Transcriptome sequencing and development of EST-SSR markers in Pinus dabeshanensis, an endangered conifer endemic to China
Abstract Pinus dabeshanensis Cheng et Law (P.dabeshanensis) is an endangered endemic occurring along the border between Anhui Province and Hubei Province (China). This species is known from only four natural populations. However, few genomic studies have been conducted on this species. In the presen...
Ausführliche Beschreibung
Gespeichert in:
| Autor*in: |
Xiang, Xiaoyan [verfasserIn] Zhang, Zhongxin [verfasserIn] Wang, Zhigao [verfasserIn] Zhang, Xiaoping [verfasserIn] Wu, Ganlin [verfasserIn] |
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| Format: |
E-Artikel |
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| Sprache: |
Englisch |
| Erschienen: |
2015 |
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| Schlagwörter: |
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| Übergeordnetes Werk: |
Enthalten in: Molecular breeding - Dordrecht : Springer Science + Business Media B.V., 1995, 35(2015), 8 vom: 18. Juli |
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| Übergeordnetes Werk: |
volume:35 ; year:2015 ; number:8 ; day:18 ; month:07 |
| Links: |
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| DOI / URN: |
10.1007/s11032-015-0351-0 |
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| Katalog-ID: |
SPR015857786 |
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| 245 | 1 | 0 | |a Transcriptome sequencing and development of EST-SSR markers in Pinus dabeshanensis, an endangered conifer endemic to China |
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| 520 | |a Abstract Pinus dabeshanensis Cheng et Law (P.dabeshanensis) is an endangered endemic occurring along the border between Anhui Province and Hubei Province (China). This species is known from only four natural populations. However, few genomic studies have been conducted on this species. In the present study, a cDNA library of P. dabeshanensis needles was sequenced using Illumina HiSeq™ 2000 paired-end sequencing technology. By mining 42,248 non-redundant unigenes, 1966 expressed sequence tag–simple sequence repeats (EST-SSRs) derived from 1835 unigenes were identified. The most abundant repeat motif was trinucleotide (41.6 %), followed by dinucleotide (23.25 %), mononucleotide (21.41 %), hexanucleotide (7.83 %), pentanucleotide (4.43 %) and tetranucleotide repeats (1.53 %). The top tri- and dinucleotide motifs included AGC/CTG and AT/AT, respectively. A total of 20,194 unigenes were assigned to three main GO categories with 153,373 GO terms. A KOG classification showed that 11,604 unigenes and 732 SSR-containing unigenes were assigned to 25 and 23 possible functional categories, respectively. Among the 1966 EST-SSRs, 431 primer pairs were successfully designed. After selecting 82 of these pairs at random for further validation, 44 pairs amplified unambiguous bands, 19 of which were polymorphic among 24 individuals of P. dabeshanensis. A total of 57 alleles were identified, varying from 2 to 5 alleles per locus with an average of 3.0. The observed and expected heterozygosity per locus ranged from 0 to 0.958 and from 0.082 to 0.759, respectively. The PIC values ranged from 0.077 to 0.707 with an average of 0.380. The generation of such large-scale sequence data in the present study provides a valuable resource for gene discovery and molecular marker development. Such markers will be robust tools for genomic research and breeding of P. dabeshanensis. | ||
| 650 | 4 | |a EST-SSRs |7 (dpeaa)DE-He213 | |
| 650 | 4 | |a Transcriptome |7 (dpeaa)DE-He213 | |
| 650 | 4 | |a Genomic research |7 (dpeaa)DE-He213 | |
| 650 | 4 | |a Breeding |7 (dpeaa)DE-He213 | |
| 700 | 1 | |a Zhang, Zhongxin |e verfasserin |4 aut | |
| 700 | 1 | |a Wang, Zhigao |e verfasserin |4 aut | |
| 700 | 1 | |a Zhang, Xiaoping |e verfasserin |4 aut | |
| 700 | 1 | |a Wu, Ganlin |e verfasserin |4 aut | |
