Mitochondrial DNA The Journal of DNA Mapping, Sequencing, and Analysis
ISSN: 1940-1736 (Print) 1940-1744 (Online) Journal homepage: http://www.tandfonline.com/loi/imdn20
Complete chloroplast genome of the Oriental white oak: Quercus aliena Blume Sihai Lu, Meng Hou, Fang K. Du, Junqing Li & Kangquan Yin To cite this article: Sihai Lu, Meng Hou, Fang K. Du, Junqing Li & Kangquan Yin (2015): Complete chloroplast genome of the Oriental white oak: Quercus aliena Blume, Mitochondrial DNA To link to this article: http://dx.doi.org/10.3109/19401736.2015.1053074
Published online: 26 Jun 2015.
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Full Terms & Conditions of access and use can be found at http://www.tandfonline.com/action/journalInformation?journalCode=imdn20 Download by: ["Queen's University Libraries, Kingston"]
Date: 08 October 2015, At: 06:56
http://informahealthcare.com/mdn ISSN: 1940-1736 (print), 1940-1744 (electronic) Mitochondrial DNA, Early Online: 1–3 ! 2015 Informa UK Ltd. DOI: 10.3109/19401736.2015.1053074
MITOGENOME ANNOUNCEMENT
Complete chloroplast genome of the Oriental white oak: Quercus aliena Blume Sihai Lu, Meng Hou, Fang K. Du, Junqing Li, and Kangquan Yin
Downloaded by ["Queen's University Libraries, Kingston"] at 06:56 08 October 2015
College of Forestry, Beijing Forestry University, Beijing, China
Abstract
Keywords
The complete chloroplast (cp) genome sequence of the Oriental white oak: Quercus aliena Blume, the first sequenced member of the section Quercus, is reported in this study. The length of cp genome size is 160,921 bp, with 36.9% GC content. A pair of 25,841 bp inverted repeat regions (IRs) is separated by a 90,258 bp large single copy region (LSC) and an 18,980 bp small single copy region (SSC). This genome contains 115 unique genes, including 89 coding genes, four rRNA genes, and 39 tRNA genes. Border analysis of cp genome of Quercus aliena and other 10 most closely related cp genomes revealed that most Fagaceae species have high similarity either in structure or distribution of these genes except for Trigonobalanus doichangensis.
Complete chloroplast genome, nextgeneration sequencing, pseudogenes
The Oriental white oak (Quercus aliena) is a perennial deciduous arbor, and mainly distributed in the mountainous regions in China, Japan and Korea at an altitude between 100 and 2000 m (Su, 2003). To date, numerous paleobotanic (Crepet & Nixon, 1989; Kvacˇek & Walther, 1989) and molecular studies (Ishida et al., 2003) about Quercus, indubitably, provide much more evidences to species classification and colonization process. However, due to a pressing need of high-resolution data, varieties of methods and materials need to be exploited (Manos et al., 2001). Since the chloroplast (cp) genome is maternally inherited in Q. aliena (Dumolin et al., 1995), it therefore can be used as an identifier for tracing the process of colonization and migration (Ferris et al., 1995; Kanno et al., 2004; Petit et al., 2002). To date, however, the GenBank database has only one complete cp genome sequence of the red oak group in the genus Quercus: Quercus rubra (Alexander & Woeste, 2014). Consequently, here, we provide the complete cp genome information of Q. aliena (GenBank accession number: KP301144): the first complete cp genome sequence of the white oak group (Quercus section Quercus). In this study, voucher specimens of Q. aliena were deposited at the herbarium of Beijing Forestry University, Beijing, China and DNA samples were properly stored at Molecular Ecology Lab of the College of Forestry, Beijing Forestry University, Beijing, China. We determine the complete cp genome sequence of Q. aliena (160,921 bp) and built the neighbor-joining (NJ) phylogenetic tree using the whole cp genome sequence data of eight Fagaceae species with three Cucumis species as out-groups (Figure 1A). A comparison of the neighbored genes distribution
History Received 1 May 2015 Accepted 4 May 2015 Published online 26 June 2015
around the borders of quadripartite genome structure of these 11 cp genomes indicated that most Fagaceae species have high similarity either in structure or distribution of these genes except for Trigonobalanus doichangensis (Figure 1B), which belongs to ancient taxonomic group (Manos et al., 2001). The ycf1 pseudogene ( ycf1) and the ndhF gene overlapped in the four Quercus species, Castanea mollissima, Castanopsis echinocarpa and Cucumis melo (Figure 1B). The cp genome of Q. aliena consists of one LSC (large single copy section, 90,258 bp), one SSC (small single copy section, 18,980 bp) and two IRs (inverted repeat regions, 25,841 bp). The overall GC contents of Q. aliena cp genome were approximate to 36.9%. GC contents in the LSC, and SSC, was 34.8% and 31% respectively, which were lower than that of the IRs (43%). The proportion of coding sequences is approximate to 57.3%, including all tRNA and rRNA regions. The cp genome contains 137 genes, including 89 coding genes, 39 tRNA genes, four rRNA, and three pseudogenes (two ycf15, one rpl22). Eighteen of these genes were duplicated in the IR regions, including four rRNA genes, seven tRNA genes, seven protein-coding genes, and two pseudogenes (two ycf15). Fifteen protein-coding genes, as well as seven tRNA genes contain intron. Moreover, two introns were found in three protein-coding genes (rps12, ycf3, clpP), and the largest intron in cp genome is 2505 bp belonging to trnK-UUU gene. Of 115 unique genes in Q. aliena cp genome, the largest gene is ycf2 with a length of 6822 bp. rps12 is the only one form of trans-splicing, of which exon 1 is located in the LSC region and 30 end exon 2 and exon 3 are in the IRs.
