Eucalyptus microsatellites mined in silico: survey and evaluation

Abstract Eucalyptus is an important short rotation pulpy woody plant, grown widely in the tropics. Recently, many genomic programmes are underway leading to the accumulation of voluminous genomic and expressed sequence tag sequences in public databases. These sequences can be utilized for analysis o...
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Autor*in:	Yasodha, R. [verfasserIn] Sumathi, R. [verfasserIn] Chezhian, P. [verfasserIn] Kavitha, S. [verfasserIn] Ghosh, M. [verfasserIn]

Format:	E-Artikel
Sprache:	Englisch

Erschienen:	2008

Schlagwörter:	EST-SSR simple sequence repeats allelic diversity

Übergeordnetes Werk:	Enthalten in: Journal of Genetics - Springer India, 1955, 87(2008), 1 vom: 01. Apr., Seite 21-25
Übergeordnetes Werk:	volume:87 ; year:2008 ; number:1 ; day:01 ; month:04 ; pages:21-25

Links:	Volltext

DOI / URN:	10.1007/s12041-008-0003-9

Katalog-ID:	SPR024135836

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allfields	10.1007/s12041-008-0003-9 doi (DE-627)SPR024135836 (SPR)s12041-008-0003-9-e DE-627 ger DE-627 rakwb eng Yasodha, R. verfasserin aut Eucalyptus microsatellites mined in silico: survey and evaluation 2008 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier Abstract Eucalyptus is an important short rotation pulpy woody plant, grown widely in the tropics. Recently, many genomic programmes are underway leading to the accumulation of voluminous genomic and expressed sequence tag sequences in public databases. These sequences can be utilized for analysis of simple sequence repeats (SSRs) and single nucleotide polymorphism (SNPs) available in the transcribed genes. In this study, in silico analysis of 15,285 sequences representing partial and full-length mRNA from Eucalyptus species for their use in developing SSRs or microsatellites were carried out. A total of 875 EST-SSRs were identified from 772 SSR containing ESTs. Motif size of 6 for dinucleotide and 5 for trinucleotide, tetranucleotide, and pentanucleotides were considered in locating the microsatellites. The average frequency of identified SSRs was 12.9%. The dinucleotide repeats were the most abundant among the dinucleotide, trinucleotide and tetranucleotide motifs and accounted for 50.9% of the Eucalyptus genome. Primer designing analysis showed that 571 sequences with SSRs had sufficient flanking regions for polymerase chain reaction (PCR) primer synthesis. Evaluation of the usefulness of the SSRs showed that EST-derived SSRs can generate polymorphic markers as all the primers showed allelic diversity among the 16 provenances of E. tereticornis. EST-SSR (dpeaa)DE-He213 simple sequence repeats (dpeaa)DE-He213 allelic diversity (dpeaa)DE-He213 Sumathi, R. verfasserin aut Chezhian, P. verfasserin aut Kavitha, S. verfasserin aut Ghosh, M. verfasserin aut Enthalten in Journal of Genetics Springer India, 1955 87(2008), 1 vom: 01. Apr., Seite 21-25 (DE-627)SPR024069582 nnns volume:87 year:2008 number:1 day:01 month:04 pages:21-25 https://dx.doi.org/10.1007/s12041-008-0003-9 lizenzpflichtig Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER GBV_ILN_11 GBV_ILN_20 GBV_ILN_21 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_30 GBV_ILN_31 GBV_ILN_32 GBV_ILN_40 GBV_ILN_65 GBV_ILN_70 GBV_ILN_2002 GBV_ILN_2004 GBV_ILN_2008 GBV_ILN_2009 GBV_ILN_2012 GBV_ILN_2014 GBV_ILN_2015 GBV_ILN_2018 GBV_ILN_2021 GBV_ILN_2088 GBV_ILN_2190 GBV_ILN_2244 AR 87 2008 1 01 04 21-25
