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 plastid genome of Astragalus mongholicus var. nakaianus (Fabaceae) In-Su Choi, Joo-Hwan Kim & Byoung-Hee Choi To cite this article: In-Su Choi, Joo-Hwan Kim & Byoung-Hee Choi (2015): Complete plastid genome of Astragalus mongholicus var. nakaianus (Fabaceae), Mitochondrial DNA To link to this article: http://dx.doi.org/10.3109/19401736.2015.1053118
Published online: 29 Jun 2015.
Submit your article to this journal
Article views: 18
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: [University of Lethbridge]
Date: 16 October 2015, At: 06:16
http://informahealthcare.com/mdn ISSN: 1940-1736 (print), 1940-1744 (electronic) Mitochondrial DNA, Early Online: 1–2 ! 2015 Informa UK Ltd. DOI: 10.3109/19401736.2015.1053118
MITOGENOME ANNOUNCEMENT
Complete plastid genome of Astragalus mongholicus var. nakaianus (Fabaceae) In-Su Choi1, Joo-Hwan Kim2, and Byoung-Hee Choi1 Department of Biological Sciences, Inha University, Incheon, Republic of Korea and 2Department of Life Science, Gachon University, Seongnam, Republic of Korea
Downloaded by [University of Lethbridge] at 06:16 16 October 2015
1
Abstract
Keywords
The first complete plastid genome (plastome) of the largest angiosperm genus, Astragalus, was sequenced for the Korean endangered endemic species A. mongholicus var. nakaianus. Its genome is relatively short (123,633 bp) because it lacks an Inverted Repeat (IR) region. It comprises 110 genes, including four unique rRNAs, 30 tRNAs, and 76 protein-coding genes. Similar to other closely related plastomes, rpl22 and rps16 are absent. The putative pseudogene with abnormal stop codons is atpE. This plastome has no additional inversions when compared with highly variable plastomes from IRLC tribes Fabeae and Trifolieae. Our phylogenetic analysis confirms the non-monophyly of Galegeae.
Astragalus, IRLC, Papilionoideae, plastid genome
Astragalus L., in subfamily Papilionoideae of Fabaceae, is nested within a radiation of predominantly herbaceous and temperate groups in Galegeae (Lock & Schrire, 2005). It is the largest genus among angiosperms, with more than 2800 species (Podlech & Zarre, 2013). Several species, e.g. A. mongholicus, are important ethnopharmacological resources in East Asia (Guo et al., 2010). Among Fabaceae members, plastid genome (plastome) rearrangements provide valuable phylogenetic evidence (Jansen & Ruhlman, 2012). For example, the Inverted Repeat-Lacking Clade (IRLC; Wojciechowski et al., 2004) comprises Galageae and closely related tribes of Cicereae, Fabeae, Hedysareae, and Trifoliae, as well as some members of Millettieae. This monophyletic group is distinguished by the absence of a 25 kb IR along with drastic structural variations in their plastomes (Sabir et al., 2014). The plastomes have been sequenced for eight genera in the IRLC taxa. However, no investigation has been made on Astragalus, which is the most diverse, evolutionarily interesting, and medicinally important genus. Therefore, we sequenced the plastome from Astragalus to enhance our understanding of its evolutionary processes and breeding. The plastome sequence was examined for A. mongholicus var. nakaianus (Y.N. Lee) I.S. Choi & B.H. Choi. Plants of this critically endangered species are herbaceous perennials endemic to the subalpine grasslands of Mt. Halla, Jeju-do, Korea (Choi et al., 2013). The entire plastome was sequenced by PCR and
Correspondence: Byoung-Hee Choi, Department of Biological Sciences, Inha University, Incheon, Republic of Korea. E-mail: [email protected] Joo-Hwan Kim, Department of Life Science, Gachon University, Korea, Republic of Korea. E-mail: [email protected]
History Received 6 May 2015 Accepted 17 May 2015 Published online 29 June 2015
traditional Sanger techniques, using primer pairs designed from IRLC reference genomes in NCBI. The contiguous sequences were assembled via Geneious 7.1.3 (Kearse et al., 2012). This plastome (GenBank accession number KR296789) is 123,633 bp long and lacks an IR region. Its 110 genes include four unique rRNAs, 30 tRNAs, and 76 protein-coding genes. Among these, atpE is a putative pseudogene caused by frame shifts and internal stop codons. Similar to other IRLC plastomes, rpl22 and rps16 are absent. Contrary to the loss of two introns from clpP in Glycyrrhiza glabra (belonging to Galegeae), this plastome retains clpP intron 2. Although IRLC taxa have highly variable plastome structures, especially within tribes Fabeae and Trifolieae, A. mongholicus var. nakaianus apparently experienced no inversions after the loss of one copy of the IR region. Phylogenetic relationships among representatives of IRLC tribes were inferred using complete plastomes and a maximum likelihood tree (Figure 1). The phylogenetic tree indicated that A. mongholicus var. nakaianus does not cluster into a single branch with another species in the Galegeae taxa, i.e. Glycyrrhiza glabra. This segregation from Glycyrrhiza was also supported by the loss of clpP intron 2. Non-monophyly of Galegeae, based on single- or multi-gene phylogeny, has previously been recognized (Lock & Schrire, 2005, and references therein), and our data are congruent with those results at the complete plastome level. The plastome of Astragalus elucidated here provides fundamental genetic information for evolutionary or biotechnological examinations of Fabaceae. Furthermore, the chloroplast microsatellite markers that could be designed from this genome, combined with our previously developed nuclear microsatellite markers (Choi & Choi, 2013), will be useful for future population genetics studies aimed at conserving the critically endangered A. mongholicus var. nakaianus.
