1
|
dos Reis LL, de Souza LSS, Fonseca FR, Nava AFD, Vicente ACP. Zoonotic assemblages A and B of Giardia duodenalis in Chiroptera from Brazilian Amazon biome. One Health 2024; 19:100853. [PMID: 39071487 PMCID: PMC11277728 DOI: 10.1016/j.onehlt.2024.100853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2024] [Revised: 07/02/2024] [Accepted: 07/02/2024] [Indexed: 07/30/2024] Open
Abstract
Bats are important reservoirs and spreaders of pathogens. Giardia duodenalis is a globally important protozoan that infects humans and other mammals with considerable public health burden, particularly on the child development. Based on genetic variation and host specificity, G. duodenalis is categorized into eight genotypes/assemblages A-H. Assemblages A and B are widespread globally and are associated with human and animal disease. There is evidence of Giardia in the bat feces from diverse geographic regions, but the G. duodenalis assemblages are unknown, which is a key point for the One Health view. Here, we successfully amplified the BG/GDH/DIS3/HCMP2/HCMP3 targets of G. duodenalis from five bat species captured in the Brazilian Amazon biome revealing the presence of zoonotic G. duodenalis assemblages A and B in the feces of these flying mammals. Our study reveals that bats may play a role in transmission of zoonotic G. duodenalis, at least in this biome.
Collapse
Affiliation(s)
- Lisiane Lappe dos Reis
- Fundação Oswaldo Cruz-Fiocruz, Instituto Leônidas & Maria Deane, Laboratório de Diversidade Microbiana da Amazônia de Importância para a Saúde - DMAIS, Manaus, AM, Brazil
- Fundação Oswaldo Cruz-Fiocruz, Instituto Oswaldo Cruz, Laboratório de Genética Molecular de Microrganismos - LGMM, Rio de Janeiro, RJ, Brazil
| | - Lirna Salvioni Silva de Souza
- Fundação Oswaldo Cruz-Fiocruz, Instituto Leônidas & Maria Deane, Laboratório de Diversidade Microbiana da Amazônia de Importância para a Saúde - DMAIS, Manaus, AM, Brazil
| | - Fernanda Rodrigues Fonseca
- Fundação Oswaldo Cruz-Fiocruz, Instituto Leônidas & Maria Deane, Laboratório de Modelagem em Estatística, Geoprocessamento e Epidemiologia - LEGEPI, Manaus, AM, Brazil
| | - Alessandra Ferreira Dales Nava
- Fundação Oswaldo Cruz-Fiocruz, Instituto Leônidas & Maria Deane, Laboratório de Ecologia de Doenças Transmissíveis na Amazônia - EDTA, Manaus, AM, Brazil
| | - Ana Carolina Paulo Vicente
- Fundação Oswaldo Cruz-Fiocruz, Instituto Oswaldo Cruz, Laboratório de Genética Molecular de Microrganismos - LGMM, Rio de Janeiro, RJ, Brazil
| |
Collapse
|
2
|
Hao X, Lu Q, Zhao H. A molecular phylogeny for all 21 families within Chiroptera (bats). Integr Zool 2024; 19:989-998. [PMID: 37853557 DOI: 10.1111/1749-4877.12772] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2023]
Abstract
Bats, members of the Chiroptera order, rank as the second most diverse group among mammals. Recent molecular systematic studies on bats have successfully classified 21 families within two suborders: Yinpterochiroptera and Yangochiroptera. Nevertheless, the phylogeny within these 21 families has remained a subject of controversy. In this study, we have employed a balanced approach to establish a robust family-level phylogenetic hypothesis for bats, utilizing a more comprehensive molecular dataset. This dataset includes representative species from all 21 bat families, resulting in a reduced level of missing genetic information. The resulting phylogenetic tree comprises 21 lineages that are strongly supported, each corresponding to one of the bat families. Our findings support to place the Emballonuroidea superfamily as the basal lineage of Yangochiroptera, and that Myzopodidae should be situated as a basal lineage of Emballonuroidea, forming a sister relationship with the clade consisting of Nycteridae and Emballonuridae. Finally, we have conducted dating analyses on this newly resolved phylogenetic tree, providing divergence times for each bat family. Collectively, our study has employed a relatively comprehensive molecular dataset to establish a more robust phylogeny encompassing all 21 bat families. This improved phylogenetic framework will significantly contribute to our understanding of evolutionary processes, ecological roles, disease dynamics, and biodiversity conservation in the realm of bats.
Collapse
Affiliation(s)
- Xiangyu Hao
- College of Life Sciences, Wuhan University, Wuhan, Hubei, China
- College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, China
| | - Qin Lu
- College of Life Sciences, Wuhan University, Wuhan, Hubei, China
| | - Huabin Zhao
- College of Life Sciences, Wuhan University, Wuhan, Hubei, China
| |
Collapse
|
3
|
Chen MN, Ye ZX, Feng KH, Yuan JN, Chen JP, Zhang CX, Li JM, Mao QZ. Genetic Characterization of Two Novel Insect-Infecting Negative-Sense RNA Viruses Identified in a Leaf Beetle, Aulacophora indica. INSECTS 2024; 15:615. [PMID: 39194819 DOI: 10.3390/insects15080615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2024] [Revised: 08/13/2024] [Accepted: 08/14/2024] [Indexed: 08/29/2024]
Abstract
Herbivorous insects harbor a variety of insect-specific viruses (ISVs) some of which are considered to be valuable biological agents for potential applications in biological defense and control strategies. Leaf beetles with chewing mouthparts are particularly known for their capacity to disrupt plant tissue while feeding, often creating openings that can act as entry points for plant pathogens. In this study, we have identified two new negative-sense RNA viruses infecting the leaf beetle Aulacophora indica, an important member of the Chrysomelidae family. These recently discovered viruses belong to the viral families Nyamiviridae and Chuviridae and have been preliminarily named Aulacophora indica nyami-like virus 1 (AINlV1) and Aulacophora indica chu-like virus 1 (AIClV1), respectively. The complete genomic sequences of these viruses were obtained using rapid amplification of cDNA ends (RACE) techniques. Detailed analysis of their genomic structures has confirmed their similarity to other members within their respective families. Furthermore, analysis of virus-derived small interfering RNA (vsiRNA) demonstrated a high abundance and typical vsiRNA pattern of AINlV1 and AIClV1, offering substantial evidence to support their classification as ISVs. This research enhances our understanding of viral diversity within insects.
Collapse
Affiliation(s)
- Meng-Nan Chen
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
| | - Zhuang-Xin Ye
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
- College of Forestry, Nanjing Forestry University, Nanjing 210037, China
| | - Ke-Hui Feng
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
| | - Jing-Na Yuan
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
| | - Jian-Ping Chen
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
- College of Forestry, Nanjing Forestry University, Nanjing 210037, China
| | - Chuan-Xi Zhang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
| | - Jun-Min Li
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
| | - Qian-Zhuo Mao
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
| |
Collapse
|
4
|
Han Y, Xie Y, Hao Z, Mao J, Wang X, Chang Y, Tian Y. The Mitochondrial Genome of Ylistrum japonicum (Bivalvia, Pectinidae) and Its Phylogenetic Analysis. Int J Mol Sci 2024; 25:8755. [PMID: 39201441 PMCID: PMC11354973 DOI: 10.3390/ijms25168755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2024] [Revised: 08/06/2024] [Accepted: 08/09/2024] [Indexed: 09/02/2024] Open
Abstract
The Ylistrum japonicum is a commercially valuable scallop known for its long-distance swimming abilities. Despite its economic importance, genetic and genomic research on this species is limited. This study presents the first complete mitochondrial genome of Y. japonicum. The mitochondrial genome is 19,475 bp long and encompasses 13 protein-coding genes, three ribosomal RNA genes, and 23 transfer RNA genes. Two distinct phylogenetic analyses were used to explore the phylogenetic position of the Y. japonicum within the family Pectinidae. Based on one mitochondrial phylogenetic analysis by selecting 15 Pectinidae species and additional outgroup taxa and one single gene phylogenetic analysis by 16S rRNA, two phylogenetic trees were constructed to provide clearer insights into the evolutionary placement of Y. japonicum within the family Pectinidae. Our analysis reveals that Ylistrum is a basal lineage to the Pectininae clade, distinct from its previously assigned tribe, Amusiini. This study offers critical insights into the genetic makeup and evolutionary history of Y. japonicum, enhancing our knowledge of this economically vital species.
Collapse
Affiliation(s)
| | | | | | | | | | - Yaqing Chang
- Key Laboratory of Mariculture & Stock Enhancement in North China Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian 116023, China; (Y.H.); (Y.X.); (Z.H.); (J.M.); (X.W.)
| | - Ying Tian
- Key Laboratory of Mariculture & Stock Enhancement in North China Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian 116023, China; (Y.H.); (Y.X.); (Z.H.); (J.M.); (X.W.)
| |
Collapse
|
5
|
Dong J, Liu Y, Tan MK, Wahab RA, Nattier R, Chifflet-Belle P, Robillard T. Museomics allows comparative analyses of mitochondrial genomes in the family Gryllidae (Insecta, Orthoptera) and confirms its phylogenetic relationships. PeerJ 2024; 12:e17734. [PMID: 39131617 PMCID: PMC11317039 DOI: 10.7717/peerj.17734] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Accepted: 06/21/2024] [Indexed: 08/13/2024] Open
Abstract
Background Next-generation sequencing technology can now be used to sequence historical specimens from natural history collections, an approach referred to as museomics. The museomics allows obtaining molecular data from old museum-preserved specimens, a resource of biomolecules largely underexploited despite the fact that these specimens are often unique samples of nomenclatural types that can be crucial for resolving scientific questions. Despite recent technical progress, cricket mitogenomes are still scarce in the databases, with only a handful of new ones generated each year from freshly collected material. Methods In this study, we used the genome skimming method to sequence and assemble three new complete mitogenomes representing two tribes of the cricket subfamily Eneopterinae: two were obtained from old, historical type material of Xenogryllus lamottei (68 years old) and X. maniema (80 years old), the third one from a freshly collected specimen of Nisitrus vittatus. We compared their genome organization and base composition, and reconstructed the molecular phylogeny of the family Gryllidae. Results Our study not only confirmed that the genome skimming method used by next generation sequencing allows us to efficiently obtain the whole mitogenome from dry-pinned historical specimens, but we also confirmed how promising it is for large-scale comparative studies of mitogenomes using resources from natural history collections. Used in a phylogenetic context the new mitogenomes attest that the mitogenomic data contain valuable information and also strongly support phylogenetic relationships at multiple time scales.