spelling	10.1007/s12041-008-0003-9 doi (DE-627)SPR024135836 (SPR)s12041-008-0003-9-e DE-627 ger DE-627 rakwb eng Yasodha, R. verfasserin aut Eucalyptus microsatellites mined in silico: survey and evaluation 2008 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier Abstract Eucalyptus is an important short rotation pulpy woody plant, grown widely in the tropics. Recently, many genomic programmes are underway leading to the accumulation of voluminous genomic and expressed sequence tag sequences in public databases. These sequences can be utilized for analysis of simple sequence repeats (SSRs) and single nucleotide polymorphism (SNPs) available in the transcribed genes. In this study, in silico analysis of 15,285 sequences representing partial and full-length mRNA from Eucalyptus species for their use in developing SSRs or microsatellites were carried out. A total of 875 EST-SSRs were identified from 772 SSR containing ESTs. Motif size of 6 for dinucleotide and 5 for trinucleotide, tetranucleotide, and pentanucleotides were considered in locating the microsatellites. The average frequency of identified SSRs was 12.9%. The dinucleotide repeats were the most abundant among the dinucleotide, trinucleotide and tetranucleotide motifs and accounted for 50.9% of the Eucalyptus genome. Primer designing analysis showed that 571 sequences with SSRs had sufficient flanking regions for polymerase chain reaction (PCR) primer synthesis. Evaluation of the usefulness of the SSRs showed that EST-derived SSRs can generate polymorphic markers as all the primers showed allelic diversity among the 16 provenances of E. tereticornis. EST-SSR (dpeaa)DE-He213 simple sequence repeats (dpeaa)DE-He213 allelic diversity (dpeaa)DE-He213 Sumathi, R. verfasserin aut Chezhian, P. verfasserin aut Kavitha, S. verfasserin aut Ghosh, M. verfasserin aut Enthalten in Journal of Genetics Springer India, 1955 87(2008), 1 vom: 01. Apr., Seite 21-25 (DE-627)SPR024069582 nnns volume:87 year:2008 number:1 day:01 month:04 pages:21-25 https://dx.doi.org/10.1007/s12041-008-0003-9 lizenzpflichtig Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER GBV_ILN_11 GBV_ILN_20 GBV_ILN_21 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_30 GBV_ILN_31 GBV_ILN_32 GBV_ILN_40 GBV_ILN_65 GBV_ILN_70 GBV_ILN_2002 GBV_ILN_2004 GBV_ILN_2008 GBV_ILN_2009 GBV_ILN_2012 GBV_ILN_2014 GBV_ILN_2015 GBV_ILN_2018 GBV_ILN_2021 GBV_ILN_2088 GBV_ILN_2190 GBV_ILN_2244 AR 87 2008 1 01 04 21-25
allfields_unstemmed	10.1007/s12041-008-0003-9 doi (DE-627)SPR024135836 (SPR)s12041-008-0003-9-e DE-627 ger DE-627 rakwb eng Yasodha, R. verfasserin aut Eucalyptus microsatellites mined in silico: survey and evaluation 2008 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier Abstract Eucalyptus is an important short rotation pulpy woody plant, grown widely in the tropics. Recently, many genomic programmes are underway leading to the accumulation of voluminous genomic and expressed sequence tag sequences in public databases. These sequences can be utilized for analysis of simple sequence repeats (SSRs) and single nucleotide polymorphism (SNPs) available in the transcribed genes. In this study, in silico analysis of 15,285 sequences representing partial and full-length mRNA from Eucalyptus species for their use in developing SSRs or microsatellites were carried out. A total of 875 EST-SSRs were identified from 772 SSR containing ESTs. Motif size of 6 for dinucleotide and 5 for trinucleotide, tetranucleotide, and pentanucleotides were considered in locating the microsatellites. The average frequency of identified SSRs was 12.9%. The dinucleotide repeats were the most abundant among the dinucleotide, trinucleotide and tetranucleotide motifs and accounted for 50.9% of the Eucalyptus genome. Primer designing analysis showed that 571 sequences with SSRs had sufficient flanking regions for polymerase chain reaction (PCR) primer synthesis. Evaluation of the usefulness of the SSRs showed that EST-derived SSRs can generate polymorphic markers as all the primers showed allelic diversity among the 16 provenances of E. tereticornis. EST-SSR (dpeaa)DE-He213 simple sequence repeats (dpeaa)DE-He213 allelic diversity (dpeaa)DE-He213 Sumathi, R. verfasserin aut Chezhian, P. verfasserin aut Kavitha, S. verfasserin aut Ghosh, M. verfasserin aut Enthalten in Journal of Genetics Springer India, 1955 87(2008), 1 vom: 01. Apr., Seite 21-25 (DE-627)SPR024069582 nnns volume:87 year:2008 number:1 day:01 month:04 pages:21-25 https://dx.doi.org/10.1007/s12041-008-0003-9 lizenzpflichtig Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER GBV_ILN_11 GBV_ILN_20 GBV_ILN_21 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_30 GBV_ILN_31 GBV_ILN_32 GBV_ILN_40 GBV_ILN_65 GBV_ILN_70 GBV_ILN_2002 GBV_ILN_2004 GBV_ILN_2008 GBV_ILN_2009 GBV_ILN_2012 GBV_ILN_2014 GBV_ILN_2015 GBV_ILN_2018 GBV_ILN_2021 GBV_ILN_2088 GBV_ILN_2190 GBV_ILN_2244 AR 87 2008 1 01 04 21-25
