1
|
Wu R, Li Y, Wang L, Li Z, Wu R, Xu K, Liu Y. The DBB Family in Populus trichocarpa: Identification, Characterization, Evolution and Expression Profiles. Molecules 2024; 29:1823. [PMID: 38675643 DOI: 10.3390/molecules29081823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2024] [Revised: 04/12/2024] [Accepted: 04/15/2024] [Indexed: 04/28/2024] Open
Abstract
The B-box proteins (BBXs) encode a family of zinc-finger transcription factors that regulate the plant circadian rhythm and early light morphogenesis. The double B-box (DBB) family is in the class of the B-box family, which contains two conserved B-box domains and lacks a CCT (CO, CO-like and TOC1) motif. In this study, the identity, classification, structures, conserved motifs, chromosomal location, cis elements, duplication events, and expression profiles of the PtrDBB genes were analyzed in the woody model plant Populus trichocarpa. Here, 12 PtrDBB genes (PtrDBB1-PtrDBB12) were identified and classified into four distinct groups, and all of them were homogeneously spread among eight out of seventeen poplar chromosomes. The collinearity analysis of the DBB family genes from P. trichocarpa and two other species (Z. mays and A. thaliana) indicated that segmental duplication gene pairs and high-level conservation were identified. The analysis of duplication events demonstrates an insight into the evolutionary patterns of DBB genes. The previously published transcriptome data showed that PtrDBB genes represented distinct expression patterns in various tissues at different stages. In addition, it was speculated that several PtrDBBs are involved in the responsive to drought stress, light/dark, and ABA and MeJA treatments, which implied that they might function in abiotic stress and phytohormone responses. In summary, our results contribute to the further understanding of the DBB family and provide a reference for potential functional studies of PtrDBB genes in P. trichocarpa.
Collapse
Affiliation(s)
- Ruihua Wu
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Yuxin Li
- Melbourne School of Design, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Lin Wang
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Zitian Li
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Runbin Wu
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Kehang Xu
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Yixin Liu
- College of Landscape Architecture and Art, Northwest A & F University, Yangling 712100, China
| |
Collapse
|
2
|
Mwamula AO, Kwon OG, Kwon C, Kim YS, Kim YH, Lee DW. A Revision of the Phylogeny of Helicotylenchus Steiner, 1945 (Tylenchida: Hoplolaimidae) as Inferred from Ribosomal and Mitochondrial DNA. Plant Pathol J 2024; 40:171-191. [PMID: 38606447 PMCID: PMC11016563 DOI: 10.5423/ppj.oa.01.2024.0013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 02/20/2024] [Accepted: 03/03/2024] [Indexed: 04/13/2024]
Abstract
Identification of Helicotylenchus species is very challenging due to phenotypic plasticity and existence of cryptic species complexes. Recently, the use of rDNA barcodes has proven to be useful for identification of Helicotylenchus. Molecular markers are a quick diagnostic tool and are crucial for discriminating related species and resolving cryptic species complexes within this speciose genus. However, DNA barcoding is not an error-free approach. The public databases appear to be marred by incorrect sequences, arising from sequencing errors, mislabeling, and misidentifications. Herein, we provide a comprehensive analysis of the newly obtained, and published DNA sequences of Helicotylenchus, revealing the potential faults in the available DNA barcodes. A total of 97 sequences (25 nearly full-length 18S-rRNA, 12 partial 28S-rRNA, 16 partial internal transcribed spacer [ITS]-rRNA, and 44 partial cytochrome c oxidase subunit I [COI] gene sequences) were newly obtained in the present study. Phylogenetic relationships between species are given as inferred from the analyses of 103 sequences of 18S-rRNA, 469 sequences of 28S-rRNA, 183 sequences of ITS-rRNA, and 63 sequences of COI. Remarks on suggested corrections of published accessions in GenBank database are given. Additionally, COI gene sequences of H. dihystera, H. asiaticus and the contentious H. microlobus are provided herein for the first time. Similar to rDNA gene analyses, the COI sequences support the genetic distinctness and validity of H. microlobus. DNA barcodes from type material are needed for resolving the taxonomic status of the unresolved taxonomic groups within the genus.
Collapse
Affiliation(s)
- Abraham Okki Mwamula
- Research Institute of Invertebrate Vector, Kyungpook National University, Sangju 37224, Korea
| | - Oh-Gyeong Kwon
- Department of Ecological Science, Kyungpook National University, Sangju 37224, Korea
| | - Chanki Kwon
- Department of Plant Protection and Quarantine, Graduate School of Plant Protection and Quarantine, Kyungpook National University, Daegu 41566, Korea
| | - Yi Seul Kim
- Research Institute of Invertebrate Vector, Kyungpook National University, Sangju 37224, Korea
| | - Young Ho Kim
- Research Institute of Invertebrate Vector, Kyungpook National University, Sangju 37224, Korea
- Department of Ecological Science, Kyungpook National University, Sangju 37224, Korea
- Department of Plant Protection and Quarantine, Graduate School of Plant Protection and Quarantine, Kyungpook National University, Daegu 41566, Korea
| | - Dong Woon Lee
- Research Institute of Invertebrate Vector, Kyungpook National University, Sangju 37224, Korea
- Department of Ecological Science, Kyungpook National University, Sangju 37224, Korea
- Department of Plant Protection and Quarantine, Graduate School of Plant Protection and Quarantine, Kyungpook National University, Daegu 41566, Korea
| |
Collapse
|
3
|
Lin L, Hao Z, Zhou L, Liu W, Liu N, Wang K, Jia R. Elucidating phylogenetic relationships within the genus Curcuma through the comprehensive analysis of the chloroplast genome of Curcuma viridiflora Roxb. 1810 (Zingiberaceae). Mitochondrial DNA B Resour 2024; 9:371-375. [PMID: 38529111 PMCID: PMC10962285 DOI: 10.1080/23802359.2024.2329674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Accepted: 03/07/2024] [Indexed: 03/27/2024] Open
Abstract
Curcuma viridiflora Roxb., a plant species of significant pharmaceutical interest, has been the subject of limited chloroplast genomic research. In this study, we present the sequencing and assembly of the C. viridiflora chloroplast genome, which is characterized by a circular chromosome spanning 162,212 base pairs and a GC content of 36.20%. The genome encodes 87 protein-coding genes (PCGs), 38 transfer RNA (tRNA) genes, and eight ribosomal RNA (rRNA) genes. A phylogenetic analysis was conducted, incorporating eight related species, and based on the complete chloroplast genome and protein-coding DNA sequences of six related taxa within the genus. Outgroup species Zingiber zerumbet and Zingiber officinale were also included in the analysis. The results indicate a close relationship between C. viridiflora and Curcuma phaeocaulis, Curcuma sichuanensis, and Curcuma yunnanensis. This study provides the first chloroplast genome of C. viridiflora, thereby contributing a valuable genomic resource for future research on medicinal plants within the Curcuma genus.
Collapse
Affiliation(s)
- Ling Lin
- Sanya Research Institution/Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Chinese Academy of Tropical Agriculture Sciences, Sanya, China
- Foshan Lianyi Biotechnology Co., Ltd., Foshan, China
| | - Zhigang Hao
- Sanya Research Institution/Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Chinese Academy of Tropical Agriculture Sciences, Sanya, China
- Sanya Institute of China Agricultural University, Sanya, China
- Hainan Seed Industry Laboratory, Sanya, China
| | - Liying Zhou
- Sanya Research Institution/Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Chinese Academy of Tropical Agriculture Sciences, Sanya, China
- Department of Horticulture and Landscape Architecture, Zhongkai University of Agriculture and Engineering, Guangzhou, China
| | - Wenyi Liu
- Foshan Lianyi Biotechnology Co., Ltd., Foshan, China
| | - Nian Liu
- Department of Horticulture and Landscape Architecture, Zhongkai University of Agriculture and Engineering, Guangzhou, China
| | - Kebao Wang
- Kenli Vocational Education Center, Dongying, China
| | - Ruizong Jia
- Sanya Research Institution/Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Chinese Academy of Tropical Agriculture Sciences, Sanya, China
| |
Collapse
|
4
|
Yang X, Zheng S, Wang X, Wang J, Ali Shah SB, Wang Y, Gao R, Xu Z. Advances in pharmacology, biosynthesis, and metabolic engineering of Scutellaria-specialized metabolites. Crit Rev Biotechnol 2024; 44:302-318. [PMID: 36581326 DOI: 10.1080/07388551.2022.2149386] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 10/11/2022] [Accepted: 11/02/2022] [Indexed: 12/31/2022]
Abstract
Scutellaria Linn., which belongs to the family Lamiaceae, is a commonly used medicinal plant for heat clearing and detoxification. In particular, the roots of S. baicalensis and the entire herb of S. barbata have been widely used in traditional medicine for thousands of years. The main active components of Scutellaria, including: baicalein, wogonin, norwogonin, scutellarein, and their glycosides have potential or existing drug usage. However, the wild resources of Scutellaria plants have been overexploited, and degenerated germplasm resources cannot fulfill the requirements of chemical extraction and clinical usage. Metabolic engineering and green production via microorganisms provide alternative strategies for greater efficiency in the production of natural products. Here, we review the progress of: pharmacological investigations, multi-omics, biosynthetic pathways, and metabolic engineering of various Scutellaria species and their active compounds. In addition, based on multi-omics data, we systematically analyze the phylogenetic relationships of Scutellaria and predict candidate transcription factors related to the regulation of active flavonoids. Finally, we propose the prospects of directed evolution of core enzymes and genome-assisted breeding to alleviate the shortage of plant resources of Scutellaria. This review provides important insights into the sustainable utilization and development of Scutellaria resources.
Collapse
Affiliation(s)
- Xinyi Yang
- Ministry of Education, Key Laboratory of Saline-alkali Vegetation Ecology Restoration (Northeast Forestry University), Harbin, China
- College of Life Science, Northeast Forestry University, Harbin, China
| | - Sihao Zheng
- China National Traditional Chinese Medicine Co., Ltd, Beijing, China
| | - Xiaotong Wang
- Ministry of Education, Key Laboratory of Saline-alkali Vegetation Ecology Restoration (Northeast Forestry University), Harbin, China
- College of Life Science, Northeast Forestry University, Harbin, China
| | - Jing Wang
- Ministry of Education, Key Laboratory of Saline-alkali Vegetation Ecology Restoration (Northeast Forestry University), Harbin, China
- College of Life Science, Northeast Forestry University, Harbin, China
| | - Syed Basit Ali Shah
- Ministry of Education, Key Laboratory of Saline-alkali Vegetation Ecology Restoration (Northeast Forestry University), Harbin, China
- College of Life Science, Northeast Forestry University, Harbin, China
| | - Yu Wang
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Ranran Gao
- The Artemisinin Research Center, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Zhichao Xu
- Ministry of Education, Key Laboratory of Saline-alkali Vegetation Ecology Restoration (Northeast Forestry University), Harbin, China
- College of Life Science, Northeast Forestry University, Harbin, China
| |
Collapse
|
5
|
Tao K, Gao Y, Yin H, Liang Q, Yang Q, Yu X. Comparative Mitogenome Analyses of Fifteen Ramshorn Snails and Insights into the Phylogeny of Planorbidae (Gastropoda: Hygrophila). Int J Mol Sci 2024; 25:2279. [PMID: 38396956 PMCID: PMC10889216 DOI: 10.3390/ijms25042279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 02/08/2024] [Accepted: 02/09/2024] [Indexed: 02/25/2024] Open
Abstract
Ramshorn snails from the family Planorbidae are important freshwater snails due to their low trophic level, and some of them act as intermediate hosts for zoonotic trematodes. There are about 250 species from 40 genera of Planorbidae, but only 14 species from 5 genera (Anisus, Biomphalaria, Bulinus, Gyraulus, and Planorbella) have sequenced complete mitochondrial genomes (mitogenomes). In this study, we sequenced and assembled a high-quality mitogenome of a ramshorn snail, Polypylis sp. TS-2018, which represented the first mitogenome of the genus. The mitogenome of Polypylis sp. TS-2018 is 13,749 bp in length, which is shorter than that of most gastropods. It contains 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, and 2 ribosomal RNA (rRNA). We compared mitogenome characteristics, selection pressure, and gene rearrangement among all of the available mitogenomes of ramshorn snails. We found that the nonsynonymous and synonymous substitution rates (Ka/Ks) of most PCGs indicated purifying and negative selection, except for atp8 of Anisus, Biomphalaria, and Gyraulus, which indicated positive selection. We observed that transpositions and reverse transpositions occurred on 10 tRNAs and rrnS, which resulted in six gene arrangement types. We reconstructed the phylogenetic trees using the sequences of PCGs and rRNAs and strongly supported the monophyly of each genus, as well as three tribes in Planorbidae. Both the gene rearrangement and phylogenetic results suggested that Polypylis had a close relationship with Anisus and Gyraulus, while Bulinus was the sister group to all of the other genera. Our results provide useful data for further investigation of species identification, population genetics, and phylogenetics among ramshorn snails.
Collapse
Affiliation(s)
| | | | | | | | - Qianqian Yang
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine, College of Life Sciences, China Jiliang University, Hangzhou 310018, China; (K.T.); (Y.G.); (H.Y.); (Q.L.)
| | - Xiaoping Yu
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine, College of Life Sciences, China Jiliang University, Hangzhou 310018, China; (K.T.); (Y.G.); (H.Y.); (Q.L.)
| |
Collapse
|
6
|
Yang X, Li X, Bao Q, Wang Z, He S, Qu X, Tang Y, Song B, Huang J, Yi G. Uncovering Evolutionary Adaptations in Common Warthogs through Genomic Analyses. Genes (Basel) 2024; 15:166. [PMID: 38397156 PMCID: PMC10888464 DOI: 10.3390/genes15020166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 01/15/2024] [Accepted: 01/20/2024] [Indexed: 02/25/2024] Open
Abstract
In the Suidae family, warthogs show significant survival adaptability and trait specificity. This study offers a comparative genomic analysis between the warthog and other Suidae species, including the Luchuan pig, Duroc pig, and Red River hog. By integrating the four genomes with sequences from the other four species, we identified 8868 single-copy orthologous genes. Based on 8868 orthologous protein sequences, phylogenetic assessments highlighted divergence timelines and unique evolutionary branches within suid species. Warthogs exist on different evolutionary branches compared to DRCs and LCs, with a divergence time preceding that of DRC and LC. Contraction and expansion analyses of warthog gene families have been conducted to elucidate the mechanisms of their evolutionary adaptations. Using GO, KEGG, and MGI databases, warthogs showed a preference for expansion in sensory genes and contraction in metabolic genes, underscoring phenotypic diversity and adaptive evolution direction. Associating genes with the QTLdb-pigSS11 database revealed links between gene families and immunity traits. The overlap of olfactory genes in immune-related QTL regions highlighted their importance in evolutionary adaptations. This work highlights the unique evolutionary strategies and adaptive mechanisms of warthogs, guiding future research into the distinct adaptability and disease resistance in pigs, particularly focusing on traits such as resistance to African Swine Fever Virus.
Collapse
Affiliation(s)
- Xintong Yang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China; (X.Y.); (X.L.); (Q.B.); (Z.W.); (S.H.); (X.Q.); (Y.T.); (B.S.)
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning 530005, China;
| | - Xingzheng Li
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China; (X.Y.); (X.L.); (Q.B.); (Z.W.); (S.H.); (X.Q.); (Y.T.); (B.S.)
| | - Qi Bao
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China; (X.Y.); (X.L.); (Q.B.); (Z.W.); (S.H.); (X.Q.); (Y.T.); (B.S.)
| | - Zhen Wang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China; (X.Y.); (X.L.); (Q.B.); (Z.W.); (S.H.); (X.Q.); (Y.T.); (B.S.)
| | - Sang He
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China; (X.Y.); (X.L.); (Q.B.); (Z.W.); (S.H.); (X.Q.); (Y.T.); (B.S.)
| | - Xiaolu Qu
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China; (X.Y.); (X.L.); (Q.B.); (Z.W.); (S.H.); (X.Q.); (Y.T.); (B.S.)
| | - Yueting Tang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China; (X.Y.); (X.L.); (Q.B.); (Z.W.); (S.H.); (X.Q.); (Y.T.); (B.S.)
- School of Life Sciences, Henan University, Kaifeng 475004, China
| | - Bangmin Song
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China; (X.Y.); (X.L.); (Q.B.); (Z.W.); (S.H.); (X.Q.); (Y.T.); (B.S.)
- School of Life Sciences, Henan University, Kaifeng 475004, China
| | - Jieping Huang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning 530005, China;
| | - Guoqiang Yi
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China; (X.Y.); (X.L.); (Q.B.); (Z.W.); (S.H.); (X.Q.); (Y.T.); (B.S.)
