Complete chloroplast genomes of three sand-fixing Salix shrubs from Northwest China: comparative and phylogenetic analysis and interspecific identification

Key message By comparing the chloroplast genomes of three willows, it is found that the genome structure is relatively conservative, and the large variations are more derived from the noncoding regions. Abstract Salix L., the largest genus in Salicaceae, has great value in ecology and economy. Here,...
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Autor*in:	Lu, Dongye [verfasserIn] Huang, Haiguang Zhang, Lei Hao, Lei Zhang, Guosheng

Format:	E-Artikel
Sprache:	Englisch

Erschienen:	2023

Schlagwörter:	Chloroplast genome Comparative analysis Phylogenetic relationship

Anmerkung:	© The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature 2023. Springer Nature or its licensor (e.g. a society or other partner) holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law.

Übergeordnetes Werk:	Enthalten in: Trees - Berlin : Springer, 1986, 37(2023), 3 vom: 19. Jan., Seite 849-861
Übergeordnetes Werk:	volume:37 ; year:2023 ; number:3 ; day:19 ; month:01 ; pages:849-861

Links:	Volltext

DOI / URN:	10.1007/s00468-023-02388-3

Katalog-ID:	SPR05155206X

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520			\|a Key message By comparing the chloroplast genomes of three willows, it is found that the genome structure is relatively conservative, and the large variations are more derived from the noncoding regions. Abstract Salix L., the largest genus in Salicaceae, has great value in ecology and economy. Here, we compared the chloroplast genomes of three important sand-fixing shrubs of the genus Salix: Salix gordejevii (size: 155,279 bp); S. cheilophila (size: 155,322 bp); and S. psammophila (size: 155,278 bp). The quadripartite circular structures of these genome sequences have the same structure and gene contents with 84 protein-coding genes, 38 tRNA genes, and eight rRNA genes. Long repeats including forward and palindromic repeats were found in three plastomes. The mononucleotide simple sequence repeats (SSRs) were dominant and accounted for more than 64% in all three plastomes, whereas hexanucleotide SSRs existed only in S. gordejevii. The noncoding and intergenic regions have greater variations than the coding regions, and eight highly variable regions were identified within the Salix chloroplast genomes, which could be utilized as potential markers for phylogenetic studies and phylogeography. In addition, we found 34 indels with more than 5 bases, which can be used to further identify S. gordejevii and S. psammophila with similar morphologies. Phylogenetic analysis based on whole cp genomes showed that S. gordejevii and S. magnifica are closely related, S. psammophila was a sister to S. suchowensis, and S. cheilophila clustered with them. The completed genomes in this study provide useful genetic resources for future research on species identification, phylogenetic relationships, and the adaptive evolution of Salix species.
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allfields	10.1007/s00468-023-02388-3 doi (DE-627)SPR05155206X (SPR)s00468-023-02388-3-e DE-627 ger DE-627 rakwb eng Lu, Dongye verfasserin aut Complete chloroplast genomes of three sand-fixing Salix shrubs from Northwest China: comparative and phylogenetic analysis and interspecific identification 2023 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature 2023. Springer Nature or its licensor (e.g. a society or other partner) holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law. Key message By comparing the chloroplast genomes of three willows, it is found that the genome structure is relatively conservative, and the large variations are more derived from the noncoding regions. Abstract Salix L., the largest genus in Salicaceae, has great value in ecology and economy. Here, we compared the chloroplast genomes of three important sand-fixing shrubs of the genus Salix: Salix gordejevii (size: 155,279 bp); S. cheilophila (size: 155,322 bp); and S. psammophila (size: 155,278 bp). The quadripartite circular