Comparative Analyses of the Chloroplast Genomes of Patchouli Plants and Their Relatives in Pogostemon (Lamiaceae)

Zhang, Caiyun; Liu, Tong-Jian; Mo, Xiaolu; Huang, Hui-Run; Yao, Gang; Lǐ, Jiànróng; Ge, Xue‐Jun; Yan, Hai‐Fei

doi:10.3390/plants9111497

Cited by 7 publications

(4 citation statements)

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“…The high stability of DNA sequences with high GC content resulted in a negative correlation between the GC content and the variability of cp genome sequences [ 43 , 50 ]. In this study, the most variable regions for Trapa were located in IGS regions with the lowest GC content.…”

Section: Discussionmentioning

confidence: 99%

Fifteen complete chloroplast genomes of Trapa species (Trapaceae): insight into genome structure, comparative analysis and phylogenetic relationships

et al. 2022

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Background Trapa L. is a floating-leaved aquatic plant with important economic and ecological values. However, the species identification and phylogenetic relationship within Trapa are still controversial, which necessitates the need for plastid genome information of Trapa. In this study, complete chloroplast genomes of 13 Trapa species/taxa were sequenced and annotated. Combined with released sequences, comparative analyses of chloroplast genomes were performed on the 15 Trapa species/taxa for the first time. Results The Trapa chloroplast genomes exhibited typical quadripartite structures with lengths from 155,453 to 155,559 bp. The gene orders and contents within Trapa were conservative, but several changes were found in the microstructure. The intron loss of rpl2, also detected in Lythraceae, was found in all Trapa species/taxa, suggesting close genetic relationship between Lythraceae and Trapaceae. Notably, two small-seed species (T. incisa and T. maximowiczii) showed the smallest genome size with 155,453 and 155,477 bp, respectively. Each cp genome contained the same 130 genes consisting of 85 protein-coding genes, 37 tRNA genes and 8 rRNA genes. Trapa species/taxa showed 37 (T. incisa and T. maximowiczii) to 41 (T. sibirica) long repeats, including forward, palindromic, reversed and complementary repeats. There were 110 (T. quadrispinosa) to 123 (T. incisa and T. maximowiczii) SSR (simple sequence repeat) loci in Trapa chloroplast genomes. Comparative analyses revealed that two hotspot regions (atpA—atpF and rps2—rpoC2) in Trapa chloroplast genomes could be served as potential molecular markers. Three phylogenetic analyses (ML, MP and BI) consistently showed that there were two clusters within Trapa, including large- and small-seed species/taxa, respectively; for the large-seed Trapa, they clustered according to their geographical origin and tubercle morphology on the surface of seeds. Conclusion In summary, we have acquired the sequences of 13 Trapa chloroplast genomes, and performed the comparative analyses within Trapa for the first time. The results have helped us better identify the Trapa species/taxa and deepen the understanding of genetic basis and phylogenetic relationship of Trapa, which will facilitate the effective management and utilization of the important genetic resources in the future.

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Section: Discussionmentioning

confidence: 99%

Fifteen complete chloroplast genomes of Trapa species (Trapaceae): insight into genome structure, comparative analysis and phylogenetic relationships

et al. 2022

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“…In most angiosperms, chloroplast (cp) genomes are quadripartite, double-helical, and spherical [17]. The chloroplast genome has been considered an "ultra-barcode" for species recognition [18] and phylogenetic analysis [19]. The chloroplast genomes are appropriate for inferring phylogenic analysis due to their conserved genetic research, slowly changing traits, and uni-parental hereditary data [17,20,21].…”

Section: Introductionmentioning

confidence: 99%

The chloroplast genome of Farsetia hamiltonii Royle, phylogenetic analysis, and comparative study with other members of Clade C of Brassicaceae