Collapse
Affiliation(s)
- Jiajia Dong
- School of Life Sciences, Jiangsu Key Laboratory of Brain Disease and Bioinformation, Research Center for Biochemistry and Molecular Biology, Xuzhou Medical University, Xuzhou, China
| | - Yong Liu
- School of Life Sciences, Jiangsu Key Laboratory of Brain Disease and Bioinformation, Research Center for Biochemistry and Molecular Biology, Xuzhou Medical University, Xuzhou, China
| | - Ming Kai Tan
- Institut de Systématique, Evolution et Biodiversité (ISYEB), Muséum national d’Histoire naturelle, CNRS, SU, EPHE-SPL, UA, Paris, France
| | - Rodzay Abdul Wahab
- Institute for Biodiversity and Environmental Research, Universiti Brunei Darussalam, Jalan Universiti, Gadong, Brunei Darussalam
| | - Romain Nattier
- Institut de Systématique, Evolution et Biodiversité (ISYEB), Muséum national d’Histoire naturelle, CNRS, SU, EPHE-SPL, UA, Paris, France
| | - Pascaline Chifflet-Belle
- Institut de Systématique, Evolution et Biodiversité (ISYEB), Muséum national d’Histoire naturelle, CNRS, SU, EPHE-SPL, UA, Paris, France
| | - Tony Robillard
- Institut de Systématique, Evolution et Biodiversité (ISYEB), Muséum national d’Histoire naturelle, CNRS, SU, EPHE-SPL, UA, Paris, France
| |
Collapse
|
6
|
Wang S, Zhao G, Niu D, Wang L, Ren X, Wu J, Qu H. Three New Species and a New Record of the Lichen Genus Peltula (Peltulaceae) from Helan Mountain in China. BIOLOGY 2024; 13:590. [PMID: 39194528 DOI: 10.3390/biology13080590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2024] [Revised: 07/22/2024] [Accepted: 08/02/2024] [Indexed: 08/29/2024]
Abstract
In this study, a systematic taxonomic analysis was carried out on the lichen genus Peltula, collected from Helan Mountain in China; three new species (Peltula helanense, P. overlappine, and P. reticulata) and a new record (P. crispatula (Nyl.) Egea) for China were identified. Four species were identified by morph-anatomical, chemical, and phylogenetic analyses by combining two gene loci (ITS and LSU). Peltula helanense is with tiny individual thalli up to 1mm, attached by creamy-white cylindrical rhizoids and apothecia filling the whole squamule. Peltula overlappine is characterized by thallus squamulose forming rosette-shaped patches and squamules with distinctive thickened margins. Peltula reticulata is characterized by brownish brown thallus and squamules with densely reticulate upper surface. P. crispatula is characterized by irregular squamules attached to a tuft of hyphae. The four species are described in detail, compared, and discussed with similar species, and images of morpho-anatomical structures of the four species are also provided. Moreover, a key to the species of Peltula from Helan Mountain is provided. The results enrich the data of the genus Peltula and also indicate that the rich diversity of lichen species in Helan Mountain is worthy of in-depth study.
Collapse
Affiliation(s)
- Siying Wang
- School of Life Sciences, Ningxia University, Yinchuan 750021, China
| | - Gege Zhao
- School of Life Sciences, Ningxia University, Yinchuan 750021, China
| | - Dongling Niu
- School of Life Sciences, Ningxia University, Yinchuan 750021, China
| | - Liang Wang
- Inner Mongolia Helan Mountain National Nature Reserve Administration, Alxa East County 750300, China
| | - Xia Ren
- Inner Mongolia Helan Mountain National Nature Reserve Administration, Alxa East County 750300, China
| | - Jinai Wu
- Inner Mongolia Helan Mountain National Nature Reserve Administration, Alxa East County 750300, China
| | - Hongbin Qu
- Inner Mongolia Helan Mountain National Nature Reserve Administration, Alxa East County 750300, China
| |
Collapse
|
7
|
Jakovlić I, Ye T, Zou H, Zhu F, Shi Y, Ma Y, Wang GT, Li WX, Zhang D. Drivers of interlineage variability in mitogenomic evolutionary rates in Platyhelminthes. Heredity (Edinb) 2024:10.1038/s41437-024-00712-2. [PMID: 39095653 DOI: 10.1038/s41437-024-00712-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Revised: 07/25/2024] [Accepted: 07/26/2024] [Indexed: 08/04/2024] Open
Abstract
Studies of forces driving interlineage variability in the evolutionary rates (both sequence and architecture) of mitochondrial genomes often produce contradictory results. Flatworms (Platyhelminthes) exhibit the fastest-evolving mitogenomic sequences among all bilaterian phyla. To test the effects of multiple factors previously associated with different aspects of mitogenomic evolution, we used mitogenomes of 223 flatworm species, phylogenetic multilevel regression models, and causal inference. Thermic host environment (endothermic vs. ectothermic) had nonsignificant impacts on both sequence evolution and mitogenomic size. Mitogenomic gene order rearrangements (GORR) were mostly positively correlated with mitogenomic size (R2 ≈ 20-30%). Longevity was not (negatively) correlated with sequence evolution in flatworms. The predominantly free-living "turbellaria" exhibited much shorter branches and faster-evolving mitogenomic architecture than parasitic Neodermata. As a result, "parasitism" had a strong explanatory power on the branch length variability (>90%), and there was a negative correlation between GORR and branch length. However, the stem branch of Neodermata comprised 63.6% of the total average branch length. This evolutionary period was also marked by a high rate of gene order rearrangements in the ancestral Neodermata. We discuss how this period of rapid evolution deep in the evolutionary history may have decoupled sequence evolution rates from longevity and GORR, and overestimated the explanatory power of "parasitism". This study shows that impacts of variables often vary across lineages, and stresses the importance accounting for the episodic nature of evolutionary patterns in studies of mitogenomic evolution.
Collapse
Affiliation(s)
- Ivan Jakovlić
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, and College of Ecology, Lanzhou University, Lanzhou, 730000, China
| | - Tong Ye
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, and College of Ecology, Lanzhou University, Lanzhou, 730000, China
| | - Hong Zou
- Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, and State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Fengyue Zhu
- National Agricultural Science Observing and Experimental Station of Chongqing, Chongqing, 401329, China
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Science, Wuhan, 430073, China
| | - Yuying Shi
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, and College of Ecology, Lanzhou University, Lanzhou, 730000, China
| | - Yiwen Ma
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, and College of Ecology, Lanzhou University, Lanzhou, 730000, China
| | - Gui-Tang Wang
- Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, and State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Wen-Xiang Li
- Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, and State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Dong Zhang
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, and College of Ecology, Lanzhou University, Lanzhou, 730000, China.
- Key Laboratory of Biodiversity and Environment on the Qinghai-Tibetan Plateau, Ministry of Education, School of Ecology and Environment, Tibet University, Lhasa, 850011, China.
| |
Collapse
|
8
|
Cheng WX, Wang J, Mao ML, Lu YB, Zou JX. The mitochondrial genome of Bottapotamon fukienense (Brachiura: Potamidae) is fragmented into two chromosomes. BMC Genomics 2024; 25:755. [PMID: 39095713 PMCID: PMC11295360 DOI: 10.1186/s12864-024-10657-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2024] [Accepted: 07/23/2024] [Indexed: 08/04/2024] Open
Abstract
BACKGROUND China is the hotspot of global freshwater crab diversity, but their wild populations are facing severe pressures associated with anthropogenic factors, necessitating the need to map their taxonomic and genetic diversity and design conservation policies. RESULTS Herein, we sequenced the mitochondrial genome of a Chinese freshwater crab species Bottapotamon fukienense, and found that it is fragmented into two chromosomes. We confirmed that fragmentation was not limited to a single specimen or population. Chromosome 1 comprised 15,111 base pairs (bp) and there were 26 genes and one pseudogene (pseudo-nad1) encoded on it. Chromosome 2 comprised 8,173 bp and there were 12 genes and two pseudogenes (pseudo-trnL2 and pseudo-rrnL) encoded on it. Combined, they comprise the largest mitogenome (23,284 bp) among the Potamidae. Bottapotamon was the only genus in the Potamidae dataset exhibiting rearrangements of protein-coding genes. Bottapotamon fukienense exhibited average rates of sequence evolution in the dataset and did not differ in selection pressures from the remaining Potamidae. CONCLUSIONS This is the first experimentally confirmed fragmentation of a mitogenome in crustaceans. While the mitogenome of B. fukienense exhibited multiple signs of elevated mitogenomic architecture evolution rates, including the exceptionally large size, duplicated genes, pseudogenisation, rearrangements of protein-coding genes, and fragmentation, there is no evidence that this is matched by elevated sequence evolutionary rates or changes in selection pressures.
Collapse
Affiliation(s)
- Wang-Xinjun Cheng
- Research Laboratory of Freshwater Crustacean Decapoda & Paragonimus, School of Basic Medical Sciences, Nanchang University, Nanchang, Jiangxi Province, 330031, China
| | - Jun Wang
- Research Laboratory of Freshwater Crustacean Decapoda & Paragonimus, School of Basic Medical Sciences, Nanchang University, Nanchang, Jiangxi Province, 330031, China
| | - Mei-Lin Mao
- Research Laboratory of Freshwater Crustacean Decapoda & Paragonimus, School of Basic Medical Sciences, Nanchang University, Nanchang, Jiangxi Province, 330031, China
| | - Yuan-Biao Lu
- Research Laboratory of Freshwater Crustacean Decapoda & Paragonimus, School of Basic Medical Sciences, Nanchang University, Nanchang, Jiangxi Province, 330031, China
| | - Jie-Xin Zou
- Research Laboratory of Freshwater Crustacean Decapoda & Paragonimus, School of Basic Medical Sciences, Nanchang University, Nanchang, Jiangxi Province, 330031, China.