- Kunpeng Institute of Modern Agriculture at Foshan, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Foshan 528226, China
- Bama Yao Autonomous County Rural Revitalization Research Institute, Bama 547500, China
| |
Collapse
|
7
|
Chen F, Lu P, Liang D, Wu Y, Jiang Z, Huang W, Gao L. Phylogenetic analysis based on the complete mitochondrial genome of Discogobio brachyphysallidos (Cypriniformes: Cyprinidae) suggests the need for taxonomic revision at the genus level. Mitochondrial DNA B Resour 2024; 9:200-203. [PMID: 38288248 PMCID: PMC10823891 DOI: 10.1080/23802359.2024.2306882] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Accepted: 01/13/2024] [Indexed: 01/31/2024] Open
Abstract
Discogobio brachyphysallidos Huang 1989 is a Cyprinidae fish species that is endemic to the upper Pearl River. In the present study, the complete mitochondrial genome of D. brachyphysallidos collected from the Nanpanjiang River was sequenced and annotated. The mitochondrial genome encompassed 13 protein-coding genes, two ribosomal RNA (rRNA) genes, 22 transfer RNA (tRNA) genes, and the control region (D-loop). The total length of the mitochondrial genome was determined to be 16,594 base pairs (bp), with a GC content of 41.7%. Phylogenetic analyses revealed that D. brachyphysallidos may be a sister to D. longibarbatus and D. macrophysallidos. These findings provide insight into the genetic information and phylogenetic relationships of D. brachyphysallidos.
Collapse
Affiliation(s)
- Fangcan Chen
- Guangdong Hanyu Ecological Technology Co., Ltd., Guangzhou, China
| | - Pingke Lu
- Guangdong Hanyu Ecological Technology Co., Ltd., Guangzhou, China
| | - Dejin Liang
- Guangdong Tilapia Breeding Farms, Guangzhou, China
| | - Yuli Wu
- Agro-Tech Extension Center of Guangdong Province, Guangzhou, China
| | - Zhiyong Jiang
- Agro-Tech Extension Center of Guangdong Province, Guangzhou, China
| | - Wei Huang
- Guangdong Tilapia Breeding Farms, Guangzhou, China
| | - Liuling Gao
- Guangdong Hanyu Ecological Technology Co., Ltd., Guangzhou, China
| |
Collapse
|
8
|
Zograf JK, Semenchenko AA, Mordukhovich VV. New deep-sea species of Aborjinia (Nematoda, Leptosomatidae) from the North-Western Pacific: an integrative taxonomy and phylogeny. Zookeys 2024; 1189:231-256. [PMID: 38282715 PMCID: PMC10809327 DOI: 10.3897/zookeys.1189.111825] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Accepted: 11/15/2023] [Indexed: 01/30/2024] Open
Abstract
Marimermithid nematodes parasitising invertebrates are mainly found in the deep-sea environments. Several adult and juvenile specimens marimermithids of the genus Aborjinia have been found in bottom sediments and inside Polychaeta during recent cruises to the Kuril-Kamchatka trench and the Kuril Basin (the Sea of Okhotsk). New species are described based on integrative study. Aborjiniaprofundasp. nov. differs from A.eulagiscae by the location of the ventral gland cell bodies (posterior to the nerve ring vs posterior to the cardia), by the smaller body size (23-28 mm vs 103-132 mm) and shorter tail (193-263 µm vs 500-850 µm). BI and ML phylogenetic analyses based on 18S and 28S rDNA suggest that genus Aborjinia belongs to the family Leptosomatidae. Based on molecular and morphological characters the new genus Paraborjiniagen. nov. is proposed for A.corallicola. Within the family Leptosomatidae the new genus differs from all genera except Aborjinia by its endoparasitic lifestyle and hologonic ovaries. Paraborjiniagen. nov. differs from Aborjinia by the position of cephalic sensitive organs (outer labial and cephalic papillae in two separate circles vs outer labial and cephalic papillae in one circle) and by the parasitic adult (vs free-living in Aborjinia).
Collapse
Affiliation(s)
- Julia K. Zograf
- A.V. Zhirmunsky National Scientific Center of Marine Biology, FEB RAS, 690041, Vladivostok, RussiaA.V. Zhirmunsky National Scientific Center of Marine BiologyVladivostokRussia
| | - Alexander A. Semenchenko
- Federal Scientific Center of the East Asia Terrestrial Biodiversity, FEB RAS, 690022, Vladivostok, RussiaFederal Scientific Center of the East Asia Terrestrial BiodiversityVladivostokRussia
| | - Vladimir V. Mordukhovich
- A.V. Zhirmunsky National Scientific Center of Marine Biology, FEB RAS, 690041, Vladivostok, RussiaA.V. Zhirmunsky National Scientific Center of Marine BiologyVladivostokRussia
- Far Eastern Federal University, 690922, Vladivostok, RussiaFar Eastern Federal UniversityVladivostokRussia
| |
Collapse
|
9
|
Xiang YN, Wang XQ, Ding LL, Bai XY, Feng YQ, Qi ZC, Sun YT, Yan XL. Deciphering the Plastomic Code of Chinese Hog-Peanut ( Amphicarpaea edgeworthii Benth., Leguminosae): Comparative Genomics and Evolutionary Insights within the Phaseoleae Tribe. Genes (Basel) 2024; 15:88. [PMID: 38254977 PMCID: PMC10815570 DOI: 10.3390/genes15010088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 01/05/2024] [Accepted: 01/08/2024] [Indexed: 01/24/2024] Open
Abstract
The classification and phylogenetic relationships within the Phaseoleae tribe (Leguminosae) have consistently posed challenges to botanists. This study addresses these taxonomic intricacies, with a specific focus on the Glycininae subtribe, by conducting a comprehensive analysis of the highly conserved plastome in Amphicarpaea edgeworthii Benth., a critical species within this subtribe. Through meticulous genomic sequencing, we identified a plastome size of 148,650 bp, composed of 128 genes, including 84 protein-coding genes, 36 tRNA genes, and 8 rRNA genes. Comparative genomic analysis across seven Glycininae species illuminated a universally conserved circular and quadripartite structure, with nine genes exhibiting notable nucleotide diversity, signifying a remarkable genomic variability. Phylogenetic reconstruction of 35 Phaseoleae species underscores the affinity of Amphicarpaea with Glycine, placing Apios as a sister lineage to all other Phaseoleae species, excluding Clitorinae and Diocleinae subtribes. Intriguingly, Apios, Butea, Erythrina, and Spatholobus, traditionally clumped together in the Erythrininae subtribe, display paraphyletic divergence, thereby contesting their taxonomic coherence. The pronounced structural differences in the quadripartite boundary genes among taxa with unresolved subtribal affiliations demand a reevaluation of Erythrininae's taxonomic classification, potentially refining the phylogenetic contours of the tribe.
Collapse
Affiliation(s)
- Yi-Nan Xiang
- Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, China; (Y.-N.X.); (L.-L.D.); (Y.-Q.F.)
- Eastern China Conservation Centre for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai 201602, China
| | - Xiao-Qun Wang
- Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, China; (Y.-N.X.); (L.-L.D.); (Y.-Q.F.)
| | - Lu-Lu Ding
- Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, China; (Y.-N.X.); (L.-L.D.); (Y.-Q.F.)
| | - Xin-Yu Bai
- Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, China; (Y.-N.X.); (L.-L.D.); (Y.-Q.F.)
| | - Yu-Qing Feng
- Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, China; (Y.-N.X.); (L.-L.D.); (Y.-Q.F.)
| | - Zhe-Chen Qi
- Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, China; (Y.-N.X.); (L.-L.D.); (Y.-Q.F.)
| | - Yong-Tao Sun
- East China Survey and Planning Institute, The National Forestry and Grassland Administration, Hangzhou 310019, China;
| | - Xiao-Ling Yan
- Eastern China Conservation Centre for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai 201602, China
| |
Collapse
|
10
|
Kuczera K, Orłowska A, Smreczak M, Frant M, Trębas P, Rola J. Prevalence of Astroviruses in Different Animal Species in Poland. Viruses 2024; 16:80. [PMID: 38257780 PMCID: PMC10819871 DOI: 10.3390/v16010080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 12/28/2023] [Accepted: 01/01/2024] [Indexed: 01/24/2024] Open
Abstract
Astroviruses (AstVs) are small RNA viruses characterized by a high mutation rate, the ability to recombine, and interspecies transmission, which allows them to infect a multitude of hosts including humans, companion animals, and farmed animals as well as wildlife. AstVs are stable in the environment, and their transmission is usually through the fecal-oral route or via contaminated water and food. Although direct zoonotic transmission was not confirmed, interspecies transmission events have occurred or have been indicated to occur in the past between wild and domestic animals and humans. They cause large economic losses, mainly in the poultry sector, due to gastroenteritis and mortality. In young children, they are the second most common cause of diarrhea. This study involved 166 intestine samples and pools of spleen, lymph node, and kidney samples collected from 352 wild animals, 52 pigs, and 31 companion animals. Astroviruses were detected in the intestine samples and were separately detected in pools of tissue samples prepared for individual animals using a heminested RT-PCR protocol. Amplicons were subjected to Sanger sequencing, and a phylogenetic analysis of 320 nt RNA-dependent RNA polymerase (RdRp) fragments referring to known nt sequences of astroviruses was performed. Astroviral RNA was detected in the intestine samples and/or tissue pools of red foxes (nine positive intestines and six positive tissue pools), rats (two positive intestines and three positive tissue pools), a cat (one AstV detected in an intestine sample), pigs (eight positive tissue pools), and wild boars (two positive pools of spleens, kidneys, and lymph nodes). No astroviral RNA was detected in wild mustelids, dogs, or other small wild animals including rodents. A phylogenetic analysis revealed that the astroviruses detected during this study were mostly host-specific, such as porcine, canine, and rat astroviruses that were highly homologous to the sequences of reference strains. In one of two wild boars, an AstV distinct to porcine species was found with the highest nt identity to Avastroviruses, i.e., turkey astroviruses, which suggests potential cross-species transmission of the virus, as previously described. Here, we present the first detection of astroviruses in the population of wild animals, companion animals, and pigs in Poland, confirming that astroviruses are frequent pathogens circulating in animals in the field. Our study also suggests potential cross-species transmission of Avaastrovirus to wild boars; however, further molecular characterization is needed.
Collapse
Affiliation(s)
- Konrad Kuczera
- Voivodship Veterinary Inspectorate Katowice, ul. Brynowska 25a, 40-585 Katowice, Poland;
| | - Anna Orłowska
- Department of Virology, National Veterinary Research Institute, 24-100 Puławy, Poland; (P.T.); (J.R.)
| | - Marcin Smreczak
- Department of Virology, National Veterinary Research Institute, 24-100 Puławy, Poland; (P.T.); (J.R.)
| | - Maciej Frant
- Department of Swine Diseases, National Veterinary Research Institute, 24-100 Puławy, Poland;
| | - Paweł Trębas
- Department of Virology, National Veterinary Research Institute, 24-100 Puławy, Poland; (P.T.); (J.R.)
| | - Jerzy Rola
- Department of Virology, National Veterinary Research Institute, 24-100 Puławy, Poland; (P.T.); (J.R.)
| |
Collapse
|
11
|
Li J, Du Y, Xie L, Jin X, Zhang Z, Yang M. Comparative plastome genomics and phylogenetic relationships of the genus Trollius. Front Plant Sci 2023; 14:1293091. [PMID: 38046610 PMCID: PMC10690957 DOI: 10.3389/fpls.2023.1293091] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Accepted: 10/31/2023] [Indexed: 12/05/2023]
Abstract
Trollius, a genus in the Ranunculaceae family, has significant medicinal and ornamental value. It is widely distributed in China with 16 different species accepted. However, due to the lack of enough samples and information sites, the molecular phylogenetic relationships of Trollius have been unresolved till now. Here we sequenced, assembled and annotated the plastomes of 16 Trollius species to investigate their genomic characteristics, inverted repeat (IR) boundaries, sequence repeats, and hypervariable loci. In addition, the phylogenetic relationships of this genus was reconstructed based on the whole plastomes and the protein-coding sequences data-sets. The plastomes of Trollius ranged between 159,597 bp and 160,202 bp in length, and contained 113 unique genes, including 79 protein coding, 30 tRNA, and 4 rRNA. The IR boundaries were relatively conserved within the genus Trollius. 959 simple sequence repeats and 657 long sequence repeats were detected in the Trollius plastomes. We identified 12 highly polymorphic loci (Pi > 0.0115) that can be used as plastid markers in molecular identification and phylogenetic investigation of the genus. Besides, Trollius was a monophyletic group with the earliest divergence clade being Trollius lilacinus Bunge, and the remaining species were divided into two strongly-supported clades. The phylogeny in our study supported the traditional classification systems based on the color of sepal, but not the previous classification system based on the types and relative lengths of the nectaries, and distribution. The genomic resources provided in our study can be used in the taxonomy of the genus Trollius, promoting the development and utilization of this genus.
Collapse
Affiliation(s)
- Jiaxin Li
- School of Pharmacy, Baotou Medical College, Baotou, Inner Mongolia, China
| | - Yan Du
- School of Pharmacy, Baotou Medical College, Baotou, Inner Mongolia, China
| | - Lei Xie
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
| | - Xiaohua Jin
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Zhirong Zhang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Meiqing Yang
- School of Pharmacy, Baotou Medical College, Baotou, Inner Mongolia, China
| |
Collapse
|
12
|
Mei Z, Sha Z, Sun S. Going deeper and further: a range and depth extension for the deep-sea feather star Paratelecrinuscubensis (Carpenter, 1881) (Comatulida, Atelecrinidae), first record from the Western Pacific. Zookeys 2023; 1184:103-113. [PMID: 38314329 PMCID: PMC10836655 DOI: 10.3897/zookeys.1184.110577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2023] [Accepted: 10/24/2023] [Indexed: 02/06/2024] Open
Abstract
A specimen belonging to the deep-sea feather-star family Atelecrinidae was collected in April 2018 at the Kocebu Guyot at 1294 m deep. Based on its morphological characters, the specimen was identified as Paratelecrinuscubensis (Carpenter, 1881). This species of feather star is restricted to the deep sea and was known only from 12 records from the Bahamas and Cuba at depths of 567-892 m. The data represent the first record from the Western Pacific Ocean and the deepest record known, extending the depth where this feather star has been found to beyond 1000 m. The morphological characteristics of the Kocebu Guyot specimen were essentially identical to the morphology of the neotype, with a slight difference in the dorsal spine at the end of the cirri. The phylogenetic analysis based on the mitochondrial cytochrome c oxidase subunit I (COI), 16S rRNA genes, 28S rRNA genes, and 18S rRNA genes reveal a close relationship of P.cubensis with P.wyvilli. Results of our molecular phylogenetic analysis are consistent with our morphological identifications. Our find extends the known geographical distribution of the feather star P.cubensis to the Western Pacific Ocean and provide insights into deep-sea biodiversity in the Kocebu Guyot.
Collapse
Affiliation(s)
- Zijie Mei
- Department of Marine Organism Taxonomy and Phylogeny, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
| | - Zhongli Sha
- Department of Marine Organism Taxonomy and Phylogeny, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- Laoshan Laboratory, Qingdao 266237, China
- Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
| | - Shao’e Sun
- Department of Marine Organism Taxonomy and Phylogeny, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- Laoshan Laboratory, Qingdao 266237, China
- Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
| |
Collapse
|
13
|
Yoichi W. The complete chloroplast genome sequence of Swertia japonica (Schult.) Makino (Gentianaceae). Mitochondrial DNA B Resour 2023; 8:1179-1182. [PMID: 38188429 PMCID: PMC10769539 DOI: 10.1080/23802359.2023.2275335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Accepted: 10/19/2023] [Indexed: 01/09/2024] Open
Abstract
Swertia japonica (Schult.) Makino is a traditional medicinal plant in Japan for which the chloroplast genome has not been previously reported. The complete chloroplast genome of S. japonica was determined using a high-throughput sequencing technique. The total length of the S. japonica chloroplast genome was 153,208 bp, and comprised a large single-copy region of 83,319 bp, and a small single-copy region of 18,375 bp, separated by a pair of 25,757 bp inverted repeat regions. A phylogenetic analysis, based on the obtained chloroplast genome, indicated that S. japonica is closely related to S. diluta, S. franchetiana, S. kouitchensis, S. mussotii, and S. punicea. The presented chloroplast genome will be useful for further taxonomic, pharmacological and evolutionary studies of Swertia.
Collapse
Affiliation(s)
- Watanabe Yoichi
- Graduate School of Horticulture, Chiba University, Matsudo, Japan
| |
Collapse
|
14
|
Phan QC, Nagasaki R, Inoue Y, Tsubota H. The complete chloroplast genome of Callicarpa dichotoma (Lour.) K.Koch (Lamiaceae). Mitochondrial DNA B Resour 2023; 8:1174-1178. [PMID: 38188443 PMCID: PMC10769526 DOI: 10.1080/23802359.2023.2275332] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 10/19/2023] [Indexed: 01/09/2024] Open
Abstract
Callicarpa dichotoma (Lour.) K.Koch is a shrub species with distribution from East Asia to Southeast Asia. We assembled and annotated for the first time the complete chloroplast (cp) genome of C. dichotoma. The cp genome of C. dichotoma is 154,110 bp long with the GC content of 38.09% and consists of four subregions: a large single-copy (LSC) region of 84,915 bp, a small single-copy (SSC) region of 17,783 bp and a pair of inverted repeats (IRs) of 25,706 bp each. The cp genome of C. dichotoma encodes a total of 114 unique genes, comprising 80 protein-coding genes, 30 tRNA genes, and four rRNA genes. Phylogenetic trees based on the coding sequences strongly support the position of C. dichotoma within the genus Callicarpa, confirming the previously reported monophyly of the genus.