et al. 2022

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Background Farsetia hamiltonii Royle is a medicinally important annual plant from the Cholistan desert that belongs to the tribe Anastaticeae and clade C of the Brassicaceae family. We provide the entire chloroplast sequence of F.hamiltonii, obtained using the Illumina HiSeq2500 and paired-end sequencing. We compared F. hamiltonii to nine other clade C species, including Farsetia occidentalis, Lobularia libyca, Notoceras bicorne, Parolinia ornata, Morettia canescens, Cochlearia borzaeana, Megacarpaea polyandra, Biscutella laevigata, and Iberis amara. We conducted phylogenetic research on the 22 Brassicaceae species, which included members from 17 tribes and six clades. Results The chloroplast genome sequence of F.hamiltonii of 154,802 bp sizes with 36.30% GC content and have a typical structure comprised of a Large Single Copy (LSC) of 83,906 bp, a Small Single Copy (SSC) of 17,988 bp, and two copies of Inverted Repeats (IRs) of 26,454 bp. The genomes of F. hamiltonii and F. occidentalis show shared amino acid frequencies and codon use, RNA editing sites, simple sequence repeats, and oligonucleotide repeats. The maximum likelihood tree revealed Farsetia as a monophyletic genus, closely linked to Morettia, with a bootstrap score of 100. The rate of transversion substitutions (Tv) was higher than the rate of transition substitutions (Ts), resulting in Ts/Tv less than one in all comparisons with F. hamiltonii, indicating that the species are closely related. The rate of synonymous substitutions (Ks) was greater than non-synonymous substitutions (Ka) in all comparisons with F. hamiltonii, with a Ka/Ks ratio smaller than one, indicating that genes underwent purifying selection. Low nucleotide diversity values range from 0.00085 to 0.08516, and IR regions comprise comparable genes on junctions with minimal change, supporting the conserved status of the selected chloroplast genomes of the clade C of the Brassicaceae family. We identified ten polymorphic regions, including rps8-rpl14, rps15-ycf1, ndhG-ndhI, psbK-psbI, ccsA-ndhD, rpl36-rps8, petA-psbJ, ndhF-rpl32, psaJ-rpl3, and ycf1 that might be exploited to construct genuine and inexpensive to solve taxonomic discrepancy and understand phylogenetic relationship amongst Brassicaceae species. Conclusion The entire chloroplast sequencing of F. hamiltonii sheds light on the divergence of genic chloroplast sequences among members of the clade C. When other Farsetia species are sequenced in the future, the full F. hamiltonii chloroplast will be used as a source for comprehensive taxonomical investigations of the genus. The comparison of F. hamiltonii and other clade C species adds new information to the phylogenetic data and evolutionary processes of the clade. The results of this study will also provide further molecular uses of clade C chloroplasts for possible plant genetic modifications and will help recognise more Brassicaceae family species.

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“…Patchouli seedling period like rain, and like the humidity environment in the long term (but the soil humidity is too high, it will also die.) [4]. Irrigation should be noted in areas with less rainfall.…”

Section: Cultivation Conditions Of Patchoulimentioning

confidence: 99%

Design and Implementation on Patchouli Growth Environment Monitoring System Based on IoT

Zhang

2021

ASP trans. Internet things

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With the development of the times, the concept of "interconnection of all things" has been deeply rooted in the hearts of people. As an early and developing Internet technology, the Internet of things(IoT) has shown its infinite potential in many fields of social life. In agriculture, the agricultural IoT is coverring a growing number of fields: greenhouse planting, climate factor collection, climate prediction and so on. Based on this idea, the design idea of "patchouli growth environment monitoring system" is put forward. In this paper, the medicinal plant "patchouli" is studied, and its medicinal value and growth factors are discussed. Meanwhile, based on zigbee technology, we design a set of feasible monitoring scheme including hardware and software. The hardware part used ZigBee wireless network design, mainly relies on the cc2530 chip and the esp8266 wifi chip to carry on the wireless distance transmission to the sensor data. It interacts between OneNET cloud server and mysql database through MQTT protocol, TCP/IP protocol and HTTP protocol.

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Comparative Analyses of the Chloroplast Genomes of Patchouli Plants and Their Relatives in Pogostemon (Lamiaceae)

Cited by 7 publications

References 50 publications

Fifteen complete chloroplast genomes of Trapa species (Trapaceae): insight into genome structure, comparative analysis and phylogenetic relationships

Fifteen complete chloroplast genomes of Trapa species (Trapaceae): insight into genome structure, comparative analysis and phylogenetic relationships

The chloroplast genome of Farsetia hamiltonii Royle, phylogenetic analysis, and comparative study with other members of Clade C of Brassicaceae

Design and Implementation on Patchouli Growth Environment Monitoring System Based on IoT

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