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Zhang Z, Zhang G, Zhang X, Zhang H, Xie J, Zeng R, Guo B, Huang L. The complete chloroplast genome sequence and phylogenetic relationship analysis of Eomecon chionantha, one species unique to China. JOURNAL OF PLANT RESEARCH 2024; 137:575-587. [PMID: 38652407 DOI: 10.1007/s10265-024-01539-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 02/29/2024] [Indexed: 04/25/2024]
Abstract
Eomecon chionantha Hance, an endemic species in China, has a long medical history in Chinese ethnic minority medicine and is known for its anti-inflammatory and analgesic effects. However, studies of E. chionantha are lacking. In this study, we investigated the characteristics of the E. chionantha chloroplast genome and determined the taxonomic position of E. chionantha in Papaveraceae via phylogenetic analysis. In addition, we determined molecular markers to identify E. chionantha at the molecular level by comparing the chloroplast genomes of E. chionantha and its closely related species. The complete chloroplast genomic information indicated that E. chionantha chloroplast DNA (178,808 bp) contains 99 protein-coding genes, 8 rRNAs, and 37 tRNAs. Meanwhile, we were able to identify a total of 54 simple sequence repeats through our analysis. Our findings from the phylogenetic analysis suggest that E. chionantha shares a close relationship with four distinct species, namely Macleaya microcarpa, Coreanomecon hylomeconoides, Hylomecon japonica, and Chelidonium majus. Additionally, using the Kimura two-parameter model, we successfully identified five hypervariable regions (ycf4-cemA, ycf3-trnS-GGA, trnC-GCA-petN, rpl32-trnL-UAG, and psbI-trnS-UGA). To the best of our knowledge, this is the first report of the complete chloroplast genome of E. chionantha, providing a scientific reference for further understanding of E. chionantha from the perspective of the chloroplast genome and establishing a solid foundation for the future identification, taxonomic determination and evolutionary analysis of this species.
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Affiliation(s)
- Zhi Zhang
- Key Laboratory of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100193, China
- School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
| | - Guoshuai Zhang
- Key Laboratory of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100193, China
| | - Xinke Zhang
- Key Laboratory of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100193, China
| | - Huihui Zhang
- Key Laboratory of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100193, China
| | - Junbo Xie
- Key Laboratory of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100193, China
| | - Rui Zeng
- College of Pharmacy, Southwest Minzu University, Chengdu, 610041, China
| | - Baolin Guo
- Key Laboratory of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100193, China.
| | - Linfang Huang
- Key Laboratory of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100193, China.
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Habib KA, Islam MJ, Sakib MN, Brishti PS, Neogi AK. DNA barcoding of reef-associated fishes of Saint Martin's Island, Northern Bay of Bengal, Bangladesh. Ecol Evol 2023; 13:e10641. [PMID: 37877103 PMCID: PMC10590961 DOI: 10.1002/ece3.10641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 10/09/2023] [Accepted: 10/10/2023] [Indexed: 10/26/2023] Open
Abstract
This study employs the DNA barcoding approach to make a molecular taxonomic catalog of reef fishes of Saint Martin's Island (SMI), an ecologically critical area (ECA), and Marine Protected Area (MPA) in Bangladesh. DNA barcoding, along with morphological analysis, confirmed 84 reef-associated fish species in SMI belonging to 16 orders, 39 families, and 67 genera. A total of 184 sequences were obtained in this study where 151 sequences (534-604 bp) of 81 species were identified from the COI barcode gene and 33 sequences (609 bp) of 19 species from the 16S rRNA gene region which were submitted to the GenBank and Barcode of Life Data System (BOLD). Among these sequences, 70 sequences of the COI gene and 16 sequences of 16S rRNA gene region from 41 species were submitted for the first time into the GenBank from Bangladesh. For molecular characterization analysis, another 37 sequences of 15 reef fish species of SMI were added from previous studies, making a total of 221 DNA sequences which comprised 179 sequences of 96 species for the COI gene and 42 sequences of 26 species for the 16S rRNA gene region. The COI sequences contain 145 haplotypes with 337 polymorphic sites, and the mean genetic distances within species, genera, and families were calculated as 0.34%, 12.26%, and 19.03%, respectively. On the contrary, 16S rRNA sequences comprised 31 haplotypes with 241 polymorphic sites, and the mean genetic divergences within species, genera, and families were 0.94%, 4.72%, and 12.43%, respectively. This study is a significant contribution to the marine biodiversity of Bangladesh which would facilitate the assessment of species diversity for strategizing management action. It is also an important input to the DNA barcode library of reef fishes of the northern Bay of Bengal.