Collapse
Affiliation(s)
- Quynh Chi Phan
- Graduate School of Integrated Sciences for Life, Hiroshima University, Hiroshima, Japan
| | - Ryohei Nagasaki
- Graduate School of Integrated Sciences for Life, Hiroshima University, Hiroshima, Japan
| | - Yuya Inoue
- Department of Botany, National Museum of Nature and Science, Ibaraki, Japan
- Hattori Botanical Laboratory, Miyazaki, Japan
| | - Hiromi Tsubota
- Graduate School of Integrated Sciences for Life, Hiroshima University, Hiroshima, Japan
- Miyajima Natural Botanical Garden, Green Innovation Division, Seto Inland Sea Carbon Neutral Research Center, Hiroshima University, Hiroshima, Japan
| |
Collapse
|
15
|
Li DM, Liu HL, Pan YG, Yu B, Huang D, Zhu GF. Comparative Chloroplast Genomics of 21 Species in Zingiberales with Implications for Their Phylogenetic Relationships and Molecular Dating. Int J Mol Sci 2023; 24:15031. [PMID: 37834481 PMCID: PMC10648771 DOI: 10.3390/ijms241915031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2023] [Revised: 09/21/2023] [Accepted: 09/22/2023] [Indexed: 10/15/2023] Open
Abstract
Zingiberales includes eight families and more than 2600 species, with many species having important economic and ecological value. However, the backbone phylogenetic relationships of Zingiberales still remain controversial, as demonstrated in previous studies, and molecular dating based on chloroplast genomes has not been comprehensively studied for the whole order. Herein, 22 complete chloroplast genomes from 21 species in Zingiberales were sequenced, assembled, and analyzed. These 22 genomes displayed typical quadripartite structures, which ranged from 161,303 bp to 163,979 bp in length and contained 111-112 different genes. The genome structures, gene contents, simple sequence repeats, long repeats, and codon usage were highly conserved, with slight differences among these genomes. Further comparative analysis of the 111 complete chloroplast genomes of Zingiberales, including 22 newly sequenced ones and the remaining ones from the national center for biotechnology information (NCBI) database, identified three highly divergent regions comprising ccsA, psaC, and psaC-ndhE. Maximum likelihood and Bayesian inference phylogenetic analyses based on chloroplast genome sequences found identical topological structures and identified a strongly supported backbone of phylogenetic relationships. Cannaceae was sister to Marantaceae, forming a clade that was collectively sister to the clade of (Costaceae, Zingiberaceae) with strong support (bootstrap (BS) = 100%, and posterior probability (PP) = 0.99-1.0); Heliconiaceae was sister to the clade of (Lowiaceae, Strelitziaceae), then collectively sister to Musaceae with strong support (BS = 94-100%, and PP = 0.93-1.0); the clade of ((Cannaceae, Marantaceae), (Costaceae, Zingiberaceae)) was sister to the clade of (Musaceae, (Heliconiaceae, (Lowiaceae, Strelitziaceae))) with robust support (BS = 100%, and PP = 1.0). The results of divergence time estimation of Zingiberales indicated that the crown node of Zingiberales occurred approximately 85.0 Mya (95% highest posterior density (HPD) = 81.6-89.3 million years ago (Mya)), with major family-level lineages becoming from 46.8 to 80.5 Mya. These findings proved that chloroplast genomes could contribute to the study of phylogenetic relationships and molecular dating in Zingiberales, as well as provide potential molecular markers for further taxonomic and phylogenetic studies of Zingiberales.
Collapse
Affiliation(s)
- Dong-Mei Li
- Guangdong Provincial Key Lab of Ornamental Plant Germplasm Innovation and Utilization, Environmental Horticulture Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China; (H.-L.L.); (Y.-G.P.); (B.Y.); (D.H.)
| | | | | | | | | | - Gen-Fa Zhu
- Guangdong Provincial Key Lab of Ornamental Plant Germplasm Innovation and Utilization, Environmental Horticulture Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China; (H.-L.L.); (Y.-G.P.); (B.Y.); (D.H.)
| |
Collapse
|
16
|
Pan S, Li X, Zhang L, Zhang Q. The complete chloroplast genome of Scutellaria barbata D. Don 1825 revealed the phylogenetic relationships of the Scutellaria genus. Mitochondrial DNA B Resour 2023; 8:1025-1028. [PMID: 37799449 PMCID: PMC10548842 DOI: 10.1080/23802359.2023.2261564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 09/17/2023] [Indexed: 10/07/2023] Open
Abstract
Scutellaria barbata D. Don 1825 is an important medicinal plant distributed in wetlands about 2000 m above sea level and used to treat various diseases. The complete chloroplast genome of S. barbata is 152,050 bp with four subregions consisting of a large single-copy region (84,053 bp), a small single-copy region (17,517 bp), and a pair of inverted repeats (25,240 bp). In the chloroplast genome of S. barbata, 131 genes were detected, comprising 87 protein-encoding genes, eight ribosomal RNA (rRNA) genes, and 36 transfer RNA (tRNA) genes. Phylogenetic analysis based on the complete chloroplast genome and protein-coding DNA sequences of 27 related taxa of the genus (out group included Holmskioldia sanguinea and Tinnea aethiopica) indicates that S. barbata was made a clade with S. orthocalyx, and S. meehanioides was a sister to them. The first chloroplast genome of S. barbata was reported in this work, serving as a potential reference for important medicinal plants within the Scutellaria genus.
Collapse
Affiliation(s)
- Shouhui Pan
- Guizhou Tobacco Corporation Anshun Company, Anshun, People’s Republic of China
| | - Xiquan Li
- Guizhou Tobacco Corporation Anshun Company, Anshun, People’s Republic of China
| | - Li Zhang
- Guizhou Tobacco Corporation Anshun Company, Anshun, People’s Republic of China
| | - Quan Zhang
- Guizhou Tobacco Corporation Anshun Company, Anshun, People’s Republic of China
| |
Collapse
|
17
|
Atopkin DM, Semenchenko AA, Solodovnik DA, Ivashko YI. A report on the complete mitochondrial genome of the trematode Azygia robusta Odhner, 1911, its new definitive host from the Russian Far East, and unexpected phylogeny of Azygiidae within Digenea, as inferred from mitogenome sequences. J Helminthol 2023; 97:e69. [PMID: 37655787 DOI: 10.1017/s0022149x23000500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
Abstract
New data on the complete mitochondrial genome of Azygia robusta (Azygiidae) were obtained by the next-generation sequencing (NGS) approach. The mitochondrial DNA (mtDNA) of A. robusta had a length of 13 857 bp and included 12 protein-coding genes, two ribosomal genes, 22 transfer RNA genes, and two non-coding regions. The nucleotide sequences of the complete mitochondrial genomes of two A. robusta specimens differed from each other by 0.12 ± 0.03%. Six of 12 protein-coding genes demonstrated intraspecific variation. The difference between the nucleotide sequences of the complete mitochondrial genomes of A. robusta and Azygia hwangtsiyui was 26.95 ± 0.35%; the interspecific variation of protein-coding genes between A. robusta and A. hwangtsiyui ranged from 20.5 ± 0.9% (cox1) to 30.7 ± 1.2% (nad5). The observed gene arrangement in the mtDNA sequence of A. robusta was identical to that of A. hwangtsiyui. Codon usage and amino acid frequencies were highly similar between A. robusta and A. hwangtsiyui. The results of phylogenetic analyses based on mtDNA protein-coding regions showed that A. robusta is closely related to A. hwangtsiyui (belonging to the same suborder, Azygiida) that formed a distinct early-diverging branch relative to all other Digenea. A preliminary morphological analysis of paratypes of the two azygiid specimens studied showed visible morphological differences between them. The specimen extracted from Sakhalin taimen (Parahucho perryi) was most similar to A. robusta. Thus, we here provide the first record of a new definitive host, P. perryi, for A. robusta and also molecular characteristics of the trematode specimens.
Collapse
Affiliation(s)
- D M Atopkin
- Federal Scientific Center of the East Asia Terrestrial Biodiversity, Far Eastern Branch, Russian Academy of Sciences, Vladivostok, Russia
- Department of Cell Biology and Genetics, Far Eastern Federal University, Vladivostok, Russia
| | - A A Semenchenko
- Federal Scientific Center of the East Asia Terrestrial Biodiversity, Far Eastern Branch, Russian Academy of Sciences, Vladivostok, Russia
| | - D A Solodovnik
- Federal Scientific Center of the East Asia Terrestrial Biodiversity, Far Eastern Branch, Russian Academy of Sciences, Vladivostok, Russia
| | - Y I Ivashko
- Federal Scientific Center of the East Asia Terrestrial Biodiversity, Far Eastern Branch, Russian Academy of Sciences, Vladivostok, Russia
| |
Collapse
|
18
|
Li Z, Tian Q, Chong P, Du W, Wei J, Huang R. Phylogenetic Partitioning of Gansu Flora: Unveiling the Core Transitional Zone of Chinese Flora. Plants (Basel) 2023; 12:3060. [PMID: 37687307 PMCID: PMC10490386 DOI: 10.3390/plants12173060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 08/21/2023] [Accepted: 08/23/2023] [Indexed: 09/10/2023]
Abstract
Floristic regions, conventionally established using species distribution patterns, have often overlooked the phylogenetic relationships among taxa. However, how phylogenetic relationships influence the historical interconnections within and among biogeographic regions remains inadequately understood. In this research, we compiled distribution data for seed plants in Gansu, a region of significant biogeographic diversity located in northwestern China.We proposed a novel framework for floristic regions within Gansu, integrating distribution data and phylogenetic relationships of genera-level native seed plants, aiming to explore the relationship between phylogenetic relatedness, taxonomic composition, and regional phylogenetic delineation. We found that (1) phylogenetic relatedness was strongly correlated with the taxonomic composition among floras in Gansu. (2) The southeastern Gansu region showed the lowest level of spatial turnover in both phylogenetic relationships and the taxonomic composition of floristic assemblages across the Gansu region. (3) Null model analyses indicated nonrandom phylogenetic structure across the region, where most areas showed higher phylogenetic turnover than expected given the underlying taxonomic composition between sites. (4) Our results demonstrated a consistent pattern across various regionalization schemes and highlighted the preference for employing the phylogenetic dissimilarity approach in biogeographical regionalization investigations. (5) Employing the phylogenetic dissimilarity approach, we identified nine distinct floristic regions in Gansu that are categorized into two broader geographical units, namely the northwest and southeast. (6) Based on the phylogenetic graphic regions of China across this area.
Collapse
Affiliation(s)
- Zizhen Li
- College of Forestry, Gansu Agricultural University, Lanzhou 730070, China; (Z.L.); (W.D.); (R.H.)
| | - Qing Tian
- College of Forestry, Gansu Agricultural University, Lanzhou 730070, China; (Z.L.); (W.D.); (R.H.)
- Jinchang Municipal People’s Government, Jinchang 737100, China
| | - Peifang Chong
- College of Forestry, Gansu Agricultural University, Lanzhou 730070, China; (Z.L.); (W.D.); (R.H.)
| | - Weibo Du
- College of Forestry, Gansu Agricultural University, Lanzhou 730070, China; (Z.L.); (W.D.); (R.H.)
| | - Jia Wei
- Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100089, China;
| | - Rong Huang
- College of Forestry, Gansu Agricultural University, Lanzhou 730070, China; (Z.L.); (W.D.); (R.H.)
- Lanzhou Institute of Landscape Gardening, Lanzhou 730070, China
| |
Collapse
|
19
|
Lin C, Guo X, Yu X, Li S, Li W, Yu X, An F, Zhao P, Ruan M. Genome-Wide Survey of the RWP-RK Gene Family in Cassava ( Manihot esculenta Crantz) and Functional Analysis. Int J Mol Sci 2023; 24:12925. [PMID: 37629106 PMCID: PMC10454212 DOI: 10.3390/ijms241612925] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 08/12/2023] [Accepted: 08/16/2023] [Indexed: 08/27/2023] Open
Abstract
The plant-specific RWP-RK transcription factor family plays a central role in the regulation of nitrogen response and gametophyte development. However, little information is available regarding the evolutionary relationships and characteristics of the RWP-RK family genes in cassava, an important tropical crop. Herein, 13 RWP-RK proteins identified in cassava were unevenly distributed across 9 of the 18 chromosomes (Chr), and these proteins were divided into two clusters based on their phylogenetic distance. The NLP subfamily contained seven cassava proteins including GAF, RWP-RK, and PB1 domains; the RKD subfamily contained six cassava proteins including the RWP-RK domain. Genes of the NLP subfamily had a longer sequence and more introns than the RKD subfamily. A large number of hormone- and stress-related cis-acting elements were found in the analysis of RWP-RK promoters. Real-time quantitative PCR revealed that all MeNLP1-7 and MeRKD1/3/5 genes responded to different abiotic stressors (water deficit, cold temperature, mannitol, polyethylene glycol, NaCl, and H2O2), hormonal treatments (abscisic acid and methyl jasmonate), and nitrogen starvation. MeNLP3/4/5/6/7 and MeRKD3/5, which can quickly and efficiently respond to different stresses, were found to be important candidate genes for further functional assays in cassava. The MeRKD5 and MeNLP6 proteins were localized to the cell nucleus in tobacco leaf. Five and one candidate proteins interacting with MeRKD5 and MeNLP6, respectively, were screened from the cassava nitrogen starvation library, including agamous-like mads-box protein AGL14, metallothionein 2, Zine finger FYVE domain containing protein, glyceraldehyde-3-phosphate dehydrogenase, E3 Ubiquitin-protein ligase HUWE1, and PPR repeat family protein. These results provided a solid basis to understand abiotic stress responses and signal transduction mediated by RWP-RK genes in cassava.
Collapse
Affiliation(s)
- Chenyu Lin
- School of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China; (C.L.); (X.G.); (X.Y.)
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; (S.L.); (W.L.); (X.Y.)
| | - Xin Guo
- School of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China; (C.L.); (X.G.); (X.Y.)
| | - Xiaohui Yu
- School of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China; (C.L.); (X.G.); (X.Y.)
| | - Shuxia Li
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; (S.L.); (W.L.); (X.Y.)
| | - Wenbin Li
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; (S.L.); (W.L.); (X.Y.)
| | - Xiaoling Yu
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; (S.L.); (W.L.); (X.Y.)
| | - Feng An
- Hainan Danzhou Agro-Ecosystem National Observation and Research Station, Rubber Research Institute of Chinese Academy of Tropical Agricultural Sciences, Danzhou 571737, China;
| | - Pingjuan Zhao
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; (S.L.); (W.L.); (X.Y.)
| | - Mengbin Ruan
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; (S.L.); (W.L.); (X.Y.)
| |
Collapse
|
20
|
Yue M, Chen H, Xuan L, Yang Y, Chong X, Li M, Yu C, Lu X, Zhang F. Novel molecular markers for Taxodium breeding from the chloroplast genomes of four artificial Taxodium hybrids. Front Genet 2023; 14:1193023. [PMID: 37600666 PMCID: PMC10433758 DOI: 10.3389/fgene.2023.1193023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 06/27/2023] [Indexed: 08/22/2023] Open
Abstract
Taxodium "Zhongshanshan" are a group of intraspecific Taxodium hybrids with superparental dominance and high ecological and economic value in southern China. Identifying the parentage of hybrids, especially the male parent, is critically important for genetic studies. However, the large nuclear genomes of members of the genus Taxodium pose a major challenge for the development of molecular markers. Here, we developed novel molecular markers by conducting a comparative analysis of the chloroplast genomes of four artificial Taxodium hybrids and their parents. The lengths of the whole chloroplast genome ranged from 131,942 to 132,128 bp, and the total guanine (GC) content of the chloroplast genomes ranged from 34.6% to 35.81%. A total of 120 unique genes were identified, including 83 protein-coding genes, 33 transfer RNAs, and four ribosomal RNAs. There were 69-71 simple sequence repeats were detected in the four hybrids. Phylogenetic analysis revealed that these hybrids clustered with their paternal parents. Similar findings were obtained by analysis of the GC content of protein-coding genes. Molecular markers were developed using the highly variable regions of the chloroplast genomes, and polymerase chain reaction (PCR) assays revealed that these markers were effective for identifying the male parents of these hybrids. Our findings indicate for the first time that the chloroplast genomes of Taxodium are paternally inherited. Generally, these molecular markers could facilitate breeding and genetic studies of Taxodium.