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10.1007/s11032-015-0351-0 doi (DE-627)SPR015857786 (SPR)s11032-015-0351-0-e DE-627 ger DE-627 rakwb eng 580 ASE 48.58 bkl 42.43 bkl Xiang, Xiaoyan verfasserin aut Transcriptome sequencing and development of EST-SSR markers in Pinus dabeshanensis, an endangered conifer endemic to China 2015 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier Abstract Pinus dabeshanensis Cheng et Law (P.dabeshanensis) is an endangered endemic occurring along the border between Anhui Province and Hubei Province (China). This species is known from only four natural populations. However, few genomic studies have been conducted on this species. In the present study, a cDNA library of P. dabeshanensis needles was sequenced using Illumina HiSeq™ 2000 paired-end sequencing technology. By mining 42,248 non-redundant unigenes, 1966 expressed sequence tag–simple sequence repeats (EST-SSRs) derived from 1835 unigenes were identified. The most abundant repeat motif was trinucleotide (41.6 %), followed by dinucleotide (23.25 %), mononucleotide (21.41 %), hexanucleotide (7.83 %), pentanucleotide (4.43 %) and tetranucleotide repeats (1.53 %). The top tri- and dinucleotide motifs included AGC/CTG and AT/AT, respectively. A total of 20,194 unigenes were assigned to three main GO categories with 153,373 GO terms. A KOG classification showed that 11,604 unigenes and 732 SSR-containing unigenes were assigned to 25 and 23 possible functional categories, respectively. Among the 1966 EST-SSRs, 431 primer pairs were successfully designed. After selecting 82 of these pairs at random for further validation, 44 pairs amplified unambiguous bands, 19 of which were polymorphic among 24 individuals of P. dabeshanensis. A total of 57 alleles were identified, varying from 2 to 5 alleles per locus with an average of 3.0. The observed and expected heterozygosity per locus ranged from 0 to 0.958 and from 0.082 to 0.759, respectively. The PIC values ranged from 0.077 to 0.707 with an average of 0.380. The generation of such large-scale sequence data in the present study provides a valuable resource for gene discovery and molecular marker development. Such markers will be robust tools for genomic research and breeding of P. dabeshanensis. EST-SSRs (dpeaa)DE-He213 Transcriptome (dpeaa)DE-He213 Genomic research (dpeaa)DE-He213 Breeding (dpeaa)DE-He213 Zhang, Zhongxin verfasserin aut Wang, Zhigao verfasserin aut Zhang, Xiaoping verfasserin aut Wu, Ganlin verfasserin aut Enthalten in Molecular breeding Dordrecht : Springer Science + Business Media B.V., 1995 35(2015), 8 vom: 18. Juli (DE-627)270930671 (DE-600)1478220-0 1572-9788 nnns volume:35 year:2015 number:8 day:18 month:07 https://dx.doi.org/10.1007/s11032-015-0351-0 lizenzpflichtig 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_31 GBV_ILN_32 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_90 GBV_ILN_95 GBV_ILN_100 GBV_ILN_105 GBV_ILN_110 GBV_ILN_120 GBV_ILN_138 GBV_ILN_150 GBV_ILN_151 GBV_ILN_152 GBV_ILN_161 GBV_ILN_170 GBV_ILN_171 GBV_ILN_187 GBV_ILN_206 GBV_ILN_213 GBV_ILN_224 GBV_ILN_230 GBV_ILN_250 GBV_ILN_281 GBV_ILN_285 GBV_ILN_293 GBV_ILN_370 GBV_ILN_602 GBV_ILN_636 GBV_ILN_647 GBV_ILN_702 GBV_ILN_2001 GBV_ILN_2003 GBV_ILN_2004 GBV_ILN_2005 GBV_ILN_2006 GBV_ILN_2007 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_2026 GBV_ILN_2027 GBV_ILN_2031 GBV_ILN_2034 GBV_ILN_2037 GBV_ILN_2038 GBV_ILN_2039 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2049 GBV_ILN_2050 GBV_ILN_2055 GBV_ILN_2057 GBV_ILN_2059 GBV_ILN_2061 GBV_ILN_2064 GBV_ILN_2065 GBV_ILN_2068 GBV_ILN_2070 GBV_ILN_2086 GBV_ILN_2088 GBV_ILN_2093 GBV_ILN_2106 GBV_ILN_2107 GBV_ILN_2108 GBV_ILN_2110 GBV_ILN_2111 GBV_ILN_2112 GBV_ILN_2113 GBV_ILN_2116 GBV_ILN_2118 GBV_ILN_2119 GBV_ILN_2122 GBV_ILN_2129 GBV_ILN_2143 GBV_ILN_2144 GBV_ILN_2147 GBV_ILN_2148 GBV_ILN_2152 GBV_ILN_2153 GBV_ILN_2188 GBV_ILN_2190 GBV_ILN_2232 GBV_ILN_2336 GBV_ILN_2446 GBV_ILN_2470 GBV_ILN_2472 GBV_ILN_2507 GBV_ILN_2522 GBV_ILN_2548 GBV_ILN_4012 GBV_ILN_4035 GBV_ILN_4037 GBV_ILN_4046 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4242 GBV_ILN_4246 GBV_ILN_4249 GBV_ILN_4251 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_4326 GBV_ILN_4333 GBV_ILN_4334 GBV_ILN_4335 GBV_ILN_4336 GBV_ILN_4338 GBV_ILN_4393 GBV_ILN_4700 48.58 ASE 42.43 ASE AR 35 2015 8 18 07 |
| spelling |
