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Mitochondrial DNA: The Journal of DNA Mapping, Sequencing, and Analysis Publication details, including instructions for authors and subscription information: http://www.tandfonline.com/loi/imdn20
The complete chloroplast genome sequence of the mulberry Morus notabilis (Moreae) a
a
a
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Chen Chen , Wen Zhou , Ying Huang & Zhe-Zhi Wang a
Key Laboratory of the Ministry of Education for Medicinal Resources and Natural Pharmaceutical Chemistry, National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest China, College of Life Sciences, Shaanxi Normal University, Xi’an, P. R. China Published online: 30 Jun 2015.
Click for updates To cite this article: Chen Chen, Wen Zhou, Ying Huang & Zhe-Zhi Wang (2015): The complete chloroplast genome sequence of the mulberry Morus notabilis (Moreae), Mitochondrial DNA: The Journal of DNA Mapping, Sequencing, and Analysis To link to this article: http://dx.doi.org/10.3109/19401736.2015.1053127
PLEASE SCROLL DOWN FOR ARTICLE Taylor & Francis makes every effort to ensure the accuracy of all the information (the “Content”) contained in the publications on our platform. However, Taylor & Francis, our agents, and our licensors make no representations or warranties whatsoever as to the accuracy, completeness, or suitability for any purpose of the Content. Any opinions and views expressed in this publication are the opinions and views of the authors, and are not the views of or endorsed by Taylor & Francis. The accuracy of the Content should not be relied upon and should be independently verified with primary sources of information. Taylor and Francis shall not be liable for any losses, actions, claims, proceedings, demands, costs, expenses, damages, and other liabilities whatsoever or howsoever caused arising directly or indirectly in connection with, in relation to or arising out of the use of the Content. This article may be used for research, teaching, and private study purposes. Any substantial or systematic reproduction, redistribution, reselling, loan, sub-licensing, systematic supply, or distribution in any form to anyone is expressly forbidden. Terms & Conditions of access and use can be found at http:// www.tandfonline.com/page/terms-and-conditions
http://informahealthcare.com/mdn ISSN: 1940-1736 (print), 1940-1744 (electronic) Mitochondrial DNA, Early Online: 1–2 ! 2015 Informa UK Ltd. DOI: 10.3109/19401736.2015.1053127
MITOGENOME ANNOUNCEMENT
The complete chloroplast genome sequence of the mulberry Morus notabilis (Moreae) Chen Chen, Wen Zhou, Ying Huang, and Zhe-Zhi Wang
Downloaded by [New York University] at 20:11 02 August 2015
Key Laboratory of the Ministry of Education for Medicinal Resources and Natural Pharmaceutical Chemistry, National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest China, College of Life Sciences, Shaanxi Normal University, Xi’an, P. R. China Abstract
Keywords
The complete chloroplast genome of the mulberry Morus notabilis (Moreae) has been reconstructed from the whole-genome Illumina sequencing data. The circular genome is 158,680 bp in size, and comprises a pair of inverted repeat (IR) regions of 25,717 bp each, a large single-copy (LSC) region of 87,470 bp and a small single-copy (SSC) region of 19,776 bp. The total A+T content is 63.6%, while the corresponding values of the LSC, SSC and IR region are 65.9%, 70.7% and 57.1%, respectively. The chloroplast genome contains 129 genes, including 84 protein-coding genes (PCGs), eight ribosomal RNA (rRNA) genes and 37 transfer RNA (tRNA) genes. The maximum likelihood (ML) phylogenetic analysis revealed that M. notabilis was more related to its congeners than to the others.