Downloaded by [University of Lethbridge] at 06:16 16 October 2015
2
I.-S. Choi et al.
Mitochondrial DNA, Early Online: 1–2
Figure 1. Maximum likelihood phylogeny tree of IRLC taxa inferred by RAxML (Stamatakis et al., 2008). Phylogenetic relationships among taxa were generated from a concatenated matrix of 64 protein-coding genes with combined aligned length of 50,979 characters. All nodes have 100% bootstrap support. GenBank accession numbers of sequences used for developing tree include: Cicer arietinum, NC_011163; Glycyrrhiza glabra, NC_024038; Lathyrus sativus, NC_014063; Lens culinaris, KF186232; Lotus japonicus, NC_002694; Medicago truncatula, NC_003119; Pisum sativum, NC_014057; Trifolium aureum, NC_024035; Trifolium subterraneum, NC_011828; Vicia faba, KF042344.
Acknowledgements We are grateful to Hoang Dang Khoa Do in the Department of Life Science, Gachon University, for assistance with our experiments and other research activities.
Declaration of interest This work was supported by an Inha University Research grant as well as grants from the Scientific Research program (KNA1-2-13,14-2) of the Korea National Arboretum. The authors declare that they have no conflicts of interests regarding the publication of this article.
References Choi IS, Choi BH. (2013). Isolation and characterization of ten microsatellite loci from Korean Astragalus mongholicus (Fabaceae). J Genet 92:e73–6. Choi IS, Kim SY, Choi BH. (2013). Taxonomic position and genetic differentiation of Korean Astragalus mongholicus Bunge. Korean J Pl Taxon 43:12–21. Guo H, Wang W, Yang N, Guo B, Zhang S, Yang R, Yuan Y, et al. (2010). DNA barcoding provides distinction between Radix astragali and its adulterants. Sci China Life Sci 53:992–9.
Jansen RK, Ruhlman TA. (2012). Plastid genomes of seed plants. In: Bock R, Knoop V, editors. Genomics of Chloroplasts and mitochondria. The Netherlands: Springer. p 103–26. Kearse M, Moir R, Wilson A, Stones-Havas S, Cheung M, Sturrock S, Buxton S, et al. (2012). Geneious basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics 28:1647–9. Lock J, Schrire B. (2005). Tribe Galegeae. In: Lewis G, Schrire B, Mackinder B, Lock M, editors. Legumes of the World. Richmond, UK: Royal Botanical Gardens, Kew. p 475–88. Podlech D, Zarre S. (2013). A taxonomic revision of the genus Astragalus L. (Leguminosae) in the Old World. Wien, Austria: Naturhistorisches Museum. Sabir J, Schwarz E, Ellison N, Zhang J, Baeshen NA, Mutwakil M, Jansen R, Ruhlman T. (2014). Evolutionary and biotechnology implications of plastid genome variation in the inverted-repeat-lacking clade of legumes. Plant Biotechnol J 12:743–54. Stamatakis A, Hoover P, Rougemont J. (2008). A rapid bootstrap algorithm for the RAxML web servers. System Biol 57:758–71. Wojciechowski MF, Lavin M, Sanderson MJ. (2004). A phylogeny of legumes (Leguminosae) based on analysis of the plastid matK gene resolves many well-supported subclades within the family. Am J Bot 91:1846–62.
