The complete chloroplast genome of <i>Magnolia delavayi</i>, a threatened species endemic to Southwest China

Xu, Xiao-lei; Wu, Shengjun; Xia, Jingjing; Yan, Bo

doi:10.1080/23802359.2019.1660252

Cited by 2 publications

(4 citation statements)

References 6 publications

(5 reference statements)

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“…The newly assembled plastomes had lengths of about 160 kb ( Table 1 ), which is consistent with the lengths observed in previously assembled Magnolia plastomes [ 40 , 41 , 42 , 43 , 44 , 45 ]; partition lengths (LSC, IR, and SSC regions) were also consistent and similar to those observed in previous studies. For the GC content, other studies have found similar values [ 40 ], while for gene content, the previously annotated Magnoliaceae plastomes presented between 113 and 131 genes [ 41 , 42 ].…”

Section: Discussionsupporting

confidence: 89%

“…WGS, followed by the use of assembly tools, has resulted in an effective manner to obtain chloroplast genomes for different families of angiosperms [ 13 , 31 , 32 , 33 ], as well as of different Magnoliaceae species [ 40 , 41 , 42 , 44 ]. In this study, the plastomes of 15 Neotropical Magnolia species were assembled through the use of short Illumina reads and the GetOrganelle assembler.…”

Section: Discussionmentioning

confidence: 99%

“…In an evolutionary context, it is of vital importance to focus on early divergent or "basal" angiosperm groups, i.e., the family Magnoliaceae [ 34 , 35 , 36 , 37 , 38 ]. For the Magnoliaceae, to date, 86 complete plastomes have been published and are available in the NCBI GenBank [ 39 ]; however, most of these correspond to Asian species [ 40 , 41 , 42 , 43 , 44 , 45 ].…”

Section: Introductionmentioning

confidence: 99%

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Comparison of Magnoliaceae Plastomes: Adding Neotropical Magnolia to the Discussion

Guzmán-Díaz

Núñez

Veltjen

et al. 2022

Plants

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Chloroplast genomes are considered to be highly conserved. Nevertheless, differences in their sequences are an important source of phylogenetically informative data. Chloroplast genomes are increasingly applied in evolutionary studies of angiosperms, including Magnoliaceae. Recent studies have focused on resolving the previously debated classification of the family using a phylogenomic approach and chloroplast genome data. However, most Neotropical clades and recently described species have not yet been included in molecular studies. We performed sequencing, assembly, and annotation of 15 chloroplast genomes from Neotropical Magnoliaceae species. We compared the newly assembled chloroplast genomes with 22 chloroplast genomes from across the family, including representatives from each genus and section. Family-wide, the chloroplast genomes presented a length of about 160 kb. The gene content in all species was constant, with 145 genes. The intergenic regions showed a higher level of nucleotide diversity than the coding regions. Differences were higher among genera than within genera. The phylogenetic analysis in Magnolia showed two main clades and corroborated that the current infrageneric classification does not represent natural groups. Although chloroplast genomes are highly conserved in Magnoliaceae, the high level of diversity of the intergenic regions still resulted in an important source of phylogenetically informative data, even for closely related taxa.

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Section: Discussionsupporting

confidence: 89%

Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Comparison of Magnoliaceae Plastomes: Adding Neotropical Magnolia to the Discussion

Guzmán-Díaz

Núñez

Veltjen

et al. 2022

Plants

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“…1 ). Identical findings have been reported in other species, such as Magnolia polytepala [ 39 ], Magnolia delavayi [ 40 ] and Datura stramonium [ 41 ].…”

Section: Discussionsupporting

confidence: 84%

Comparative analysis of the complete chloroplast genomes of six threatened subgenus Gynopodium (Magnolia) species

Xie

Zhang

et al. 2022

BMC Genomics

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Background The subgenus Gynopodium belonging to genus Magnolia have high ornamental, economic, and ecological value. Subgenus Gynopodium contains eight species, but six of these species are threatened. No studies to date have characterized the characteristics of the chloroplast genomes (CPGs) within subgenus Gynopodium species. In this study, we compared the structure of CPGs, identified the mutational hotspots and resolved the phylogenetic relationship of subgenus Gynopodium. Results The CPGs of six subgenus Gynopodium species ranged in size from 160,027 bp to 160,114 bp. A total of 131 genes were identified, including 86 protein-coding genes, eight ribosomal RNA genes, and 37 transfer RNA genes. We detected neither major expansions or contractions in the inverted repeat region, nor rearrangements or insertions in the CPGs of six subgenus Gynopodium species. A total of 300 large repeat sequences (forward, reverse, and palindrome repeats), 847 simple sequence repeats, and five highly variable regions were identified. One gene (ycf1) and four intergenic regions (psbA-trnH-GUG, petA-psbJ, rpl32-trnL-UAG, and ccsA-ndhD) were identified as mutational hotspots by their high nucleotide diversity (Pi) values (≥ 0.004), which were useful for species discrimination. Maximum likelihood and Bayesian inference trees were concordant and indicated that Magnoliaceae consisted of two genera Liriodendron and Magnolia. Six species of subgenus Gynopodium clustered as a monophyletic clade, forming a sister clade with subgenus Yulania (BS = 100%, PP = 1.00). Due to the non-monophyly of subgenus Magnolia, subgenus Gynopodium should be treated as a section of Magnolia. Within section Gynopodium, M. sinica diverged first (posterior probability = 1, bootstrap = 100), followed by M. nitida, M. kachirachirai and M. lotungensis. M. omeiensis was sister to M. yunnanensis (posterior probability = 0.97, bootstrap = 50). Conclusion The CPGs and characteristics information provided by our study could be useful in species identification, conservation genetics and resolving phylogenetic relationships of Magnoliaceae species.

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The complete chloroplast genome of Magnolia delavayi, a threatened species endemic to Southwest China

Cited by 2 publications

References 6 publications

Comparison of Magnoliaceae Plastomes: Adding Neotropical Magnolia to the Discussion

Comparison of Magnoliaceae Plastomes: Adding Neotropical Magnolia to the Discussion

Comparative analysis of the complete chloroplast genomes of six threatened subgenus Gynopodium (Magnolia) species

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