Correspondence: Fang K. Du and Kangquan Yin, College of Forestry, Beijing Forestry University, Beijing, China. Fax: 86-10-62338191. E-mail: [email protected] (F. K. Du); [email protected] (K. Yin)
S. Lu et al.
Mitochondrial DNA, Early Online: 1–3
Downloaded by ["Queen's University Libraries, Kingston"] at 06:56 08 October 2015
2
Figure 1. (A) The NJ phylogenetic tree was built using the whole cp genome sequence data of 11 species, including three Cucumis species as outgroups. Numbers above the branches are the bootstrap values of NJ tree built using MEGA6 (Tamura et al., 2013) under the p-distance model. (B) Comparison of the borders of LSC, SSC and IR regions among 11 cp genomes, number above the gene features means the distance between the ends of genes and the borders sites. ycf1 gene was stretched across the IRb/LSC. Various lengths of rps19, rpl2 and trnH genes were created at the LSC/IRa and IRb/LSC borders. These features are not to scale.
DOI: 10.3109/19401736.2015.1053074
Declaration of interest This work is supported by grants from Beijing Nova Programme (China) and National Natural Science Foundation of China (grant number 41201051) to Fang K. Du. The authors report no conflict of interest and are responsible for the content.
Downloaded by ["Queen's University Libraries, Kingston"] at 06:56 08 October 2015
References Alexander LW, Woeste KE. (2014). Pyrosequencing of the northern red oak (Quercus rubra L.) chloroplast genome reveals high quality polymorphisms for population management. Tree Genet Genomes 10: 803–12. Crepet WL, Nixon KC. (1989). Earliest megafossil evidence of Fagaceae: Phylogenetic and biogeographic implications. Am J Bot 76:842–55. Dumolin S, Demesure B, Petit RJ. (1995). Inheritance of chloroplast and mitochondrial genomes in pedunculate oak investigated with an efficient PCR method. Theor Appl Genet 91:1253–6. Ferris C, Oliver RP, Davy AJ, Hewitt GM. (1995). Using chloroplast DNA to trace postglacial migration routes of oaks into Britain. Mol Ecol 4:731–8.
Oriental white oak cp genome
3
Ishida TA, Hattori K, Sato H, Kimura MT. (2003). Differentiation and hybridization between Quercus crispula and Q. dentata (Fagaceae): Insights from morphological traits, amplified fragment length polymorphism markers, and leafminer composition. Am J Bot 90:769–76. Kanno M, Yokoyama J, Suyama Y, Ohyama M, Itoh T, Suzuki M. (2004). Geographical distribution of two haplotypes of chloroplast DNA in four oak species (Quercus) in Japan. J Plant Res 117:311–17. Kvacˇek Z, Walther H. (1989). Paleobotanical studies in Fagaceae of the European Tertiary. Plant Syst Evol 162:213–29. Manos PS, Zhou ZK, Cannon CH. (2001). Systematics of Fagaceae: Phylogenetic tests of reproductive trait evolution. Int J Plant Sci 162: 1361–79. Petit RJ, Brewer S, Borda´cs S, Burg K, Cheddadi R, Coart E, Cottrell J, et al. (2002). Identification of refugia and post-glacial colonisation routes of European white oaks based on chloroplast DNA and fossil pollen evidence. For Ecol Manage 156:49–74. Su MH, Wu SC, Hsieh CF, Chen SI, Yang KC. (2003). Rediscovery of Quercus aliena Blume (Fagaceae) in Taiwan. Taiwania 48:112–17. 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.
