_ILN_2038 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2050 GBV_ILN_2055 GBV_ILN_2056 GBV_ILN_2057 GBV_ILN_2061 GBV_ILN_2111 GBV_ILN_2113 GBV_ILN_2190 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 16 2015 1 25 03
allfieldsGer	10.1186/s12864-015-1401-z doi (DE-627)SPR027104729 (SPR)s12864-015-1401-z-e DE-627 ger DE-627 rakwb eng Wachowiak, Witold verfasserin aut Comparative transcriptomics of a complex of four European pine species 2015 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © Wachowiak et al. 2015 Background Pinus sylvestris, P. mugo, P. uliginosa and P. uncinata are closely related but phenotypically and ecologically very distinct European pine species providing an excellent study system for analysis of the genetic basis of adaptive variation and speciation. For comparative genomic analysis of the species, transcriptome sequence was generated for 17 samples collected across the European distribution range using Illumina paired-end sequencing technology. Results De novo transcriptome assembly of a reference sample of P. sylvestris contained 40968 unigenes, of which fewer than 0.5% were identified as putative retrotransposon sequences. Based on gene annotation approaches, 19659 contigs were identified and assigned to unique genes covering a broad range of gene ontology categories. About 80% of the reads from each sample were successfully mapped to the reference transcriptome of P. sylvestris. Single nucleotide polymorphisms were identified in 22041-24096 of the unigenes providing a set of ~220-262 k SNPs identified for each species. Very similar levels of nucleotide polymorphism were observed across species (π=0.0044-0.0053) and highest pairwise nucleotide divergence (0.006) was found between P. mugo and P. sylvestris at a common set of unigenes. Conclusions The study provides whole transcriptome sequence and a large set of SNPs to advance population and association genetic studies in pines. Our study demonstrates that transcriptome sequencing can be a very useful approach for development of novel genomic resources in species with large and complex genomes. Whole transcriptome sequencing (dpeaa)DE-He213 Ontology (dpeaa)DE-He213 SNPs (dpeaa)DE-He213 Nucleotide divergence (dpeaa)DE-He213 Species complex (dpeaa)DE-He213 Trivedi, Urmi aut Perry, Annika aut Cavers, Stephen aut Enthalten in BMC genomics London : BioMed Central, 2000 16(2015), 1 vom: 25. März (DE-627)326644954 (DE-600)2041499-7 1471-2164 nnns volume:16 year:2015 number:1 day:25 month:03 https://dx.doi.org/10.1186/s12864-015-1401-z kostenfrei Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER SSG-OLC-PHA GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_702 GBV_ILN_2001 GBV_ILN_2003 GBV_ILN_2005 GBV_ILN_2006 GBV_ILN_2008 GBV_ILN_2009 GBV_ILN_2010 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2015 GBV_ILN_2020 GBV_ILN_2021 GBV_ILN_2025 GBV_ILN_2031 GBV_ILN_2038 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2050 GBV_ILN_2055 GBV_ILN_2056 GBV_ILN_2057 GBV_ILN_2061 GBV_ILN_2111 GBV_ILN_2113 GBV_ILN_2190 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 16 2015 1 25 03
allfieldsSound	10.1186/s12864-015-1401-z doi (DE-627)SPR027104729 (SPR)s12864-015-1401-z-e DE-627 ger DE-627 rakwb eng Wachowiak, Witold verfasserin aut Comparative transcriptomics of a complex of four European pine species 2015 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © Wachowiak et al. 2015 Background Pinus sylvestris, P. mugo, P. uliginosa and P. uncinata are closely related but phenotypically and ecologically very distinct European pine species providing an excellent study system for analysis of the genetic basis of adaptive variation and speciation. For comparative genomic analysis of the species, transcriptome sequence was generated for 17 samples collected across the European distribution range using Illumina paired-end sequencing technology. Results De novo transcriptome assembly of a reference sample of P. sylvestris contained 40968 unigenes, of which fewer than 0.5% were identified as putative retrotransposon sequences. Based on gene annotation approaches, 19659 contigs were identified and assigned to unique genes covering a broad range of gene ontology categories. About 80% of the reads from each sample were successfully mapped to the reference transcriptome of P. sylvestris. Single nucleotide polymorphisms were identified in 22041-24096 of the unigenes providing a set of ~220-262 