- Provincial Key Laboratory for Drug Targeting and Drug Screening, Jiangxi Medical College, Nanchang University, Nanchang, 330031, China.
| |
Collapse
|
9
|
Zhan L, Chen Y, He J, Guo Z, Wu L, Storey KB, Zhang J, Yu D. The Phylogenetic Relationships of Major Lizard Families Using Mitochondrial Genomes and Selection Pressure Analyses in Anguimorpha. Int J Mol Sci 2024; 25:8464. [PMID: 39126033 PMCID: PMC11312734 DOI: 10.3390/ijms25158464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2024] [Revised: 07/29/2024] [Accepted: 07/31/2024] [Indexed: 08/12/2024] Open
Abstract
Anguimorpha, within the order Squamata, represents a group with distinct morphological and behavioral characteristics in different ecological niches among lizards. Within Anguimorpha, there is a group characterized by limb loss, occupying lower ecological niches, concentrated within the subfamily Anguinae. Lizards with limbs and those without exhibit distinct locomotor abilities when adapting to their habitats, which in turn necessitate varying degrees of energy expenditure. Mitochondria, known as the metabolic powerhouses of cells, play a crucial role in providing approximately 95% of an organism's energy. Functionally, mitogenomes (mitochondrial genomes) can serve as a valuable tool for investigating potential adaptive evolutionary selection behind limb loss in reptiles. Due to the variation of mitogenome structures among each species, as well as its simple genetic structure, maternal inheritance, and high evolutionary rate, the mitogenome is increasingly utilized to reconstruct phylogenetic relationships of squamate animals. In this study, we sequenced the mitogenomes of two species within Anguimorpha as well as the mitogenomes of two species in Gekkota and four species in Scincoidea. We compared these data with the mitogenome content and evolutionary history of related species. Within Anguimorpha, between the mitogenomes of limbless and limbed lizards, a branch-site model analysis supported the presence of 10 positively selected sites: Cytb protein (at sites 183 and 187), ND2 protein (at sites 90, 155, and 198), ND3 protein (at site 21), ND5 protein (at sites 12 and 267), and ND6 protein (at sites 72 and 119). These findings suggested that positive selection of mitogenome in limbless lizards may be associated with the energy requirements for their locomotion. Additionally, we acquired data from 205 mitogenomes from the NCBI database. Bayesian inference (BI) and Maximum Likelihood (ML) trees were constructed using the 13 mitochondrial protein-coding genes (PCGs) and two rRNAs (12S rRNA and 16S rRNA) from 213 mitogenomes. Our phylogenetic tree and the divergence time estimates for Squamata based on mitogenome data are consistent with results from previous studies. Gekkota was placed at the root of Squamata in both BI and ML trees. However, within the Toxicofera clade, due to long-branch attraction, Anguimorpha and (Pleurodonta + (Serpentes + Acrodonta)) were closely related groupings, which might indicate errors and also demonstrate that mitogenome-based phylogenetic trees may not effectively resolve long-branch attraction issues. Additionally, we reviewed the origin and diversification of Squamata throughout the Mesozoic era, suggesting that Squamata originated in the Late Triassic (206.05 Mya), with the diversification of various superfamilies occurring during the Cretaceous period. Future improvements in constructing squamate phylogenetic relationships using mitogenomes will rely on identifying snake and acrodont species with slower evolutionary rates, ensuring comprehensive taxonomic coverage of squamate diversity, and increasing the number of genes analyzed.
Collapse
Affiliation(s)
- Lemei Zhan
- College of Life Sciences, Zhejiang Normal University, Jinhua 321004, China
| | - Yuxin Chen
- College of Life Sciences, Zhejiang Normal University, Jinhua 321004, China
| | - Jingyi He
- College of Life Sciences, Zhejiang Normal University, Jinhua 321004, China
| | - Zhiqiang Guo
- College of Life Sciences, Zhejiang Normal University, Jinhua 321004, China
| | - Lian Wu
- College of Life Sciences, Zhejiang Normal University, Jinhua 321004, China
| | - Kenneth B. Storey
- Department of Biology, Carleton University, Ottawa, ON K1S5B6, Canada
| | - Jiayong Zhang
- College of Life Sciences, Zhejiang Normal University, Jinhua 321004, China
- Key Laboratory of Wildlife Biotechnology, Conservation and Utilization of Zhejiang Province, Zhejiang Normal University, Jinhua 321004, China
| | - Danna Yu
- College of Life Sciences, Zhejiang Normal University, Jinhua 321004, China
- Key Laboratory of Wildlife Biotechnology, Conservation and Utilization of Zhejiang Province, Zhejiang Normal University, Jinhua 321004, China
| |
Collapse
|
10
|
Chen CZ, Yin MH, Niu LJ, Wang JX, Liu L, Sun YJ, Ju WM, Li P, Li ZH. Exploring seasonal variations, assembly dynamics, and relationships of bacterial communities in different habitats of marine ranching. MARINE POLLUTION BULLETIN 2024; 205:116658. [PMID: 38964192 DOI: 10.1016/j.marpolbul.2024.116658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Revised: 06/22/2024] [Accepted: 06/25/2024] [Indexed: 07/06/2024]
Abstract
Offshore coastal marine ranching ecosystems provide habitat for diverse and active bacterial communities. In this study, 16S rRNA gene sequencing and multiple bioinformatics methods were applied to investigate assembly dynamics and relationships in different habitats. The higher number of edges in the water network, more balanced ratio of positive and negative links, and more keystone species included in the co-occurrence network of water. Stochastic processes dominated in shaping gut and sediment community assembly (R2 < 0.5), while water bacterial community assembly were dominated by deterministic processes (R2 > 0.5). Dissimilarity-overlap curve model indicated that the communities in different habitats have general dynamics and interspecific interaction (P < 0.001). Bacterial source-tracking analysis revealed that the gut was more similar to the sediment than the water bacterial communities. In summary, this study provides basic data for the ecological study of marine ranching through the study of bacterial community dynamics.
Collapse
Affiliation(s)
| | - Ming-Hao Yin
- Marine College, Shandong University, Weihai, Shandong 264209, China
| | - Lin-Jing Niu
- Marine College, Shandong University, Weihai, Shandong 264209, China
| | - Jin-Xin Wang
- Marine College, Shandong University, Weihai, Shandong 264209, China
| | - Ling Liu
- Marine College, Shandong University, Weihai, Shandong 264209, China.
| | - Yong-Jun Sun
- Homey Group Co. Ltd, Rongcheng, Shandong 264306, China
| | - Wen-Ming Ju
- Homey Group Co. Ltd, Rongcheng, Shandong 264306, China
| | - Ping Li
- Marine College, Shandong University, Weihai, Shandong 264209, China
| | - Zhi-Hua Li
- Marine College, Shandong University, Weihai, Shandong 264209, China.
| |
Collapse
|
11
|
Song WL, Yan SZ, Chen SL. Morphological and phylogenetic analyses reveal four species of myxomycetes new to China. Arch Microbiol 2024; 206:364. [PMID: 39080072 DOI: 10.1007/s00203-024-04083-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2024] [Revised: 07/09/2024] [Accepted: 07/14/2024] [Indexed: 08/15/2024]
Abstract
Four species of myxomycetes (Arcyria pseudodenudata, Diderma europaeum, Lycogala irregulare, and Trichia armillata) new to China were observed via light microscope and scanning electron microscope, and detailed descriptions and illustrations are provided, along with comparisons with related species. Among them, A. pseudodenudata was discovered for the first time outside of the type locality, D. europaeum was discovered for the first time outside of Europe, and L. irregulare and T. armillata were reported again after being named. Phylogenetic analyses based on nuclear 18S rDNA and elongation factor-1 alpha sequences or nuclear 18S rDNA and cytochrome oxidase subunit I sequences was performed to provide a molecular basis for morphological identification. These specimens were deposited in the Herbarium of Fungi of Nanjing Normal University.
Collapse
Affiliation(s)
- Wen-Long Song
- School of Life Sciences, Nanjing Normal University, Nanjing, 210023, Jiangsu Province, China
| | - Shu-Zhen Yan
- School of Life Sciences, Nanjing Normal University, Nanjing, 210023, Jiangsu Province, China
| | - Shuang-Lin Chen
- School of Life Sciences, Nanjing Normal University, Nanjing, 210023, Jiangsu Province, China.
| |
Collapse
|
12
|
Lu G, Wang W, Zhang S, Yang G, Zhang K, Que Y, Deng L. The first complete mitochondrial genome of Grossulariaceae: Molecular features, structure recombination, and genetic evolution. BMC Genomics 2024; 25:744. [PMID: 39080514 PMCID: PMC11290076 DOI: 10.1186/s12864-024-10654-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2023] [Accepted: 07/22/2024] [Indexed: 08/02/2024] Open
Abstract
BACKGROUND Mitochondria play crucial roles in the growth, development, and adaptation of plants. Blackcurrant (Ribes nigrum L.) stands out as a significant berry species due to its rich nutritional profile, medicinal properties, and health benefits. Despite its importance, the mitochondrial genome of blackcurrant remains unassembled. RESULTS This study presents the first assembly of the mitochondrial genome of R. nigrum in the Grossulariaceae family. The genome spans 450,227 base pairs (bp) and encompasses 39 protein-coding genes (PCGs), 19 transfer RNAs (tRNAs), and three ribosomal RNAs (rRNAs). Protein-coding regions constitute 8.88% of the entire genome. Additionally, we identified 180 simple sequence repeats, 12 tandem repeats, and 432 pairs of dispersed repeats. Notably, the dispersed sequence R1 (cotig3, 1,129 bp) mediated genome recombination, resulting in the formation of two major conformations, namely master and double circles. Furthermore, we identified 731 C-to-U RNA editing sites within the PCGs. Among these, cox1-2, nad1-2, and nad4L-2 were associated with the creation of start codons, whereas atp6-718 and rps10-391 were linked to termination codons. We also detected fourteen plastome fragments within the mitogenome, constituting 1.11% of the total length. Phylogenetic analysis suggests that R. nigrum might have undergone multiple genomic reorganization and/or gene transfer events, resulting in the loss of two PCGs (rps2 and rps11) during its evolutionary history. CONCLUSIONS This investigation unveils the molecular characteristics of the R. nigrum mitogenome, shedding light on its evolutionary trajectory and phylogenetic implications. Furthermore, it serves as a valuable reference for evolutionary research and germplasm identification within the genus.