Chloroplast genome, Illumina sequencing, MITObim, Morus notabilis
Mulberry trees have been exploited as economic crop in East Asia for thousands of years. Morus notabilis is native to Southwest China’s Sichuan and Yunnan provinces, with a distribution elevation of 1300–2800 m. In this article, we reconstructed its complete chloroplast genome from the previously published whole-genome Illumina sequencing data (He et al., 2013). A total of 102.8 M 50 bp raw reads were downloaded from the Sequence Read Archive (SRA) of GenBank (Accession number: SRR847539), and trimmed with CLC Genomics Workbench v7.5 (CLC Bio, Aarhus, Denmark). A subset of 21.4 M trimmed reads were used for reconstructing the chloroplast genome with MITObim v1.7 (Hahn et al., 2013), with that of its congener M. mongolica (GenBank: KM491711) as the initial reference sequence. A total of 567,470 individual chloroplast reads yielded an average coverage of 176.3X. The chloroplast genome was annotated in GENEIOUS R8 (Biomatters Ltd., Auckland, New Zealand) by aligning with that of M. mongolica (KM491711). The chloroplast genome of M. notabilis is a doublestranded circular DNA molecule with a length of 158,680 bp
Correspondence: Zhe-Zhi Wang, College of Life Sciences, Shaanxi Normal University, No.620, Western Chang’an Street, Chang’an District, Xi’an, Shaanxi 710119, P. R. China. Tel: +86 29 85310260. Fax: +86 29 85310623. E-mail: [email protected]
History Received 14 May 2015 Accepted 17 May 2015 Published online 29 June 2015
(GenBank: KP939360), which is similar to that of its congeners M. indica (DQ226511) and M. mongolica (KM491711). It shows a typical quadripartite structure, and comprises a pair of inverted repeat (IR) regions of 25,717 bp each, separated by a large singlecopy (LSC) region of 87,470 bp and a small single-copy (SSC) region of 19,776 bp. The total A+T content is 63.6%, while the corresponding values of the LSC, SSC and IR region are 65.9%, 70.7% and 57.1%, respectively. This is similar to those previously reported for the chloroplast genomes of most other vascular plants (Young et al., 2014; Yu et al., 2015). This chloroplast genome harbors 129 functional genes, including 84 protein-coding genes (PCGs), 37 tRNA genes and eight rRNA genes. Six PCGs, seven tRNA genes and all rRNA genes are duplicated in the IR regions. The LSC region possesses 61 PCGs and 22 tRNA genes, while the SSC region contains 12 PCGs and one tRNA gene. Out of those genes, 21 are involved in photosynthesis, four in transcription and two in substance metabolism. Moreover, 11 genes contain one intron, while another two genes harbor two introns; all the other genes are intronless. The phylogenetic placement of M. notabilis was deduced by its comparison with other 17 chloroplast genomes (downloaded from the GenBank of NCBI database) using 65 protein-coding genes (Figure 1). A maximum likelihood (ML) analysis was performed with MEGA6 (Tamura et al., 2013) using 500 bootstrap replicates and setting Salvia miltiorrhiza (Lamiaceae) as the outgroup. And as expected, M. notabilis was more related to its congeners than to the others in the order Rosales. Our genomic data of M. notabilis would contribute to the further studies on its phylogenetics, molecular breeding and genetic engineering.
2
C. Chen et al.
Mitochondrial DNA, Early Online: 1–2
Downloaded by [New York University] at 20:11 02 August 2015
Figure 1. Phylogenetic tree of the Rosales and related families based on maximum likelihood (ML) analysis of 65 protein-coding genes in 17 chloroplast genome sequences. Numbers next to each node are bootstrap support values based on 500 resamplings. Salvia miltiorrhiza was used as the outgroup.
Declaration of interest The authors report no conflicts of interest, and alone are responsible for the content and writing of the paper. The authors were financially supported by the Fundamental Research Funds for the Central Universities in China (GK201204004) and Innovation Funds of Graduate Programs, Shaanxi Normal University (CXS20120048) and the ‘‘Foundation for Excellent Doctoral Degree Dissertation’’ of Shaanxi Normal University (X2012YB01), Shaanxi, P. R. China.
References Hahn C, Bachmann L, Chevreux B. (2013). Reconstructing mitochondrial genomes directly from genomic next-generation sequencing
reads—A baiting and iterative mapping approach. Nucl Acids Res 41:e129. He N, Zhang C, Qi X, Zhao S, Tao Y, Yang G, Lee T-H, et al. (2013). Draft genome sequence of the mulberry tree Morus notabilis. Nat Commun 4:2445–54. Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. (2013). MEGA6: Molecular evolutionary genetics analysis version 6.0. Mol Biol Evol 30:2725–9. Young MJ, Chung WH, Mun JH, Kim N, Yu HJ. (2014). De novo assembly and characterization of the complete chloroplast genome of radish (Raphanus sativus L.). Gene 551:39–48. Yu CW, Lian Q, Wu KC, Yu SH, Xie LY, Wu ZJ. (2015). The complete chloroplast genome sequence of Anoectochilus roxburghii. Mitochondrial DNA. [Epub ahead of print]. doi: 10.3109/19401736. 2015.1033706.