10.1007/s11032-015-0351-0 doi (DE-627)SPR015857786 (SPR)s11032-015-0351-0-e DE-627 ger DE-627 rakwb eng 580 ASE 48.58 bkl 42.43 bkl Xiang, Xiaoyan verfasserin aut Transcriptome sequencing and development of EST-SSR markers in Pinus dabeshanensis, an endangered conifer endemic to China 2015 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier Abstract Pinus dabeshanensis Cheng et Law (P.dabeshanensis) is an endangered endemic occurring along the border between Anhui Province and Hubei Province (China). This species is known from only four natural populations. However, few genomic studies have been conducted on this species. In the present study, a cDNA library of P. dabeshanensis needles was sequenced using Illumina HiSeq™ 2000 paired-end sequencing technology. By mining 42,248 non-redundant unigenes, 1966 expressed sequence tag–simple sequence repeats (EST-SSRs) derived from 1835 unigenes were identified. The most abundant repeat motif was trinucleotide (41.6 %), followed by dinucleotide (23.25 %), mononucleotide (21.41 %), hexanucleotide (7.83 %), pentanucleotide (4.43 %) and tetranucleotide repeats (1.53 %). The top tri- and dinucleotide motifs included AGC/CTG and AT/AT, respectively. A total of 20,194 unigenes were assigned to three main GO categories with 153,373 GO terms. A KOG classification showed that 11,604 unigenes and 732 SSR-containing unigenes were assigned to 25 and 23 possible functional categories, respectively. Among the 1966 EST-SSRs, 431 primer pairs were successfully designed. After selecting 82 of these pairs at random for further validation, 44 pairs amplified unambiguous bands, 19 of which were polymorphic among 24 individuals of P. dabeshanensis. A total of 57 alleles were identified, varying from 2 to 5 alleles per locus with an average of 3.0. The observed and expected heterozygosity per locus ranged from 0 to 0.958 and from 0.082 to 0.759, respectively. The PIC values ranged from 0.077 to 0.707 with an average of 0.380. The generation of such large-scale sequence data in the present study provides a valuable resource for gene discovery and molecular marker development. Such markers will be robust tools for genomic research and breeding of P. dabeshanensis. EST-SSRs (dpeaa)DE-He213 Transcriptome (dpeaa)DE-He213 Genomic research (dpeaa)DE-He213 Breeding (dpeaa)DE-He213 Zhang, Zhongxin verfasserin aut Wang, Zhigao verfasserin aut Zhang, Xiaoping verfasserin aut Wu, Ganlin verfasserin aut Enthalten in Molecular breeding Dordrecht : Springer Science + Business Media B.V., 1995 35(2015), 8 vom: 18. Juli (DE-627)270930671 (DE-600)1478220-0 1572-9788 nnns volume:35 year:2015 number:8 day:18 month:07 https://dx.doi.org/10.1007/s11032-015-0351-0 lizenzpflichtig 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_31 GBV_ILN_32 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_90 GBV_ILN_95 GBV_ILN_100 GBV_ILN_105 GBV_ILN_110 GBV_ILN_120 GBV_ILN_138 GBV_ILN_150 GBV_ILN_151 GBV_ILN_152 GBV_ILN_161 GBV_ILN_170 GBV_ILN_171 GBV_ILN_187 GBV_ILN_206 GBV_ILN_213 GBV_ILN_224 GBV_ILN_230 GBV_ILN_250 GBV_ILN_281 GBV_ILN_285 GBV_ILN_293 GBV_ILN_370 GBV_ILN_602 GBV_ILN_636 GBV_ILN_647 GBV_ILN_702 GBV_ILN_2001 GBV_ILN_2003 GBV_ILN_2004 GBV_ILN_2005 GBV_ILN_2006 GBV_ILN_2007 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_2026 GBV_ILN_2027 GBV_ILN_2031 GBV_ILN_2034 GBV_ILN_2037 GBV_ILN_2038 GBV_ILN_2039 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2049 GBV_ILN_2050 GBV_ILN_2055 GBV_ILN_2057 GBV_ILN_2059 GBV_ILN_2061 GBV_ILN_2064 GBV_ILN_2065 GBV_ILN_2068 GBV_ILN_2070 GBV_ILN_2086 GBV_ILN_2088 GBV_ILN_2093 GBV_ILN_2106 GBV_ILN_2107 GBV_ILN_2108 GBV_ILN_2110 GBV_ILN_2111 GBV_ILN_2112 GBV_ILN_2113 GBV_ILN_2116 GBV_ILN_2118 GBV_ILN_2119 GBV_ILN_2122 GBV_ILN_2129 GBV_ILN_2143 GBV_ILN_2144 GBV_ILN_2147 GBV_ILN_2148 GBV_ILN_2152 GBV_ILN_2153 GBV_ILN_2188 GBV_ILN_2190 GBV_ILN_2232 GBV_ILN_2336 GBV_ILN_2446 GBV_ILN_2470 GBV_ILN_2472 GBV_ILN_2507 GBV_ILN_2522 GBV_ILN_2548 GBV_ILN_4012 GBV_ILN_4035 GBV_ILN_4037 GBV_ILN_4046 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4242 GBV_ILN_4246 GBV_ILN_4249 GBV_ILN_4251 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_4326 GBV_ILN_4333 GBV_ILN_4334 GBV_ILN_4335 GBV_ILN_4336 GBV_ILN_4338 GBV_ILN_4393 GBV_ILN_4700 48.58 ASE 42.43 ASE AR 35 2015 8 18 07 |