ISSN: 1940-1736 (Print) 1940-1744 (Online) Journal homepage: http://www.tandfonline.com/loi/imdn20
Complete chloroplast genome of the Oriental white oak: Quercus aliena Blume Sihai Lu, Meng Hou, Fang K. Du, Junqing Li & Kangquan Yin To cite this article: Sihai Lu, Meng Hou, Fang K. Du, Junqing Li & Kangquan Yin (2015): Complete chloroplast genome of the Oriental white oak: Quercus aliena Blume, Mitochondrial DNA To link to this article: http://dx.doi.org/10.3109/19401736.2015.1053074
Published online: 26 Jun 2015.
Submit your article to this journal
Article views: 14
View related articles
View Crossmark data
Full Terms & Conditions of access and use can be found at http://www.tandfonline.com/action/journalInformation?journalCode=imdn20 Download by: ["Queen's University Libraries, Kingston"]
Date: 08 October 2015, At: 06:56
http://informahealthcare.com/mdn ISSN: 1940-1736 (print), 1940-1744 (electronic) Mitochondrial DNA, Early Online: 1–3 ! 2015 Informa UK Ltd. DOI: 10.3109/19401736.2015.1053074
MITOGENOME ANNOUNCEMENT
Complete chloroplast genome of the Oriental white oak: Quercus aliena Blume Sihai Lu, Meng Hou, Fang K. Du, Junqing Li, and Kangquan Yin
Downloaded by ["Queen's University Libraries, Kingston"] at 06:56 08 October 2015
College of Forestry, Beijing Forestry University, Beijing, China
Abstract
Keywords
The complete chloroplast (cp) genome sequence of the Oriental white oak: Quercus aliena Blume, the first sequenced member of the section Quercus, is reported in this study. The length of cp genome size is 160,921 bp, with 36.9% GC content. A pair of 25,841 bp inverted repeat regions (IRs) is separated by a 90,258 bp large single copy region (LSC) and an 18,980 bp small single copy region (SSC). This genome contains 115 unique genes, including 89 coding genes, four rRNA genes, and 39 tRNA genes. Border analysis of cp genome of Quercus aliena and other 10 most closely related cp genomes revealed that most Fagaceae species have high similarity either in structure or distribution of these genes except for Trigonobalanus doichangensis.
Complete chloroplast genome, nextgeneration sequencing, pseudogenes
The Oriental white oak (Quercus aliena) is a perennial deciduous arbor, and mainly distributed in the mountainous regions in China, Japan and Korea at an altitude between 100 and 2000 m (Su, 2003). To date, numerous paleobotanic (Crepet & Nixon, 1989; Kvacˇek & Walther, 1989) and molecular studies (Ishida et al., 2003) about Quercus, indubitably, provide much more evidences to species classification and colonization process. However, due to a pressing need of high-resolution data, varieties of methods and materials need to be exploited (Manos et al., 2001). Since the chloroplast (cp) genome is maternally inherited in Q. aliena (Dumolin et al., 1995), it therefore can be used as an identifier for tracing the process of colonization and migration (Ferris et al., 1995; Kanno et al., 2004; Petit et al., 2002). To date, however, the GenBank database has only one complete cp genome sequence of the red oak group in the genus Quercus: Quercus rubra (Alexander & Woeste, 2014). Consequently, here, we provide the complete cp genome information of Q. aliena (GenBank accession number: KP301144): the first complete cp genome sequence of the white oak group (Quercus section Quercus). In this study, voucher specimens of Q. aliena were deposited at the herbarium of Beijing Forestry University, Beijing, China and DNA samples were properly stored at Molecular Ecology Lab of the College of Forestry, Beijing Forestry University, Beijing, China. We determine the complete cp genome sequence of Q. aliena (160,921 bp) and built the neighbor-joining (NJ) phylogenetic tree using the whole cp genome sequence data of eight Fagaceae species with three Cucumis species as out-groups (Figure 1A). A comparison of the neighbored genes distribution
History Received 1 May 2015 Accepted 4 May 2015 Published online 26 June 2015
around the borders of quadripartite genome structure of these 11 cp genomes indicated that most Fagaceae species have high similarity either in structure or distribution of these genes except for Trigonobalanus doichangensis (Figure 1B), which belongs to ancient taxonomic group (Manos et al., 2001). The ycf1 pseudogene ( ycf1) and the ndhF gene overlapped in the four Quercus species, Castanea mollissima, Castanopsis echinocarpa and Cucumis melo (Figure 1B). The cp genome of Q. aliena consists of one LSC (large single copy section, 90,258 bp), one SSC (small single copy section, 18,980 bp) and two IRs (inverted repeat regions, 25,841 bp). The overall GC contents of Q. aliena cp genome were approximate to 36.9%. GC contents in the LSC, and SSC, was 34.8% and 31% respectively, which were lower than that of the IRs (43%). The proportion of coding sequences is approximate to 57.3%, including all tRNA and rRNA regions. The cp genome contains 137 genes, including 89 coding genes, 39 tRNA genes, four rRNA, and three pseudogenes (two ycf15, one rpl22). Eighteen of these genes were duplicated in the IR regions, including four rRNA genes, seven tRNA genes, seven protein-coding genes, and two pseudogenes (two ycf15). Fifteen protein-coding genes, as well as seven tRNA genes contain intron. Moreover, two introns were found in three protein-coding genes (rps12, ycf3, clpP), and the largest intron in cp genome is 2505 bp belonging to trnK-UUU gene. Of 115 unique genes in Q. aliena cp genome, the largest gene is ycf2 with a length of 6822 bp. rps12 is the only one form of trans-splicing, of which exon 1 is located in the LSC region and 30 end exon 2 and exon 3 are in the IRs.