Mitochondrial DNA: The Journal of DNA Mapping, Sequencing, and Analysis Publication details, including instructions for authors and subscription information: http://www.tandfonline.com/loi/imdn20
The complete chloroplast genome sequence of the mulberry Morus notabilis (Moreae) a
a
a
a
Chen Chen , Wen Zhou , Ying Huang & Zhe-Zhi Wang a
Key Laboratory of the Ministry of Education for Medicinal Resources and Natural Pharmaceutical Chemistry, National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest China, College of Life Sciences, Shaanxi Normal University, Xi’an, P. R. China Published online: 30 Jun 2015.
Click for updates To cite this article: Chen Chen, Wen Zhou, Ying Huang & Zhe-Zhi Wang (2015): The complete chloroplast genome sequence of the mulberry Morus notabilis (Moreae), Mitochondrial DNA: The Journal of DNA Mapping, Sequencing, and Analysis To link to this article: http://dx.doi.org/10.3109/19401736.2015.1053127
PLEASE SCROLL DOWN FOR ARTICLE Taylor & Francis makes every effort to ensure the accuracy of all the information (the “Content”) contained in the publications on our platform. However, Taylor & Francis, our agents, and our licensors make no representations or warranties whatsoever as to the accuracy, completeness, or suitability for any purpose of the Content. Any opinions and views expressed in this publication are the opinions and views of the authors, and are not the views of or endorsed by Taylor & Francis. The accuracy of the Content should not be relied upon and should be independently verified with primary sources of information. Taylor and Francis shall not be liable for any losses, actions, claims, proceedings, demands, costs, expenses, damages, and other liabilities whatsoever or howsoever caused arising directly or indirectly in connection with, in relation to or arising out of the use of the Content. This article may be used for research, teaching, and private study purposes. Any substantial or systematic reproduction, redistribution, reselling, loan, sub-licensing, systematic supply, or distribution in any form to anyone is expressly forbidden. Terms & Conditions of access and use can be found at http:// www.tandfonline.com/page/terms-and-conditions
http://informahealthcare.com/mdn ISSN: 1940-1736 (print), 1940-1744 (electronic) Mitochondrial DNA, Early Online: 1–2 ! 2015 Informa UK Ltd. DOI: 10.3109/19401736.2015.1053127
MITOGENOME ANNOUNCEMENT
The complete chloroplast genome sequence of the mulberry Morus notabilis (Moreae) Chen Chen, Wen Zhou, Ying Huang, and Zhe-Zhi Wang
Downloaded by [New York University] at 20:11 02 August 2015
Key Laboratory of the Ministry of Education for Medicinal Resources and Natural Pharmaceutical Chemistry, National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest China, College of Life Sciences, Shaanxi Normal University, Xi’an, P. R. China Abstract
Keywords
The complete chloroplast genome of the mulberry Morus notabilis (Moreae) has been reconstructed from the whole-genome Illumina sequencing data. The circular genome is 158,680 bp in size, and comprises a pair of inverted repeat (IR) regions of 25,717 bp each, a large single-copy (LSC) region of 87,470 bp and a small single-copy (SSC) region of 19,776 bp. The total A+T content is 63.6%, while the corresponding values of the LSC, SSC and IR region are 65.9%, 70.7% and 57.1%, respectively. The chloroplast genome contains 129 genes, including 84 protein-coding genes (PCGs), eight ribosomal RNA (rRNA) genes and 37 transfer RNA (tRNA) genes. The maximum likelihood (ML) phylogenetic analysis revealed that M. notabilis was more related to its congeners than to the others.