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10.1007/s11032-015-0351-0 doi (DE-627)SPR015857786 (SPR)s11032-015-0351-0-e DE-627 ger DE-627 rakwb eng 580 ASE 48.58 bkl 42.43 bkl Xiang, Xiaoyan verfasserin aut Transcriptome sequencing and development of EST-SSR markers in Pinus dabeshanensis, an endangered conifer endemic to China 2015 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier Abstract Pinus dabeshanensis Cheng et Law (P.dabeshanensis) is an endangered endemic occurring along the border between Anhui Province and Hubei Province (China). This species is known from only four natural populations. However, few genomic studies have been conducted on this species. In the present study, a cDNA library of P. dabeshanensis needles was sequenced using Illumina HiSeq™ 2000 paired-end sequencing technology. By mining 42,248 non-redundant unigenes, 1966 expressed sequence tag–simple sequence repeats (EST-SSRs) derived from 1835 unigenes were identified. The most abundant repeat motif was trinucleotide (41.6 %), followed by dinucleotide (23.25 %), mononucleotide (21.41 %), hexanucleotide (7.83 %), pentanucleotide (4.43 %) and tetranucleotide repeats (1.53 %). The top tri- and dinucleotide motifs included AGC/CTG and AT/AT, respectively. A total of 20,194 unigenes were assigned to three main GO categories with 153,373 GO terms. A KOG classification showed that 11,604 unigenes and 732 SSR-containing unigenes were assigned to 25 and 23 possible functional categories, respectively. Among the 1966 EST-SSRs, 431 primer pairs were successfully designed. After selecting 82 of these pairs at random for further validation, 44 pairs amplified unambiguous bands, 19 of which were polymorphic among 24 individuals of P. dabeshanensis. A total of 57 alleles were identified, varying from 2 to 5 alleles per locus with an average of 3.0. The observed and expected heterozygosity per locus ranged from 0 to 0.958 and from 0.082 to 0.759, respectively. The PIC values ranged from 0.077 to 0.707 with an average of 0.380. The generation of such large-scale sequence data in the present study provides a valuable resource for gene discovery and molecular marker development. Such markers will be robust tools for genomic research and breeding of P. dabeshanensis. EST-SSRs (dpeaa)DE-He213 Transcriptome (dpeaa)DE-He213 Genomic research (dpeaa)DE-He213 Breeding (dpeaa)DE-He213 Zhang, Zhongxin verfasserin aut Wang, Zhigao verfasserin aut Zhang, Xiaoping verfasserin aut Wu, Ganlin verfasserin aut Enthalten in Molecular breeding Dordrecht : Springer Science + Business Media B.V., 1995 35(2015), 8 vom: 18. Juli (DE-627)270930671 (DE-600)1478220-0 1572-9788 nnns volume:35 year:2015 number:8 day:18 month:07 https://dx.doi.org/10.1007/s11032-015-0351-0 lizenzpflichtig 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_31 GBV_ILN_32 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_90 GBV_ILN_95 GBV_ILN_100 GBV_ILN_105 GBV_ILN_110 GBV_ILN_120 GBV_ILN_138 GBV_ILN_150 GBV_ILN_151 GBV_ILN_152 GBV_ILN_161 GBV_ILN_170 GBV_ILN_171 GBV_ILN_187 GBV_ILN_206 GBV_ILN_213 GBV_ILN_224 GBV_ILN_230 GBV_ILN_250 GBV_ILN_281 GBV_ILN_285 GBV_ILN_293 GBV_ILN_370 GBV_ILN_602 GBV_ILN_636 GBV_ILN_647 GBV_ILN_702 GBV_ILN_2001 GBV_ILN_2003 GBV_ILN_2004 GBV_ILN_2005 GBV_ILN_2006 GBV_ILN_2007 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_2026 GBV_ILN_2027 GBV_ILN_2031 GBV_ILN_2034 GBV_ILN_2037 GBV_ILN_2038 GBV_ILN_2039 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2049 GBV_ILN_2050 GBV_ILN_2055 GBV_ILN_2057 GBV_ILN_2059 GBV_ILN_2061 GBV_ILN_2064 GBV_ILN_2065 GBV_ILN_2068 GBV_ILN_2070 GBV_ILN_2086 GBV_ILN_2088 GBV_ILN_2093 GBV_ILN_2106 GBV_ILN_2107 GBV_ILN_2108 GBV_ILN_2110 GBV_ILN_2111 GBV_ILN_2112 GBV_ILN_2113 GBV_ILN_2116 GBV_ILN_2118 GBV_ILN_2119 GBV_ILN_2122 GBV_ILN_2129 GBV_ILN_2143 GBV_ILN_2144 GBV_ILN_2147 GBV_ILN_2148 GBV_ILN_2152 GBV_ILN_2153 GBV_ILN_2188 GBV_ILN_2190 GBV_ILN_2232 GBV_ILN_2336 GBV_ILN_2446 GBV_ILN_2470 GBV_ILN_2472 GBV_ILN_2507 GBV_ILN_2522 GBV_ILN_2548 GBV_ILN_4012 GBV_ILN_4035 GBV_ILN_4037 GBV_ILN_4046 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4242 GBV_ILN_4246 GBV_ILN_4249 GBV_ILN_4251 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_4326 GBV_ILN_4333 GBV_ILN_4334 GBV_ILN_4335 GBV_ILN_4336 GBV_ILN_4338 GBV_ILN_4393 GBV_ILN_4700 48.58 ASE 42.43 ASE AR 35 2015 8 18 07 |
