Figure 1 - available via license: Creative Commons Attribution 4.0 International
Content may be subject to copyright.
Chloroplast genome map of M. chuanchienensis. Genes on the outside of the main circle are transcribed clockwise, while genes on the inside are transcribed counterclockwise. The Organellar Genome Draw (OGDraw) online software was used to draw this map. Genes with different functions are represented by different colors. The gray portion of the inner circle indicates the GC content of the chloroplast genome.
Source publication
Machilus chuanchienensis is an ecological tree distributed in southwestern China. It has a significant valuation with making Hawk tea using its leaves, an ethnic traditional tea-like beverage with a long history in Chinese tea culture. The whole chloroplast (cp) genome is an ideal model for the phylogenetic study of Lauraceae because of its simple...
Contexts in source publication
Context 1
... M. chuanchienensis cp genome, like that of most angiosperms, is a covalently closed double-stranded cyclic molecule with a total length of 152,748 bp, including a small single-copy (SSC) region (18,803 bp), a large single-copy (LSC) region (93,811 bp) and a pair of inverted repeats (IRs) regions (20,067 bp) (Figure 1). The total GC content of the chloroplast genome was 39.15%, and the AT content was 60.85%, which had evident AT bias. ...
Context 2
... genes Note: + Exon is transcribed counterclockwise in Figure 1; − Exon is transcribed clockwise in Figure 1; -spliceosomal intron; # rps12 is a trans-spliced gene with the 5 end located in the large single copy (LSC) region; it is duplicated in the 3 end in the IR regions. ...
Citations
... In this study, the chloroplast genomes of two Belians from Java and Kalimantan were newly assembled and compared with another previously published one. The chloroplast genome of Belian had a typical quadripartite structure with a size of 157,535~157,577 bp, containing a total of 130 genes, including 85 CDS genes, 37 tRNA genes and eight rRNA genes, which was similar to the chloroplast genomes of other Lauraceae species [40,41]. Song et al. (2017) found that the chloroplasts of the core Lauraceae were 150,749 bp to 152,739 bp in length, with trnI-CAU, rpl23, rpl2, and ycf2 fragments and their intergenic regions lost in the IRb region, and that the chloroplasts of the basal Lauraceae were 157,577 bp to 158,530 bp in length, with rpl2 lost in the IRa region [17], which is supported by the results of the present study. ...
In our article in Genome Biology Ecology six years ago, one complete plastid genome of Belian was assembled for comparative analyses of the plastomes in Lauraceae. However, Ariati et al. (2023) concluded that our sequenced Belian individual could be located in the clade of Myristicaceae instead of that of Lauraceae. Here, we performed re-analyses of additional two Belian plastomes, along with 42 plastomes from plants spanning ten families of the Magnoliids. The plastomes of the three Belian individuals range from 157,535 to 157,577 bp in length. Comparative genomic analysis revealed 170 mutation sites in their plastomes, which include 111 substitutions, 53 indels, and six microinversions. Phylogeny was reconstructed using maximum likelihood and Bayesian approaches for 44 magnoliids species indicated that our three Belian individuals are nested among the species in the family Lauraceae rather than Myristicaceae.
... These hypervariable regions can be used as candidate molecular markers for the development of specific DNA barcodes to aid in the taxonomic identification of Neocinnamomum samples. Among these, the highly-variable petA-psbJ was previously identified as a variation hotspot in the Lauraceae species Litsea glutinosa, Persea americana, and Machilus chuanchienensis (Hinsinger et al., 2017;Song et al., 2016;Bai et al., 2022). The variability of the IR region was significantly lower than that of the SSC and LSC regions, and the variability of the coding regions was much lower than that of the noncoding regions, in the Neocinnamomum cp genome. ...