allfieldsGer	10.1007/s12041-008-0003-9 doi (DE-627)SPR024135836 (SPR)s12041-008-0003-9-e DE-627 ger DE-627 rakwb eng Yasodha, R. verfasserin aut Eucalyptus microsatellites mined in silico: survey and evaluation 2008 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier Abstract Eucalyptus is an important short rotation pulpy woody plant, grown widely in the tropics. Recently, many genomic programmes are underway leading to the accumulation of voluminous genomic and expressed sequence tag sequences in public databases. These sequences can be utilized for analysis of simple sequence repeats (SSRs) and single nucleotide polymorphism (SNPs) available in the transcribed genes. In this study, in silico analysis of 15,285 sequences representing partial and full-length mRNA from Eucalyptus species for their use in developing SSRs or microsatellites were carried out. A total of 875 EST-SSRs were identified from 772 SSR containing ESTs. Motif size of 6 for dinucleotide and 5 for trinucleotide, tetranucleotide, and pentanucleotides were considered in locating the microsatellites. The average frequency of identified SSRs was 12.9%. The dinucleotide repeats were the most abundant among the dinucleotide, trinucleotide and tetranucleotide motifs and accounted for 50.9% of the Eucalyptus genome. Primer designing analysis showed that 571 sequences with SSRs had sufficient flanking regions for polymerase chain reaction (PCR) primer synthesis. Evaluation of the usefulness of the SSRs showed that EST-derived SSRs can generate polymorphic markers as all the primers showed allelic diversity among the 16 provenances of E. tereticornis. EST-SSR (dpeaa)DE-He213 simple sequence repeats (dpeaa)DE-He213 allelic diversity (dpeaa)DE-He213 Sumathi, R. verfasserin aut Chezhian, P. verfasserin aut Kavitha, S. verfasserin aut Ghosh, M. verfasserin aut Enthalten in Journal of Genetics Springer India, 1955 87(2008), 1 vom: 01. Apr., Seite 21-25 (DE-627)SPR024069582 nnns volume:87 year:2008 number:1 day:01 month:04 pages:21-25 https://dx.doi.org/10.1007/s12041-008-0003-9 lizenzpflichtig Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER GBV_ILN_11 GBV_ILN_20 GBV_ILN_21 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_30 GBV_ILN_31 GBV_ILN_32 GBV_ILN_40 GBV_ILN_65 GBV_ILN_70 GBV_ILN_2002 GBV_ILN_2004 GBV_ILN_2008 GBV_ILN_2009 GBV_ILN_2012 GBV_ILN_2014 GBV_ILN_2015 GBV_ILN_2018 GBV_ILN_2021 GBV_ILN_2088 GBV_ILN_2190 GBV_ILN_2244 AR 87 2008 1 01 04 21-25
allfieldsSound	10.1007/s12041-008-0003-9 doi (DE-627)SPR024135836 (SPR)s12041-008-0003-9-e DE-627 ger DE-627 rakwb eng Yasodha, R. verfasserin aut Eucalyptus microsatellites mined in silico: survey and evaluation 2008 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier Abstract Eucalyptus is an important short rotation pulpy woody plant, grown widely in the tropics. Recently, many genomic programmes are underway leading to the accumulation of voluminous genomic and expressed sequence tag sequences in public databases. These sequences can be utilized for analysis of simple sequence repeats (SSRs) and single nucleotide polymorphism (SNPs) available in the transcribed genes. In this study, in silico analysis of 15,285 sequences representing partial and full-length mRNA from Eucalyptus species for their use in developing SSRs or microsatellites were carried out. A total of 875 EST-SSRs were identified from 772 SSR containing ESTs. Motif size of 6 for dinucleotide and 5 for trinucleotide, tetranucleotide, and pentanucleotides were