| allfieldsGer |
10.1007/s11032-015-0351-0 doi (DE-627)SPR015857786 (SPR)s11032-015-0351-0-e DE-627 ger DE-627 rakwb eng 580 ASE 48.58 bkl 42.43 bkl Xiang, Xiaoyan verfasserin aut Transcriptome sequencing and development of EST-SSR markers in Pinus dabeshanensis, an endangered conifer endemic to China 2015 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier Abstract Pinus dabeshanensis Cheng et Law (P.dabeshanensis) is an endangered endemic occurring along the border between Anhui Province and Hubei Province (China). This species is known from only four natural populations. However, few genomic studies have been conducted on this species. In the present study, a cDNA library of P. dabeshanensis needles was sequenced using Illumina HiSeq™ 2000 paired-end sequencing technology. By mining 42,248 non-redundant unigenes, 1966 expressed sequence tag–simple sequence repeats (EST-SSRs) derived from 1835 unigenes were identified. The most abundant repeat motif was trinucleotide (41.6 %), followed by dinucleotide (23.25 %), mononucleotide (21.41 %), hexanucleotide (7.83 %), pentanucleotide (4.43 %) and tetranucleotide repeats (1.53 %). The top tri- and dinucleotide motifs included AGC/CTG and AT/AT, respectively. A total of 20,194 unigenes were assigned to three main GO categories with 153,373 GO terms. A KOG classification showed that 11,604 unigenes and 732 SSR-containing unigenes were assigned to 25 and 23 possible functional categories, respectively. Among the 1966 EST-SSRs, 431 primer pairs were successfully designed. After selecting 82 of these pairs at random for further validation, 44 pairs amplified unambiguous bands, 19 of which were polymorphic among 24 individuals of P. dabeshanensis. A total of 57 alleles were identified, varying from 2 to 5 alleles per locus with an average of 3.0. The observed and expected heterozygosity per locus ranged from 0 to 0.958 and from 0.082 to 0.759, respectively. The PIC values ranged from 0.077 to 0.707 with an average of 0.380. The generation of such large-scale sequence data in the present study provides a valuable resource for gene discovery and molecular marker development. Such markers will be robust tools for genomic research and breeding of P. dabeshanensis. EST-SSRs (dpeaa)DE-He213 Transcriptome (dpeaa)DE-He213 Genomic research (dpeaa)DE-He213 Breeding (dpeaa)DE-He213 Zhang, Zhongxin verfasserin aut Wang, Zhigao verfasserin aut Zhang, Xiaoping verfasserin aut Wu, Ganlin verfasserin aut Enthalten in Molecular breeding Dordrecht : Springer Science + Business Media B.V., 1995 35(2015), 8 vom: 18. Juli (DE-627)270930671 (DE-600)1478220-0 1572-9788 nnns volume:35 year:2015 number:8 day:18 month:07 https://dx.doi.org/10.1007/s11032-015-0351-0 lizenzpflichtig 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_31 GBV_ILN_32 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_90 GBV_ILN_95 GBV_ILN_100 GBV_ILN_105 GBV_ILN_110 GBV_ILN_120 GBV_ILN_138 GBV_ILN_150 GBV_ILN_151 GBV_ILN_152 GBV_ILN_161 GBV_ILN_170 GBV_ILN_171 GBV_ILN_187 GBV_ILN_206 GBV_ILN_213 GBV_ILN_224 GBV_ILN_230 GBV_ILN_250 GBV_ILN_281 GBV_ILN_285 GBV_ILN_293 GBV_ILN_370 GBV_ILN_602 GBV_ILN_636 GBV_ILN_647 GBV_ILN_702 GBV_ILN_2001 GBV_ILN_2003 GBV_ILN_2004 GBV_ILN_2005 GBV_ILN_2006 GBV_ILN_2007 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_2026 GBV_ILN_2027 GBV_ILN_2031 GBV_ILN_2034 GBV_ILN_2037 GBV_ILN_2038 GBV_ILN_2039 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2049 GBV_ILN_2050 GBV_ILN_2055 GBV_ILN_2057 GBV_ILN_2059 GBV_ILN_2061 GBV_ILN_2064 GBV_ILN_2065 GBV_ILN_2068 GBV_ILN_2070 GBV_ILN_2086 GBV_ILN_2088 GBV_ILN_2093 GBV_ILN_2106 GBV_ILN_2107 GBV_ILN_2108 GBV_ILN_2110 GBV_ILN_2111 GBV_ILN_2112 GBV_ILN_2113 GBV_ILN_2116 GBV_ILN_2118 GBV_ILN_2119 GBV_ILN_2122 GBV_ILN_2129 GBV_ILN_2143 GBV_ILN_2144 GBV_ILN_2147 GBV_ILN_2148 GBV_ILN_2152 GBV_ILN_2153 GBV_ILN_2188 GBV_ILN_2190 GBV_ILN_2232 GBV_ILN_2336 GBV_ILN_2446 GBV_ILN_2470 GBV_ILN_2472 GBV_ILN_2507 GBV_ILN_2522 GBV_ILN_2548 GBV_ILN_4012 GBV_ILN_4035 GBV_ILN_4037 GBV_ILN_4046 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4242 GBV_ILN_4246 GBV_ILN_4249 GBV_ILN_4251 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_4326 GBV_ILN_4333 GBV_ILN_4334 GBV_ILN_4335 GBV_ILN_4336 GBV_ILN_4338 GBV_ILN_4393 GBV_ILN_4700 48.58 ASE 42.43 ASE AR 35 2015 8 18 07 |