structures of these genome sequences have the same structure and gene contents with 84 protein-coding genes, 38 tRNA genes, and eight rRNA genes. Long repeats including forward and palindromic repeats were found in three plastomes. The mononucleotide simple sequence repeats (SSRs) were dominant and accounted for more than 64% in all three plastomes, whereas hexanucleotide SSRs existed only in S. gordejevii. The noncoding and intergenic regions have greater variations than the coding regions, and eight highly variable regions were identified within the Salix chloroplast genomes, which could be utilized as potential markers for phylogenetic studies and phylogeography. In addition, we found 34 indels with more than 5 bases, which can be used to further identify S. gordejevii and S. psammophila with similar morphologies. Phylogenetic analysis based on whole cp genomes showed that S. gordejevii and S. magnifica are closely related, S. psammophila was a sister to S. suchowensis, and S. cheilophila clustered with them. The completed genomes in this study provide useful genetic resources for future research on species identification, phylogenetic relationships, and the adaptive evolution of Salix species. Chloroplast genome (dpeaa)DE-He213 Comparative analysis (dpeaa)DE-He213 Phylogenetic relationship (dpeaa)DE-He213 Huang, Haiguang aut Zhang, Lei aut Hao, Lei aut Zhang, Guosheng (orcid)0000-0002-4506-6885 aut Enthalten in Trees Berlin : Springer, 1986 37(2023), 3 vom: 19. Jan., Seite 849-861 (DE-627)265505755 (DE-600)1463920-8 1432-2285 nnns volume:37 year:2023 number:3 day:19 month:01 pages:849-861 https://dx.doi.org/10.1007/s00468-023-02388-3 lizenzpflichtig Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER 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_213 GBV_ILN_224 GBV_ILN_230 GBV_ILN_250 GBV_ILN_267 GBV_ILN_281 GBV_ILN_285 GBV_ILN_293 GBV_ILN_370 GBV_ILN_602 GBV_ILN_636 GBV_ILN_702 GBV_ILN_2001 GBV_ILN_2003 GBV_ILN_2004 GBV_ILN_2005 GBV_ILN_2006 GBV_ILN_2007 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_2056 GBV_ILN_2057 GBV_ILN_2059 GBV_ILN_2061 GBV_ILN_2064 GBV_ILN_2065 GBV_ILN_2068 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_2118 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_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_4328 GBV_ILN_4333 GBV_ILN_4334 GBV_ILN_4335 GBV_ILN_4336 GBV_ILN_4338 GBV_ILN_4393 GBV_ILN_4700 AR 37 2023 3 19 01 849-861
spelling	10.1007/s00468-023-02388-3 doi (DE-627)SPR05155206X (SPR)s00468-023-02388-3-e DE-627 ger DE-627 rakwb eng Lu, Dongye verfasserin aut Complete chloroplast genomes of three sand-fixing Salix shrubs from Northwest China: comparative and phylogenetic analysis and interspecific identification 2023 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature 2023. Springer Nature or its licensor (e.g. a society or other partner) holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law. Key message By comparing the chloroplast genomes of three willows, it is found that the genome structure is relatively conservative, and the large variations are more derived from the noncoding regions. Abstract Salix L., the largest genus in Salicaceae, has great value in ecology and economy. Here, we compared the chloroplast genomes of three important sand-fixing shrubs of the genus Salix: Salix gordejevii (size: 155,279 bp); S. cheilophila (size: 155,322 bp); and S. psammophila (size: 155,278 bp). The quadripartite circular structures of these genome sequences have the same structure and gene contents with 84 protein-coding genes, 38 tRNA genes, and eight rRNA genes. Long repeats including forward and palindromic repeats were found in three plastomes. The mononucleotide simple sequence repeats (SSRs) were dominant and accounted for more than 64% in all three plastomes, whereas hexanucleotide SSRs existed only in S. gordejevii. The noncoding and intergenic regions have greater variations than the coding regions, and eight highly variable regions were identified within the Salix chloroplast genomes, which could be utilized as potential markers for phylogenetic studies and phylogeography. In