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Affiliation(s)
- Kazi Ahsan Habib
- Department of Fisheries Biology and Genetics, Faculty of Fisheries, Aquaculture and Marine ScienceSher‐e‐Bangla Agricultural UniversityDhakaBangladesh
- Aquatic Bioresource Research Lab, Department of Fisheries Biology and GeneticsSher‐e‐Bangla Agricultural UniversityDhakaBangladesh
| | - Md. Jayedul Islam
- Aquatic Bioresource Research Lab, Department of Fisheries Biology and GeneticsSher‐e‐Bangla Agricultural UniversityDhakaBangladesh
| | - Md. Nazmus Sakib
- Department of Fisheries Biology and Genetics, Faculty of Fisheries, Aquaculture and Marine ScienceSher‐e‐Bangla Agricultural UniversityDhakaBangladesh
- Aquatic Bioresource Research Lab, Department of Fisheries Biology and GeneticsSher‐e‐Bangla Agricultural UniversityDhakaBangladesh
| | - Parsha Shanjana Brishti
- Aquatic Bioresource Research Lab, Department of Fisheries Biology and GeneticsSher‐e‐Bangla Agricultural UniversityDhakaBangladesh
| | - Amit Kumer Neogi
- Aquatic Bioresource Research Lab, Department of Fisheries Biology and GeneticsSher‐e‐Bangla Agricultural UniversityDhakaBangladesh
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Cruz MM, Hoffmann LS, de Freitas TRO. Saint Peter and Saint Paul Archipelago barcoded: Fish diversity in the remoteness and DNA barcodes reference library for metabarcoding monitoring. Genet Mol Biol 2022; 45:e20210349. [PMID: 36205729 PMCID: PMC9540803 DOI: 10.1590/1678-4685-gmb-2021-0349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Accepted: 08/04/2022] [Indexed: 11/04/2022] Open
Abstract
In order to monitor the effects of anthropogenic pressures in ecosystems,
molecular techniques can be used to characterize species composition. Among
molecular markers capable of identifying species, the cytochrome c oxidase I
(COI) is the most used. However, new possibilities of
biodiversity profiling have become possible, in which molecular fragments of
medium and short-length can now be analyzed in metabarcoding studies. Here, a
survey of fishes from the Saint Peter and Saint Paul Archipelago was barcoded
using the COI marker, which allowed the identification of 21
species. This paved the way to further investigate the fish biodiversity of the
archipelago, transitioning from barcoding to metabarcoding analysis. As
preparatory steps for future metabarcoding studies, the first extensive
COI library of fishes listed for these islands was
constructed and includes new data generated in this survey as well as previously
available data, resulting in a final database with 9,183 sequences from 169
species and 63 families of fish. A new primer specifically designed for those
fishes was tested in silico to amplify a region of 262 bp. The
new approach should guarantee a reliable surveillance of the archipelago and can
be used to generate policies that will enhance the archipelago’s protection.
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Affiliation(s)
- Marcelo Merten Cruz
- Universidade Federal do Rio Grande do Sul, Programa de
Pós-Graduação em Genética e Biologia Molecular, Departamento de Genética, Porto
Alegre, RS, Brazil
| | - Lilian Sander Hoffmann
- Universidade Federal do Rio Grande do Sul, Programa de
Pós-Graduação em Genética e Biologia Molecular, Departamento de Genética, Porto
Alegre, RS, Brazil
| | - Thales R. O. de Freitas
- Universidade Federal do Rio Grande do Sul, Programa de
Pós-Graduação em Genética e Biologia Molecular, Departamento de Genética, Porto
Alegre, RS, Brazil
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Descriptions of Two New Species, Sillago muktijoddhai sp. nov. and Sillago mengjialensis sp. nov. (Perciformes: Sillaginidae) from the Bay of Bengal, Bangladesh. FISHES 2022. [DOI: 10.3390/fishes7030093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Due to difficulty in recognition, many true species have been covered under the synonyms of wide-spread species. To justify the identification of a widely distributed species, Sillago sihama from the Bay of Bengal, Bangladesh, an integrated approach including morphology and DNA barcoding was used. Two unrecognized species of Sillago, i.e., Sillagomuktijoddhai sp. nov. and S. mengjialensis sp. nov., were identified from the coastal area of Bangladesh. S. muktijoddhai sp. nov. has marked differences in the body color, anal fin color, number of gill rakers, snout length, and swimbladder. S. mengjialensis sp. nov. has notable differences in the anal fin color, snout length, and swimbladder and is distinguished from S. muktijoddhai sp. nov. by the body color and swimbladder. The morphological characters of 14 documented Sillago species with two posterior extensions of the swimbladder were referenced and distinguished to accredit the two new species. Genetic analyses of partial mitochondrial cytochrome oxidase subunit I and 16S ribosomal RNA also supported the validity of the new species. This study has increased the number of recognized species of Sillago in the world and confirmed the prevailing misidentification of these two new species in Bangladesh as so-called S. sihama. Moreover, the study confirmed the misidentification of S. mengjialensis sp. nov. in Indonesia as S. sihama and the identification of unknown Sillago sp.1 in India.
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