ISSN: 1940-1736 (Print) 1940-1744 (Online) Journal homepage: http://www.tandfonline.com/loi/imdn20
Complete plastid genome of Astragalus mongholicus var. nakaianus (Fabaceae) In-Su Choi, Joo-Hwan Kim & Byoung-Hee Choi To cite this article: In-Su Choi, Joo-Hwan Kim & Byoung-Hee Choi (2015): Complete plastid genome of Astragalus mongholicus var. nakaianus (Fabaceae), Mitochondrial DNA To link to this article: http://dx.doi.org/10.3109/19401736.2015.1053118
Published online: 29 Jun 2015.
Submit your article to this journal
Article views: 18
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: [University of Lethbridge]
Date: 16 October 2015, At: 06:16
http://informahealthcare.com/mdn ISSN: 1940-1736 (print), 1940-1744 (electronic) Mitochondrial DNA, Early Online: 1–2 ! 2015 Informa UK Ltd. DOI: 10.3109/19401736.2015.1053118
MITOGENOME ANNOUNCEMENT
Complete plastid genome of Astragalus mongholicus var. nakaianus (Fabaceae) In-Su Choi1, Joo-Hwan Kim2, and Byoung-Hee Choi1 Department of Biological Sciences, Inha University, Incheon, Republic of Korea and 2Department of Life Science, Gachon University, Seongnam, Republic of Korea
Downloaded by [University of Lethbridge] at 06:16 16 October 2015
1
Abstract
Keywords
The first complete plastid genome (plastome) of the largest angiosperm genus, Astragalus, was sequenced for the Korean endangered endemic species A. mongholicus var. nakaianus. Its genome is relatively short (123,633 bp) because it lacks an Inverted Repeat (IR) region. It comprises 110 genes, including four unique rRNAs, 30 tRNAs, and 76 protein-coding genes. Similar to other closely related plastomes, rpl22 and rps16 are absent. The putative pseudogene with abnormal stop codons is atpE. This plastome has no additional inversions when compared with highly variable plastomes from IRLC tribes Fabeae and Trifolieae. Our phylogenetic analysis confirms the non-monophyly of Galegeae.
Astragalus, IRLC, Papilionoideae, plastid genome
Astragalus L., in subfamily Papilionoideae of Fabaceae, is nested within a radiation of predominantly herbaceous and temperate groups in Galegeae (Lock & Schrire, 2005). It is the largest genus among angiosperms, with more than 2800 species (Podlech & Zarre, 2013). Several species, e.g. A. mongholicus, are important ethnopharmacological resources in East Asia (Guo et al., 2010). Among Fabaceae members, plastid genome (plastome) rearrangements provide valuable phylogenetic evidence (Jansen & Ruhlman, 2012). For example, the Inverted Repeat-Lacking Clade (IRLC; Wojciechowski et al., 2004) comprises Galageae and closely related tribes of Cicereae, Fabeae, Hedysareae, and Trifoliae, as well as some members of Millettieae. This monophyletic group is distinguished by the absence of a 25 kb IR along with drastic structural variations in their plastomes (Sabir et al., 2014). The plastomes have been sequenced for eight genera in the IRLC taxa. However, no investigation has been made on Astragalus, which is the most diverse, evolutionarily interesting, and medicinally important genus. Therefore, we sequenced the plastome from Astragalus to enhance our understanding of its evolutionary processes and breeding. The plastome sequence was examined for A. mongholicus var. nakaianus (Y.N. Lee) I.S. Choi & B.H. Choi. Plants of this critically endangered species are herbaceous perennials endemic to the subalpine grasslands of Mt. Halla, Jeju-do, Korea (Choi et al., 2013). The entire plastome was sequenced by PCR and
Correspondence: Byoung-Hee Choi, Department of Biological Sciences, Inha University, Incheon, Republic of Korea. E-mail: [email protected] Joo-Hwan Kim, Department of Life Science, Gachon University, Korea, Republic of Korea. E-mail: [email protected]
History Received 6 May 2015 Accepted 17 May 2015 Published online 29 June 2015
traditional Sanger techniques, using primer pairs designed from IRLC reference genomes in NCBI. The contiguous sequences were assembled via Geneious 7.1.3 (Kearse et al., 2012). This plastome (GenBank accession number KR296789) is 123,633 bp long and lacks an IR region. Its 110 genes include four unique rRNAs, 30 tRNAs, and 76 protein-coding genes. Among these, atpE is a putative pseudogene caused by frame shifts and internal stop codons. Similar to other IRLC plastomes, rpl22 and rps16 are absent. Contrary to the loss of two introns from clpP in Glycyrrhiza glabra (belonging to Galegeae), this plastome retains clpP intron 2. Although IRLC taxa have highly variable plastome structures, especially within tribes Fabeae and Trifolieae, A. mongholicus var. nakaianus apparently experienced no inversions after the loss of one copy of the IR region. Phylogenetic relationships among representatives of IRLC tribes were inferred using complete plastomes and a maximum likelihood tree (Figure 1). The phylogenetic tree indicated that A. mongholicus var. nakaianus does not cluster into a single branch with another species in the Galegeae taxa, i.e. Glycyrrhiza glabra. This segregation from Glycyrrhiza was also supported by the loss of clpP intron 2. Non-monophyly of Galegeae, based on single- or multi-gene phylogeny, has previously been recognized (Lock & Schrire, 2005, and references therein), and our data are congruent with those results at the complete plastome level. The plastome of Astragalus elucidated here provides fundamental genetic information for evolutionary or biotechnological examinations of Fabaceae. Furthermore, the chloroplast microsatellite markers that could be designed from this genome, combined with our previously developed nuclear microsatellite markers (Choi & Choi, 2013), will be useful for future population genetics studies aimed at conserving the critically endangered A. mongholicus var. nakaianus.