Collapse
Affiliation(s)
- Guilong Lu
- School of Horticulture and Landscape Architecture, Henan Institute of Science and Technology, Xinxiang, 453003, China
- Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, 890032, China
| | - Wenhua Wang
- Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, 890032, China
| | - Shanshan Zhang
- Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, 890032, China
| | - Guang Yang
- Institute of Rural Revitalization Science and Technology, Heilongjiang Academy of Agricultural Sciences, Harbin, 150086, China
| | - Kun Zhang
- Institute of Rural Revitalization Science and Technology, Heilongjiang Academy of Agricultural Sciences, Harbin, 150086, China
| | - Youxiong Que
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
| | - Lan Deng
- Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, 890032, China.
| |
Collapse
|
13
|
Chi ZH, Zhang CH, Chen ZP, Cui WY, Wang HY, Zu GH. The complete mitochondrial genome of Exoristobia philippinensis (Hymenoptera: Chalcidoidea: Encyrtidae) and phylogenetic analysis. Mitochondrial DNA B Resour 2024; 9:920-923. [PMID: 39077059 PMCID: PMC11285288 DOI: 10.1080/23802359.2024.2381821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Accepted: 07/13/2024] [Indexed: 07/31/2024] Open
Abstract
Exoristobia philippinensis (Hymenoptera: Encyrtidae) is a worldwide parasitic wasp. This work presents the mitochondrial genome (mitogenome) of E. philippinensis for the first time. The complete mitochondrial genome of E. philippinensis was sequenced and annotated, which was 15,751 bp in length, and encoded 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), and two ribosomal RNA genes (rRNAs). All 13 PCGs were initiated by the ATN (ATG, ATT, and ATA) codon, terminated with the stop codon TAA except for ND1 which ends with TAG. Phylogenetic analysis showed that E. philippinensis has a sister relationship with the genus Lamennaisia.
Collapse
Affiliation(s)
- Zhi-Hao Chi
- College of Horticulture and Landscape, Tianjin Agricultural University, Tianjin, PR China
| | - Cheng-Hui Zhang
- College of Horticulture and Landscape, Tianjin Agricultural University, Tianjin, PR China
| | - Zhi-Peng Chen
- College of Horticulture and Landscape, Tianjin Agricultural University, Tianjin, PR China
| | - Wen-Yu Cui
- College of Horticulture and Landscape, Tianjin Agricultural University, Tianjin, PR China
| | - Hai-Yang Wang
- College of Horticulture and Landscape, Tianjin Agricultural University, Tianjin, PR China
| | - Guo-Hao Zu
- College of Horticulture and Landscape, Tianjin Agricultural University, Tianjin, PR China
| |
Collapse
|
14
|
Luo L, Qu Q, Lin H, Chen J, Lin Z, Shao E, Lin D. Exploring the Evolutionary History and Phylogenetic Relationships of Giant Reed ( Arundo donax) through Comprehensive Analysis of Its Chloroplast Genome. Int J Mol Sci 2024; 25:7936. [PMID: 39063178 PMCID: PMC11277011 DOI: 10.3390/ijms25147936] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2024] [Revised: 07/12/2024] [Accepted: 07/18/2024] [Indexed: 07/28/2024] Open
Abstract
Giant reed (Arundo donax) is widely distributed across the globe and is considered an important energy crop. This study presents the first comprehensive analysis of the chloroplast genome of giant reed, revealing detailed characteristics of this species' chloroplast genome. The chloroplast genome has a total length of 137,153 bp, containing 84 protein-coding genes, 38 tRNA genes, and 8 rRNA genes, with a GC content of 39%. Functional analysis indicates that a total of 45 photosynthesis-related genes and 78 self-replication-related genes were identified, which may be closely associated with its adaptability and growth characteristics. Phylogenetic analysis confirmed that Arundo donax cv. Lvzhou No.1 belongs to the Arundionideae clade and occupies a distinct evolutionary position compared to other Arundo species. The findings of this study not only enhance our understanding of the giant reed genome but also provide valuable genetic resources for its application in biotechnology, bioenergy crop development, and ecological restoration.
Collapse
Affiliation(s)
| | | | | | | | | | - Ensi Shao
- Juncao Science and Ecology College, National Engineering Research Center of JUNCAO, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (L.L.); (Q.Q.); (H.L.); (J.C.); (Z.L.)
| | - Dongmei Lin
- Juncao Science and Ecology College, National Engineering Research Center of JUNCAO, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (L.L.); (Q.Q.); (H.L.); (J.C.); (Z.L.)
| |
Collapse
|
15
|
Cheng Z, Li J, Xu C, Zhang L, Gong Q, Long C. Coptisaustrogaoligongensis (Ranunculaceae), a new species from West Yunnan, China. PHYTOKEYS 2024; 244:225-235. [PMID: 39070103 PMCID: PMC11283624 DOI: 10.3897/phytokeys.244.127978] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/21/2024] [Accepted: 07/03/2024] [Indexed: 07/30/2024]
Abstract
Based on morphological and plastid data, we have described and confirmed that Coptisaustrogaoligongensis distributed in Tongbiguan Provincial Nature Reserve, Yingjiang County, Yunnan Province, is a new species of Coptis. It is distinctly different from C.teetasubsp.teeta and C.teetasubsp.lohitensis with differences mainly reflected in the following features: former leaf segment lobes contiguous to each other, and lateral segments equal to central one; plants without developed stolons; inflorescences with only 1-3 flowers; petals have short claws. Phylogenetic analysis indicated that C.austrogaoligongensis is a sister to C.teetasubsp.teeta and C.teetasubsp.lohitensis.
Collapse
Affiliation(s)
- Zhuo Cheng
- Key Laboratory of Ecology and Environment in Minority Areas (Minzu University of China), National Ethnic Affairs Commission of China, Beijing, 100081, ChinaMinzu University of ChinaBeijingChina
| | - Jiahua Li
- College of Life and Environmental Sciences, Minzu University of China, Beijing, 100081, ChinaGaoligongshan National Nature ReserveYunnanChina
| | - Congli Xu
- College of Life and Environmental Sciences, Minzu University of China, Beijing, 100081, ChinaGaoligongshan National Nature ReserveYunnanChina
| | - Lixiang Zhang
- Gaoligongshan National Nature Reserve (Longyang Sub-bureau), Yunnan, 678000, ChinaYunnan Tongbiguan Provincial Nature Reserve Management and Protection BureauYunnanChina
| | - Qiangbang Gong
- Gaoligongshan National Nature Reserve (Longyang Sub-bureau), Yunnan, 678000, ChinaYunnan Tongbiguan Provincial Nature Reserve Management and Protection BureauYunnanChina
| | - Chunlin Long
- Key Laboratory of Ecology and Environment in Minority Areas (Minzu University of China), National Ethnic Affairs Commission of China, Beijing, 100081, ChinaMinzu University of ChinaBeijingChina
| |
Collapse
|
16
|
Zhang L, Huang Y, Gai Y, Hou S, Zhan Q. First complete mitochondrial genome of Pselliophora (Diptera, Tipulidae): genome description and phylogenetic implications. Mitochondrial DNA B Resour 2024; 9:897-901. [PMID: 39040483 PMCID: PMC11262202 DOI: 10.1080/23802359.2024.2381817] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Accepted: 07/13/2024] [Indexed: 07/24/2024] Open
Abstract
Pselliophora is widely distributed in Eurasia and China. To explore the characteristics of the mitogenome of Pselliophora and reveal phylogenetic relationships, the mitogenome of Pselliophora bifascipennis Brunetti, 1911 was sequenced and annotated. This is the first complete mitochondrial genome in this genus. Its mitogenome is 15821 bp in length, containing 13 protein-coding genes, 22 tRNA and 2 rRNA genes. Nucleotide compositions of its whole mitogenome are 39.09% for A, 38.49% for T, 13.42% for C, and 9.01% for G. Consistent with previous observations of Tipulidae species, the mitogenome of Pselliophora bifascipennis is highly conserved in gene size, organization and codon usage, and secondary structures of tRNAs. Most tRNAs have the typical clover-leaf structure. The control region is 1006 bp long with an A + T content of 92.7%. Phylogenetic tree analysis using the sequences of the mitochondrial genomes of Pselliophora bifascipennis and other Tipulidae species showed that Pselliophora bifascipennis is closely related to Tanyptera hebeiensis. These two species are grouped on the same branch, which is in accordance with the traditional morphological classification. The results of this study lay a foundation for screening molecular markers of mitochondrion for molecular identification and genetic structure research in Tipulidae species.
Collapse
Affiliation(s)
- Lei Zhang
- Department of Public Safety, Nanjing Police University, Nanjing, China
| | - Yalin Huang
- Department of Criminal Science and Technology, Nanjing Police University, Nanjing, China
- Key Laboratory of State Forestry and Grassland Administration on Wildlife Evidence Technology, Nanjing, China
| | - Yunpeng Gai
- School of Grassland Science, Beijing Forestry University, Beijing, China
| | - Senlin Hou
- Department of Criminal Science and Technology, Nanjing Police University, Nanjing, China
- Key Laboratory of State Forestry and Grassland Administration on Wildlife Evidence Technology, Nanjing, China
| | - Qingbin Zhan
- Department of Criminal Science and Technology, Nanjing Police University, Nanjing, China
- Key Laboratory of State Forestry and Grassland Administration on Wildlife Evidence Technology, Nanjing, China
| |
Collapse
|
17
|
Zhang X, Zhou HM, Ghobad-Nejhad M, Liu HG, Vlasák J, Dai YC, Yuan Y. Molecular and morphological data reveal two new polypores (Polyporales, Basidiomycota) with reddish brown to orange basidiomata from China. MycoKeys 2024; 107:75-94. [PMID: 39045085 PMCID: PMC11263816 DOI: 10.3897/mycokeys.107.126176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2024] [Accepted: 07/03/2024] [Indexed: 07/25/2024] Open
Abstract
Two taxonomically controversial polypore genera with reddish brown to orange basidiomata that stain reddish with KOH solution, Aurantiporus and Hapalopilus, are revised based on additional sampling, morphological examination, and phylogenetic analysis of a combined dataset of ITS1-5.8S-ITS2-nLSU sequences. Hapalopilus is a monophyletic genus belonging to Phanerochaetaceae, whereas Aurantiporus is a polyphyletic genus belonging to Meruliaceae. Hapalopilus and Aurantiporus s. str. are circumscribed, and two new species - Aurantiporusorientalis and Hapalopilustabuliformis - are described and illustrated from temperate China. In addition, four new combinations, viz. Aurantiporusalboaurantius, A.mutans, A.tropicus and Luteoporiaalbocitrina, are proposed based on morphology and phylogenetic analysis. The relationships between Aurantiporus and Hapalopilus are discussed.
