The complete plastid genome of Magnolia omeiensis (Magnoliaceae)

Abstract

Magnolia omeiensis (W. C. Cheng) Dandy, belonging to Magnolia sect. Gynopodium Dandy (Magnoliaceae), is a critically endangered species. In this study, we assembled the complete plastid genome sequence of M. omeiensis. The plastid genome was 160,091 bp in length, consisting of a large single-copy (LSC) region of 88,160 bp, a small single-copy (SSC) region of 18,763 bp, and two inverted repeat (IR) regions of 26,584 bp. It contained 112 unique genes, including 80 protein-coding genes, 28 tRNA genes, and 4 rRNA genes. Overall GC content was 39.3%. Phylogenetic analysis showed that M. omeiensis was closely related to Magnolia Yunnanensis, which was identified in the same section Gynopodium.

Keywords:

• Magnolia omeiensis
• plastid genome
• phylogenetic analysis

Magnolia omeiensis (W. C. Cheng) Dandy, belonging to Magnolia sect. Gynopodium Dandy (Magnoliaceae) (Figlar and Nooteboom 2004), is endemic to China, and has an extremely restricted distribution range in Emei Mountain (Xiao and Li 2017). Due to habitat loss, M. omeiensis was categorized as Critically Endangered plant to China, according to the latest version of IUCN Red List of threatened species (China Expert Workshop 2014). Conservation studies on M. omeiensis have mainly focused on phytocoenological characteristics and breeding (Zhang et al. 1993; Wade et al. 2016; Yu et al. 2018). In addition, genetic structure and phylogeographical patterns of sect. Gynopodium from subtropical China were detected by using chloroplast psbA-trnH sequences (Xiao and Li 2017). Understanding the plastid genome of M. omeiensis is also crucial for its conservation concerns, but so far there is no plastid genome resource for this species. Therefore, we assembled the whole plastid genome of M. omeiensis in this study.

Voucher specimen (SCBG00000853, IBSC) and leaves of M. omeiensis were sampled from South China Botanical Garden (N23°11′, E113°22′). Total genomic DNA was extracted from leaves dried by silica gel, then sequenced on an Illumina Hiseq X Ten platform. c.2 Gb of paired-end (PE = 150 bp) sequence reads were obtained and was used to assemble the plastid genome by NOVOPlasty 2.7.2 (Dierckxsens et al. 2017). The complete plastid genome sequence of Magnolia yunnanensis (GenBank Accession Number KF753638) was set as a seed sequence in the seed-and-extend algorithm implemented in NOVOPlasty. The genes in the plastid genome were annotated using the online tool GeSeq (Tillich et al. 2017), with manual adjustment using Geneious 11.0.2 (Kearse et al. 2012). ARAGORN (Laslett and Canback 2004) was used to detect transfer RNA (tRNA). The annotated plastid genome of M. omeiensis has been deposited in GenBank (Accession Number: MK713973).

The complete plastid genome of M. omeiensis was 160,091 bp in length. It typically consisted of a large single-copy (LSC) region of 88,160 bp, a small single-copy (SSC) region of 18,763 bp, and a pair of inverted repeat (IRa and IRb) of 26,584 bp. Overall GC content was 39.3%. The plastid genome contains 112 unique genes, including 80 protein-coding genes, 28 tRNA genes, and 4 ribosomal RNA (rRNA) genes.

Phylogenomic analysis was performed using the complete plastid genomes from 34 samples in the subfamily Magnolioideae (including M. omeiensis in this study). Liriodendron tulipifera and Liriodendron chinense from subfamily Liriodendroidae were used as outgroups. Whole plastid genome sequences from all the above-menioned species were aligned using MAFFT (Katoh and Standley 2013). Maximum likelihood phylogeny was constructed using RAxML (Stamatakis 2014) with GTR + G model. The bootstrap support values were based on 1000 replicates. The phylogeny tree showed that M. omeiensis was closely releated to Magnolia Yunnanensis (Figure 1), which was identified in the same section Gynopodium (Figlar and Nooteboom 2004). The plastid genome of M. omeiensis is of significance for its conservation and evolutionary studies.

Figure 1. Maximum likelihood tree of 36 complete plastid genome of Magnoliaceae. The bootstrap values were based on 1000 replicates.

Disclosure statement

No potential conflict of interest was reported by the authors.

Additional information

Funding

This study was financially supported by the International Partnership Program of Chinese Academy of Sciences [Grant No. GJHZ1620].