addition, we found 34 indels with more than 5 bases, which can be used to further identify S. gordejevii and S. psammophila with similar morphologies. Phylogenetic analysis based on whole cp genomes showed that S. gordejevii and S. magnifica are closely related, S. psammophila was a sister to S. suchowensis, and S. cheilophila clustered with them. The completed genomes in this study provide useful genetic resources for future research on species identification, phylogenetic relationships, and the adaptive evolution of Salix species. Chloroplast genome (dpeaa)DE-He213 Comparative analysis (dpeaa)DE-He213 Phylogenetic relationship (dpeaa)DE-He213 Huang, Haiguang aut Zhang, Lei aut Hao, Lei aut Zhang, Guosheng (orcid)0000-0002-4506-6885 aut Enthalten in Trees Berlin : Springer, 1986 37(2023), 3 vom: 19. Jan., Seite 849-861 (DE-627)265505755 (DE-600)1463920-8 1432-2285 nnns volume:37 year:2023 number:3 day:19 month:01 pages:849-861 https://dx.doi.org/10.1007/s00468-023-02388-3 lizenzpflichtig Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER 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_213 GBV_ILN_224 GBV_ILN_230 GBV_ILN_250 GBV_ILN_267 GBV_ILN_281 GBV_ILN_285 GBV_ILN_293 GBV_ILN_370 GBV_ILN_602 GBV_ILN_636 GBV_ILN_702 GBV_ILN_2001 GBV_ILN_2003 GBV_ILN_2004 GBV_ILN_2005 GBV_ILN_2006 GBV_ILN_2007 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_2056 GBV_ILN_2057 GBV_ILN_2059 GBV_ILN_2061 GBV_ILN_2064 GBV_ILN_2065 GBV_ILN_2068 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_2118 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_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_4328 GBV_ILN_4333 GBV_ILN_4334 GBV_ILN_4335 GBV_ILN_4336 GBV_ILN_4338 GBV_ILN_4393 GBV_ILN_4700 AR 37 2023 3 19 01 849-861
allfields_unstemmed	10.1007/s00468-023-02388-3 doi (DE-627)SPR05155206X (SPR)s00468-023-02388-3-e DE-627 ger DE-627 rakwb eng Lu, Dongye verfasserin aut Complete chloroplast genomes of three sand-fixing Salix shrubs from Northwest China: comparative and phylogenetic analysis and interspecific identification 2023 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature 2023. Springer Nature or its licensor (e.g. a society or other partner) holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law. Key message By comparing the chloroplast genomes of three willows, it is found that the genome structure is relatively conservative, and the large variations are more derived from the noncoding regions. Abstract Salix L., the largest genus in Salicaceae, has great value in ecology and economy. Here, we compared the chloroplast genomes of three important sand-fixing shrubs of the genus Salix: Salix gordejevii (size: 155,279 bp); S. cheilophila (size: 155,322 bp); and S. psammophila (size: 155,278 bp). The quadripartite circular structures of these genome sequences have the same structure and gene contents with 84 protein-coding genes, 38 tRNA genes, and eight rRNA genes. Long repeats including forward and palindromic repeats were found in three plastomes. The mononucleotide simple sequence repeats (SSRs) were dominant and accounted for more than 64% in all three plastomes, whereas hexanucleotide SSRs existed only in S. gordejevii. The noncoding and intergenic regions have greater variations than the coding regions, and eight highly variable regions were identified within the Salix chloroplast genomes, which could be utilized as potential markers for phylogenetic studies and phylogeography. In addition, we found 34 indels with more than 5 bases, which can be used to further identify S. gordejevii and S. psammophila with similar morphologies. Phylogenetic analysis based on whole cp genomes showed that S. gordejevii and S. magnifica are closely related, S. psammophila was a sister to S. suchowensis, and S. cheilophila clustered with them. The completed genomes in this study provide useful genetic resources for future research on species identification, phylogenetic relationships, and the adaptive evolution of Salix species. Chloroplast genome (dpeaa)DE-He213 Comparative analysis (dpeaa)DE-He213 Phylogenetic relationship (dpeaa)DE-He213 