Collapse
Affiliation(s)
- Xin Zhang
- State Key Laboratory of Efficient Production of Forest Resources, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, ChinaBeijing Forestry UniversityBeijingChina
| | - Hong-Min Zhou
- College of Biodiversity Conservation, Southwest Forestry University, Kunming 650224, ChinaSouthwest Forestry UniversityKunmingChina
| | - Masoomeh Ghobad-Nejhad
- Department of Biotechnology, Iranian Research Organization for Science and Technology (IROST), Tehran 3353-5111, IranIranian Research Organization for Science and Technology (IROST)TehranIran
| | - Hong-Gao Liu
- Yunnan Key Laboratory of Gastrodia and Fungi Symbiotic Biology, Zhaotong University, Zhaotong 657000, ChinaZhaotong UniversityZhaotongChina
| | - Josef Vlasák
- Biology Centre of the Academy of Sciences of the Czech Republic, Branišovská 31, CZ-370 05 České Budějovice, Czech RepublicBiology Centre of the Czech Academy of SciencesČeské BudějoviceCzech Republic
| | - Yu-Cheng Dai
- State Key Laboratory of Efficient Production of Forest Resources, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, ChinaBeijing Forestry UniversityBeijingChina
| | - Yuan Yuan
- State Key Laboratory of Efficient Production of Forest Resources, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, ChinaBeijing Forestry UniversityBeijingChina
| |
Collapse
|
18
|
Jiang C, Kang H, Zhou Y, Zhu W, Zhao X, Mohamed N, Li B. Selected Lark Mitochondrial Genomes Provide Insights into the Evolution of Second Control Region with Tandem Repeats in Alaudidae (Aves, Passeriformes). Life (Basel) 2024; 14:881. [PMID: 39063634 PMCID: PMC11278119 DOI: 10.3390/life14070881] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2024] [Revised: 06/30/2024] [Accepted: 07/05/2024] [Indexed: 07/28/2024] Open
Abstract
The control region (CR) regulates the replication and transcription of the mitochondrial genome (mitogenome). Some avian mitogenomes possess two CRs, and the second control region (CR2) may enhance replication and transcription; however, the CR2 in lark mitogenome appears to be undergoing loss and is accompanied by tandem repeats. Here, we characterized six lark mitogenomes from Alaudala cheleensis, Eremophila alpestris, Alauda razae, and Calandrella cinerea and reconstructed the phylogeny of Passerida. Through further comparative analysis among larks, we traced the evolutionary process of CR2. The mitochondrial gene orders were conserved in all published lark mitogenomes, with Cytb-trnT-CR1-trnP-ND6-trnE-remnant CR2 with tandem repeat-trnF-rrnS. Phylogenetic analysis revealed Alaudidae and Panuridae are sister groups at the base of Sylvioidea, and sporadic losses of CR2 may occur in their common ancestor. CR sequence and phylogeny analysis indicated CR2 tandem repeats were generated within CR2, originating in the ancestor of all larks, rather than inherited from CR1. The secondary structure comparison of tandem repeat units within and between species suggested slipped-strand mispairing and DNA turnover as suitable models for explaining the origin and evolution of these repeats. This study reveals the evolutionary process of the CR2 containing tandem repeat in Alaudidae, providing reference for understanding the evolutionary characteristics and dynamics of tandem repeats.
Collapse
Affiliation(s)
- Chuan Jiang
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin 150040, China; (C.J.); (H.K.); (X.Z.); (N.M.)
| | - Hui Kang
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin 150040, China; (C.J.); (H.K.); (X.Z.); (N.M.)
| | - Yang Zhou
- BGI Research, Shenzhen 518083, China;
- BGI Research, Wuhan 430074, China
| | - Wenwen Zhu
- School of Life Sciences, Heilongjiang University, Harbin 150080, China;
| | - Xilong Zhao
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin 150040, China; (C.J.); (H.K.); (X.Z.); (N.M.)
| | - Nassoro Mohamed
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin 150040, China; (C.J.); (H.K.); (X.Z.); (N.M.)
| | - Bo Li
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin 150040, China; (C.J.); (H.K.); (X.Z.); (N.M.)
- State Forestry and Grassland Administration Detecting Center of Wildlife, Harbin 150040, China
| |
Collapse
|
19
|
Ji L, Jia Z, Bai X. Comparative Analysis of the Mitochondrial Genomes of Three Species of Yangiella (Hemiptera: Aradidae) and the Phylogenetic Implications of Aradidae. INSECTS 2024; 15:533. [PMID: 39057266 PMCID: PMC11276747 DOI: 10.3390/insects15070533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2024] [Revised: 07/09/2024] [Accepted: 07/12/2024] [Indexed: 07/28/2024]
Abstract
The mitochondrial genomes of three species of Yangiella were sequenced, annotated, and analyzed. The genome length of the three species of the genus is 15,070-15,202 bp, with a typical gene number, including a control region, 2 ribosomal RNA genes (rRNAs), 22 transfer RNA genes (tRNAs), and 13 protein-coding genes (PCGs). It was found that the mitochondrial genome of Yangiella had AT bias. Except for the lack of a DHU arm of the trnS1 gene, the other tRNAs had a typical cloverleaf structure, and the codon usage preferences of the three species exhibited high similarity. In addition, tRNA gene rearrangements were observed among the three subfamilies of Aradidae (Mezirinae, Calisiinae, Aradinae), and it was found that codon usage preferences appeared to be less affected by base mutation and more by natural selection. The Pi and Ka/Ks values indicated that cox1 was the most conserved gene in the mitochondrial genome of Aradidae, while atp8 and nad6 were rapidly evolved genes. Substitution saturation level analysis showed that the nucleic acid sequence of mitochondrial protein-coding genes in Aradidae did not reach saturation, suggesting the rationality of the phylogenetic analysis data. Bayesian and maximum likelihood methods were used to analyze the phylogeny of 16 species of Hemiptera insects, which supported the monophyly of Aneurinae, Carventinae, and Mezirinae, as well as the monophyly of Yangiella. Based on fossils and previous studies, the differentiation time was inferred, indicating that Yangiella diverged about 57 million years ago.
Collapse
Affiliation(s)
| | | | - Xiaoshuan Bai
- College of Life Sciences and Technology, Inner Mongolia Normal University, Hohhot 010022, China; (L.J.); (Z.J.)
| |
Collapse
|
20
|
Wang ZH, Zhong QQ, Li YL, Xu JJ, Sun QW. Ixeridiumnujiangense (Crepidinae, Cichorieae, Asteraceae), a new species from southwest Yunnan, China. PHYTOKEYS 2024; 244:163-174. [PMID: 39035362 PMCID: PMC11258457 DOI: 10.3897/phytokeys.244.126940] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/06/2024] [Accepted: 06/24/2024] [Indexed: 07/23/2024]
Abstract
In this paper, we describe Ixeridiumnujiangense, a novel species identified in southwestern Yunnan, China. Two populations have been found along the riverbanks of the Nujiang River in Yongde and Zhenkang Counties. Morphologically, I.nujiangense is most similar to the recently described I.malingheense, but it can be readily distinguished by its mostly divided basal leaves, narrower non-clasping cauline leaves, notably shorter corolla tube, pale brown anthers, and considerably longer beak of achenes.
Collapse
Affiliation(s)
- Ze-Huan Wang
- Department of Traditional Chinese Medicine Resources and Development, College of Pharmacy, Guizhou University of Traditional Chinese Medicine, Guiyang 550025, Guizhou, ChinaGuizhou University of Traditional Chinese MedicineGuiyangChina
| | - Qian-Qian Zhong
- Department of Traditional Chinese Medicine Resources and Development, College of Pharmacy, Guizhou University of Traditional Chinese Medicine, Guiyang 550025, Guizhou, ChinaGuizhou University of Traditional Chinese MedicineGuiyangChina
| | - Yong-Liang Li
- Administration Bureau of Yongde Daxueshan National Nature Reserve, Yongde 677600, Yunnan, ChinaAdministration Bureau of Yongde Daxueshan National Nature ReserveYongdeChina
| | - Jia-Ju Xu
- Department of Traditional Chinese Medicine Resources and Development, College of Pharmacy, Guizhou University of Traditional Chinese Medicine, Guiyang 550025, Guizhou, ChinaGuizhou University of Traditional Chinese MedicineGuiyangChina
| | - Qing-Wen Sun
- Department of Traditional Chinese Medicine Resources and Development, College of Pharmacy, Guizhou University of Traditional Chinese Medicine, Guiyang 550025, Guizhou, ChinaGuizhou University of Traditional Chinese MedicineGuiyangChina
| |
Collapse
|
21
|
Yang Z, Ren J, Lu S, Feng Y, Fan Y, Liu TX, Jing X. In vivo functional analysis of the cotton bollworm Helicoverpa armigera 24-dehydrocholesterol reductase (HaDHCR24) in phytosterol metabolism. INSECT SCIENCE 2024. [PMID: 38973264 DOI: 10.1111/1744-7917.13405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Revised: 05/03/2024] [Accepted: 05/10/2024] [Indexed: 07/09/2024]
Abstract
Insects have to obtain sterols from food due to the inability to synthesize this essential nutrient de novo. For lepidopteran insects, they can convert a variety of phytosterols into cholesterol to meet their growth needs. The final step of the cholesterol biosynthesis is the metabolism of desmosterol catalyzed by 24-dehydrocholesterol reductase (DHCR24). In this study, we identified a DHCR24 homolog in the cotton bollworm Helicoverpa armigera, designated as H. armigera 24-dehydrocholesterol reductase (HaDHCR24)-1. The quantitative expression analyses indicated that HaDHCR24-1 was highly enriched in the midgut where dietary sterol uptake occurs. Compared to the control, the DHCR24-1 mutant larvae generated by clustered regularly interspaced palindromic repeats (CRISPR) / CRISPR-associated nuclease 9 technology accumulated more desmosterol in the gut, while the content of cholesterol was significantly reduced. A similar phenomenon was observed when the DHCR24 inhibitor, amiodarone, was applied to the insects. Moreover, DHCR24-1 played an important role for the usage of β-sitosterol, a major sterol in plants, in H. armigera, and loss of function of DHCR24-1 resulted in higher mortality on β-sitosterol. However, the DHCR24 homolog does not necessarily exist in the genomes of all insects. The loss of this gene occurred more frequently in the insects feeding on animals, which further support the role of DHCR24-1 in using phytosterols. This gene may have important potential in developing new strategies to control herbivory pests in Lepidoptera and other insect orders.