Collapse
Affiliation(s)
- Minghua Yue
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
- Nanjing Botanical Garden Mem. Sun Yat-Sen, Nanjing, China
| | - Hong Chen
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
| | - Lei Xuan
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Nanjing, China
| | - Ying Yang
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Nanjing, China
| | - Xinran Chong
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
| | - Mingzhi Li
- Guangzhou Bio&Data Technology Co., Ltd., Guangzhou, China
| | - ChaoGuang Yu
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Nanjing, China
| | - Xiaoqing Lu
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
| | - Fan Zhang
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
| |
Collapse
|
21
|
Sun Y, Chen J, Ye Y, Xu K, Li J. Comparison of Mitochondrial Genome Sequences between Two Palaemon Species of the Family Palaemonidae (Decapoda: Caridea): Gene Rearrangement and Phylogenetic Implications. Genes (Basel) 2023; 14:1499. [PMID: 37510403 PMCID: PMC10379425 DOI: 10.3390/genes14071499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2023] [Revised: 07/19/2023] [Accepted: 07/20/2023] [Indexed: 07/30/2023] Open
Abstract
To further understand the origin and evolution of Palaemonidae (Decapoda: Caridea), we determined the mitochondrial genome sequence of Palaemon macrodactylus and Palaemon tenuidactylus. The entire mitochondrial genome sequences of these two Palaemon species encompassed 37 typical genes, including 13 protein-coding genes (PCGs), 2 ribosomal RNA genes (rRNAs), and 22 transfer RNA genes (tRNAs), and a control region (CR). The lengths of their mitochondrial genomes were 15,744 bp (P. macrodactylus) and 15,735 bp (P. tenuidactylus), respectively. We analyzed their genomic features and structural functions. In comparison with the ancestral Decapoda, these two newly sequenced Palaemon species exhibited a translocation event, where the gene order was trnK-trnD instead of trnD-trnK. Based on phylogenetic analysis constructed from 13 PCGs, the 12 families from Caridea can be divided into four major clades. Furthermore, it was revealed that Alpheidae and Palaemonidae formed sister groups, supporting the monophyly of various families within Caridea. These findings highlight the significant gene rearrangements within Palaemonidae and provide valuable evidence for the phylogenetic relationships within Caridea.
Collapse
Affiliation(s)
- Yuman Sun
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan 316022, China
| | - Jian Chen
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan 316022, China
| | - Yingying Ye
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan 316022, China
| | - Kaida Xu
- Key Laboratory of Sustainable Utilization of Technology Research for Fisheries Resources of Zhejiang Province, Scientific Observing and Experimental Station of Fishery Resources for Key Fishing Grounds, Ministry of Agriculture and Rural Affairs of China, Zhejiang Marine Fisheries Research Institute, Zhoushan 316021, China
| | - Jiji Li
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan 316022, China
| |
Collapse
|
22
|
Romanov MN, Abdelmanova AS, Fisinin VI, Gladyr EA, Volkova NA, Anshakov DV, Stanishevskaya OI, Vakhrameev AB, Dotsev AV, Griffin DK, Zinovieva NA. Whole Genome Screening Procures a Holistic Hold of the Russian Chicken Gene Pool Heritage and Demographic History. Biology (Basel) 2023; 12:979. [PMID: 37508409 PMCID: PMC10376169 DOI: 10.3390/biology12070979] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 07/01/2023] [Accepted: 07/08/2023] [Indexed: 07/30/2023]
Abstract
A study for genomic variation that may reflect putative selective signaling and be associated with economically important traits is instrumental for obtaining information about demographic and selection history in domestic animal species and populations. A rich variety of the Russian chicken gene pool breeds warrants a further detailed study. Specifically, their genomic features can derive implications from their genome architecture and selective footprints for their subsequent breeding and practical efficient exploitation. In the present work, whole genome genotyping of 19 chicken breeds (20 populations with up to 71 samples each) was performed using the Chicken 50 K BeadChip DNA chip. The studied breed sample included six native Russian breeds of chickens developed in the 17th-19th centuries, as well as eight Russian chicken breeds, including the Russian White (RW), created in the 20th century on the basis of improving local chickens using breeds of foreign selection. Five specialized foreign breeds of chickens, including the White Leghorn (WL), were used along with other breeds representing the Russian gene pool. The characteristics of the genetic diversity and phylogenetic relationships of the native breeds of chickens were represented in comparison with foreign breeds. It was established that the studied native breeds demonstrate their own genetic structure that distinguishes them from foreign breeds, and from each other. For example, we previously made an assumption on what could cause the differences between two RW populations, RW1 and RW2. From the data obtained here, it was verified that WL was additionally crossed to RW2, unlike RW1. Thus, inherently, RW1 is a purer population of this improved Russian breed. A significant contribution of the gene pool of native breeds to the global genetic diversity of chickens was shown. In general, based on the results of a multilateral survey of this sample of breeds, it can be concluded that phylogenetic relationships based on their genetic structure and variability robustly reflect the known, previously postulated and newly discovered patterns of evolution of native chickens. The results herein presented will aid selection and breeding work using this gene pool.
Collapse
Affiliation(s)
- Michael N Romanov
- L. K. Ernst Federal Research Center for Animal Husbandry, Dubrovitsy, Podolsk 142132, Moscow Oblast, Russia
- School of Biosciences, University of Kent, Canterbury CT2 7NJ, Kent, UK
| | - Alexandra S Abdelmanova
- L. K. Ernst Federal Research Center for Animal Husbandry, Dubrovitsy, Podolsk 142132, Moscow Oblast, Russia
| | - Vladimir I Fisinin
- Center "All-Russian Poultry Research and Technological Institute" of the Russian Academy of Sciences, Sergiev Posad 141311, Moscow Oblast, Russia
| | - Elena A Gladyr
- L. K. Ernst Federal Research Center for Animal Husbandry, Dubrovitsy, Podolsk 142132, Moscow Oblast, Russia
| | - Natalia A Volkova
- L. K. Ernst Federal Research Center for Animal Husbandry, Dubrovitsy, Podolsk 142132, Moscow Oblast, Russia
| | - Dmitry V Anshakov
- Breeding and Genetic Center "Zagorsk Experimental Breeding Farm"-Branch of the Federal Research Centre "All-Russian Poultry Research and Technological Institute" of the Russian Academy of Sciences, Sergiev Posad 141311, Moscow Oblast, Russia
| | - Olga I Stanishevskaya
- Russian Research Institute of Farm Animal Genetics and Breeding-Branch of the L. K. Ernst Federal Research Center for Animal Husbandry, Pushkin, Saint Petersburg 196601, Russia
| | - Anatoly B Vakhrameev
- Russian Research Institute of Farm Animal Genetics and Breeding-Branch of the L. K. Ernst Federal Research Center for Animal Husbandry, Pushkin, Saint Petersburg 196601, Russia
| | - Arsen V Dotsev
- L. K. Ernst Federal Research Center for Animal Husbandry, Dubrovitsy, Podolsk 142132, Moscow Oblast, Russia
| | - Darren K Griffin
- School of Biosciences, University of Kent, Canterbury CT2 7NJ, Kent, UK
| | - Natalia A Zinovieva
- L. K. Ernst Federal Research Center for Animal Husbandry, Dubrovitsy, Podolsk 142132, Moscow Oblast, Russia
| |
Collapse
|
23
|
Castrillo ML, Bich GÁ, Amerio NS, Barengo MP, Zapata PD, Saparrat MCN, Villalba LL. Trichoderma koningiopsis (Hypocreaceae) has the smallest mitogenome of the genus Trichoderma. Front Microbiol 2023; 14:1141087. [PMID: 37383640 PMCID: PMC10294050 DOI: 10.3389/fmicb.2023.1141087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 04/24/2023] [Indexed: 06/30/2023] Open
Abstract
Introduction Fungal mitogenomes exhibit remarkable variation in conformation, size, gene content, arrangement and expression, including their intergenic spacers and introns. Methods The complete mitochondrial genome sequence of the mycoparasitic fungus Trichoderma koningiopsis was determined using the Illumina next-generation sequencing technology. We used data from our recent Illumina NGS-based project of T. koningiopsis genome sequencing to study its mitochondrial genome. The mitogenome was assembled, annotated, and compared with other fungal mitogenomes. Results T. koningiopsis strain POS7 mitogenome is a circular molecule of 27,560 bp long with a GC content of 27.80%. It harbors the whole complement of the 14 conserved mitochondrial protein-coding genes (PCG) such as atp6, atp8, atp9, cox1, cox2, cox3, cob, nad1, nad2, nad3, nad4, nad4L, nad5, and nad6, also found in the same gene order to other Hypocreales. The mitogenome also contains 26 transfer RNA genes (tRNAs), 5 of them with more than one copy. Other genes also present in the assembled mitochondrial genome are a small rRNA subunit and a large rRNA subunit containing ribosomal protein S3 gene. Despite the small genome size, two introns were detected in the T. koningiopsis POS7 mitogenome, one of them in cox3 gene and the other in rnl gene, accounting 7.34% of this mitogenome with a total size of 2,024 bp. A phylogenetic analysis was done using the 14 PCGs genes of T. koningiopsis strain POS7 mitogenome to compare them with those from other fungi of the Subphyla Pezizomycotina and Saccharomycotina. T. koningiopsis strain POS7 was clustered together with other representatives of Trichoderma lineage, within the Hypocreales group, which is also supported by previous phylogenetic studies based on nuclear markers. Discussion The mitochondrial genome of T. koningiopsis POS7 will allow further investigations into the taxonomy, phylogenetics, conservation genetics, and evolutionary biology of this important genus as well as other closely related species.
Collapse
Affiliation(s)
- María Lorena Castrillo
- Laboratorio de Biotecnología Molecular, Instituto de Biotecnología Misiones “Dra. María Ebe Reca”-InBioMis, Universidad Nacional de Misiones, Posadas, Misiones, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Gustavo Ángel Bich
- Laboratorio de Biotecnología Molecular, Instituto de Biotecnología Misiones “Dra. María Ebe Reca”-InBioMis, Universidad Nacional de Misiones, Posadas, Misiones, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Natalia Soledad Amerio
- Laboratorio de Biotecnología Molecular, Instituto de Biotecnología Misiones “Dra. María Ebe Reca”-InBioMis, Universidad Nacional de Misiones, Posadas, Misiones, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Marcela Paola Barengo
- Laboratorio de Biotecnología Molecular, Instituto de Biotecnología Misiones “Dra. María Ebe Reca”-InBioMis, Universidad Nacional de Misiones, Posadas, Misiones, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Pedro Darío Zapata
- Laboratorio de Biotecnología Molecular, Instituto de Biotecnología Misiones “Dra. María Ebe Reca”-InBioMis, Universidad Nacional de Misiones, Posadas, Misiones, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Mario Carlos Nazareno Saparrat
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
- Facultad de Ciencias Agrarias y Forestales, Instituto de Fisiología Vegetal, Universidad Nacional de La Plata, La Plata, Buenos Aires, Argentina
- Facultad de Ciencias Naturales y Museo, Instituto de Botánica Carlos Spegazzini, Universidad Nacional de La Plata, La Plata, Buenos Aires, Argentina
- Cátedra de Microbiología Agrícola, Facultad de Ciencias Agrarias y Forestales, Universidad Nacional de La Plata, La Plata, Buenos Aires, Argentina
| | - Laura Lidia Villalba
- Laboratorio de Biotecnología Molecular, Instituto de Biotecnología Misiones “Dra. María Ebe Reca”-InBioMis, Universidad Nacional de Misiones, Posadas, Misiones, Argentina
| |
Collapse
|
24
|
Yuan Y, Zhang L, Li K, Hong Y, Storey KB, Zhang J, Yu D. Nine Mitochondrial Genomes of Phasmatodea with Two Novel Mitochondrial Gene Rearrangements and Phylogeny. Insects 2023; 14:insects14050485. [PMID: 37233113 DOI: 10.3390/insects14050485] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 05/12/2023] [Accepted: 05/15/2023] [Indexed: 05/27/2023]
Abstract
The classification of stick and leaf insects (Order Phasmatodea) is flawed at various taxonomic ranks due to a lack of robust phylogenetic relationships and convergent morphological characteristics. In this study, we sequenced nine new mitogenomes that ranged from 15,011 bp to 17,761 bp in length. In the mitogenome of Carausis sp., we found a translocation of trnR and trnA, which can be explained by the tandem duplication/random loss (TDRL) model. In the Stheneboea repudiosa Brunner von Wattenwyl, 1907, a novel mitochondrial structure of 12S rRNA-CR1-trnI-CR2-trnQ-trnM was found for the first time in Phasmatodea. Due to the low homology of CR1 and CR2, we hypothesized that trnI was inverted through recombination and then translocated into the middle of the control region. Control region repeats were frequently detected in the newly sequenced mitogenomes. To explore phylogenetic relationships in Phasmatodea, mtPCGs from 56 Phasmatodean species (composed of 9 stick insects from this study, 31 GenBank data, and 16 data derived from transcriptome splicing) were used for Bayesian inference (BI), and maximum likelihood (ML) analyses. Both analyses supported the monophyly of Lonchodinae and Necrosciinae, but Lonchodidae was polyphyletic. Phasmatidae was monophyletic, and Clitumninae was paraphyletic. Phyllidae was located at the base of Neophasmatodea and formed a sister group with the remaining Neophasmatodea. Bacillidae and Pseudophasmatidae were recovered as a sister group. Heteroptergidae was monophyletic, and the Heteropteryginae sister to the clade (Obriminae + Dataminae) was supported by BI analysis and ML analysis.
Collapse
Affiliation(s)
- Yani Yuan
- College of Life Science, Zhejiang Normal University, Jinhua 321004, China
| | - Lihua Zhang
- Taishun County Forestry Bureau, Wenzhou 325500, China
| | - Ke Li
- College of Life Science, Zhejiang Normal University, Jinhua 321004, China
| | - Yuehuan Hong
- College of Life Science, Zhejiang Normal University, Jinhua 321004, China
| | - Kenneth B Storey
- Department of Biology, Carleton University, Ottawa, ON K1S 5B6, Canada
| | - Jiayong Zhang
- College of Life Science, Zhejiang Normal University, Jinhua 321004, China
- Key Lab of Wildlife Biotechnology, Conservation and Utilization of Zhejiang Province, Zhejiang Normal University, Jinhua 321004, China
| | - Danna Yu
- College of Life Science, Zhejiang Normal University, Jinhua 321004, China
- Key Lab of Wildlife Biotechnology, Conservation and Utilization of Zhejiang Province, Zhejiang Normal University, Jinhua 321004, China
| |
Collapse
|
25
|
Guidalevich V, Nagahama N, López AS, Angeli JP, Marchelli P, Azpilicueta MM. Intraspecific phylogeny of a Patagonian fescue: differentiation at molecular markers and morphological traits suggests hybridization at peripheral populations. Ann Bot 2023:7174887. [PMID: 37209108 DOI: 10.1093/aob/mcad060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Indexed: 05/22/2023]
Abstract
BACKGROUND AND AIMS Grasses of the Festuca genus have complex phylogenetic relations due to morphological similarities among species and inter-specific hybridization processes. Within Patagonian fescues, information concerning phylogenetic relationships is very scarce. In Festuca pallescens, a widely distributed species, the high phenotypic variability and the occurrence of interspecific hybridization preclude a clear identification of the populations. Given the relevance of natural rangelands for livestock production and their high degradation due to climate change, conservation actions are needed and knowledge about genetic variation required. METHODS To ravel out the intraspecific phylogenetic relations and to detect genetic differences, we studied 21 populations of the species along its natural geographic distribution by coupling both molecular (ITS and trnL-F markers) and morpho-anatomical analyses. Bayesian inference, maximum likelihood, and maximum parsimony methods were applied to assemble a phylogenetic tree, including other native species. The morphological data set was analysed by discriminant and cluster analyses. KEY RESULTS The combined information of the Bayesian tree (ITS marker), the geographic distribution of haplotype variants (trnL-F marker) and the morpho-anatomical traits, distinguished populations located at the margins of the distribution. Some of the variants detected were shared with other sympatric species of fescues. CONCLUSIONS These results suggest the occurrence of hybridization processes between species of the genus at peripheral sites characterized by suboptimal conditions, which might be key to the survival of these populations.
Collapse
Affiliation(s)
- V Guidalevich
- INTA Bariloche - IFAB (INTA-CONICET), Modesta Victoria 4450, 8400, Bariloche, Argentina
| | - N Nagahama
- EEAf Esquel INTA, Chacabuco 513, 9200, Esquel, Argentina
| | - A S López
- INTA Bariloche - IFAB (INTA-CONICET), Modesta Victoria 4450, 8400, Bariloche, Argentina
| | - J P Angeli
- EEAf Esquel INTA, Chacabuco 513, 9200, Esquel, Argentina
| | - P Marchelli
- INTA Bariloche - IFAB (INTA-CONICET), Modesta Victoria 4450, 8400, Bariloche, Argentina
| | - M M Azpilicueta
- INTA Bariloche - IFAB (INTA-CONICET), Modesta Victoria 4450, 8400, Bariloche, Argentina
| |
Collapse
|
26
|
Chen X, Kuang J, Tao W, Xiong Z, Mao K. A new species of Megastigmus (Hymenoptera, Megastigmidae) from China. Biodivers Data J 2023; 11:e102828. [PMID: 38327380 PMCID: PMC10848687 DOI: 10.3897/bdj.11.e102828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 04/06/2023] [Indexed: 02/09/2024] Open
Abstract
Background Most species of Megastigmus are considered important economic pests that grow in seeds, especially of conifers. Accurate identification of species is a crucial step for the biological research of parasitic pests and the further application of biological control. However, their large variety, small size, similar morphology and different growth and development stages have brought great challenges to taxonomic research. Traditional morphological identification often takes a long time and this requires us to seek a new method for rapid and accurate identification. Therefore, the better identification of Megastigmus urgently needs to be combined with molecular methods to help taxonomic development. New information Here, Megastigmusdaduheensis sp. n. (Chalcidoidea: Megastigmidae) was identified, based on morphology and molecular markers, such as COI and Cytb. M.daduheensis sp. n. is distinct from other known species of the same genus in the morphology. The results of the molecular phylogenetic tree, similarity alignment and genetic distance indicate that the COI and Cytb sequences of M.daduheensis sp. n. are highly similar to M.sobinae and M.duclouxiana, but there are some genetic differences. The genetic distances of M.daduheensis sp. nov. with M.duclouxiana and M.sabinae were 0.34 and 0.33 and the percentages of shared base pairs were 76.3% and 76.8%, respectively. Both morphological and molecular data classified M.daduheensis sp. n. as a new species. The obtained COI and Cytb sequences of M.daduheensis sp. n. can be used as DNA barcodes, providing molecular data for rapid and accurate identification of this species in the future.