| allfieldsSound |
10.1007/s11032-015-0351-0 doi (DE-627)SPR015857786 (SPR)s11032-015-0351-0-e DE-627 ger DE-627 rakwb eng 580 ASE 48.58 bkl 42.43 bkl Xiang, Xiaoyan verfasserin aut Transcriptome sequencing and development of EST-SSR markers in Pinus dabeshanensis, an endangered conifer endemic to China 2015 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier Abstract Pinus dabeshanensis Cheng et Law (P.dabeshanensis) is an endangered endemic occurring along the border between Anhui Province and Hubei Province (China). This species is known from only four natural populations. However, few genomic studies have been conducted on this species. In the present study, a cDNA library of P. dabeshanensis needles was sequenced using Illumina HiSeq™ 2000 paired-end sequencing technology. By mining 42,248 non-redundant unigenes, 1966 expressed sequence tag–simple sequence repeats (EST-SSRs) derived from 1835 unigenes were identified. The most abundant repeat motif was trinucleotide (41.6 %), followed by dinucleotide (23.25 %), mononucleotide (21.41 %), hexanucleotide (7.83 %), pentanucleotide (4.43 %) and tetranucleotide repeats (1.53 %). The top tri- and dinucleotide motifs included AGC/CTG and AT/AT, respectively. A total of 20,194 unigenes were assigned to three main GO categories with 153,373 GO terms. A KOG classification showed that 11,604 unigenes and 732 SSR-containing unigenes were assigned to 25 and 23 possible functional categories, respectively. Among the 1966 EST-SSRs, 431 primer pairs were successfully designed. After selecting 82 of these pairs at random for further validation, 44 pairs amplified unambiguous bands, 19 of which were polymorphic among 24 individuals of P. dabeshanensis. A total of 57 alleles were identified, varying from 2 to 5 alleles per locus with an average of 3.0. The observed and expected heterozygosity per locus ranged from 0 to 0.958 and from 0.082 to 0.759, respectively. The PIC values ranged from 0.077 to 0.707 with an average of 0.380. The generation of such large-scale sequence data in the present study provides a valuable resource for gene discovery and molecular marker development. Such markers will be robust tools for genomic research and breeding of P. dabeshanensis. EST-SSRs (dpeaa)DE-He213 Transcriptome (dpeaa)DE-He213 Genomic research (dpeaa)DE-He213 Breeding (dpeaa)DE-He213 Zhang, Zhongxin verfasserin aut Wang, Zhigao verfasserin aut Zhang, Xiaoping verfasserin aut Wu, Ganlin verfasserin aut Enthalten in Molecular breeding Dordrecht : Springer Science + Business Media B.V., 1995 35(2015), 8 vom: 18. Juli (DE-627)270930671 (DE-600)1478220-0 1572-9788 nnns volume:35 year:2015 number:8 day:18 month:07 https://dx.doi.org/10.1007/s11032-015-0351-0 lizenzpflichtig 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_31 GBV_ILN_32 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_90 GBV_ILN_95 GBV_ILN_100 GBV_ILN_105 GBV_ILN_110 GBV_ILN_120 GBV_ILN_138 GBV_ILN_150 GBV_ILN_151 GBV_ILN_152 GBV_ILN_161 GBV_ILN_170 GBV_ILN_171 GBV_ILN_187 GBV_ILN_206 GBV_ILN_213 GBV_ILN_224 GBV_ILN_230 GBV_ILN_250 GBV_ILN_281 GBV_ILN_285 GBV_ILN_293 GBV_ILN_370 GBV_ILN_602 GBV_ILN_636 GBV_ILN_647 GBV_ILN_702 GBV_ILN_2001 GBV_ILN_2003 GBV_ILN_2004 GBV_ILN_2005 GBV_ILN_2006 GBV_ILN_2007 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_2026 GBV_ILN_2027 GBV_ILN_2031 GBV_ILN_2034 GBV_ILN_2037 GBV_ILN_2038 GBV_ILN_2039 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2049 GBV_ILN_2050 GBV_ILN_2055 GBV_ILN_2057 GBV_ILN_2059 GBV_ILN_2061 GBV_ILN_2064 GBV_ILN_2065 GBV_ILN_2068 GBV_ILN_2070 GBV_ILN_2086 GBV_ILN_2088 GBV_ILN_2093 GBV_ILN_2106 GBV_ILN_2107 GBV_ILN_2108 GBV_ILN_2110 GBV_ILN_2111 GBV_ILN_2112 GBV_ILN_2113 GBV_ILN_2116 GBV_ILN_2118 GBV_ILN_2119 GBV_ILN_2122 GBV_ILN_2129 GBV_ILN_2143 GBV_ILN_2144 GBV_ILN_2147 GBV_ILN_2148 GBV_ILN_2152 GBV_ILN_2153 GBV_ILN_2188 GBV_ILN_2190 GBV_ILN_2232 GBV_ILN_2336 GBV_ILN_2446 GBV_ILN_2470 GBV_ILN_2472 GBV_ILN_2507 GBV_ILN_2522 GBV_ILN_2548 GBV_ILN_4012 GBV_ILN_4035 GBV_ILN_4037 GBV_ILN_4046 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4242 GBV_ILN_4246 GBV_ILN_4249 GBV_ILN_4251 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_4326 GBV_ILN_4333 GBV_ILN_4334 GBV_ILN_4335 GBV_ILN_4336 GBV_ILN_4338 GBV_ILN_4393 GBV_ILN_4700 48.58 ASE 42.43 ASE AR 35 2015 8 18 07 |