The genus Neocinnamomum is considered to be one of the most enigmatic groups in Lauraceae, mainly distributed in tropical and subtropical regions of Southeast Asia. The genus contains valuable oilseed and medicinal tree species. However, there are few studies on the genus Neocinnamomum at present, and its interspecific relationship is still unclear. In order to explore the genetic structure and evolutionary characteristics of the Neocinnamomum chloroplast genome and to resolve the species relationships within the genus, comparative genomic and phylogenetic analyses were performed on the whole chloroplast genome sequences of 51 samples representing seven Neocinnamomum taxa. The whole Neocinnamomum chloroplast genome size ranged from 150,753-150,956 bp, with a GC content of 38.8%-38.9%. A total of 128 genes were annotated within the Neocinnamomum chloroplast genome, including 84 protein coding genes, 8 rRNA genes, and 36 tRNA genes. Between 71-82 SSRs were detected, among which A/T base repeats were the most common. The chloroplast genome contained a total of 31 preferred codons. Three highly variable regions, trnN-GUU-ndhF, petA-psbJ, and ccsA-ndhD, were identified with Pi values > 0.004. Based on the whole chloroplast genome phylogenetic tree, the phylogenetic relationships among the seven Neocinnamomum taxa were determined. N. delavayi and N. fargesii were the most closely related species, and N. lecomtei was identified as the most basal taxon. In this study, the characteristics and sequence variation of the chloroplast genomes of seven Neocinnamomum taxa were revealed, and the genetic relationship among the species was clarified. The results of this study will provide a reference for subsequent molecular marker development and phylogenetic research of Neocinnamomum.
Justicia procumbens L. is a traditional medicinal plant that is widely distributed in China. However, little is known about the genetic diversity and evolution of this genus, and no genomic studies have been carried out on J. procumbens previously. In this study, we aimed to assemble and annotate the first complete chloroplast genome (cpDNA) of J. procumbens and compare it with all previously published cpDNAs within the tribe Justicieae. Genome structure and comparative and phylogenetic analyses were performed. The 150,454 bp-long J. procumbens cpDNA has a circular and quadripartite structure consisting of a large single copy, a small single copy, and two inverted repeat regions. It contains 133 genes, of which 88 are protein-coding genes, 37 are tRNA genes, and eight are rRNA genes. Twenty-four simple sequence repeats (SSRs) and 81 repeat sequences were identified. Comparative analyses with other Justicieae species revealed that the non-coding regions of J. procumbens cpDNA showed greater variation than did the coding regions. Moreover, phylogenetic analysis based on 14 cpDNA sequences from Justicieae species showed that J. procumbens and J. flava were most closely related. This study provides valuable genetic information to support further research on the genetic diversity and evolutionary development of the tribe Justicieae.
The Belian (Eusideroxylon zwageri Teijsm. & Binn.) is a commercially important timber species in Southeast Asia that was listed on the IUCN Red List of threatened species in 1998. Six years ago, we published an article in Genome Biology Evolution entitled “Evolutionary Comparisons of the Chloroplast Genome in Lauraceae and Insights into Loss Events in the Magnoliids” in which one complete plastid genome of Belian was assembled for comparative analyses of the plastomes in Lauraceae. However, Ariati et al. (2023) concluded that our sequenced Belian individual can be located in the clade of Myristicaceae instead of that of Lauraceae. Here, we performed reanalyses of an additional two Belian plastomes, along with 42 plastomes from plants spanning 10 families of the Magnoliids. The three Belian plastomes are 39% CG and vary in length from 157,535 to 157,577 bp. A total of 37 tRNA genes, 8 rRNA genes, and 85 protein-coding genes were among the 130 annotated genes. There were 95–101 repeat sequences and 56–61 simple repeat sequences (SSRs). Comparative genomic analysis revealed 170 mutation sites in their plastomes, which include 111 substitutions, 53 indels, and 6 microinversions. Phylogeny was reconstructed using maximum-likelihood and Bayesian approaches for 44 magnoliids species, indicating that the 3 Belian individuals were nested among the species in the Lauraceae family rather than Myristicaceae.