Collapse
Affiliation(s)
- Xiaoxiao Chen
- Key Laboratory for Bio-Resource and Eco-Environment of Ministry of Education & Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, College of Life Science, Sichuan University, Chengdu 610065, Sichuan, ChinaKey Laboratory for Bio-Resource and Eco-Environment of Ministry of Education & Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, College of Life Science, Sichuan UniversityChengdu 610065, SichuanChina
| | - Jingge Kuang
- Key Laboratory for Bio-Resource and Eco-Environment of Ministry of Education & Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, College of Life Science, Sichuan University, Chengdu 610065, Sichuan, ChinaKey Laboratory for Bio-Resource and Eco-Environment of Ministry of Education & Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, College of Life Science, Sichuan UniversityChengdu 610065, SichuanChina
| | - Wenjing Tao
- Key Laboratory for Bio-Resource and Eco-Environment of Ministry of Education & Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, College of Life Science, Sichuan University, Chengdu 610065, Sichuan, ChinaKey Laboratory for Bio-Resource and Eco-Environment of Ministry of Education & Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, College of Life Science, Sichuan UniversityChengdu 610065, SichuanChina
| | - Zhongping Xiong
- College of Forests, Southwest Forestry University, Kunming 650224,Yunnan, ChinaCollege of Forests, Southwest Forestry UniversityKunming 650224,YunnanChina
| | - Kangshan Mao
- Key Laboratory for Bio-Resource and Eco-Environment of Ministry of Education & Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, College of Life Science, Sichuan University, Chengdu 610065, Sichuan, ChinaKey Laboratory for Bio-Resource and Eco-Environment of Ministry of Education & Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, College of Life Science, Sichuan UniversityChengdu 610065, SichuanChina
| |
Collapse
|
27
|
Yu J, Chen X, Liu R, Tang Y, Nie G, Zhou C. Mitochondrial genome of Acheilognathusbarbatulus (Cypriniformes, Cyprinidae, Acheilognathinae): characterisation and phylogenetic analysis. Biodivers Data J 2023; 11:e93947. [PMID: 38327321 PMCID: PMC10848848 DOI: 10.3897/bdj.11.e93947] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Accepted: 02/01/2023] [Indexed: 02/23/2023] Open
Abstract
Acheilognathusbarbatulus is distributed in Yangtze River, Yellow River and Pearl River systems in China. Genome data can help to understand the phylogenetic relationships of A.barbatulus, but its complete mitochondrial genome has not been published. We determined the complete mitochondrial genome structure and characteristics of this species and constructed a comprehensive phylogenetic tree, based on mitochondrial genome data of several species of Acheilognathus, Rhodeus and Pseudorasboraparva. The complete length of the mitochondrial genome of A.barbatulus is 16726 bp. The genome is a covalently closed double-stranded circular molecule containing 13 protein-coding genes, two ribosomal RNAs, 22 transfer RNAs, a D-loop and a light strand replication initiation region. The base composition of the complete mitochondrial genome is A (29.33%) > T (27.6%) > C (26.12%) > G (16.95%), showing a strong AT preference and anti-G bias. All 13 PCGs have different degrees of codon preference, except for cytochrome c oxidase 1, which uses GTG as the start codon. All the PCGs use ATG as the start codon and the stop codon is dominated by TAG. The encoded amino acids Leu and Ser exist in two types, whereas the rest are all present as one type, except for tRNASer (GCT), which lacks the D-arm and has an incomplete secondary structure, all other tRNAs can be folded to form a typical cloverleaf secondary structure. Based on the 13 PCG tandems, the Maximum Likelihood and Bayesian trees were constructed, based on the concatenated sequence of 13 PCGs for the genera Acheilognathus and Rhodeus, with Pseudorasboraparva as the outgroup. Acheilognathusbarbatulus, Acheilognathustonkinensis and Acheilognathuscf.macropterus were clustered together and the most closely related. The results of this study enrich the mitochondrial genomic data of Acheilognathus and provide molecular and genetic base information for species conservation, molecular identification and species evolution of Acheilognathinae.
Collapse
Affiliation(s)
- Jinhui Yu
- College of Fisheries, Henan Normal University, Xinxiang, ChinaCollege of Fisheries, Henan Normal UniversityXinxiangChina
| | - Xin Chen
- College of Fisheries, Henan Normal University, Xinxiang, ChinaCollege of Fisheries, Henan Normal UniversityXinxiangChina
| | - Ruyao Liu
- College of Fisheries, Henan Normal University, Xinxiang, ChinaCollege of Fisheries, Henan Normal UniversityXinxiangChina
| | - Yongtao Tang
- College of Fisheries, Henan Normal University, Xinxiang, ChinaCollege of Fisheries, Henan Normal UniversityXinxiangChina
| | - Guoxing Nie
- College of Fisheries, Henan Normal University, Xinxiang, ChinaCollege of Fisheries, Henan Normal UniversityXinxiangChina
| | - Chuanjiang Zhou
- College of Life sciences, Henan Normal University, Xinxiang City, ChinaCollege of Life sciences, Henan Normal UniversityXinxiang CityChina
| |
Collapse
|
28
|
Li S, Chai S, Yu L, Zhang T, Liu Z, Lei Y, Chen K, Zhang H, Liu Y, Chen P. Genetic diversity of 23 STR loci of the Guizhou Tujia ethnic minority and the phylogenetic relationships with 22 other populations. Ann Hum Biol 2023; 50:345-350. [PMID: 37431941 DOI: 10.1080/03014460.2023.2224971] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/12/2023]
Abstract
BACKGROUND Short tandem repeats (STR) are highly polymorphic DNA markers utilised in forensic personal identification and human population genetic research. Guizhou Tujia is one of the ancient minority groups in southwest China, however, the population has not been studied using the highly discriminating 23 STR Huaxia Platinum Kit. AIM To obtain genetic data from 23 autosomal STRs in Guizhou Tujia and examine the population's relationship with others. SUBJECTS AND METHODS A total of 480 individuals from the Guizhou Tujia population were analysed using 23 STR loci of Huaxia Platinum Kit. Allele frequencies and forensic parameters were estimated. Population genetic relationships were calculated by Nei's genetic distances and visualised using a variety of biostatistical methods. RESULTS A total of 264 alleles were found, with allelic frequencies ranging from 0.0010 to 0.5104. The combined discrimination power (CDP) and the combined probability of paternity (CPE) of 23 STR loci were 0.9999999999999999999999999996 and 0.999999999710422, respectively. Guizhou Tujia showed closer genetic relationships with Hubei Tujia, Guizhou Gelao, and Guizhou Miao than with other populations. CONCLUSION We first obtained the population genetic data of Guizhou Tujia using the 23 STR system and demonstrated its value in forensic applications. Comprehensive population comparisons showed an evident genetic affinity pattern between populations that are geographically, ethnically and linguistically related.
Collapse
Affiliation(s)
- Shuhua Li
- Key Laboratory of Cell Engineering of Guizhou Province, Clinical Stem Cell Research Institute, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou, P.R. China
- Collaborative Innovation Center of Chinese Ministry of Education, Zunyi Medical University, Zunyi, Guizhou, P.R. China
- Center of Forensic Expertise, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou, P.R. China
| | - Siyu Chai
- Key Laboratory of Cell Engineering of Guizhou Province, Clinical Stem Cell Research Institute, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou, P.R. China
- Collaborative Innovation Center of Chinese Ministry of Education, Zunyi Medical University, Zunyi, Guizhou, P.R. China
- Center of Forensic Expertise, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou, P.R. China
| | - Limei Yu
- Key Laboratory of Cell Engineering of Guizhou Province, Clinical Stem Cell Research Institute, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou, P.R. China
- Collaborative Innovation Center of Chinese Ministry of Education, Zunyi Medical University, Zunyi, Guizhou, P.R. China
| | - Tao Zhang
- Key Laboratory of Cell Engineering of Guizhou Province, Clinical Stem Cell Research Institute, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou, P.R. China
- Collaborative Innovation Center of Chinese Ministry of Education, Zunyi Medical University, Zunyi, Guizhou, P.R. China
| | - Zulin Liu
- Key Laboratory of Cell Engineering of Guizhou Province, Clinical Stem Cell Research Institute, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou, P.R. China
- Collaborative Innovation Center of Chinese Ministry of Education, Zunyi Medical University, Zunyi, Guizhou, P.R. China
| | - Yinlei Lei
- Key Laboratory of Cell Engineering of Guizhou Province, Clinical Stem Cell Research Institute, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou, P.R. China
- Collaborative Innovation Center of Chinese Ministry of Education, Zunyi Medical University, Zunyi, Guizhou, P.R. China
- Center of Forensic Expertise, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou, P.R. China
| | - Kaiqin Chen
- Key Laboratory of Cell Engineering of Guizhou Province, Clinical Stem Cell Research Institute, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou, P.R. China
- Collaborative Innovation Center of Chinese Ministry of Education, Zunyi Medical University, Zunyi, Guizhou, P.R. China
- Center of Forensic Expertise, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou, P.R. China
| | - Hao Zhang
- Key Laboratory of Cell Engineering of Guizhou Province, Clinical Stem Cell Research Institute, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou, P.R. China
- Collaborative Innovation Center of Chinese Ministry of Education, Zunyi Medical University, Zunyi, Guizhou, P.R. China
- Center of Forensic Expertise, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou, P.R. China
| | - YanFei Liu
- Key Laboratory of Cell Engineering of Guizhou Province, Clinical Stem Cell Research Institute, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou, P.R. China
- Collaborative Innovation Center of Chinese Ministry of Education, Zunyi Medical University, Zunyi, Guizhou, P.R. China
| | - Pengyu Chen
- Key Laboratory of Cell Engineering of Guizhou Province, Clinical Stem Cell Research Institute, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou, P.R. China
- Collaborative Innovation Center of Chinese Ministry of Education, Zunyi Medical University, Zunyi, Guizhou, P.R. China
- Center of Forensic Expertise, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou, P.R. China
| |
Collapse
|
29
|
Inoue Y, Nakahara-Tsubota M, Ogiso-Tanaka E, Tsubota H. Complete chloroplast and mitochondrial genomes of Ditrichum rhynchostegium Kindb. (Ditrichaceae, Bryophyta). Mitochondrial DNA B Resour 2023; 8:383-388. [PMID: 36926643 PMCID: PMC10013369 DOI: 10.1080/23802359.2023.2185465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/10/2023] Open
Abstract
The moss family Pottiaceae is one of the most diverse lineages of the subclass Dicranidae (haplolepideous mosses). Nevertheless, the phylogenetic relationships of Pottiaceae with other Dicranidae families remain unclear. To better understand the ancestral genomic structure and evolution of the Pottiaceae, herein, we present the chloroplast and mitochondrial genomes of Ditrichum rhynchostegium (Ditrichaceae, Bryophyta). The chloroplast genome is 124,628 bp long and displayed a circular structure composed of a large single-copy region, a small single-copy region, and a pair of inverted repeats. It has 118 genes, including 82 protein-coding genes, 32 tRNA genes, and four rRNA genes. The mitochondrial genome is 106,246 bp long and has a circular structure. It contains 67 genes, including 40 protein-coding genes, 24 tRNA genes, and three rRNA genes. Phylogenetic trees based on the coding sequences strongly support the sister relationship of D. rhynchostegium with all Pottiaceous accessions, and the dextrosely arranged operculum cells suggest its affinity for Pottiaceae. This study also demonstrates that long-read sequencing employing the Nanopore platform facilitates the repair of unassembled or misassembled organellar genomic regions.
Collapse
Affiliation(s)
- Yuya Inoue
- Department of Botany, National Museum of Nature and Science, Ibaraki, Japan.,Hattori Botanical Laboratory, Miyazaki, Japan
| | | | - Eri Ogiso-Tanaka
- Center for Molecular Biodiversity Research, National Museum of Nature and Science, Ibaraki, Japan
| | - Hiromi Tsubota
- Miyajima Natural Botanical Garden, Graduate School of Integrated Sciences for Life, Hiroshima University, Hiroshima, Japan
| |
Collapse
|
30
|
Xie Y, Wang L, Chen Y, Wang Z, Zhu P, Hu Z, Han X, Wang Z, Zhou X, Zuo Z. The Complete Mitogenome of Toxocara vitulorum: Novel In-Sights into the Phylogenetics in Toxocaridae. Animals (Basel) 2022; 12. [PMID: 36552470 DOI: 10.3390/ani12243546] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 12/09/2022] [Accepted: 12/13/2022] [Indexed: 12/23/2022] Open
Abstract
Toxocara vitulorum (Ascaridida: Nematoda) is one of the most common intestinal nematodes of cattle and buffalos and, therefore, represents a serious threat to their populations worldwide. Despite its significance in veterinary health the epidemiology, population genetics, and molecular ecology of this nematode remain poorly understood. The mitogenome can yield a foundation for studying these areas and assist in the surveillance and control of T. vitulorum. Herein, the first whole mitogenome of T. vitulorum was sequenced utilizing Illumina technology and characterized with bioinformatic pipeline analyses. The entire genome of T. vitulorum was 15,045 bp in length and contained 12 protein-coding genes (PCGs), 22 transfer RNAs (tRNAs), and two ribosomal RNAs (rRNAs). The gene arrangement (GA) of T. vitulorum was similar to those of other Toxocara species under GA3. The whole genome showed significant levels of AT and GC skew. Comparative mitogenomics including sequence identities, Ka/Ks, and sliding window analysis, indicated a purifying selection of 12 PCGs with cox1 and nad6 having the lowest and highest evolutionary rate, respectively. Whole amino acid sequence-based phylogenetic analysis supported a novel sister-species relationship of T. vitulorum with the congeneric species Toxocara canis, Toxocara cati, and Toxocara malaysiensis in the family Toxocaridae. Further, 12 (PCGs) single gene-based phylogenies suggested that nad4 and nad6 genes shared same topological trees with that of the whole genome, suggesting that these genes were suitable as novel genetic markers for phylogenetic and evolutionary studies of Ascaridida species. This complete mitogenome of T. vitulorum refined phylogenetic relationships in Toxocaridae and provided the resource of markers for population genetics, systematics, and epidemiology of this bovine nematode.
Collapse
|
31
|
Scholz T, Kuchta R. Fish tapeworms (Cestoda) in the molecular era: achievements, gaps and prospects. Parasitology 2022; 149:1876-1893. [PMID: 36004800 PMCID: PMC11010522 DOI: 10.1017/s0031182022001202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 08/11/2022] [Accepted: 08/15/2022] [Indexed: 12/29/2022]
Abstract
The tapeworms of fishes (Chondrichthyes and Actinopterygii) account one-third (1670 from around 5000) of the total tapeworm (Platyhelminthes: Cestoda) species diversity. In total 1186 species from 9 orders occur as adults in elasmobranchs (sharks, rays and chimaeras), and 484 species from 8 orders mature in ray-finned fishes (referred to here as teleosts). Teleost tapeworms are dominated by freshwater species (78%), but only 3% of elasmobranch tapeworms are known from freshwater rays of South America and Asia (Borneo). In the last 2 decades, vast progress has been made in understanding species diversity, host associations and interrelationships among fish tapeworms. In total, 172 new species have been described since 2017 (149 from elasmobranchs and 23 from teleosts; invalidly described taxa are not included, especially those from the Oriental region). Molecular data, however, largely limited to a few molecular markers (mainly 28S rDNA, but also 18S and cox1), are available for about 40% of fish tapeworm species. They allowed us to significantly improve our understanding of their interrelationships, including proposals of a new, more natural classification at the higher-taxonomy level (orders and families) as well as at the lower-taxonomy level (genera). In this review, we summarize the main advances and provide perspectives for future research.
Collapse
Affiliation(s)
- Tomáš Scholz
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Branišovská 31, 370 05 České Budějovice, Czech Republic
| | - Roman Kuchta
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Branišovská 31, 370 05 České Budějovice, Czech Republic
| |
Collapse
|
32
|
Liu Y, Zhang Z, Fang K, Shan Q, He L, Dai X, Zou X, Liu F. Genome-Wide Analysis of the MYB-Related Transcription Factor Family in Pepper and Functional Studies of CaMYB37 Involvement in Capsaicin Biosynthesis. Int J Mol Sci 2022; 23:ijms231911667. [PMID: 36232967 PMCID: PMC9569548 DOI: 10.3390/ijms231911667] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 09/22/2022] [Accepted: 09/28/2022] [Indexed: 11/05/2022] Open
Abstract
Chili pepper is an important economic vegetable worldwide. MYB family gene members play an important role in the metabolic processes in plant growth and development. In this study, 103 pepper MYB-related members were identified and grouped into nine subfamilies according to phylogenetic relationships. Additionally, a total of 80, 20, and 37 collinear gene pairs were identified between pepper and tomato, pepper and Arabidopsis, and tomato and Arabidopsis, respectively. We performed promoter cis-element analysis and showed that CaMYB-related members may be involved in multiple biological processes such as growth and development, secondary metabolism, and circadian rhythm regulation. Expression pattern analysis indicated that CaMYB37 is significantly more enriched in fruit placenta, suggesting that this gene may be involved in capsaicin biosynthesis. Through VIGS, we confirmed that CaMYB37 is critical for the biosynthesis of capsaicin in placenta. Our subcellular localization studies revealed that CaMYB37 localized in the nucleus. On the basis of yeast one-hybrid and dual-luciferase reporter assays, we found that CaMYB37 directly binds to the promoter of capsaicin biosynthesis gene AT3 and activates its transcription, thereby regulating capsaicin biosynthesis. In summary, we systematically identified members of the CaMYB-related family, predicted their possible biological functions, and revealed that CaMYB37 is critical for the transcriptional regulation of capsaicin biosynthesis. This work provides a foundation for further studies of the CaMYB-related family in pepper growth and development.