Correspondence: Fang K. Du and Kangquan Yin, College of Forestry, Beijing Forestry University, Beijing, China. Fax: 86-10-62338191. E-mail: [email protected] (F. K. Du); [email protected] (K. Yin)
S. Lu et al.
Mitochondrial DNA, Early Online: 1–3
Downloaded by ["Queen's University Libraries, Kingston"] at 06:56 08 October 2015
2
Figure 1. (A) The NJ phylogenetic tree was built using the whole cp genome sequence data of 11 species, including three Cucumis species as outgroups. Numbers above the branches are the bootstrap values of NJ tree built using MEGA6 (Tamura et al., 2013) under the p-distance model. (B) Comparison of the borders of LSC, SSC and IR regions among 11 cp genomes, number above the gene features means the distance between the ends of genes and the borders sites. ycf1 gene was stretched across the IRb/LSC. Various lengths of rps19, rpl2 and trnH genes were created at the LSC/IRa and IRb/LSC borders. These features are not to scale.
DOI: 10.3109/19401736.2015.1053074
Declaration of interest This work is supported by grants from Beijing Nova Programme (China) and National Natural Science Foundation of China (grant number 41201051) to Fang K. Du. The authors report no conflict of interest and are responsible for the content.
Downloaded by ["Queen's University Libraries, Kingston"] at 06:56 08 October 2015
References Alexander LW, Woeste KE. (2014). Pyrosequencing of the northern red oak (Quercus rubra L.) chloroplast genome reveals high quality polymorphisms for population management. Tree Genet Genomes 10: 803–12. Crepet WL, Nixon KC. (1989). Earliest megafossil evidence of Fagaceae: Phylogenetic and biogeographic implications. Am J Bot 76:842–55. Dumolin S, Demesure B, Petit RJ. (1995). Inheritance of chloroplast and mitochondrial genomes in pedunculate oak investigated with an efficient PCR method. Theor Appl Genet 91:1253–6. Ferris C, Oliver RP, Davy AJ, Hewitt GM. (1995). Using chloroplast DNA to trace postglacial migration routes of oaks into Britain. Mol Ecol 4:731–8.
Oriental white oak cp genome
3
Ishida TA, Hattori K, Sato H, Kimura MT. (2003). Differentiation and hybridization between Quercus crispula and Q. dentata (Fagaceae): Insights from morphological traits, amplified fragment length polymorphism markers, and leafminer composition. Am J Bot 90:769–76. Kanno M, Yokoyama J, Suyama Y, Ohyama M, Itoh T, Suzuki M. (2004). Geographical distribution of two haplotypes of chloroplast DNA in four oak species (Quercus) in Japan. J Plant Res 117:311–17. Kvacˇek Z, Walther H. (1989). Paleobotanical studies in Fagaceae of the European Tertiary. Plant Syst Evol 162:213–29. Manos PS, Zhou ZK, Cannon CH. (2001). Systematics of Fagaceae: Phylogenetic tests of reproductive trait evolution. Int J Plant Sci 162: 1361–79. Petit RJ, Brewer S, Borda´cs S, Burg K, Cheddadi R, Coart E, Cottrell J, et al. (2002). Identification of refugia and post-glacial colonisation routes of European white oaks based on chloroplast DNA and fossil pollen evidence. For Ecol Manage 156:49–74. Su MH, Wu SC, Hsieh CF, Chen SI, Yang KC. (2003). Rediscovery of Quercus aliena Blume (Fagaceae) in Taiwan. Taiwania 48:112–17. 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.