Collapse
Affiliation(s)
- Zhen Yang
- Key Laboratory of Plant Protection Resources and Pest Management of Ministry of Education, Key Laboratory of Integrated Pest Management on Crops in Northwestern Loess Plateau of Ministry of Agriculture and Rural Affairs, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, China
| | - Jinchan Ren
- Key Laboratory of Plant Protection Resources and Pest Management of Ministry of Education, Key Laboratory of Integrated Pest Management on Crops in Northwestern Loess Plateau of Ministry of Agriculture and Rural Affairs, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, China
| | - Shuning Lu
- Key Laboratory of Plant Protection Resources and Pest Management of Ministry of Education, Key Laboratory of Integrated Pest Management on Crops in Northwestern Loess Plateau of Ministry of Agriculture and Rural Affairs, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, China
| | - Yuanze Feng
- Key Laboratory of Plant Protection Resources and Pest Management of Ministry of Education, Key Laboratory of Integrated Pest Management on Crops in Northwestern Loess Plateau of Ministry of Agriculture and Rural Affairs, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, China
| | - Yongliang Fan
- Key Laboratory of Plant Protection Resources and Pest Management of Ministry of Education, Key Laboratory of Integrated Pest Management on Crops in Northwestern Loess Plateau of Ministry of Agriculture and Rural Affairs, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, China
| | - Tong-Xian Liu
- Key Laboratory of Plant Protection Resources and Pest Management of Ministry of Education, Key Laboratory of Integrated Pest Management on Crops in Northwestern Loess Plateau of Ministry of Agriculture and Rural Affairs, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, China
| | - Xiangfeng Jing
- Key Laboratory of Plant Protection Resources and Pest Management of Ministry of Education, Key Laboratory of Integrated Pest Management on Crops in Northwestern Loess Plateau of Ministry of Agriculture and Rural Affairs, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, China
| |
Collapse
|
22
|
Ghosh A, Tyagi K, Dubey AK, Sweet AD, Singha D, Goswami P, Kumar V. Purifying selection drove the adaptation of mitochondrial genes along with correlation of gene rearrangements and evolutionary rates in two subfamilies of Whitefly (Insecta: Hemiptera). Funct Integr Genomics 2024; 24:121. [PMID: 38976062 DOI: 10.1007/s10142-024-01400-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Revised: 05/06/2024] [Accepted: 06/27/2024] [Indexed: 07/09/2024]
Abstract
Insect mitochondrial genomes (mitogenomes) are usually represented by a conserved gene order. Whiteflies exhibit gene rearrangement in their mitogenomes; however, understanding how nucleotide substitution rates shape gene rearrangement in whiteflies is unclear due to the limited number of mitogenomes. Additionally, the mechanisms by which selection pressure drives adaptations in mitochondrial genes in the two subfamilies of whiteflies are not yet known. Here, we analyzed 18 whitefly mitogenomes, including one newly generated mitogenome, to compare nucleotide substitution rates, selection pressure, and gene arrangements. The newly generated mitogenome is reported along with reannotation of Pealius mori and comparisons to other whitefly mitogenomes. Comparative studies on nucleotide composition of 18 whiteflies revealed the positive GC skewness, confirming the reversal of strand asymmetry. We found 11 rearranged gene orders within two subfamilies of whiteflies with 8-18 breakpoints of gene rearrangements. Members of the subfamily Aleyrodinae exhibit more complex pathways in the evolution of gene order as compared to the subfamily Aleurodicinae. Our findings also revealed that the increase or reduction of nucleotide substitution rates does not have an impact on any of the gene rearrangement scenarios depicting neutral correlation. Selection pressure analysis revealed that the mitogenomes from members of both the subfamilies Aleurodicinae and Aleyrodinae are characterized by intense purifying selection pressure.
Collapse
Affiliation(s)
- Abhishek Ghosh
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, Kolkata, West Bengal, India
- Department of Zoology, University of Calcutta, Kolkata, West Bengal, India
| | - Kaomud Tyagi
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, Kolkata, West Bengal, India.
| | - Anil Kumar Dubey
- Hemiptera Section, Zoological Survey of India, West Bengal, Kolkata, India
| | | | - Devkant Singha
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, Kolkata, West Bengal, India
| | - Prathana Goswami
- Lepidoptera Section, Zoological Survey of India, Kolkata, West Bengal, India
- Department of Zoology, Gauhati University, Guwahati, Assam, India
| | - Vikas Kumar
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, Kolkata, West Bengal, India.
| |
Collapse
|
23
|
Li R, Li X, Tang J, Xie C, Wang J. The Development of a Fluorescent Microsatellite Marker Assay for the Pitaya Canker Pathogen ( Neoscytalidium dimidiatum). Genes (Basel) 2024; 15:885. [PMID: 39062664 PMCID: PMC11275628 DOI: 10.3390/genes15070885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2024] [Revised: 06/24/2024] [Accepted: 07/03/2024] [Indexed: 07/28/2024] Open
Abstract
Pitaya canker, caused by Neoscytalidium dimidiatum, is a destructive disease that significantly threatens the safety of the pitaya industry. The authors of previous studies have mainly focused on its biological characteristics and chemical control. However, there are no molecular markers available thus far that can be used for the population genetics study of this pathogen. In the present study, a draft genome of N. dimidiatum with a total length of 41.46 MB was assembled in which 9863 coding genes were predicted and annotated. In particular, the microsatellite sequences in the draft genome were investigated. To improve the successful screening rate of potentially polymorphic microsatellite makers, another five N. dimidiatum isolates were resequenced and assembled. A total of eight pairs of polymorphic microsatellite primers were screened out based on the polymorphic microsatellite loci after investigating the sequencing and resequencing assemblies of the six isolates. A total of thirteen representative isolates sampled from different pitaya plantations were genotyped in order to validate the polymorphism of the resulting eight markers. The results indicated that these markers were able to distinguish the isolates well. Lastly, a neighbor-joining tree of 35 isolates, sampled from different pitaya plantations located in different regions, was constructed according to the genotypes of the eight molecular markers. The developed tree indicated that these molecular markers had sufficient genotyping capabilities for our test panel of isolates. In summary, we developed a set of polymorphic microsatellite markers in the following study that can effectively genotype and distinguish N. dimidiatum isolates and be utilized in the population genetics study of N. dimidiatum.
Collapse
Affiliation(s)
- Rui Li
- School of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China; (R.L.); (X.L.); (J.T.); (C.X.)
- Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests, Ministry of Education of China, Haikou 570228, China
| | - Xi Li
- School of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China; (R.L.); (X.L.); (J.T.); (C.X.)
- Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests, Ministry of Education of China, Haikou 570228, China
| | - Jingcheng Tang
- School of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China; (R.L.); (X.L.); (J.T.); (C.X.)
- Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests, Ministry of Education of China, Haikou 570228, China
| | - Changping Xie
- School of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China; (R.L.); (X.L.); (J.T.); (C.X.)
- Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests, Ministry of Education of China, Haikou 570228, China
| | - Jianan Wang
- School of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China; (R.L.); (X.L.); (J.T.); (C.X.)
- Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests, Ministry of Education of China, Haikou 570228, China
| |
Collapse
|
24
|
Xi O, Zhang S, Li J, Hu H, Bai M. Geometric Morphometrics and Genetic Diversity Analysis of Chalcidoidea ( Diglyphus and Pachyneuron) at Various Elevations. INSECTS 2024; 15:497. [PMID: 39057230 PMCID: PMC11277471 DOI: 10.3390/insects15070497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2024] [Revised: 06/20/2024] [Accepted: 06/29/2024] [Indexed: 07/28/2024]
Abstract
Eulophidae and Pteromalidae are parasitic wasps with a global distribution and import for the biological control of pests. They can be distributed in different altitude regions, but their morphological and genetic adaptations to different altitudes are unclear. Here, we collected specimens that belong to Eulophidae and Pteromalidae from various altitudinal gradients, based on integrated taxonomic approaches to determine the species composition, and we analyzed their body shape and size from different altitudes using geometric morphometrics. Then, we performed an analysis of the D. isaea population's haplotype genes to illustrate their genetic diversity. As a result, eight species that belong to two genera, Diglyphus Walker (Eulophidae) and Pachyneuron Walker (Pteromalidae), were identified, including two newly recorded species from China (D. chabrias and D. sabulosus). Through a geometric morphometrics analysis of body shape, we found that a narrow forewing shape and a widened thorax are the significant characteristics of adaptation to high-altitude environments in D. isaea and P. aphidis. Additionally, the body size studies showed a principal relationship between centroid size and altitude; the size of the forewings and thorax increases at higher altitudes. Next, using haplotype analysis, 32 haplotypes were found in seven geographic populations with high genetic diversity of this species. Our research provides preliminary evidence for the morphological and genetic diversity adaptation of parasitic wasps to extreme environments, and these data can provide important references for investigations on the ecological adaptability of parasitic wasps.
Collapse
Affiliation(s)
- Ouyan Xi
- College of Life Science and Technology, Xinjiang University, Urumqi 830017, China; (O.X.); (S.Z.); (J.L.)
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, Urumqi 830017, China
| | - Shuli Zhang
- College of Life Science and Technology, Xinjiang University, Urumqi 830017, China; (O.X.); (S.Z.); (J.L.)
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, Urumqi 830017, China
| | - Jinzhe Li
- College of Life Science and Technology, Xinjiang University, Urumqi 830017, China; (O.X.); (S.Z.); (J.L.)
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, Urumqi 830017, China
| | - Hongying Hu
- College of Life Science and Technology, Xinjiang University, Urumqi 830017, China; (O.X.); (S.Z.); (J.L.)