Collapse
Affiliation(s)
- Yi Liu
- Longping Branch, Graduate School of Hunan University, Changsha 410125, China
- Key Laboratory for Vegetable Biology of Hunan Province, Engineering Research Center for Germplasm Innovation and New Varieties Breeding of Horticultural Crops, College of Horticulture, Hunan Agricultural University, Changsha 410125, China
| | - Zhishuo Zhang
- Longping Branch, Graduate School of Hunan University, Changsha 410125, China
- Key Laboratory for Vegetable Biology of Hunan Province, Engineering Research Center for Germplasm Innovation and New Varieties Breeding of Horticultural Crops, College of Horticulture, Hunan Agricultural University, Changsha 410125, China
| | - Ke Fang
- Key Laboratory for Vegetable Biology of Hunan Province, Engineering Research Center for Germplasm Innovation and New Varieties Breeding of Horticultural Crops, College of Horticulture, Hunan Agricultural University, Changsha 410125, China
| | - Qingyun Shan
- Key Laboratory for Vegetable Biology of Hunan Province, Engineering Research Center for Germplasm Innovation and New Varieties Breeding of Horticultural Crops, College of Horticulture, Hunan Agricultural University, Changsha 410125, China
| | - Lun He
- Key Laboratory for Vegetable Biology of Hunan Province, Engineering Research Center for Germplasm Innovation and New Varieties Breeding of Horticultural Crops, College of Horticulture, Hunan Agricultural University, Changsha 410125, China
| | - Xiongze Dai
- Key Laboratory for Vegetable Biology of Hunan Province, Engineering Research Center for Germplasm Innovation and New Varieties Breeding of Horticultural Crops, College of Horticulture, Hunan Agricultural University, Changsha 410125, China
| | - Xuexiao Zou
- Longping Branch, Graduate School of Hunan University, Changsha 410125, China
- Key Laboratory for Vegetable Biology of Hunan Province, Engineering Research Center for Germplasm Innovation and New Varieties Breeding of Horticultural Crops, College of Horticulture, Hunan Agricultural University, Changsha 410125, China
- Correspondence: (X.Z.); (F.L.)
| | - Feng Liu
- Longping Branch, Graduate School of Hunan University, Changsha 410125, China
- Key Laboratory for Vegetable Biology of Hunan Province, Engineering Research Center for Germplasm Innovation and New Varieties Breeding of Horticultural Crops, College of Horticulture, Hunan Agricultural University, Changsha 410125, China
- Correspondence: (X.Z.); (F.L.)
| |
Collapse
|
33
|
Fang H, Wang P, Ye F, Li J, Zhang M, Wang C, Liao W. Genome-Wide Identification and Characterization of the Calmodulin-Binding Transcription Activator (CAMTA) Gene Family in Plants and the Expression Pattern Analysis of CAMTA3/SR1 in Tomato under Abiotic Stress. Int J Mol Sci 2022; 23:6264. [PMID: 35682943 DOI: 10.3390/ijms23116264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 05/28/2022] [Accepted: 05/31/2022] [Indexed: 12/03/2022] Open
Abstract
Calmodulin-binding transcription activator (CAMTA) plays an important regulatory role in plant growth, development, and stress response. This study identified the phylogenetic relationships of the CAMTA family in 42 plant species using a genome-wide search approach. Subsequently, the evolutionary relationships, gene structures, and conservative structural domain of CAMTA3/SR1 in different plants were analyzed. Meanwhile, in the promoter region, the cis-acting elements, protein clustering interaction, and tissue-specific expression of CAMTA3/SR1 in tomato were identified. The results show that SlCAMTA3/SR1 genes possess numerous cis-acting elements related to hormones, light response, and stress in the promoter regions. SlCAMTA3 might act together with other Ca2+ signaling components to regulate Ca2+-related biological processes. Then, the expression pattern of SlCAMTA3/SR1 was also investigated by quantitative real-time PCR (qRT-PCR) analysis. The results show that SlCAMTA3/SR1 might respond positively to various abiotic stresses, especially Cd stress. The expression of SlCAMTA3/SR1 was scarcely detected in tomato leaf at the seedling and flowering stages, whereas SlCAMTA3/SR1 was highly expressed in the root at the seedling stage. In addition, SlCAMTA3/SR1 had the highest expression levels in flowers at the reproductive stage. Here, we provide a basic reference for further studies about the functions of CAMTA3/SR1 proteins in plants.
Collapse
|
34
|
Fernández CJ, García BA. Variation in the Mitochondrial Genome of the Chagas Disease Vector Triatoma infestans (Hemiptera: Reduviidae). Neotrop Entomol 2022; 51:483-492. [PMID: 35360894 DOI: 10.1007/s13744-022-00953-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Accepted: 03/03/2022] [Indexed: 06/14/2023]
Abstract
Chagas' disease is transmitted mainly by members of the subfamily Triatominae (Hemiptera: Reduviidae). Among them, Triatoma infestans (Klug) is the main vector of the disease in Southern Cone of Latin America. In order to contribute to knowledge of the genetic variation between triatomine vectors, in the present study, we analyzed the intraspecific and interspecific variations of the seven mitogenomes available from Triatominae. In addition, in order to examine their evolutionary relationships with others species of Reduviidae and to estimate the divergence time of the main lineages, we constructed phylogenetic trees including mitogenome sequences of 30 species from Reduviidae. Comparative analysis between mitochondrial DNA sequences from two specimens of T. infestans revealed a total of 54 variable sites. Triatoma infestans, Triatoma dimidiata (Latreille), Triatoma rubrofasciata (De Geer), Triatoma migrans (Breddin), Rhodnius pictipes (Stål), and Panstrongylus rufotuberculatus (Champion) present similar mitogenome organization and the length differences observed among these species are primarily caused by variations in control region (CR) and intergenic spacers (IGS). The relative synonymous codon usage values (RSCU) were similar in the six species of Triatominae, and in agreement with the observed in other insects, a biased use of A and C nucleotides in the majority strand was detected. The monophyly of five subfamilies was strongly supported (Phymatinae, Peiratinae, Triatominae, Stenopodainae, and Harpactorinae), while the sampled species of Reduviinae were grouped with one specie from the Salyavatinae subfamily. The oldest subfamily is Phymatinae at 100.3 Mya (99.6-102.2 Mya) and the youngest is Triatominae and Stenopodainae at 52.6 Mya (42.5-63.7 Mya). The estimated diversification time for the Triatominae subfamily agrees with the Andean uplift geological event. An analysis with more mitogenomes from more Triatominae species would be necessary to provide sufficient evidence to support this finding.
Collapse
Affiliation(s)
- Cintia Judith Fernández
- Cátedra de Bioquímica y Biología Molecular, Facultad de Ciencias Médicas, Univ. Nacional de Córdoba, Córdoba, Argentina
| | - Beatriz Alicia García
- Cátedra de Bioquímica y Biología Molecular, Facultad de Ciencias Médicas, Univ. Nacional de Córdoba, Córdoba, Argentina.
- Instituto de Investigaciones en Ciencias de la Salud (INICSA), Consejo Nacional de Investigaciones Científicas y Técnicas, Univ. Nacional de Córdoba (CONICET-UNC), Córdoba, Argentina.
| |
Collapse
|
35
|
Dong Z, Qu S, Landrein S, Yu WB, Xin J, Zhao W, Song Y, Tan Y, Xin P. Increasing Taxa Sampling Provides New Insights on the Phylogenetic Relationship Between Eriobotrya and Rhaphiolepis. Front Genet 2022; 13:831206. [PMID: 35368713 PMCID: PMC8964991 DOI: 10.3389/fgene.2022.831206] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 02/28/2022] [Indexed: 11/13/2022] Open
Abstract
Eriobotrya (Rosaceae) is an economically important genus with around 30 species. It is widely distributed in tropical and warm temperate regions of Asia, with most of its species in China, Myanmar, and Vietnam. However, Eriobotrya is often confused with the smaller genus Rhaphiolepis, and the phylogenetic relationships between the two genera are controversial. Here we present phylogenetic analyses of 38 newly generated Eriobotrya and Rhaphiolepis nrDNA together with 16 sequences of nrDNA and 28 sequences of ITS obtained from GenBank, representing 28 species of Eriobotrya and 12 species of Rhaphiolepis, in order to reconstruct highly supported relationships for the two genera. Contrary to previous research based on limited sampling, our results highlight the monophyly of Eriobotrya as well as Rhaphiolepis. The topology recovered here is consistent with key morphological synapomorphies such as the persistent sepals in Eriobotrya. Our findings show that increased sampling of taxa can provide a more robust phylogeny through reducing phylogenetic error and increasing overall phylogenetic accuracy.
Collapse
Affiliation(s)
- Zhanghong Dong
- Southwest Research Center for Landscape Architecture Engineering, National Forestry and Grassland Administration, Southwest Forestry University, Kunming, China
| | - Shaohong Qu
- Southwest Research Center for Landscape Architecture Engineering, National Forestry and Grassland Administration, Southwest Forestry University, Kunming, China
| | - Sven Landrein
- Center for Integrative Conservation and Horticulture Department, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, China
| | - Wen-Bin Yu
- Center for Integrative Conservation and Horticulture Department, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, China
| | - Jing Xin
- Southwest Research Center for Landscape Architecture Engineering, National Forestry and Grassland Administration, Southwest Forestry University, Kunming, China
| | - Wenzhi Zhao
- Southwest Research Center for Landscape Architecture Engineering, National Forestry and Grassland Administration, Southwest Forestry University, Kunming, China
| | - Yu Song
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Ministry of Education), Guangxi Normal University, Guilin, China
| | - Yunhong Tan
- Center for Integrative Conservation and Horticulture Department, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, China.,Southeast Asia Biodiversity Research Institute, Chinese Academy of Sciences, Yezin, Myanmar
| | - Peiyao Xin
- Southwest Research Center for Landscape Architecture Engineering, National Forestry and Grassland Administration, Southwest Forestry University, Kunming, China
| |
Collapse
|
36
|
Ruang-areerate P, Yoocha T, Kongkachana W, Phetchawang P, Maknual C, Meepol W, Jiumjamrassil D, Pootakham W, Tangphatsornruang S. Comparative Analysis and Phylogenetic Relationships of Ceriops Species (Rhizophoraceae) and Avicennia lanata (Acanthaceae): Insight into the Chloroplast Genome Evolution between Middle and Seaward Zones of Mangrove Forests. Biology (Basel) 2022; 11:biology11030383. [PMID: 35336757 PMCID: PMC8945693 DOI: 10.3390/biology11030383] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Revised: 02/19/2022] [Accepted: 02/24/2022] [Indexed: 02/04/2023]
Abstract
Ceriops and Avicennia are true mangroves in the middle and seaward zones of mangrove forests, respectively. The chloroplast genomes of Ceriops decandra, Ceriops zippeliana, and Ceriops tagal were assembled into lengths of 166,650, 166,083 and 164,432 bp, respectively, whereas Avicennia lanata was 148,264 bp in length. The gene content and gene order are highly conserved among these species. The chloroplast genome contains 125 genes in A. lanata and 129 genes in Ceriops species. Three duplicate genes (rpl2, rpl23, and trnM-CAU) were found in the IR regions of the three Ceriops species, resulting in expansion of the IR regions. The rpl32 gene was lost in C. zippeliana, whereas the infA gene was present in A. lanata. Short repeats (<40 bp) and a lower number of SSRs were found in A. lanata but not in Ceriops species. The phylogenetic analysis supports that all Ceriops species are clustered in Rhizophoraceae and A. lanata is in Acanthaceae. In a search for genes under selective pressures of coastal environments, the rps7 gene was under positive selection compared with non-mangrove species. Finally, two specific primer sets were developed for species identification of the three Ceriops species. Thus, this finding provides insightful genetic information for evolutionary relationships and molecular markers in Ceriops and Avicennia species.
Collapse
Affiliation(s)
- Panthita Ruang-areerate
- National Omics Center, National Science and Technology Development Agency (NSTDA), Pathum Thani 12120, Thailand; (P.R.-a.); (T.Y.); (W.K.); (P.P.)
| | - Thippawan Yoocha
- National Omics Center, National Science and Technology Development Agency (NSTDA), Pathum Thani 12120, Thailand; (P.R.-a.); (T.Y.); (W.K.); (P.P.)
| | - Wasitthee Kongkachana
- National Omics Center, National Science and Technology Development Agency (NSTDA), Pathum Thani 12120, Thailand; (P.R.-a.); (T.Y.); (W.K.); (P.P.)
| | - Phakamas Phetchawang
- National Omics Center, National Science and Technology Development Agency (NSTDA), Pathum Thani 12120, Thailand; (P.R.-a.); (T.Y.); (W.K.); (P.P.)
| | - Chatree Maknual
- Department of Marine and Coastal Resources, 120 The Government Complex, Chaengwatthana Rd., Thung Song Hong, Bangkok 10210, Thailand;
| | - Wijarn Meepol
- Department of Marine and Coastal Resources, Ranong Mangrove Forest Research Center, Tambon Ngao, Muang District, Ranong 85000, Thailand;
| | - Darunee Jiumjamrassil
- Marine and Coastal Resources Office 5, 199/6 Khanom, Khanom, Nakhon Si Thammarat 80210, Thailand;
| | - Wirulda Pootakham
- National Omics Center, National Science and Technology Development Agency (NSTDA), Pathum Thani 12120, Thailand; (P.R.-a.); (T.Y.); (W.K.); (P.P.)
- Correspondence: (W.P.); (S.T.)
| | - Sithichoke Tangphatsornruang
- National Omics Center, National Science and Technology Development Agency (NSTDA), Pathum Thani 12120, Thailand; (P.R.-a.); (T.Y.); (W.K.); (P.P.)
- Correspondence: (W.P.); (S.T.)
| |
Collapse
|
37
|
Dmitrieva E, Sanna D, Vodiasova E, Prokhorova D, Casu M, Burreddu C, Piras MC, Garippa G, Merella P. Morphological and genetic variability of the cryptic Gyrodactylus sphinx and Gyrodactylus gerasevi n. sp. (Platyhelminthes: Monogenea) from the Mediterranean Sea and Black Sea: two new members of the cross-ocean distributed Gyrodactylus orecchiae species group. J Helminthol 2022; 96:e9. [PMID: 35115061 DOI: 10.1017/S0022149X21000778] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Gyrodactylus sphinx Dmitrieva & Gerasev, 2000 is the only species of Gyrodactylus originally described from Aidablennius sphynx (Valenciennes) in the Black Sea. In the present study, monogeneans similar to G. sphinx are reported from the same host and from two other species of Blenniidae from the Black Sea, as well as from the Mediterranean Sea. This study aims to verify the taxonomic status of the specimens found in different hosts and localities, other than the type ones of G. sphinx. Twenty-two measurements of the haptoral structures of 169 gyrodactylids were used for the morphological study. Morphometric variability between different samples was analysed using analysis of variance, multivariate analysis of variance (MANOVA) and principal component analysis (PCA). Molecular studies were carried out using the nuclear internal transcribed spacer 2 and 5.8S ribosomal DNA regions. Network, Bayesian phylogenetic and species delimitation analyses were performed to infer the number of taxonomic units and the phylogeographic relationships occurring within and among them. MANOVA revealed a significant dependence of the morphometry of hamuli and marginal hooks on host species and regions, but a clear differentiation between samples was not confirmed by PCA. Moreover, the ranges of all dimensions overlapped between samples. However, molecular analyses suggested the occurrence of at least two taxonomic entities. The most common entity was present in individuals of the Black and Mediterranean seas, and is described here as Gyrodactylus gerasevi n. sp., whereas a second entity recognized as a G. sphinx was found only in individuals from two localities off Crimea. The monophyletic cluster grouping of these two species was placed within a large clade that also included a separate sister cluster with seven other species of the Gyrodactylus orecchiae cross-ocean species group.