Huang, Haiguang aut Zhang, Lei aut Hao, Lei aut Zhang, Guosheng (orcid)0000-0002-4506-6885 aut Enthalten in Trees Berlin : Springer, 1986 37(2023), 3 vom: 19. Jan., Seite 849-861 (DE-627)265505755 (DE-600)1463920-8 1432-2285 nnns volume:37 year:2023 number:3 day:19 month:01 pages:849-861 https://dx.doi.org/10.1007/s00468-023-02388-3 lizenzpflichtig Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER 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_213 GBV_ILN_224 GBV_ILN_230 GBV_ILN_250 GBV_ILN_267 GBV_ILN_281 GBV_ILN_285 GBV_ILN_293 GBV_ILN_370 GBV_ILN_602 GBV_ILN_636 GBV_ILN_702 GBV_ILN_2001 GBV_ILN_2003 GBV_ILN_2004 GBV_ILN_2005 GBV_ILN_2006 GBV_ILN_2007 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_2056 GBV_ILN_2057 GBV_ILN_2059 GBV_ILN_2061 GBV_ILN_2064 GBV_ILN_2065 GBV_ILN_2068 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_2118 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_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_4328 GBV_ILN_4333 GBV_ILN_4334 GBV_ILN_4335 GBV_ILN_4336 GBV_ILN_4338 GBV_ILN_4393 GBV_ILN_4700 AR 37 2023 3 19 01 849-861
allfieldsGer	10.1007/s00468-023-02388-3 doi (DE-627)SPR05155206X (SPR)s00468-023-02388-3-e DE-627 ger DE-627 rakwb eng Lu, Dongye verfasserin aut Complete chloroplast genomes of three sand-fixing Salix shrubs from Northwest China: comparative and phylogenetic analysis and interspecific identification 2023 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature 2023. Springer Nature or its licensor (e.g. a society or other partner) holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law. Key message By comparing the chloroplast genomes of three willows, it is found that the genome structure is relatively conservative, and the large variations are more derived from the noncoding regions. Abstract Salix L., the largest genus in Salicaceae, has great value in ecology and economy. Here, we compared the chloroplast genomes of three important sand-fixing shrubs of the genus Salix: Salix gordejevii (size: 155,279 bp); S. cheilophila (size: 155,322 bp); and S. psammophila (size: 155,278 bp). The quadripartite circular structures of these genome sequences have the same structure and gene contents with 84 protein-coding genes, 38 tRNA genes, and eight rRNA genes. Long repeats including forward and palindromic repeats were found in three plastomes. The mononucleotide simple sequence repeats (SSRs) were dominant and accounted for more than 64% in all three plastomes, whereas hexanucleotide SSRs existed only in S. gordejevii. The noncoding and intergenic regions have greater variations than the coding regions, and eight highly variable regions were identified within the Salix chloroplast genomes, which could be utilized as potential markers for phylogenetic studies and phylogeography. In addition, we found 34 indels with more than 5 bases, which can be used to further identify S. gordejevii and S. psammophila with similar morphologies. Phylogenetic analysis based on whole cp genomes showed that S. gordejevii and S. magnifica are closely related, S. psammophila was a sister to S. suchowensis, and S. cheilophila clustered with them. The completed genomes in this study provide useful genetic resources for future research on species identification, phylogenetic relationships, and the adaptive evolution of Salix species. Chloroplast genome (dpeaa)DE-He213 Comparative analysis (dpeaa)DE-He213 Phylogenetic relationship (dpeaa)DE-He213 Huang, Haiguang aut Zhang, Lei aut Hao, Lei aut Zhang, Guosheng (orcid)0000-0002-4506-6885 aut Enthalten in Trees Berlin : Springer, 1986 37(2023), 3 vom: 19. Jan., Seite 849-861 (DE-627)265505755 (DE-600)1463920-8 1432-2285 nnns volume:37 year:2023 number:3 day:19 month:01 pages:849-861 https://dx.doi.org/10.1007/s00468-023-02388-3 lizenzpflichtig Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER 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_213 GBV_ILN_224 GBV_ILN_230 GBV_ILN_250 GBV_ILN_267 GBV_ILN_281 GBV_ILN_285 GBV_ILN_293 GBV_ILN_370 GBV_ILN_602 GBV_ILN_636 GBV_ILN_702 GBV_ILN_2001 GBV_ILN_2003 GBV_ILN_2004 GBV_ILN_2005 GBV_ILN_2006 GBV_ILN_2007 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_2056 GBV_ILN_2057 GBV_ILN_2059 GBV_ILN_2061 GBV_ILN_2064 GBV_ILN_2065 GBV_ILN_2068 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_2118 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_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_4328 GBV_ILN_4333 GBV_ILN_4334 GBV_ILN_4335 GBV_ILN_4336 GBV_ILN_4338 GBV_ILN_4393 GBV_ILN_4700 AR 37 2023 3 19 01 849-861