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, Urumqi 830017, China
| | - Ming Bai
- Institute of Zoology, Chinese Academy of Sciences, Beijing 100864, China;
| |
Collapse
|
25
|
Li Q, Jiang P, Li M, Du J, Sun J, Chen N, Wu Y, Chang Q, Hu C. Structure and Phylogenetic Relationships of Scolopacidae Mitogenomes (Charadriiformes: Scolopacidae). Curr Issues Mol Biol 2024; 46:6186-6198. [PMID: 38921040 PMCID: PMC11202466 DOI: 10.3390/cimb46060369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2024] [Revised: 06/09/2024] [Accepted: 06/15/2024] [Indexed: 06/27/2024] Open
Abstract
The family Scolopacidae presents a valuable subject for evolutionary research; however, molecular studies of Scolopacidae are still relatively understudied, and the phylogenetic relationships of certain species remain unclear. In this study, we sequenced and obtained complete mitochondrial DNA (mtDNA) from Actitis hypoleucos and partial mtDNA from Numenius arquata, Limosa limosa, and Limnodromus semipalmatus. The complete mtDNA contained 13 protein-coding genes (PCGs), two ribosomal RNA genes, 22 tRNA genes, and a control region. Scolopacidae contained three types of start codons and five types of stop codons (including one incomplete stop codon, T--). In 13 protein-coding genes, average uncorrected pairwise distances (Aupd) revealed that ATP8 was the least conserved while COX3 had the lowest evolutionary rate. The ratio of Ka/Ks suggested that all PCGs were under purifying selection. Using two methods (maximum likelihood and Bayesian inference) to analyze the phylogenetic relationships of the family Scolopacidae, it was found that the genera Xenus and Actitis were clustered into another sister group, while the genus Phalaropus is more closely related to the genus Tringa. The genera Limnodromus, Gallinago, and Scolopax form a monophyletic group. This study improves our understanding of the evolutionary patterns and phylogenetic relationships of the family Scolopacidae.
Collapse
Affiliation(s)
- Quanheng Li
- School of Life Sciences, Nanjing Normal University, Nanjing 210023, China; (Q.L.); (M.L.); (J.D.); (J.S.); (N.C.); (Y.W.)
| | - Peiyue Jiang
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, School of Life Sciences, Nanjing Normal University, Nanjing 210023, China;
| | - Mingxuan Li
- School of Life Sciences, Nanjing Normal University, Nanjing 210023, China; (Q.L.); (M.L.); (J.D.); (J.S.); (N.C.); (Y.W.)
| | - Jingjing Du
- School of Life Sciences, Nanjing Normal University, Nanjing 210023, China; (Q.L.); (M.L.); (J.D.); (J.S.); (N.C.); (Y.W.)
| | - Jianxiang Sun
- School of Life Sciences, Nanjing Normal University, Nanjing 210023, China; (Q.L.); (M.L.); (J.D.); (J.S.); (N.C.); (Y.W.)
| | - Nuo Chen
- School of Life Sciences, Nanjing Normal University, Nanjing 210023, China; (Q.L.); (M.L.); (J.D.); (J.S.); (N.C.); (Y.W.)
| | - Yu Wu
- School of Life Sciences, Nanjing Normal University, Nanjing 210023, China; (Q.L.); (M.L.); (J.D.); (J.S.); (N.C.); (Y.W.)
| | - Qing Chang
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, School of Life Sciences, Nanjing Normal University, Nanjing 210023, China;
| | - Chaochao Hu
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, School of Life Sciences, Nanjing Normal University, Nanjing 210023, China;
- Analytical and Testing Center, Nanjing Normal University, Nanjing 210046, China
| |
Collapse
|
26
|
Hu W, Mao K, Dou L. Complete mitochondrial genome of the Minois paupera Alphéraky, 1888 (nymphalidae: satyrinae) and its phylogenetic analysis. Mitochondrial DNA B Resour 2024; 9:738-742. [PMID: 38881576 PMCID: PMC11177703 DOI: 10.1080/23802359.2024.2361704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Accepted: 05/25/2024] [Indexed: 06/18/2024] Open
Abstract
The present study firstly reported a complete mitochondrial genome of Minois paupera (Alphéraky, 1888), a Satyrinae species endemic to China. This mitogenome is circular, 15,213 bp in length, and consists of 37 typical mitochondrial genes, including 13 protein-coding genes (PCGs), 22 tRNAs, and two rRNAs. The phylogenetic position was inferred using 31 previously published complete mitogenomes, and the results reveal that M. paupera is the most closely related to Minois dryas. The complete mitogenome of M. paupera provides useful genetic information for further research on the phylogeography and phylogeny of the genus Minois.
Collapse
Affiliation(s)
- Wenqian Hu
- College of Life Sciences, Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, Key Laboratory of Conservation Biology on Endangered Wildlife of Sichuan Province, Sichuan University, Chengdu, China
| | - Kangshan Mao
- College of Life Sciences, Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, Key Laboratory of Conservation Biology on Endangered Wildlife of Sichuan Province, Sichuan University, Chengdu, China
| | - Liang Dou
- College of Life Sciences, Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, Key Laboratory of Conservation Biology on Endangered Wildlife of Sichuan Province, Sichuan University, Chengdu, China
| |
Collapse
|
27
|
Rahmouni C, Seifertová M, Bean MG, Šimková A. Intraspecific variation in Gyrodactylus mediotorus and G. crysoleucas (Gyrodactylidae) from Nearctic shiners (Leuciscidae): evidence for ongoing speciation, host-switching, and parasite translocation. Parasite 2024; 31:29. [PMID: 38860920 PMCID: PMC11166112 DOI: 10.1051/parasite/2024023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Accepted: 04/21/2024] [Indexed: 06/12/2024] Open
Abstract
A parasitological investigation of Cyprinella venusta and Notropis cf. stramineus sampled in Texas, USA, in the Guadalupe River, revealed the presence of Gyrodactylus crysoleucas Mizelle and Kritsky, 1967 on C. venusta, and Gyrodactylus mediotorus King, Marcogliese, Forest, McLaughlin & Bentzen, 2013 on both fish species. This represents new leuscicid fish hosts and locality records for these two gyrodactylids. Gyrodactylus crysoleucas previously identified from both non-native Californian Notemigonus crysoleucas and from farmed stocks in Minnesota demonstrated intraspecific variability in terms of morphology and genetics as a local adaptation associated with isolation by distance. Results further confirmed G. crysoleucas as alien in the western USA and suggested host-switching involving C. venusta and N. crysoleucas. Conservative morphology and genetics on the part of G. mediotorus from C. venusta and N. cf. stramineus (Guadalupe River) was observed, while higher genetic divergence in the ITS sequences associated with morphological discrepancy was found between the studied G. mediotorus specimens and those of Notropis hudsonius than when considering the parasites of Notropis texanus. The separation of G. mediotorus into geographical subgroups may indicate ongoing speciation linked to the Pleistocene glaciations in North America, and to hydrographic barriers that facilitated separate evolutionary paths leading to speciation. We suggest that deep investigations of Gyrodactylus populations will help to understand the speciation of these parasites and their adaptation to Nearctic fish hosts.
Collapse
Affiliation(s)
- Chahrazed Rahmouni
- Department of Botany and Zoology, Faculty of Science, Masaryk University Kotlářská 2 611 37 Brno Czech Republic
| | - Mária Seifertová
- Department of Botany and Zoology, Faculty of Science, Masaryk University Kotlářská 2 611 37 Brno Czech Republic
| | - Megan G. Bean
- Texas Parks and Wildlife Department 5103 Junction Highway Mountain Home TX 78058 USA
| | - Andrea Šimková
- Department of Botany and Zoology, Faculty of Science, Masaryk University Kotlářská 2 611 37 Brno Czech Republic
| |
Collapse
|
28
|
Li Y, He J, Zhang X, Deng X. The draft genome of Nitzschia closterium f. minutissima and transcriptome analysis reveals novel insights into diatom biosilicification. BMC Genomics 2024; 25:560. [PMID: 38840265 PMCID: PMC11151724 DOI: 10.1186/s12864-024-10479-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Accepted: 05/30/2024] [Indexed: 06/07/2024] Open
Abstract
BACKGROUND Nitzschia closterium f. minutissima is a commonly available diatom that plays important roles in marine aquaculture. It was originally classified as Nitzschia (Bacillariaceae, Bacillariophyta) but is currently regarded as a heterotypic synonym of Phaeodactylum tricornutum. The aim of this study was to obtain the draft genome of the marine microalga N. closterium f. minutissima to understand its phylogenetic placement and evolutionary specialization. Given that the ornate hierarchical silicified cell walls (frustules) of diatoms have immense applications in nanotechnology for biomedical fields, biosensors and optoelectric devices, transcriptomic data were generated by using reference genome-based read mapping to identify significantly differentially expressed genes and elucidate the molecular processes involved in diatom biosilicification. RESULTS In this study, we generated 13.81 Gb of pass reads from the PromethION sequencer. The draft genome of N. closterium f. minutissima has a total length of 29.28 Mb, and contains 28 contigs with an N50 value of 1.23 Mb. The GC content was 48.55%, and approximately 18.36% of the genome assembly contained repeat sequences. Gene annotation revealed 9,132 protein-coding genes. The results of comparative genomic analysis showed that N. closterium f. minutissima was clustered as a sister lineage of Phaeodactylum tricornutum and the divergence time between them was estimated to be approximately 17.2 million years ago (Mya). CAFF analysis demonstrated that 220 gene families that significantly changed were unique to N. closterium f. minutissima and that 154 were specific to P. tricornutum, moreover, only 26 gene families overlapped between these two species. A total of 818 DEGs in response to silicon were identified in N. closterium f. minutissima through RNA sequencing, these genes are involved in various molecular processes such as transcription regulator activity. Several genes encoding proteins, including silicon transporters, heat shock factors, methyltransferases, ankyrin repeat domains, cGMP-mediated signaling pathways-related proteins, cytoskeleton-associated proteins, polyamines, glycoproteins and saturated fatty acids may contribute to the formation of frustules in N. closterium f. minutissima. CONCLUSIONS Here, we described a draft genome of N. closterium f. minutissima and compared it with those of eight other diatoms, which provided new insight into its evolutionary features. Transcriptome analysis to identify DEGs in response to silicon will help to elucidate the underlying molecular mechanism of diatom biosilicification in N. closterium f. minutissima.