k SNPs identified for each species. Very similar levels of nucleotide polymorphism were observed across species (π=0.0044-0.0053) and highest pairwise nucleotide divergence (0.006) was found between P. mugo and P. sylvestris at a common set of unigenes. Conclusions The study provides whole transcriptome sequence and a large set of SNPs to advance population and association genetic studies in pines. Our study demonstrates that transcriptome sequencing can be a very useful approach for development of novel genomic resources in species with large and complex genomes. Whole transcriptome sequencing (dpeaa)DE-He213 Ontology (dpeaa)DE-He213 SNPs (dpeaa)DE-He213 Nucleotide divergence (dpeaa)DE-He213 Species complex (dpeaa)DE-He213 Trivedi, Urmi aut Perry, Annika aut Cavers, Stephen aut Enthalten in BMC genomics London : BioMed Central, 2000 16(2015), 1 vom: 25. März (DE-627)326644954 (DE-600)2041499-7 1471-2164 nnns volume:16 year:2015 number:1 day:25 month:03 https://dx.doi.org/10.1186/s12864-015-1401-z kostenfrei Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER SSG-OLC-PHA GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_702 GBV_ILN_2001 GBV_ILN_2003 GBV_ILN_2005 GBV_ILN_2006 GBV_ILN_2008 GBV_ILN_2009 GBV_ILN_2010 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2015 GBV_ILN_2020 GBV_ILN_2021 GBV_ILN_2025 GBV_ILN_2031 GBV_ILN_2038 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2050 GBV_ILN_2055 GBV_ILN_2056 GBV_ILN_2057 GBV_ILN_2061 GBV_ILN_2111 GBV_ILN_2113 GBV_ILN_2190 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 16 2015 1 25 03
language	English
source	Enthalten in BMC genomics 16(2015), 1 vom: 25. März volume:16 year:2015 number:1 day:25 month:03
sourceStr	Enthalten in BMC genomics 16(2015), 1 vom: 25. März volume:16 year:2015 number:1 day:25 month:03
format_phy_str_mv	Article
institution	findex.gbv.de
topic_facet	Whole transcriptome sequencing Ontology SNPs Nucleotide divergence Species complex
isfreeaccess_bool	true
container_title	BMC genomics
authorswithroles_txt_mv	Wachowiak, Witold @@aut@@ Trivedi, Urmi @@aut@@ Perry, Annika @@aut@@ Cavers, Stephen @@aut@@
publishDateDaySort_date	2015-03-25T00:00:00Z
hierarchy_top_id	326644954
id	SPR027104729
language_de	englisch
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author	Wachowiak, Witold
spellingShingle	Wachowiak, Witold misc Whole transcriptome sequencing misc Ontology misc SNPs misc Nucleotide divergence misc Species complex Comparative transcriptomics of a complex of four European pine species
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topic_title	Comparative transcriptomics of a complex of four European pine species Whole transcriptome sequencing (dpeaa)DE-He213 Ontology (dpeaa)DE-He213 SNPs (dpeaa)DE-He213 Nucleotide divergence (dpeaa)DE-He213 Species complex (dpeaa)DE-He213
topic	misc Whole transcriptome sequencing misc Ontology misc SNPs misc Nucleotide divergence misc Species complex
topic_unstemmed	misc Whole transcriptome sequencing misc Ontology misc SNPs misc Nucleotide divergence misc Species complex
topic_browse	misc Whole transcriptome sequencing misc Ontology misc SNPs misc Nucleotide divergence misc Species complex
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title	Comparative transcriptomics of a complex of four European pine species
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title_full	Comparative transcriptomics of a complex of four European pine species
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author_browse	Wachowiak, Witold Trivedi, Urmi Perry, Annika Cavers, Stephen
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title_sort	comparative transcriptomics of a complex of four european pine species
title_auth	Comparative transcriptomics of a complex of four European pine species