allfieldsSound	10.1007/s00468-023-02388-3 doi (DE-627)SPR05155206X (SPR)s00468-023-02388-3-e DE-627 ger DE-627 rakwb eng Lu, Dongye verfasserin aut Complete chloroplast genomes of three sand-fixing Salix shrubs from Northwest China: comparative and phylogenetic analysis and interspecific identification 2023 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature 2023. Springer Nature or its licensor (e.g. a society or other partner) holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law. Key message By comparing the chloroplast genomes of three willows, it is found that the genome structure is relatively conservative, and the large variations are more derived from the noncoding regions. Abstract Salix L., the largest genus in Salicaceae, has great value in ecology and economy. Here, we compared the chloroplast genomes of three important sand-fixing shrubs of the genus Salix: Salix gordejevii (size: 155,279 bp); S. cheilophila (size: 155,322 bp); and S. psammophila (size: 155,278 bp). The quadripartite circular structures of these genome sequences have the same structure and gene contents with 84 protein-coding genes, 38 tRNA genes, and eight rRNA genes. Long repeats including forward and palindromic repeats were found in three plastomes. The mononucleotide simple sequence repeats (SSRs) were dominant and accounted for more than 64% in all three plastomes, whereas hexanucleotide SSRs existed only in S. gordejevii. The noncoding and intergenic regions have greater variations than the coding regions, and eight highly variable regions were identified within the Salix chloroplast genomes, which could be utilized as potential markers for phylogenetic studies and phylogeography. In addition, we found 34 indels with more than 5 bases, which can be used to further identify S. gordejevii and S. psammophila with similar morphologies. Phylogenetic analysis based on whole cp genomes showed that S. gordejevii and S. magnifica are closely related, S. psammophila was a sister to S. suchowensis, and S. cheilophila clustered with them. The completed genomes in this study provide useful genetic resources for future research on species identification, phylogenetic relationships, and the adaptive evolution of Salix species. Chloroplast genome (dpeaa)DE-He213 Comparative analysis (dpeaa)DE-He213 Phylogenetic relationship (dpeaa)DE-He213 Huang, Haiguang aut Zhang, Lei aut Hao, Lei aut Zhang, Guosheng (orcid)0000-0002-4506-6885 aut Enthalten in Trees Berlin : Springer, 1986 37(2023), 3 vom: 19. Jan., Seite 849-861 (DE-627)265505755 (DE-600)1463920-8 1432-2285 nnns volume:37 year:2023 number:3 day:19 month:01 pages:849-861 https://dx.doi.org/10.1007/s00468-023-02388-3 lizenzpflichtig Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER 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_213 GBV_ILN_224 GBV_ILN_230 GBV_ILN_250 GBV_ILN_267 GBV_ILN_281 GBV_ILN_285 GBV_ILN_293 GBV_ILN_370 GBV_ILN_602 GBV_ILN_636 GBV_ILN_702 GBV_ILN_2001 GBV_ILN_2003 GBV_ILN_2004 GBV_ILN_2005 GBV_ILN_2006 GBV_ILN_2007 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_2056 GBV_ILN_2057 GBV_ILN_2059 GBV_ILN_2061 GBV_ILN_2064 GBV_ILN_2065 GBV_ILN_2068 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_2118 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_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_4328 GBV_ILN_4333 GBV_ILN_4334 GBV_ILN_4335 GBV_ILN_4336 GBV_ILN_4338 GBV_ILN_4393 GBV_ILN_4700 AR 37 2023 3 19 01 849-861
language	English
source	Enthalten in Trees 37(2023), 3 vom: 19. Jan., Seite 849-861 volume:37 year:2023 number:3 day:19 month:01 pages:849-861
sourceStr	Enthalten in Trees 37(2023), 3 vom: 19. Jan., Seite 849-861 volume:37 year:2023 number:3 day:19 month:01 pages:849-861