Collapse
|
38
|
Gani M, Rovie-Ryan JJ, Sitam FT, Kulaimi NAM, Zheng CC, Atiqah AN, Rahim NMA, Mohammed AA. Taxonomic and genetic assessment of captive White-Handed Gibbons ( Hylobateslar) in Peninsular Malaysia with implications towards conservation translocation and reintroduction programmes. Zookeys 2022; 1076:25-41. [PMID: 34975272 PMCID: PMC8674214 DOI: 10.3897/zookeys.1076.73262] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 10/25/2021] [Indexed: 11/29/2022] Open
Abstract
Conservation translocation and reintroduction for the purpose of repopulating and reinforcing extirpated or depleted populations has been recognised as an important conservation tool, particularly for gibbon conservation in the immediate future. Feasibility assessments involving multiple factors, including taxonomic and genetic assessment of rescued and captive gibbons, are imperative prior to translocation and reintroduction programmes. In this study, we attempt to determine the subspecies and origin of captive Hylobateslar, White-handed gibbons, from Peninsular Malaysia to assist in future translocation and reintroduction programmes. A total of 12 captive and rescued H.lar samples were analysed using the control region segment of mitochondrial DNA. Sequence analyses and phylogenetic trees constructed using neighbour-joining, maximum likelihood, Bayesian inference, and network methods congruently differentiate all 12 captive individuals used in this study from other H.lar subspecies suggesting that these individuals belong to the H.larlar subspecies. In addition, two populations of H.l.lar were observed: (1) a southern population consisting of all 12 individuals from Peninsular Malaysia, and (2) a possible northern population represented by three individuals (from previous studies), which might have originated from the region between the Isthmus of Kra, Surat Thani-Krabi depression, and Kangar-Pattani. Our findings suggest that the complete control region segment can be used to determine the subspecies and origin of captive H.lar.
Collapse
Affiliation(s)
- Millawati Gani
- National Wildlife Forensic Laboratory, Ex-Situ Conservation Division, Department of Wildlife and National Parks, KM 10 Jalan Cheras, 56100 Kuala Lumpur, Malaysia Department of Wildlife and National Parks Cheras Malaysia
| | - Jeffrine J Rovie-Ryan
- National Wildlife Forensic Laboratory, Ex-Situ Conservation Division, Department of Wildlife and National Parks, KM 10 Jalan Cheras, 56100 Kuala Lumpur, Malaysia Department of Wildlife and National Parks Cheras Malaysia
| | - Frankie Thomas Sitam
- National Wildlife Forensic Laboratory, Ex-Situ Conservation Division, Department of Wildlife and National Parks, KM 10 Jalan Cheras, 56100 Kuala Lumpur, Malaysia Department of Wildlife and National Parks Cheras Malaysia
| | - Noor Azleen Mohd Kulaimi
- National Wildlife Forensic Laboratory, Ex-Situ Conservation Division, Department of Wildlife and National Parks, KM 10 Jalan Cheras, 56100 Kuala Lumpur, Malaysia Department of Wildlife and National Parks Cheras Malaysia
| | - Chew Cheah Zheng
- National Wildlife Forensic Laboratory, Ex-Situ Conservation Division, Department of Wildlife and National Parks, KM 10 Jalan Cheras, 56100 Kuala Lumpur, Malaysia Department of Wildlife and National Parks Cheras Malaysia.,Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 UKM, Bangi Selangor, Malaysia Universiti Kebangsaan Malaysia Bangi Malaysia
| | - Aida Nur Atiqah
- National Wildlife Forensic Laboratory, Ex-Situ Conservation Division, Department of Wildlife and National Parks, KM 10 Jalan Cheras, 56100 Kuala Lumpur, Malaysia Department of Wildlife and National Parks Cheras Malaysia.,Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 UKM, Bangi Selangor, Malaysia Universiti Kebangsaan Malaysia Bangi Malaysia
| | - Nur Maisarah Abd Rahim
- National Wildlife Forensic Laboratory, Ex-Situ Conservation Division, Department of Wildlife and National Parks, KM 10 Jalan Cheras, 56100 Kuala Lumpur, Malaysia Department of Wildlife and National Parks Cheras Malaysia.,Faculty of Science, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia Universiti Putra Malaysia Serdang Malaysia
| | - Ahmad Azhar Mohammed
- National Wildlife Forensic Laboratory, Ex-Situ Conservation Division, Department of Wildlife and National Parks, KM 10 Jalan Cheras, 56100 Kuala Lumpur, Malaysia Department of Wildlife and National Parks Cheras Malaysia
| |
Collapse
|
39
|
Wang J, Fu CN, Mo ZQ, Möller M, Yang JB, Zhang ZR, Li DZ, Gao LM. Testing the Complete Plastome for Species Discrimination, Cryptic Species Discovery and Phylogenetic Resolution in Cephalotaxus (Cephalotaxaceae). Front Plant Sci 2022; 13:768810. [PMID: 35599857 PMCID: PMC9116380 DOI: 10.3389/fpls.2022.768810] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 03/07/2022] [Indexed: 05/17/2023]
Abstract
Species of Cephalotaxus have great economic and ecological values. However, the taxonomy and interspecific phylogenetic relationships within the genus have been controversial and remained not fully resolved until now. To date, no study examined the efficiency of the complete plastome as super-barcode across Cephalotaxus species with multiple samples per taxon. In this study, we have evaluated the complete plastome in species discrimination and phylogenetic resolution in Cephalotaxus by including 32 individuals of all eight recognized species and five varieties following Farjon's classification (2010) with multiple samples per taxon. Our results indicated that not all species recognized in recent taxonomic revisions of Cephalotaxus could be distinguished and not all were monophyletic. Based on the plastome phylogeny, a new taxonomic classification for the genus comprising nine species and two varieties, including a cryptic species, was proposed. The phylogeny also resolved all interspecific relationships. Compared to the plastome based classification, standard DNA barcodes, alone or in combination, only recognized a maximum of seven out of the nine species. Moreover, two highly variable single loci, ycf1 and rps16, each alone achieved full species discrimination. With the moderate length of 1079 bp, rps16 is proposed as a specific barcode to discriminate Cephalotaxus species. The super-barcodes and specific barcode candidates will aid in the identification of endangered Cephalotaxus species, and to help focus conservation measures.
Collapse
Affiliation(s)
- Jie Wang
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Chao-Nan Fu
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Zhi-Qiong Mo
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Michael Möller
- Royal Botanic Garden Edinburgh, Edinburgh, United Kingdom
| | - Jun-Bo Yang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Zhi-Rong Zhang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - De-Zhu Li
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Lian-Ming Gao
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- Lijiang Forest Biodiversity National Observation and Research Station, Kunming Institute of Botany, Chinese Academy of Sciences, Lijiang, China
- *Correspondence: Lian-Ming Gao,
| |
Collapse
|
40
|
Somboon P, Phanitchakun T, Saingamsook J, Namgay R, Harbach RE. Culex (Culex) longitubus, A New Species of the Mimeticus Subgroup (Diptera: Culicidae) From Bhutan. J Med Entomol 2021; 58:2196-2205. [PMID: 33982746 DOI: 10.1093/jme/tjab080] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Indexed: 06/12/2023]
Abstract
Culex longitubus Somboon, Namgay & Harbach is described as a new species of the Mimeticus Subgroup of the subgenus Culex. The larva is most similar to the larva of Cx. tianpingensis Chen from China, but is distinguished by the length of the siphon and the anal papillae, the form of the comb scales and pecten spines, and the development of setae 7-P, 13-T, 1-X, and 4-X. The adults have wing markings and male genitalia similar to those of species of the Mimeticus Complex. Phylogenetic analysis of COI sequences revealed that the new species is closely related to Cx. murrelli Lien of the Mimulus Complex. The immature stages of the new species were found in stagnant pools and marshes at high altitudes in several districts of Bhutan.
Collapse
Affiliation(s)
- Pradya Somboon
- Center of Insect Vector Study, Department of Parasitology, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200,Thailand
| | - Thanari Phanitchakun
- Center of Insect Vector Study, Department of Parasitology, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200,Thailand
| | - Jassada Saingamsook
- Center of Insect Vector Study, Department of Parasitology, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200,Thailand
| | - Rinzin Namgay
- Vector-Borne Disease Control Programme, Ministry of Health, Gelephu 31101,Bhutan
| | - Ralph E Harbach
- Department of Life Sciences, Natural History Museum, Cromwell Road, London SW7 5BD,UK
| |
Collapse
|
41
|
Fitzner A, Kwit E, Niedbalski W, Bigoraj E, Kęsy A, Rzeżutka A. Phylogenetic Analysis of European Brown Hare Syndrome Virus Strains from Poland (1992-2004). Viruses 2021; 13:1999. [PMID: 34696431 DOI: 10.3390/v13101999] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 09/19/2021] [Accepted: 09/27/2021] [Indexed: 11/25/2022] Open
Abstract
European brown hare syndrome (EBHS) is lethal to several species of free-living hares worldwide. The genetic characterization of its virus (EBHSV) strains in European circulation and epidemiological knowledge of EBHSV infections is not yet complete. The study determined the nucleotide sequences of the genomes of EBHSV strains from Poland and analyzed their genetic and phylogenetic relationships to a group of hare lagoviruses. The genome of five virus strains detected in Poland between 1992 and 2004 was obtained by RT-PCR and sequencing of the obtained amplicons. The genetic relationships of the EBHSV strains were analyzed using the full genome and VP60 gene sequences. Additionally, the amino acid sequence of the VP60 gene was analyzed to identify mutations specific to recognized EBHSV subgroups. Partial amplification of the virus open reading frame (ORF)1 and ORF2 regions obtained nearly complete nucleotide genome sequences of the EBHSV strains. Phylogenetic analysis placed them in a GII.1 cluster with other European strains related to nonpathogenic hare caliciviruses. VP60 gene analysis allocated these EBHSV strains to the G1.2, G2.2–2.3 or G3 virus genetic groups. The amino acid sequence differences in the entire genome ranged from 1.1 to 2.6%. Compared to a reference French EBHSV-GD strain, 22 variable amino acid sites were identified in the VP60 region of the Polish strains, but only six were in VP10. Single amino acid changes appeared in different sequence positions among Polish and other European virus strains from different genetic groups, as well as in VP10 sequences of nonpathogenic hare caliciviruses. The results of the study showed a high genetic homogeneity of EBHSV strains from Poland despite their different location occurrence and initial detection times. These strains are also phylogenetically closely related to other EBHSV strains circulating in Europe, likely confirming the slow evolutionary dynamics of this lagovirus species.
Collapse
|
42
|
Kretschmer R, Franz I, de Souza MS, Garnero ADV, Gunski RJ, de Oliveira EHC, O’Connor RE, Griffin DK, de Freitas TRO. Cytogenetic Evidence Clarifies the Phylogeny of the Family Rhynchocyclidae (Aves: Passeriformes). Cells 2021; 10:2650. [PMID: 34685630 PMCID: PMC8534115 DOI: 10.3390/cells10102650] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 09/27/2021] [Accepted: 09/30/2021] [Indexed: 11/16/2022] Open
Abstract
The phylogenetic position and taxonomic status of Rhynchocyclidae (Aves: Passeriformes) have been the subject of debate since their first description. In most models, Rhynchocyclidae represents a subfamily-level taxon placed within the Tyrant Flycatchers (Tyrannidae). Considering that this classification does not include cytotaxonomic characters, we tested the hypothesis that the chromosome organization of Rhynchocyclidae members differs from that of Tyrannidae. Hence, we selected two species, Tolmomyias sulphurescens, and Pitangus sulphuratus, representing Rhynchocyclidae and Tyrannidae, respectively. Results revealed a diploid number (2n) of 60 in T. sulphurescens and 2n = 80 in P. sulphuratus, indicating significant chromosomal differences. Chromosome mapping of Gallus gallus (GGA) and Taeniopygia guttata bacterial artificial chromosome (BAC) corresponding to chromosomes GGA1-28 (except 16) revealed that the genome evolution of T. sulphurescens involved extensive chromosome fusions of macrochromosomes and microchromosomes. On the other hand, P. sulphuratus retained the ancestral pattern of organization of macrochromosomes (except the centric fission involving GGA1) and microchromosomes. In conclusion, comparing our results with previous studies in Tyrant Flycatchers and allies indicates that P. sulphuratus has similar karyotypes to other Tyrannidae members. However, T. sulphurescens does not resemble the Tyrannidae family, reinforcing family status to the clade named Rhynchocyclidae.
Collapse
Affiliation(s)
- Rafael Kretschmer
- School of Biosciences, University of Kent, Canterbury CT2 7NJ, UK; (R.K.); (R.E.O.)
- Laboratório de Citogenética e Evolução, Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre 91509-900, RS, Brazil;
| | - Ismael Franz
- Departamento de Zoologia, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre 91509-900, RS, Brazil;
| | - Marcelo Santos de Souza
- Laboratório de Diversidade Genética Animal, Universidade Federal do Pampa, São Gabriel 97300-162, RS, Brazil; (M.S.d.S.); (A.D.V.G.); (R.J.G.)
| | - Analía Del Valle Garnero
- Laboratório de Diversidade Genética Animal, Universidade Federal do Pampa, São Gabriel 97300-162, RS, Brazil; (M.S.d.S.); (A.D.V.G.); (R.J.G.)
| | - Ricardo José Gunski
- Laboratório de Diversidade Genética Animal, Universidade Federal do Pampa, São Gabriel 97300-162, RS, Brazil; (M.S.d.S.); (A.D.V.G.); (R.J.G.)
| | - Edivaldo Herculano Corrêa de Oliveira
- Instituto de Ciências Exatas e Naturais, Universidade Federal do Pará, Belém 66075-110, PA, Brazil;
- Laboratório de Cultura de Tecidos e Citogenética, SAMAM, Instituto Evandro Chagas, Ananindeua 67030-000, PA, Brazil
| | - Rebecca E. O’Connor
- School of Biosciences, University of Kent, Canterbury CT2 7NJ, UK; (R.K.); (R.E.O.)
| | - Darren K. Griffin
- School of Biosciences, University of Kent, Canterbury CT2 7NJ, UK; (R.K.); (R.E.O.)
| | - Thales Renato Ochotorena de Freitas
- Laboratório de Citogenética e Evolução, Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre 91509-900, RS, Brazil;
| |
Collapse
|
43
|
Abstract
Caylusea hexagyna and Ochradenus baccatus are two species in the Resedaceae family. In this study, we analysed the complete plastid genomes of these two species using high-throughput sequencing technology and compared their genomic data. The length of the plastid genome of C. hexagyna was 154,390 bp while that of O. baccatus was 153,380 bp. The lengths of the inverted repeats (IR) regions were 26,526 bp and 26,558 bp, those of the large single copy (LSC) regions were 83,870 bp and 83,023 bp; and those of the small single copy (SSC) regions were 17,468 bp and 17,241 bp in C. hexagyna and O. baccatus, respectively. Both genomes consisted of 113 genes: 79 protein-coding genes, 30 tRNA genes and 4 rRNA genes. Repeat analysis showed that the plastid genome included all types of repeats, with more frequent occurrences of palindromic sequences. Comparative studies of SSR markers showed that there were 256 markers in C. hexagyna and 255 in O. baccatus; the majority of the SSRs in these plastid genomes were mononucleotide repeats (A/T). All the clusters in the phylogenetic tree had high support. This study reported the first complete plastid genomes of the genera Caylusea and Ochradenus and the first for the Resedaceae family.
Collapse
Affiliation(s)
- Dhafer Alzahrani
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Enas Albokhari
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Biological Sciences, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Abidina Abba
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Biological Sciences, Federal University Lokoja, Lokoja, Kogi State, Nigeria
| | - Samaila Yaradua
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
- Centre for Biodiversity and Conservation, Department of Biology, Umaru Musa Yaradua University, Katsina, Nigeria
| |
Collapse
|
44
|
Izrailskaia AV, Besprozvannykh VV, Tatonova YV. Echinostoma chankensis nom. nov., other Echinostoma spp. and Isthmiophora hortensis in East Asia: morphology, molecular data and phylogeny within Echinostomatidae. Parasitology 2021; 148:1366-1382. [PMID: 34103113 PMCID: PMC11010142 DOI: 10.1017/s0031182021000950] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 06/01/2021] [Accepted: 06/01/2021] [Indexed: 11/06/2022]
Abstract
Life cycles, and morphological and molecular data were obtained for Echinostoma chankensis nom. nov., Echinostoma cinetorchis, Echinostoma miyagawai and Isthmiophora hortensis from East Asia. It was established that, based on both life cycle and morphology data, one of the trematodes is identical to the worms designated as Euparyphium amurensis. Genetic data showed that this trematode belongs to Echinostoma. The complex data on biological, morphological and genetic characterizations establish that the distribution of the morphologically similar species, I. hortensis and Isthmiophora melis, in the Old World are limited by the East Asian and European regions, respectively. Data on mature worms of East Asian E. miyagawai revealed morphological and genetic identity with E. miyagawai from Europe. However, E. miyagawai from Europe differs from E. miyagawai from the type locality (East Asia) in terms of reaching maturity and the morphology of cercariae. These data indicate that the European worm, designated E. miyagawai, does not belong to this species. An analysis of the phylogenetic relationships of Echinostomatidae was conducted based on the 28S, ITS2 and nad1 markers. Analysis using the nad1 gene for the known representatives of Echinostomatidae is carried out for the first time, showing that nuclear markers are ineffective separate from mitochondrial ones.