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English |
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Enthalten in Molecular breeding 35(2015), 8 vom: 18. Juli volume:35 year:2015 number:8 day:18 month:07 |
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Enthalten in Molecular breeding 35(2015), 8 vom: 18. Juli volume:35 year:2015 number:8 day:18 month:07 |
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EST-SSRs Transcriptome Genomic research Breeding |
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Molecular breeding |
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Xiang, Xiaoyan @@aut@@ Zhang, Zhongxin @@aut@@ Wang, Zhigao @@aut@@ Zhang, Xiaoping @@aut@@ Wu, Ganlin @@aut@@ |
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2015-07-18T00:00:00Z |
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Xiang, Xiaoyan |
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Xiang, Xiaoyan ddc 580 bkl 48.58 bkl 42.43 misc EST-SSRs misc Transcriptome misc Genomic research misc Breeding Transcriptome sequencing and development of EST-SSR markers in Pinus dabeshanensis, an endangered conifer endemic to China |
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580 ASE 48.58 bkl 42.43 bkl Transcriptome sequencing and development of EST-SSR markers in Pinus dabeshanensis, an endangered conifer endemic to China EST-SSRs (dpeaa)DE-He213 Transcriptome (dpeaa)DE-He213 Genomic research (dpeaa)DE-He213 Breeding (dpeaa)DE-He213 |
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Transcriptome sequencing and development of EST-SSR markers in Pinus dabeshanensis, an endangered conifer endemic to China |
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Transcriptome sequencing and development of EST-SSR markers in Pinus dabeshanensis, an endangered conifer endemic to China |
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| title_sort |
transcriptome sequencing and development of est-ssr markers in pinus dabeshanensis, an endangered conifer endemic to china |
| title_auth |
Transcriptome sequencing and development of EST-SSR markers in Pinus dabeshanensis, an endangered conifer endemic to China |
| abstract |
Abstract Pinus dabeshanensis Cheng et Law (P.dabeshanensis) is an endangered endemic occurring along the border between Anhui Province and Hubei Province (China). This species is known from only four natural populations. However, few genomic studies have been conducted on this species. In the present study, a cDNA library of P. dabeshanensis needles was sequenced using Illumina HiSeq™ 2000 paired-end sequencing technology. By mining 42,248 non-redundant unigenes, 1966 expressed sequence tag–simple sequence repeats (EST-SSRs) derived from 1835 unigenes were identified. The most abundant repeat motif was trinucleotide (41.6 %), followed by dinucleotide (23.25 %), mononucleotide (21.41 %), hexanucleotide (7.83 %), pentanucleotide (4.43 %) and tetranucleotide repeats (1.53 %). The top tri- and dinucleotide motifs included AGC/CTG and AT/AT, respectively. A total of 20,194 unigenes were assigned to three main GO categories with 153,373 GO terms. A KOG classification showed that 11,604 unigenes and 732 SSR-containing unigenes were assigned to 25 and 23 possible functional categories, respectively. Among the 1966 EST-SSRs, 431 primer pairs were successfully designed. After selecting 82 of these pairs at random for further validation, 44 pairs amplified unambiguous bands, 19 of which were polymorphic among 24 individuals of P. dabeshanensis. A total of 57 alleles were identified, varying from 2 to 5 alleles per locus with an average of 3.0. The observed and expected heterozygosity per locus ranged from 0 to 0.958 and from 0.082 to 0.759, respectively. The PIC values ranged from 0.077 to 0.707 with an average of 0.380. The generation of such large-scale sequence data in the present study provides a valuable resource for gene discovery and molecular marker development. Such markers will be robust tools for genomic research and breeding of P. dabeshanensis. |