format_phy_str_mv	Article
institution	findex.gbv.de
topic_facet	Chloroplast genome Comparative analysis Phylogenetic relationship
isfreeaccess_bool	false
container_title	Trees
authorswithroles_txt_mv	Lu, Dongye @@aut@@ Huang, Haiguang @@aut@@ Zhang, Lei @@aut@@ Hao, Lei @@aut@@ Zhang, Guosheng @@aut@@
publishDateDaySort_date	2023-01-19T00:00:00Z
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author	Lu, Dongye
spellingShingle	Lu, Dongye misc Chloroplast genome misc Comparative analysis misc Phylogenetic relationship Complete chloroplast genomes of three sand-fixing Salix shrubs from Northwest China: comparative and phylogenetic analysis and interspecific identification
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topic_title	Complete chloroplast genomes of three sand-fixing Salix shrubs from Northwest China: comparative and phylogenetic analysis and interspecific identification Chloroplast genome (dpeaa)DE-He213 Comparative analysis (dpeaa)DE-He213 Phylogenetic relationship (dpeaa)DE-He213
topic	misc Chloroplast genome misc Comparative analysis misc Phylogenetic relationship
topic_unstemmed	misc Chloroplast genome misc Comparative analysis misc Phylogenetic relationship
topic_browse	misc Chloroplast genome misc Comparative analysis misc Phylogenetic relationship
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title	Complete chloroplast genomes of three sand-fixing Salix shrubs from Northwest China: comparative and phylogenetic analysis and interspecific identification
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title_full	Complete chloroplast genomes of three sand-fixing Salix shrubs from Northwest China: comparative and phylogenetic analysis and interspecific identification
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title_sort	complete chloroplast genomes of three sand-fixing salix shrubs from northwest china: comparative and phylogenetic analysis and interspecific identification
title_auth	Complete chloroplast genomes of three sand-fixing Salix shrubs from Northwest China: comparative and phylogenetic analysis and interspecific identification
abstract	Key message By comparing the chloroplast genomes of three willows, it is found that the genome structure is relatively conservative, and the large variations are more derived from the noncoding regions. Abstract Salix L., the largest genus in Salicaceae, has great value in ecology and economy. Here, we compared the chloroplast genomes of three important sand-fixing shrubs of the genus Salix: Salix gordejevii (size: 155,279 bp); S. cheilophila (size: 155,322 bp); and S. psammophila (size: 155,278 bp). The quadripartite circular structures of these genome sequences have the same structure and gene contents with 84 protein-coding genes, 38 tRNA genes, and eight rRNA genes. Long repeats including forward and palindromic repeats were found in three plastomes. The mononucleotide simple sequence repeats (SSRs) were dominant and accounted for more than 64% in all three plastomes, whereas hexanucleotide SSRs existed only in S. gordejevii. The noncoding and intergenic regions have greater variations than the coding regions, and eight highly variable regions were identified within the Salix chloroplast genomes, which could be utilized as potential markers for phylogenetic studies and phylogeography. In addition, we found 34 indels with more than 5 bases, which can be used to further identify S. gordejevii and S. psammophila with similar morphologies. Phylogenetic analysis based on whole cp genomes showed that S. gordejevii and S. magnifica are closely related, S. psammophila was a sister to S. suchowensis, and S. cheilophila clustered with them. The completed genomes in this study provide useful genetic resources for future research on species identification, phylogenetic relationships, and the adaptive evolution of Salix species. © The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature 2023. Springer Nature or its licensor (e.g. a society or other partner) holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law.