considered in locating the microsatellites. The average frequency of identified SSRs was 12.9%. The dinucleotide repeats were the most abundant among the dinucleotide, trinucleotide and tetranucleotide motifs and accounted for 50.9% of the Eucalyptus genome. Primer designing analysis showed that 571 sequences with SSRs had sufficient flanking regions for polymerase chain reaction (PCR) primer synthesis. Evaluation of the usefulness of the SSRs showed that EST-derived SSRs can generate polymorphic markers as all the primers showed allelic diversity among the 16 provenances of E. tereticornis. EST-SSR (dpeaa)DE-He213 simple sequence repeats (dpeaa)DE-He213 allelic diversity (dpeaa)DE-He213 Sumathi, R. verfasserin aut Chezhian, P. verfasserin aut Kavitha, S. verfasserin aut Ghosh, M. verfasserin aut Enthalten in Journal of Genetics Springer India, 1955 87(2008), 1 vom: 01. Apr., Seite 21-25 (DE-627)SPR024069582 nnns volume:87 year:2008 number:1 day:01 month:04 pages:21-25 https://dx.doi.org/10.1007/s12041-008-0003-9 lizenzpflichtig Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER GBV_ILN_11 GBV_ILN_20 GBV_ILN_21 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_30 GBV_ILN_31 GBV_ILN_32 GBV_ILN_40 GBV_ILN_65 GBV_ILN_70 GBV_ILN_2002 GBV_ILN_2004 GBV_ILN_2008 GBV_ILN_2009 GBV_ILN_2012 GBV_ILN_2014 GBV_ILN_2015 GBV_ILN_2018 GBV_ILN_2021 GBV_ILN_2088 GBV_ILN_2190 GBV_ILN_2244 AR 87 2008 1 01 04 21-25
language	English
source	Enthalten in Journal of Genetics 87(2008), 1 vom: 01. Apr., Seite 21-25 volume:87 year:2008 number:1 day:01 month:04 pages:21-25
sourceStr	Enthalten in Journal of Genetics 87(2008), 1 vom: 01. Apr., Seite 21-25 volume:87 year:2008 number:1 day:01 month:04 pages:21-25
format_phy_str_mv	Article
institution	findex.gbv.de
topic_facet	EST-SSR simple sequence repeats allelic diversity
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container_title	Journal of Genetics
authorswithroles_txt_mv	Yasodha, R. @@aut@@ Sumathi, R. @@aut@@ Chezhian, P. @@aut@@ Kavitha, S. @@aut@@ Ghosh, M. @@aut@@
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author	Yasodha, R.
spellingShingle	Yasodha, R. misc EST-SSR misc simple sequence repeats misc allelic diversity Eucalyptus microsatellites mined in silico: survey and evaluation
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topic_title	Eucalyptus microsatellites mined in silico: survey and evaluation EST-SSR (dpeaa)DE-He213 simple sequence repeats (dpeaa)DE-He213 allelic diversity (dpeaa)DE-He213
topic	misc EST-SSR misc simple sequence repeats misc allelic diversity
topic_unstemmed	misc EST-SSR misc simple sequence repeats misc allelic diversity
topic_browse	misc EST-SSR misc simple sequence repeats misc allelic diversity
format_facet	Elektronische Aufsätze Aufsätze Elektronische Ressource
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title	Eucalyptus microsatellites mined in silico: survey and evaluation
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title_full	Eucalyptus microsatellites mined in silico: survey and evaluation
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author_browse	Yasodha, R. Sumathi, R. Chezhian, P. Kavitha, S. Ghosh, M.
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title_sort	eucalyptus microsatellites mined in silico: survey and evaluation
title_auth	Eucalyptus microsatellites mined in silico: survey and evaluation
