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Complete chloroplast genomes of two medicinal Swertia species: The comparative evolutionary analysis of Swertia genus in the Gentianaceae family
19th International Conference on CANCER AND CANCER THERAPY
December 07, 2022 | Dubai, UAE
Qing Du
Peking Union Medical College, China
Keynote : J Can Clinical Res
Abstract:
Background/Aims: We developed the comparative research of Swertia kouitchensis chloroplast genome with that of 22 Swertia species in the Gentianaceae family from the aspects of phenotype characteristics, structural and genetic features, and evolutionary relationship. Thus, we could exploit the distinctive differentia and identified traits to fully illustrate the relevance and distinction among these species on account of the complete database statement for these chloroplast genomes. Methods: Total genomic DNA was extracted using the plant genomic DNA kit (Tiangen Biotech, Beijing, China) (Vieira et al. 2014). The DNA purity was detected with 1.0% agarose gel and the concentration of cpDNA was determined using a Nanodrop spectrophotometer 2000 (Rowan et al. 2011). DNA extracts were fragmented for 300 bp short-insert library construction. The library was sequenced in pair-end mode with the read length of 150 bp on an Illumina Hiseq 2500 platform (Cronn et al. 2008). The raw reads were filtered using Trimmomatic 0.35 with default parameters to remove adapters and low-quality bases (Bolger 2014). Then, the chloroplast genome of S. kouitchensis was assembled using the NOVOPlasty (v 4.2) software (Dierckxsens et al. 2017) with default parameters and the rbcL sequences as the seed. We used Gepard software to draw dot plots between the assembled genome and reference genomes to identify the structure of the chloroplast genome (Krumsiek et al. 2007). The chloroplast genome can be annotated using the CPGAVAS2 web service (http:// www. herba lgeno mics. org/cpgav as2) (Shi et al. 2019). The annotation was manually corrected using the Apollo software (Firtina et al. 2020). We calculated the GC content using BioXM software (Losko and Heumann 2009). Lastly, the assembly and annotation results of the S. kouitchensis chloroplast genome was submitted to GenBank and the accession number OM617848 was acquired. Then, the comparative data of S. bimaculata chloroplast genome was downloaded from the NCBI database (MW344296.1), which was developed by the team of professor Weizhen from Zhengzhou University. Results: The significant distinction in the specification between Strigoptera bimaculata and Swertia kouitchensis lies in the shape of the stem (1), pedicel (2), and leaf (3); The color of corolla (4) and seeds, spots (5), and the shape of the seed surface. In the species of S. bimaculata, it has a round stem (1), thick pedicel (2), erect or oblique extension, unequal length, oval to ovate-lanceolate leaf (3), mostly small purple spots (5) in the upper part of the yellow corolla (4), two semicircular yellow–green large gland spots (5) in the middle, and the brown round seeds with protruding on the surface. Meanwhile, the species of S. kouitchensis has four-angular erect stems (1); narrow pedicel wings (2), lanceolate leaf (3), yellow, white, and green corolla (4), apex and long pointed fruit that slightly increases with two glands (5) at the base; and yellow– brown seeds with a nearly smooth surface. The chloroplast genome of S. kouitchensis encodes a total of 131 genes (110 unique genes), which include 88 PCGs (80 unique genes), 37 tRNAs (29 unique genes), and 8 genes encoding ribosome RNA (4 unique genes). The 88 PCGs encoded a total of 26,243 and 25,961 codons in the S. kouitchensis and S. bimaculata chloroplast genome. The most abundant codon of the two species was for isoleucine, and the least abundant codon was for cysteine. The number of microsatellites repeat sequences was twenty-eight and thirty-two identified in the chloroplast genomes of S. kouitchensis and S. bimaculata, respectively. A total of 1127 repeat sequences were identified in all the 23 Swertia chloroplast genomes, and they fell into four categories. Furthermore, five divergence hotspot regions can be applied to discriminate these 23 Swertia species through genomes comparison. One pair of genus-specific DNA barcodes primer has been accurately identified. Therefore, the diverse regions cloned by a specific primer may become an effective and powerful molecular marker for the identification of Swertia genus. Moreover, four genes (ccsA, ndhK, rpoC1, and rps12) were positive selective pressure. The phylogenetic tree showed that the 23 Swertia species were clustered into a large clade including four evident subbranches, whereas the two species of S. kouitchensis and S. bimaculata were separately clustered into the diverse but correlated species group. Conclusion: The complete chloroplast genome of Swertia kouitchensis has been sequenced and assembled, compared with that of S. bimaculata to determine the evolutionary relationships among species of the Swertia in the Gentianaceae family.
Recent Publications :
1. Du Q, ZENG J, Wang L, et al. Comparative genomics and phylogenetic analysis of the chloroplast genomes in three medicinal Salvia species for bioexploration. Research Square; 2022. DOI: 10.21203/ rs.3.rs-1582501/v1
2. Du Q, Li J, Wang L, et al. Complete chloroplast genomes of two medicinal Swertia species: the comparative evolutionary analysis of Swertia genus in the Gentianaceae family. Planta. 2022 Sep;256(4):73. DOI: 10.1007/s00425-022-03987-z. PMID: 36083348.
3. Du Q, Jiang M, Sun S, et al. The complete chloroplast genome sequence of Clerodendranthus spicatus, a medicinal plant for preventing and treating kidney diseases from Lamiaceae family. Molecular Biology Reports. 2022 Apr;49(4):3073-3083. DOI: 10.1007/s11033-022-07135-4. PMID: 35059973.
Biography:
Quing Du is from IMPLAD and QHNU Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, College of Pharmacy, Qinghai Minzu University.
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