Chloroplast genome, Illumina sequencing, MITObim, Morus notabilis
Mulberry trees have been exploited as economic crop in East Asia for thousands of years. Morus notabilis is native to Southwest China’s Sichuan and Yunnan provinces, with a distribution elevation of 1300–2800 m. In this article, we reconstructed its complete chloroplast genome from the previously published whole-genome Illumina sequencing data (He et al., 2013). A total of 102.8 M 50 bp raw reads were downloaded from the Sequence Read Archive (SRA) of GenBank (Accession number: SRR847539), and trimmed with CLC Genomics Workbench v7.5 (CLC Bio, Aarhus, Denmark). A subset of 21.4 M trimmed reads were used for reconstructing the chloroplast genome with MITObim v1.7 (Hahn et al., 2013), with that of its congener M. mongolica (GenBank: KM491711) as the initial reference sequence. A total of 567,470 individual chloroplast reads yielded an average coverage of 176.3X. The chloroplast genome was annotated in GENEIOUS R8 (Biomatters Ltd., Auckland, New Zealand) by aligning with that of M. mongolica (KM491711). The chloroplast genome of M. notabilis is a doublestranded circular DNA molecule with a length of 158,680 bp
Correspondence: Zhe-Zhi Wang, College of Life Sciences, Shaanxi Normal University, No.620, Western Chang’an Street, Chang’an District, Xi’an, Shaanxi 710119, P. R. China. Tel: +86 29 85310260. Fax: +86 29 85310623. E-mail: [email protected]
History Received 14 May 2015 Accepted 17 May 2015 Published online 29 June 2015
(GenBank: KP939360), which is similar to that of its congeners M. indica (DQ226511) and M. mongolica (KM491711). It shows a typical quadripartite structure, and comprises a pair of inverted repeat (IR) regions of 25,717 bp each, separated by a large singlecopy (LSC) region of 87,470 bp and a small single-copy (SSC) region of 19,776 bp. The total A+T content is 63.6%, while the corresponding values of the LSC, SSC and IR region are 65.9%, 70.7% and 57.1%, respectively. This is similar to those previously reported for the chloroplast genomes of most other vascular plants (Young et al., 2014; Yu et al., 2015). This chloroplast genome harbors 129 functional genes, including 84 protein-coding genes (PCGs), 37 tRNA genes and eight rRNA genes. Six PCGs, seven tRNA genes and all rRNA genes are duplicated in the IR regions. The LSC region possesses 61 PCGs and 22 tRNA genes, while the SSC region contains 12 PCGs and one tRNA gene. Out of those genes, 21 are involved in photosynthesis, four in transcription and two in substance metabolism. Moreover, 11 genes contain one intron, while another two genes harbor two introns; all the other genes are intronless. The phylogenetic placement of M. notabilis was deduced by its comparison with other 17 chloroplast genomes (downloaded from the GenBank of NCBI database) using 65 protein-coding genes (Figure 1). A maximum likelihood (ML) analysis was performed with MEGA6 (Tamura et al., 2013) using 500 bootstrap replicates and setting Salvia miltiorrhiza (Lamiaceae) as the outgroup. And as expected, M. notabilis was more related to its congeners than to the others in the order Rosales. Our genomic data of M. notabilis would contribute to the further studies on its phylogenetics, molecular breeding and genetic engineering.
2
C. Chen et al.
Mitochondrial DNA, Early Online: 1–2
Downloaded by [New York University] at 20:11 02 August 2015
Figure 1. Phylogenetic tree of the Rosales and related families based on maximum likelihood (ML) analysis of 65 protein-coding genes in 17 chloroplast genome sequences. Numbers next to each node are bootstrap support values based on 500 resamplings. Salvia miltiorrhiza was used as the outgroup.
Declaration of interest The authors report no conflicts of interest, and alone are responsible for the content and writing of the paper. The authors were financially supported by the Fundamental Research Funds for the Central Universities in China (GK201204004) and Innovation Funds of Graduate Programs, Shaanxi Normal University (CXS20120048) and the ‘‘Foundation for Excellent Doctoral Degree Dissertation’’ of Shaanxi Normal University (X2012YB01), Shaanxi, P. R. China.
References Hahn C, Bachmann L, Chevreux B. (2013). Reconstructing mitochondrial genomes directly from genomic next-generation sequencing
reads—A baiting and iterative mapping approach. Nucl Acids Res 41:e129. He N, Zhang C, Qi X, Zhao S, Tao Y, Yang G, Lee T-H, et al. (2013). Draft genome sequence of the mulberry tree Morus notabilis. Nat Commun 4:2445–54. Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. (2013). MEGA6: Molecular evolutionary genetics analysis version 6.0. Mol Biol Evol 30:2725–9. Young MJ, Chung WH, Mun JH, Kim N, Yu HJ. (2014). De novo assembly and characterization of the complete chloroplast genome of radish (Raphanus sativus L.). Gene 551:39–48. Yu CW, Lian Q, Wu KC, Yu SH, Xie LY, Wu ZJ. (2015). The complete chloroplast genome sequence of Anoectochilus roxburghii. Mitochondrial DNA. [Epub ahead of print]. doi: 10.3109/19401736. 2015.1033706.