abstractGer	Key message By comparing the chloroplast genomes of three willows, it is found that the genome structure is relatively conservative, and the large variations are more derived from the noncoding regions. Abstract Salix L., the largest genus in Salicaceae, has great value in ecology and economy. Here, we compared the chloroplast genomes of three important sand-fixing shrubs of the genus Salix: Salix gordejevii (size: 155,279 bp); S. cheilophila (size: 155,322 bp); and S. psammophila (size: 155,278 bp). The quadripartite circular structures of these genome sequences have the same structure and gene contents with 84 protein-coding genes, 38 tRNA genes, and eight rRNA genes. Long repeats including forward and palindromic repeats were found in three plastomes. The mononucleotide simple sequence repeats (SSRs) were dominant and accounted for more than 64% in all three plastomes, whereas hexanucleotide SSRs existed only in S. gordejevii. The noncoding and intergenic regions have greater variations than the coding regions, and eight highly variable regions were identified within the Salix chloroplast genomes, which could be utilized as potential markers for phylogenetic studies and phylogeography. In addition, we found 34 indels with more than 5 bases, which can be used to further identify S. gordejevii and S. psammophila with similar morphologies. Phylogenetic analysis based on whole cp genomes showed that S. gordejevii and S. magnifica are closely related, S. psammophila was a sister to S. suchowensis, and S. cheilophila clustered with them. The completed genomes in this study provide useful genetic resources for future research on species identification, phylogenetic relationships, and the adaptive evolution of Salix species. © The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature 2023. Springer Nature or its licensor (e.g. a society or other partner) holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law.
abstract_unstemmed	Key message By comparing the chloroplast genomes of three willows, it is found that the genome structure is relatively conservative, and the large variations are more derived from the noncoding regions. Abstract Salix L., the largest genus in Salicaceae, has great value in ecology and economy. Here, we compared the chloroplast genomes of three important sand-fixing shrubs of the genus Salix: Salix gordejevii (size: 155,279 bp); S. cheilophila (size: 155,322 bp); and S. psammophila (size: 155,278 bp). The quadripartite circular structures of these genome sequences have the same structure and gene contents with 84 protein-coding genes, 38 tRNA genes, and eight rRNA genes. Long repeats including forward and palindromic repeats were found in three plastomes. The mononucleotide simple sequence repeats (SSRs) were dominant and accounted for more than 64% in all three plastomes, whereas hexanucleotide SSRs existed only in S. gordejevii. The noncoding and intergenic regions have greater variations than the coding regions, and eight highly variable regions were identified within the Salix chloroplast genomes, which could be utilized as potential markers for phylogenetic studies and phylogeography. In addition, we found 34 indels with more than 5 bases, which can be used to further identify S. gordejevii and S. psammophila with similar morphologies. Phylogenetic analysis based on whole cp genomes showed that S. gordejevii and S. magnifica are closely related, S. psammophila was a sister to S. suchowensis, and S. cheilophila clustered with them. The completed genomes in this study provide useful genetic resources for future research on species identification, phylogenetic relationships, and the adaptive evolution of Salix species. © The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature 2023. Springer Nature or its licensor (e.g. a society or other partner) holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law.
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container_issue	3
title_short	Complete chloroplast genomes of three sand-fixing Salix shrubs from Northwest China: comparative and phylogenetic analysis and interspecific identification
url	https://dx.doi.org/10.1007/s00468-023-02388-3
remote_bool	true
author2	Huang, Haiguang Zhang, Lei Hao, Lei Zhang, Guosheng
author2Str	Huang, Haiguang Zhang, Lei Hao, Lei Zhang, Guosheng
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doi_str	10.1007/s00468-023-02388-3
up_date	2024-07-03T22:27:52.293Z
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Complete chloroplast genomes of three sand-fixing Salix shrubs from Northwest China: comparative and phylogenetic analysis and interspecific identification

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