abstract	Abstract Eucalyptus is an important short rotation pulpy woody plant, grown widely in the tropics. Recently, many genomic programmes are underway leading to the accumulation of voluminous genomic and expressed sequence tag sequences in public databases. These sequences can be utilized for analysis of simple sequence repeats (SSRs) and single nucleotide polymorphism (SNPs) available in the transcribed genes. In this study, in silico analysis of 15,285 sequences representing partial and full-length mRNA from Eucalyptus species for their use in developing SSRs or microsatellites were carried out. A total of 875 EST-SSRs were identified from 772 SSR containing ESTs. Motif size of 6 for dinucleotide and 5 for trinucleotide, tetranucleotide, and pentanucleotides were considered in locating the microsatellites. The average frequency of identified SSRs was 12.9%. The dinucleotide repeats were the most abundant among the dinucleotide, trinucleotide and tetranucleotide motifs and accounted for 50.9% of the Eucalyptus genome. Primer designing analysis showed that 571 sequences with SSRs had sufficient flanking regions for polymerase chain reaction (PCR) primer synthesis. Evaluation of the usefulness of the SSRs showed that EST-derived SSRs can generate polymorphic markers as all the primers showed allelic diversity among the 16 provenances of E. tereticornis.
abstractGer	Abstract Eucalyptus is an important short rotation pulpy woody plant, grown widely in the tropics. Recently, many genomic programmes are underway leading to the accumulation of voluminous genomic and expressed sequence tag sequences in public databases. These sequences can be utilized for analysis of simple sequence repeats (SSRs) and single nucleotide polymorphism (SNPs) available in the transcribed genes. In this study, in silico analysis of 15,285 sequences representing partial and full-length mRNA from Eucalyptus species for their use in developing SSRs or microsatellites were carried out. A total of 875 EST-SSRs were identified from 772 SSR containing ESTs. Motif size of 6 for dinucleotide and 5 for trinucleotide, tetranucleotide, and pentanucleotides were considered in locating the microsatellites. The average frequency of identified SSRs was 12.9%. The dinucleotide repeats were the most abundant among the dinucleotide, trinucleotide and tetranucleotide motifs and accounted for 50.9% of the Eucalyptus genome. Primer designing analysis showed that 571 sequences with SSRs had sufficient flanking regions for polymerase chain reaction (PCR) primer synthesis. Evaluation of the usefulness of the SSRs showed that EST-derived SSRs can generate polymorphic markers as all the primers showed allelic diversity among the 16 provenances of E. tereticornis.
abstract_unstemmed	Abstract Eucalyptus is an important short rotation pulpy woody plant, grown widely in the tropics. Recently, many genomic programmes are underway leading to the accumulation of voluminous genomic and expressed sequence tag sequences in public databases. These sequences can be utilized for analysis of simple sequence repeats (SSRs) and single nucleotide polymorphism (SNPs) available in the transcribed genes. In this study, in silico analysis of 15,285 sequences representing partial and full-length mRNA from Eucalyptus species for their use in developing SSRs or microsatellites were carried out. A total of 875 EST-SSRs were identified from 772 SSR containing ESTs. Motif size of 6 for dinucleotide and 5 for trinucleotide, tetranucleotide, and pentanucleotides were considered in locating the microsatellites. The average frequency of identified SSRs was 12.9%. The dinucleotide repeats were the most abundant among the dinucleotide, trinucleotide and tetranucleotide motifs and accounted for 50.9% of the Eucalyptus genome. Primer designing analysis showed that 571 sequences with SSRs had sufficient flanking regions for polymerase chain reaction (PCR) primer synthesis. Evaluation of the usefulness of the SSRs showed that EST-derived SSRs can generate polymorphic markers as all the primers showed allelic diversity among the 16 provenances of E. tereticornis.
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title_short	Eucalyptus microsatellites mined in silico: survey and evaluation
url	https://dx.doi.org/10.1007/s12041-008-0003-9
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author2	Sumathi, R. Chezhian, P. Kavitha, S. Ghosh, M.
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up_date	2024-07-03T23:36:30.462Z
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