abstract	Background Pinus sylvestris, P. mugo, P. uliginosa and P. uncinata are closely related but phenotypically and ecologically very distinct European pine species providing an excellent study system for analysis of the genetic basis of adaptive variation and speciation. For comparative genomic analysis of the species, transcriptome sequence was generated for 17 samples collected across the European distribution range using Illumina paired-end sequencing technology. Results De novo transcriptome assembly of a reference sample of P. sylvestris contained 40968 unigenes, of which fewer than 0.5% were identified as putative retrotransposon sequences. Based on gene annotation approaches, 19659 contigs were identified and assigned to unique genes covering a broad range of gene ontology categories. About 80% of the reads from each sample were successfully mapped to the reference transcriptome of P. sylvestris. Single nucleotide polymorphisms were identified in 22041-24096 of the unigenes providing a set of ~220-262 k SNPs identified for each species. Very similar levels of nucleotide polymorphism were observed across species (π=0.0044-0.0053) and highest pairwise nucleotide divergence (0.006) was found between P. mugo and P. sylvestris at a common set of unigenes. Conclusions The study provides whole transcriptome sequence and a large set of SNPs to advance population and association genetic studies in pines. Our study demonstrates that transcriptome sequencing can be a very useful approach for development of novel genomic resources in species with large and complex genomes. © Wachowiak et al. 2015
abstractGer	Background Pinus sylvestris, P. mugo, P. uliginosa and P. uncinata are closely related but phenotypically and ecologically very distinct European pine species providing an excellent study system for analysis of the genetic basis of adaptive variation and speciation. For comparative genomic analysis of the species, transcriptome sequence was generated for 17 samples collected across the European distribution range using Illumina paired-end sequencing technology. Results De novo transcriptome assembly of a reference sample of P. sylvestris contained 40968 unigenes, of which fewer than 0.5% were identified as putative retrotransposon sequences. Based on gene annotation approaches, 19659 contigs were identified and assigned to unique genes covering a broad range of gene ontology categories. About 80% of the reads from each sample were successfully mapped to the reference transcriptome of P. sylvestris. Single nucleotide polymorphisms were identified in 22041-24096 of the unigenes providing a set of ~220-262 k SNPs identified for each species. Very similar levels of nucleotide polymorphism were observed across species (π=0.0044-0.0053) and highest pairwise nucleotide divergence (0.006) was found between P. mugo and P. sylvestris at a common set of unigenes. Conclusions The study provides whole transcriptome sequence and a large set of SNPs to advance population and association genetic studies in pines. Our study demonstrates that transcriptome sequencing can be a very useful approach for development of novel genomic resources in species with large and complex genomes. © Wachowiak et al. 2015
abstract_unstemmed	Background Pinus sylvestris, P. mugo, P. uliginosa and P. uncinata are closely related but phenotypically and ecologically very distinct European pine species providing an excellent study system for analysis of the genetic basis of adaptive variation and speciation. For comparative genomic analysis of the species, transcriptome sequence was generated for 17 samples collected across the European distribution range using Illumina paired-end sequencing technology. Results De novo transcriptome assembly of a reference sample of P. sylvestris contained 40968 unigenes, of which fewer than 0.5% were identified as putative retrotransposon sequences. Based on gene annotation approaches, 19659 contigs were identified and assigned to unique genes covering a broad range of gene ontology categories. About 80% of the reads from each sample were successfully mapped to the reference transcriptome of P. sylvestris. Single nucleotide polymorphisms were identified in 22041-24096 of the unigenes providing a set of ~220-262 k SNPs identified for each species. Very similar levels of nucleotide polymorphism were observed across species (π=0.0044-0.0053) and highest pairwise nucleotide divergence (0.006) was found between P. mugo and P. sylvestris at a common set of unigenes. Conclusions The study provides whole transcriptome sequence and a large set of SNPs to advance population and association genetic studies in pines. Our study demonstrates that transcriptome sequencing can be a very useful approach for development of novel genomic resources in species with large and complex genomes. © Wachowiak et al. 2015
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title_short	Comparative transcriptomics of a complex of four European pine species
url	https://dx.doi.org/10.1186/s12864-015-1401-z
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