Abstract
Chromolaena odorata is a perennial noxious invasive weed to south China. In this study, we assembled the complete chloroplast (cp) genome of C. odorata by next-generation sequencing technologies. The whole cp genome is 151,270 bp in size, consisting of a pair of inverted repeats (IR 25,080 bp), a large single-copy region (LSC 82,663 bp), and a small single-copy region (SSC 18,447 bp). The genome contains a total of 132 genes, including 88 protein-coding genes, 36 tRNAs, and 8 rRNAs. Furthermore, a maximum likelihood phylogenetic analysis demonstrated that C. odorata was closely related to Praxelis clematidea and Ageratina adenophora. The cp genome will provide reference for the further investigation and research of C. odorata.
Chromolaena odorata is one of the most serious 100 invasive alien species in the world (Lowe et al. Citation2000). It is an extremely fast-growing, high-reproducing, and long-lived perennial herbaceous shrub of Compositae family native to Central and South America (Yu et al. Citation2016). In China, C. odorata was first discovered in Yunnan and Hainan provinces in 1934, and now it is rapidly spreading throughout the southern China. It not only affects the production of agriculture, forestry and husbandry and causes great economic loss, but also threatens the health of human and livestock (Yu et al. Citation2010). Currently, studies on C. odorata focus in its invasion mechanism, ecological impacts and control methods, such as phenotypic plasticity (Liao et al. Citation2019), genetic variation (Paterson and Zachariades Citation2013), plant–soil interaction (Te Beest et al. Citation2015), biodiversity (Rozen-Rechels et al. Citation2017), and biological control (Aigbedion-Atalor et al. Citation2019). However, its phylogenetic relationships are rather limited. In this study, we reported the complete chloroplast (cp) genome sequence of C. odorata, which would be helpful for its genetic and evolutionary research.
The leaves of C. odorata were collected from the suburb of Yangjiang city (21°89’76.35″N, 112°00’56.63″E), Guangdong province, China. The specimen was stored at Guangzhou City Polytechnic (specimen code GCP0636). The genomic DNA of C. odorata was extracted from leaves by plant genomic DNA kit (Tiangen Biotech, China) and sequenced using the Novaseq platform (Illumina, San Diego, CA) following the manufacturer’s recommendations. The plastome was assembled by the GetOrganelle (Jin et al. Citation2019) and annotated with the Geseq (Tillich et al. Citation2017). Finally, a complete chloroplast genome of C. odorata was obtained and submitted to GenBank with the accession number MN885889.
The complete cp genome of C. odorata is 151,270 bp in length, containing a large single-copy (LSC) region of 82,663 bp, a small single-copy (SSC) region of 18,447 bp, and two inverted repeat (IR) regions of 25,080 bp. The new sequence has 132 genes in total, including 88 protein-coding genes, 36 tRNA genes, and 8 rRNA genes. In addition, the overall GC content of the genome is 37.48%, whereas the corresponding values of the LSC, SSC, and IR regions are 54.65%, 12.19%, and 16.58%, respectively.
To further investigate its phylogenetic position, 12 complete cp genomes of Compositae species (Sphagneticola calendulacea, Guizotia abyssinica, Tagetes erecta, Marshallia caespitosa, Marshallia obovate, Praxelis clematidea, Ageratina adenophora, Chromolaena odorata, Ageratum conyhzoides, Mikania micrantha, Ambrosia trifida, Helianthus annuus) were aligned using MAFFT (Katoh and Standley Citation2013). All the data were downloaded from NCBI GenBank. A maximum likelihood analysis was performed by RAxML (Stamatakis Citation2014) with 1000 bootstrap replicates (Minh et al. Citation2013; Chernomor et al. Citation2016). The results showed that C. odorata was closely related to Praxelis clematidea and Ageratina adenophora with 100% bootstrap support ().
Figure 1. A phylogenetic tree was constructed based on 12 complete chloroplast genome sequences of Compositae. All the sequences were downloaded from NCBI GenBank.
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No potential conflict of interest was reported by the author(s).
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References
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