Downloaded by [University of Lethbridge] at 06:16 16 October 2015
2
I.-S. Choi et al.
Mitochondrial DNA, Early Online: 1–2
Figure 1. Maximum likelihood phylogeny tree of IRLC taxa inferred by RAxML (Stamatakis et al., 2008). Phylogenetic relationships among taxa were generated from a concatenated matrix of 64 protein-coding genes with combined aligned length of 50,979 characters. All nodes have 100% bootstrap support. GenBank accession numbers of sequences used for developing tree include: Cicer arietinum, NC_011163; Glycyrrhiza glabra, NC_024038; Lathyrus sativus, NC_014063; Lens culinaris, KF186232; Lotus japonicus, NC_002694; Medicago truncatula, NC_003119; Pisum sativum, NC_014057; Trifolium aureum, NC_024035; Trifolium subterraneum, NC_011828; Vicia faba, KF042344.
Acknowledgements We are grateful to Hoang Dang Khoa Do in the Department of Life Science, Gachon University, for assistance with our experiments and other research activities.
Declaration of interest This work was supported by an Inha University Research grant as well as grants from the Scientific Research program (KNA1-2-13,14-2) of the Korea National Arboretum. The authors declare that they have no conflicts of interests regarding the publication of this article.
References Choi IS, Choi BH. (2013). Isolation and characterization of ten microsatellite loci from Korean Astragalus mongholicus (Fabaceae). J Genet 92:e73–6. Choi IS, Kim SY, Choi BH. (2013). Taxonomic position and genetic differentiation of Korean Astragalus mongholicus Bunge. Korean J Pl Taxon 43:12–21. Guo H, Wang W, Yang N, Guo B, Zhang S, Yang R, Yuan Y, et al. (2010). DNA barcoding provides distinction between Radix astragali and its adulterants. Sci China Life Sci 53:992–9.
Jansen RK, Ruhlman TA. (2012). Plastid genomes of seed plants. In: Bock R, Knoop V, editors. Genomics of Chloroplasts and mitochondria. The Netherlands: Springer. p 103–26. Kearse M, Moir R, Wilson A, Stones-Havas S, Cheung M, Sturrock S, Buxton S, et al. (2012). Geneious basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics 28:1647–9. Lock J, Schrire B. (2005). Tribe Galegeae. In: Lewis G, Schrire B, Mackinder B, Lock M, editors. Legumes of the World. Richmond, UK: Royal Botanical Gardens, Kew. p 475–88. Podlech D, Zarre S. (2013). A taxonomic revision of the genus Astragalus L. (Leguminosae) in the Old World. Wien, Austria: Naturhistorisches Museum. Sabir J, Schwarz E, Ellison N, Zhang J, Baeshen NA, Mutwakil M, Jansen R, Ruhlman T. (2014). Evolutionary and biotechnology implications of plastid genome variation in the inverted-repeat-lacking clade of legumes. Plant Biotechnol J 12:743–54. Stamatakis A, Hoover P, Rougemont J. (2008). A rapid bootstrap algorithm for the RAxML web servers. System Biol 57:758–71. Wojciechowski MF, Lavin M, Sanderson MJ. (2004). A phylogeny of legumes (Leguminosae) based on analysis of the plastid matK gene resolves many well-supported subclades within the family. Am J Bot 91:1846–62.