Collapse
Affiliation(s)
- Anna V. Izrailskaia
- Federal Scientific Center of the East Asia Terrestrial Biodiversity, Far Eastern Branch, Russian Academy of Sciences, 100-letiya Street, 159, Vladivostok, 690022, Russian Federation
- Far Eastern Federal University, School of Biomedicine, Sukhanova, 8, Vladivostok, 690091, Russian Federation
| | - Vladimir V. Besprozvannykh
- Federal Scientific Center of the East Asia Terrestrial Biodiversity, Far Eastern Branch, Russian Academy of Sciences, 100-letiya Street, 159, Vladivostok, 690022, Russian Federation
| | - Yulia V. Tatonova
- Federal Scientific Center of the East Asia Terrestrial Biodiversity, Far Eastern Branch, Russian Academy of Sciences, 100-letiya Street, 159, Vladivostok, 690022, Russian Federation
- Far Eastern Federal University, School of Biomedicine, Sukhanova, 8, Vladivostok, 690091, Russian Federation
| |
Collapse
|
45
|
Xu KK, Chen QP, Ayivi SPG, Guan JY, Storey KB, Yu DN, Zhang JY. Three Complete Mitochondrial Genomes of Orestes guangxiensis, Peruphasma schultei, and Phryganistria guangxiensis (Insecta: Phasmatodea) and Their Phylogeny. Insects 2021; 12:779. [PMID: 34564219 PMCID: PMC8471129 DOI: 10.3390/insects12090779] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 08/26/2021] [Accepted: 08/28/2021] [Indexed: 01/21/2023]
Abstract
Insects of the order Phasmatodea are mainly distributed in the tropics and subtropics and are best known for their remarkable camouflage as plants. In this study, we sequenced three complete mitochondrial genomes from three different families: Orestes guangxiensis, Peruphasma schultei, and Phryganistria guangxiensis. The lengths of the three mitochondrial genomes were 15,896 bp, 16,869 bp, and 17,005 bp, respectively, and the gene composition and structure of the three stick insects were identical to those of the most recent common ancestor of insects. The phylogenetic relationships among stick insects have been chaotic for a long time. In order to discuss the intra- and inter-ordinal relationship of Phasmatodea, we used the 13 protein-coding genes (PCGs) of 85 species for maximum likelihood (ML) and Bayesian inference (BI) analyses. Results showed that the internal topological structure of Phasmatodea had a few differences in both ML and BI trees and long-branch attraction (LBA) appeared between Embioptera and Zoraptera, which led to a non-monophyletic Phasmatodea. Consequently, after removal of the Embioptera and Zoraptera species, we re-performed ML and BI analyses with the remaining 81 species, which showed identical topology except for the position of Tectarchus ovobessus (Phasmatodea). We recovered the monophyly of Phasmatodea and the sister-group relationship between Phasmatodea and Mantophasmatodea. Our analyses also recovered the monophyly of Heteropterygidae and the paraphyly of Diapheromeridae, Phasmatidae, Lonchodidae, Lonchodinae, and Clitumninae. In this study, Peruphasma schultei (Pseudophasmatidae), Phraortes sp. YW-2014 (Lonchodidae), and species of Diapheromeridae clustered into the clade of Phasmatidae. Within Heteropterygidae, O. guangxiensis was the sister clade to O. mouhotii belonging to Dataminae, and the relationship of (Heteropteryginae + (Dataminae + Obriminae)) was recovered.
Collapse
Affiliation(s)
- Ke-Ke Xu
- College of Chemistry and Life Science, Zhejiang Normal University, Jinhua 321004, China; (K.-K.X.); (Q.-P.C.); (S.P.G.A.); (J.-Y.G.); (D.-N.Y.)
| | - Qing-Ping Chen
- College of Chemistry and Life Science, Zhejiang Normal University, Jinhua 321004, China; (K.-K.X.); (Q.-P.C.); (S.P.G.A.); (J.-Y.G.); (D.-N.Y.)
| | - Sam Pedro Galilee Ayivi
- College of Chemistry and Life Science, Zhejiang Normal University, Jinhua 321004, China; (K.-K.X.); (Q.-P.C.); (S.P.G.A.); (J.-Y.G.); (D.-N.Y.)
| | - Jia-Yin Guan
- College of Chemistry and Life Science, Zhejiang Normal University, Jinhua 321004, China; (K.-K.X.); (Q.-P.C.); (S.P.G.A.); (J.-Y.G.); (D.-N.Y.)
| | - Kenneth B. Storey
- Department of Biology, Carleton University, Ottawa, ON K1S 5B6, Canada;
| | - Dan-Na Yu
- College of Chemistry and Life Science, Zhejiang Normal University, Jinhua 321004, China; (K.-K.X.); (Q.-P.C.); (S.P.G.A.); (J.-Y.G.); (D.-N.Y.)
- Key Lab of Wildlife Biotechnology, Conservation and Utilization of Zhejiang Province, Zhejiang Normal University, Jinhua 321004, China
| | - Jia-Yong Zhang
- College of Chemistry and Life Science, Zhejiang Normal University, Jinhua 321004, China; (K.-K.X.); (Q.-P.C.); (S.P.G.A.); (J.-Y.G.); (D.-N.Y.)
- Key Lab of Wildlife Biotechnology, Conservation and Utilization of Zhejiang Province, Zhejiang Normal University, Jinhua 321004, China
| |
Collapse
|
46
|
Abstract
Since 1817, cholera, caused by Vibrio cholerae, has been characterized by seven distinct pandemics. The ongoing seventh pandemic (7P) began in 1961. In this study, we developed a Multilevel Genome Typing (MGT) tool for classifying the V. cholerae species with a focus on the 7P. MGT is based on multilocus sequence typing (MLST), but the concept has been expanded to include a series of MLST schemes that compare population structure from broad to fine resolutions. The V. cholerae MGT consists of eight levels, with the lowest, MGT1, composed of 7 loci and the highest, MGT8, consisting of the 7P core genome (3,759 loci). We used MGT to analyze 5,771 V. cholerae genomes. The genetic relationships revealed by lower MGT levels recapitulated previous findings of large-scale 7P transmission across the globe. Furthermore, the higher MGT levels provided an increased discriminatory power to differentiate subgroups within a national outbreak. Additionally, we demonstrated the usefulness of MGT for non-7P classification. In a large non-7P MGT1 type, MGT2 and MGT3 described continental and regional distributions, respectively. Finally, MGT described trends of 7P in virulence, and MGT2 to MGT3 sequence types (STs) grouped isolates of the same ctxB, tcpA, and ctxB-tcpA genotypes and characterized their trends over the pandemic. MGT offers a range of resolutions for typing V. cholerae. The MGT nomenclature is stable, transferable, and directly comparable between investigations. The MGT database (https://mgtdb.unsw.edu.au/) can accept and process newly submitted samples. MGT allows tracking of existing and new isolates and will be useful for understanding future spread of cholera. IMPORTANCE In 2017, the World Health Organization launched the “Ending Cholera” initiative to reduce cholera-related deaths by 90% by 2030. This strategy emphasized the importance of the speed and accessibility of newer technologies to contain outbreaks. Here, we present a new tool named Multilevel Genome Typing (MGT), which classifies isolates of the cholera-causing agent, Vibrio cholerae. MGT is a freely available online database that groups genetically similar V. cholerae isolates to quickly indicate the origins of outbreaks. We validated the MGT database retrospectively in an outbreak setting, showcasing rapid confirmation of the Nepalese origins for the 2010 Haiti outbreak. In the past 5 years, thousands of V. cholerae genomes have been submitted to the NCBI database, which underscores the importance of and need for proper genome data classification for cholera epidemiology. The V. cholerae MGT database can assist in early decision making that directly impacts controlling both the local and global spread of cholera.
Collapse
|
47
|
Caputi L, Osca D, Ceruso M, Venuti I, Sepe RM, Anastasio A, D'Aniello S, Crocetta F, Pepe T, Sordino P. The complete mitochondrial genome of the white seabream Diplodus sargus (Perciformes: Sparidae) from the Tyrrhenian sea. Mitochondrial DNA B Resour 2021; 6:2581-2583. [PMID: 34409152 PMCID: PMC8366610 DOI: 10.1080/23802359.2021.1915209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The white seabream Diplodus sargus (Linnaeus, 1758) is a species of interest for commercial fisheries throughout its range of distribution and it is also reared using aquaculture techniques. Herein, we present the first complete sequence and annotation of the mitochondrial genome of this species. The D. sargus mitogenome is 16,515 base pairs in length and contains 13 protein-coding genes, 2 rRNA, 22 tRNA, and 2 non-coding regions (D-loop and L-origin). The overall nucleotide composition is: 27.3% A, 28.9% C, 26.8% T, and 17.0% G. Maximum likelihood analyses placed D. sargus as a sister species of Diplodus puntazzo. This study provides valuable information for further studying identification methods and evolutionary relationships of Sparidae species.
Collapse
Affiliation(s)
- Luigi Caputi
- Biology and Evolution of Marine Organisms, Naples, Italy
| | - David Osca
- Integrative Marine Ecology, Naples, Italy
| | - Marina Ceruso
- Department of Veterinary Medicine and Animal Production, University 'Federico II', Naples, Italy
| | - Iolanda Venuti
- Department of Veterinary Medicine and Animal Production, University 'Federico II', Naples, Italy
| | | | - Aniello Anastasio
- Department of Veterinary Medicine and Animal Production, University 'Federico II', Naples, Italy
| | | | | | - Tiziana Pepe
- Department of Veterinary Medicine and Animal Production, University 'Federico II', Naples, Italy
| | - Paolo Sordino
- Biology and Evolution of Marine Organisms, Naples, Italy.,Biology and Evolution of Marine Organisms, Sicily Marine Centre, Messina, Italy
| |
Collapse
|
48
|
Li J, Zhou J, Chen S, Shen H, Peng Y, Zhang K, Huang W, Liang X, Liu B, Zhang C. Characterization of the complete mitogenome of Gammarus lacustris (G.O. Sars, 1863) (Amphipoda: Gammaridae) and its phylogenetic position within Amphipoda. Mitochondrial DNA B Resour 2021; 6:2501-2502. [PMID: 34377806 PMCID: PMC8330746 DOI: 10.1080/23802359.2021.1958083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Gammarus lacustris is native to the Qinghai-Tibet Plateau (QTP), widely distributed in alpine lakes. The complete mitochondrial DNA sequence of G. lacustris was 15,349 base pairs in length and comprised 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes, and 1 control region. The BI tree showed that G. lacustris was most closely related to Gammarus duebeni, and indicated that Gammarus, Gmelinoides, Brachyuropus, Pallaseopsis, and Eulimnogammarus evolved from a common ancestor. The mitogenome of G. lacustris provides new molecular data for further taxonomic and phylogenetic studies of Amphipoda.
Collapse
Affiliation(s)
- Jiasheng Li
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan, China
| | - Jianshe Zhou
- Institute of Fisheries Science, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, P. R. China
| | - Shiyi Chen
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan, China
| | - Haodi Shen
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan, China
| | - Ying Peng
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan, China
| | - Kun Zhang
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan, China
| | - Wenhua Huang
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan, China
| | - Xudong Liang
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan, China
| | - Bingjian Liu
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan, China
| | - Chi Zhang
- Institute of Fisheries Science, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, P. R. China
| |
Collapse
|
49
|
Alves-Barroco C, Caço J, Roma-Rodrigues C, Fernandes AR, Bexiga R, Oliveira M, Chambel L, Tenreiro R, Mato R, Santos-Sanches I. New Insights on Streptococcus dysgalactiae subsp. dysgalactiae Isolates. Front Microbiol 2021; 12:686413. [PMID: 34335512 PMCID: PMC8319831 DOI: 10.3389/fmicb.2021.686413] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 06/15/2021] [Indexed: 12/14/2022] Open
Abstract
Streptococcus dysgalactiae subsp. dysgalactiae (SDSD) has been considered a strict animal pathogen. Nevertheless, the recent reports of human infections suggest a niche expansion for this subspecies, which may be a consequence of the virulence gene acquisition that increases its pathogenicity. Previous studies reported the presence of virulence genes of Streptococcus pyogenes phages among bovine SDSD (collected in 2002-2003); however, the identity of these mobile genetic elements remains to be clarified. Thus, this study aimed to characterize the SDSD isolates collected in 2011-2013 and compare them with SDSD isolates collected in 2002-2003 and pyogenic streptococcus genomes available at the National Center for Biotechnology Information (NCBI) database, including human SDSD and S. dysgalactiae subsp. equisimilis (SDSE) strains to track temporal shifts on bovine SDSD genotypes. The very close genetic relationships between humans SDSD and SDSE were evident from the analysis of housekeeping genes, while bovine SDSD isolates seem more divergent. The results showed that all bovine SDSD harbor Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/Cas IIA system. The widespread presence of this system among bovine SDSD isolates, high conservation of repeat sequences, and the polymorphism observed in spacer can be considered indicators of the system activity. Overall, comparative analysis shows that bovine SDSD isolates carry speK, speC, speL, speM, spd1, and sdn virulence genes of S. pyogenes prophages. Our data suggest that these genes are maintained over time and seem to be exclusively a property of bovine SDSD strains. Although the bovine SDSD genomes characterized in the present study were not sequenced, the data set, including the high homology of superantigens (SAgs) genes between bovine SDSD and S. pyogenes strains, may indicate that events of horizontal genetic transfer occurred before habitat separation. All bovine SDSD isolates were negative for genes of operon encoding streptolysin S, except for sagA gene, while the presence of this operon was detected in all SDSE and human SDSD strains. The data set of this study suggests that the separation between the subspecies "dysgalactiae" and "equisimilis" should be reconsidered. However, a study including the most comprehensive collection of strains from different environments would be required for definitive conclusions regarding the two taxa.
Collapse
Affiliation(s)
- Cinthia Alves-Barroco
- UCIBIO, Departamento de Ciências da Vida, NOVA School of Science and Technology/FCT NOVA, Universidade NOVA de Lisboa, Caparica, Portugal
| | - João Caço
- UCIBIO, Departamento de Ciências da Vida, NOVA School of Science and Technology/FCT NOVA, Universidade NOVA de Lisboa, Caparica, Portugal
| | - Catarina Roma-Rodrigues
- UCIBIO, Departamento de Ciências da Vida, NOVA School of Science and Technology/FCT NOVA, Universidade NOVA de Lisboa, Caparica, Portugal
| | - Alexandra R Fernandes
- UCIBIO, Departamento de Ciências da Vida, NOVA School of Science and Technology/FCT NOVA, Universidade NOVA de Lisboa, Caparica, Portugal
| | - Ricardo Bexiga
- Centro de Investigação Interdisciplinar em Sanidade Animal, Faculdade de Medicina Veterinária, Universidade de Lisboa, Lisbon, Portugal
| | - Manuela Oliveira
- Centro de Investigação Interdisciplinar em Sanidade Animal, Faculdade de Medicina Veterinária, Universidade de Lisboa, Lisbon, Portugal
| | - Lélia Chambel
- Biosystems and Integrative Sciences Institute, Faculdade de Ciências, Universidade de Lisboa, Edifício TecLabs, Lisbon, Portugal
| | - Rogério Tenreiro
- Biosystems and Integrative Sciences Institute, Faculdade de Ciências, Universidade de Lisboa, Edifício TecLabs, Lisbon, Portugal
| | - Rosario Mato
- UCIBIO, Departamento de Ciências da Vida, NOVA School of Science and Technology/FCT NOVA, Universidade NOVA de Lisboa, Caparica, Portugal
| | - Ilda Santos-Sanches
- UCIBIO, Departamento de Ciências da Vida, NOVA School of Science and Technology/FCT NOVA, Universidade NOVA de Lisboa, Caparica, Portugal
| |
Collapse
|
50
|
de Souza UJB, Dos Santos RN, de Araújo Filho RN, Dos Santos GR, Almeida Sarmento R, De Bellis F, Campos FS. The complete chloroplast genome of Artocarpus altilis (Moraceae) and phylogenetic relationships. Mitochondrial DNA B Resour 2021; 6:2291-2293. [PMID: 34345682 PMCID: PMC8284141 DOI: 10.1080/23802359.2021.1945504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
The chloroplast (cp) is an essential organelle in higher plants. The genes of the plastome are well suited to infer phylogenetic relationships among taxa. In this study, we report the assembly of the cp genome of Artocarpus altilis and its phylogeny among species from Moraceae family. The cp genome of A. altilis was 160,822 base pair (bp) in length, comprising one large single-copy region of 88,692 bp, one small single-copy region of 19,290 bp, and a pair of inverted repeat regions (IRs) of 26,420 bp. A total of 113 different genes were predicted, including 79 protein-coding genes, 30 tRNA genes, and four rRNA genes. The phylogenetic analysis of 19 species belonging to the Moraceae family confirmed the phylogenetic proximity of the genus Artocarpus and Morus and the genetic similarity of A. camansi and A. altilis.
Collapse
Affiliation(s)
| | - Raíssa Nunes Dos Santos
- Laboratory of Bioinformatics & Biotechnology, Federal University of Tocantins, Gurupi, Brazil
| | | | | | - Renato Almeida Sarmento
- Department of Forestry Engineering, Federal University of Tocantins, Gurupi, Brazil.,Post-Graduate Program in Plant Production, Federal University of Tocantins, Gurupi, Brazil
| | - Fabien De Bellis
- CIRAD, UMR AGAP Institute, Montpellier, France.,UMR AGAP Institute, University of Montpellier, CIRAD, INRAE, L'Institut Agro, Montpellier, France
| | - Fabrício Souza Campos
- Laboratory of Bioinformatics & Biotechnology, Federal University of Tocantins, Gurupi, Brazil
| |
Collapse
|