| abstractGer |
Abstract Pinus dabeshanensis Cheng et Law (P.dabeshanensis) is an endangered endemic occurring along the border between Anhui Province and Hubei Province (China). This species is known from only four natural populations. However, few genomic studies have been conducted on this species. In the present study, a cDNA library of P. dabeshanensis needles was sequenced using Illumina HiSeq™ 2000 paired-end sequencing technology. By mining 42,248 non-redundant unigenes, 1966 expressed sequence tag–simple sequence repeats (EST-SSRs) derived from 1835 unigenes were identified. The most abundant repeat motif was trinucleotide (41.6 %), followed by dinucleotide (23.25 %), mononucleotide (21.41 %), hexanucleotide (7.83 %), pentanucleotide (4.43 %) and tetranucleotide repeats (1.53 %). The top tri- and dinucleotide motifs included AGC/CTG and AT/AT, respectively. A total of 20,194 unigenes were assigned to three main GO categories with 153,373 GO terms. A KOG classification showed that 11,604 unigenes and 732 SSR-containing unigenes were assigned to 25 and 23 possible functional categories, respectively. Among the 1966 EST-SSRs, 431 primer pairs were successfully designed. After selecting 82 of these pairs at random for further validation, 44 pairs amplified unambiguous bands, 19 of which were polymorphic among 24 individuals of P. dabeshanensis. A total of 57 alleles were identified, varying from 2 to 5 alleles per locus with an average of 3.0. The observed and expected heterozygosity per locus ranged from 0 to 0.958 and from 0.082 to 0.759, respectively. The PIC values ranged from 0.077 to 0.707 with an average of 0.380. The generation of such large-scale sequence data in the present study provides a valuable resource for gene discovery and molecular marker development. Such markers will be robust tools for genomic research and breeding of P. dabeshanensis. |
| abstract_unstemmed |
Abstract Pinus dabeshanensis Cheng et Law (P.dabeshanensis) is an endangered endemic occurring along the border between Anhui Province and Hubei Province (China). This species is known from only four natural populations. However, few genomic studies have been conducted on this species. In the present study, a cDNA library of P. dabeshanensis needles was sequenced using Illumina HiSeq™ 2000 paired-end sequencing technology. By mining 42,248 non-redundant unigenes, 1966 expressed sequence tag–simple sequence repeats (EST-SSRs) derived from 1835 unigenes were identified. The most abundant repeat motif was trinucleotide (41.6 %), followed by dinucleotide (23.25 %), mononucleotide (21.41 %), hexanucleotide (7.83 %), pentanucleotide (4.43 %) and tetranucleotide repeats (1.53 %). The top tri- and dinucleotide motifs included AGC/CTG and AT/AT, respectively. A total of 20,194 unigenes were assigned to three main GO categories with 153,373 GO terms. A KOG classification showed that 11,604 unigenes and 732 SSR-containing unigenes were assigned to 25 and 23 possible functional categories, respectively. Among the 1966 EST-SSRs, 431 primer pairs were successfully designed. After selecting 82 of these pairs at random for further validation, 44 pairs amplified unambiguous bands, 19 of which were polymorphic among 24 individuals of P. dabeshanensis. A total of 57 alleles were identified, varying from 2 to 5 alleles per locus with an average of 3.0. The observed and expected heterozygosity per locus ranged from 0 to 0.958 and from 0.082 to 0.759, respectively. The PIC values ranged from 0.077 to 0.707 with an average of 0.380. The generation of such large-scale sequence data in the present study provides a valuable resource for gene discovery and molecular marker development. Such markers will be robust tools for genomic research and breeding of P. dabeshanensis. |
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Transcriptome sequencing and development of EST-SSR markers in Pinus dabeshanensis, an endangered conifer endemic to China |
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Zhang, Zhongxin Wang, Zhigao Zhang, Xiaoping Wu, Ganlin |
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| score |
7.3985004 |