Collapse
Affiliation(s)
- Yajun Li
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences (CATAS) & Key Laboratory of Biology and Genetic Resources of Tropical Crops of Hainan Province, Haikou, 571101, China.
- Hainan Provincial Key Laboratory for Functional Components Research and Utilization of Marine Bioresources, Haikou, 571101, China.
| | - Jinman He
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences (CATAS) & Key Laboratory of Biology and Genetic Resources of Tropical Crops of Hainan Province, Haikou, 571101, China
- Hainan Provincial Key Laboratory for Functional Components Research and Utilization of Marine Bioresources, Haikou, 571101, China
| | - Xiuxia Zhang
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences (CATAS) & Key Laboratory of Biology and Genetic Resources of Tropical Crops of Hainan Province, Haikou, 571101, China
- Hainan Provincial Key Laboratory for Functional Components Research and Utilization of Marine Bioresources, Haikou, 571101, China
| | - Xiaodong Deng
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences (CATAS) & Key Laboratory of Biology and Genetic Resources of Tropical Crops of Hainan Province, Haikou, 571101, China.
- Hainan Provincial Key Laboratory for Functional Components Research and Utilization of Marine Bioresources, Haikou, 571101, China.
| |
Collapse
|
29
|
Shi L, Wang X, Yang X, Lyu T, Wang L, Zhou S, Dong Y, Wu X, Shang Y, Zhang H. Effect of locomotor preference on the evolution of mitochondrial genes in Bovidae. Sci Rep 2024; 14:12944. [PMID: 38839875 PMCID: PMC11153648 DOI: 10.1038/s41598-024-63937-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 06/03/2024] [Indexed: 06/07/2024] Open
Abstract
Locomotor preferences and habitat types may drive animal evolution. In this study, we speculated that locomotor preference and habitat type may have diverse influences on Bovidae mitochondrial genes. We used selection pressure and statistical analysis to explore the evolution of mitochondrial DNA (mtDNA) protein-coding genes (PCGs) from diverse locomotor preferences and habitat types. Our study demonstrates that locomotor preference (energy demand) drives the evolution of Bovidae in mtDNA PCGs. The habitat types had no significant effect on the rate of evolution in Bovidae mitochondrial genes. Our study provides deep insight into the adaptation of Bovidae.
Collapse
Affiliation(s)
- Lupeng Shi
- College of Life Sciences, Qufu Normal University, Qufu, Shandong, China
| | - Xibao Wang
- College of Life Sciences, Qufu Normal University, Qufu, Shandong, China
| | - Xiufeng Yang
- College of Life Sciences, Qufu Normal University, Qufu, Shandong, China
| | - Tianshu Lyu
- College of Life Sciences, Qufu Normal University, Qufu, Shandong, China
| | - Lidong Wang
- College of Life Sciences, Qufu Normal University, Qufu, Shandong, China
| | - Shengyang Zhou
- College of Life Sciences, Qufu Normal University, Qufu, Shandong, China
| | - Yuehuan Dong
- College of Life Sciences, Qufu Normal University, Qufu, Shandong, China
| | - Xiaoyang Wu
- College of Life Sciences, Qufu Normal University, Qufu, Shandong, China
| | - Yongquan Shang
- College of Life Sciences, Qufu Normal University, Qufu, Shandong, China
| | - Honghai Zhang
- College of Life Sciences, Qufu Normal University, Qufu, Shandong, China.
| |
Collapse
|
30
|
Tao K, Tao L, Huang J, Duan H, Luo Y, Li L. Complete chloroplast genome structural characterization of two Aerides (Orchidaceae) species with a focus on phylogenetic position of Aerides flabellata. BMC Genomics 2024; 25:552. [PMID: 38825700 PMCID: PMC11145882 DOI: 10.1186/s12864-024-10458-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Accepted: 05/27/2024] [Indexed: 06/04/2024] Open
Abstract
BACKGROUND The disputed phylogenetic position of Aerides flabellata Rolfe ex Downie, due to morphological overlaps with related species, was investigated based on evidence of complete chloroplast (cp) genomes. The structural characterization of complete cp genomes of A. flabellata and A. rosea Lodd. ex Lindl. & Paxton were analyzed and compared with those of six related species in "Vanda-Aerides alliance" to provide genomic information on taxonomy and phylogeny. RESULTS The cp genomes of A. flabellata and A. rosea exhibited conserved quadripartite structures, 148,145 bp and 147,925 bp in length, with similar GC content (36.7 ~ 36.8%). Gene annotations revealed 110 single-copy genes, 18 duplicated in inverted regions, and ten with introns. Comparative analysis across related species confirmed stable sequence identity and higher variation in single-copy regions. However, there are notable differences in the IR regions between two Aerides Lour. species and the other six related species. The phylogenetic analysis based on CDS from complete cp genomes indicated that Aerides species except A. flabellata formed a monophyletic clade nested in the subtribe Aeridinae, being a sister group to Renanthera Lour., consistent with previous studies. Meanwhile, a separate clade consisted of A. flabellata and six Vanda R. Br. species was formed, as a sister taxon to Holcoglossum Schltr. CONCLUSIONS This research was the first report on the complete cp genomes of A. flabellata. The results provided insights into understanding of plastome evolution and phylogenetic relationships of Aerides. The phylogenetic analysis based on complete cp genomes showed that A. flabellata should be placed in Vanda rather than in Aerides.
Collapse
Affiliation(s)
- Kaifeng Tao
- College of Forestry, Southwest Forestry University, Kunming, Yunnan, 650224, China
| | - Lei Tao
- College of Forestry, Southwest Forestry University, Kunming, Yunnan, 650224, China
| | - Jialin Huang
- School of Chemistry, Biology and Environment, Yuxi Normal University, Yuxi, Yunnan, 653100, China
| | - Hanning Duan
- College of Forestry, Southwest Forestry University, Kunming, Yunnan, 650224, China
| | - Yan Luo
- Southeast Asia Biodiversity Research Institute, Chinese Academy of Sciences & Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, Yunnan, China.
| | - Lu Li
- College of Forestry, Southwest Forestry University, Kunming, Yunnan, 650224, China.
| |
Collapse
|
31
|
Zhan L, He J, Meng S, Guo Z, Chen Y, Storey KB, Zhang J, Yu D. Mitochondrial Protein-Coding Gene Expression in the Lizard Sphenomorphus incognitus (Squamata:Scincidae) Responding to Different Temperature Stresses. Animals (Basel) 2024; 14:1671. [PMID: 38891717 PMCID: PMC11170996 DOI: 10.3390/ani14111671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2024] [Revised: 05/25/2024] [Accepted: 05/31/2024] [Indexed: 06/21/2024] Open
Abstract
In the context of global warming, the frequency of severe weather occurrences, such as unexpected cold spells and heat waves, will grow, as well as the intensity of these natural disasters. Lizards, as a large group of reptiles, are ectothermic. Their body temperatures are predominantly regulated by their environment and temperature variations directly impact their behavior and physiological activities. Frequent cold periods and heat waves can affect their biochemistry and physiology, and often their ability to maintain their body temperature. Mitochondria, as the center of energy metabolism, are crucial for maintaining body temperature, regulating metabolic rate, and preventing cellular oxidative damage. Here, we used RT-qPCR technology to investigate the expression patterns and their differences for the 13 mitochondrial PCGs in Sphenomorphus incognitus (Squamata:Scincidae), also known as the brown forest skink, under extreme temperature stress at 4 °C, 8 °C, 34 °C, and 38 °C for 24 h, compared to the control group at 25 °C. In southern China, for lizards, 4 °C is close to lethal, and 8 °C induces hibernation, while 34/38 °C is considered hot and environmentally realistic. Results showed that at a low temperature of 4 °C for 24 h, transcript levels of ATP8, ND1, ND4, COI, and ND4L significantly decreased, to values of 0.52 ± 0.08, 0.65 ± 0.04, 0.68 ± 0.10, 0.28 ± 0.02, and 0.35 ± 0.02, respectively, compared with controls. By contrast, transcript levels of COIII exhibited a significant increase, with a mean value of 1.86 ± 0.21. However, exposure to 8 °C for 24 h did not lead to an increase in transcript levels. Indeed, transcript levels of ATP6, ATP8, ND1, ND3, and ND4 were significantly downregulated, to 0.48 ± 0.11, 0.68 ± 0.07, 0.41 ± 0.08, 0.54 ± 0.10, and 0.52 ± 0.07, respectively, as compared with controls. Exposure to a hot environment of 34 °C for 24 h led to an increase in transcript levels of COI, COII, COIII, ND3, ND5, CYTB, and ATP6, with values that were 3.3 ± 0.24, 2.0 ± 0.2, 2.70 ± 1.06, 1.57 ± 0,08, 1.47 ± 0.13, 1.39 ± 0.56, and 1.86 ± 0.12, respectively, over controls. By contrast, ND4L exhibited a significant decrease (to 0.31 ± 0.01) compared with controls. When exposed to 38 °C, the transcript levels of the 13 PCGs significantly increased, ranging from a 2.04 ± 0.23 increase in ND1 to a 6.30 ± 0.96 rise in ND6. Under two different levels of cold and heat stress, the expression patterns of mitochondrial genes in S. incognitus vary, possibly associated with different strategies employed by this species in response to low and high temperatures, allowing for rapid compensatory adjustments in mitochondrial electron transport chain proteins in response to temperature changes. Furthermore, this underscores once again the significant role of mitochondrial function in determining thermal plasticity in reptiles.
Collapse
Affiliation(s)
- Lemei Zhan
- College of Life Sciences, Zhejiang Normal University, Jinhua 321004, China; (L.Z.)
| | - Jingyi He
- College of Life Sciences, Zhejiang Normal University, Jinhua 321004, China; (L.Z.)
| | - Siqi Meng
- College of Life Sciences, Zhejiang Normal University, Jinhua 321004, China; (L.Z.)
| | - Zhiqiang Guo
- College of Life Sciences, Zhejiang Normal University, Jinhua 321004, China; (L.Z.)
| | - Yuxin Chen
- College of Life Sciences, Zhejiang Normal University, Jinhua 321004, China; (L.Z.)
| | - Kenneth B. Storey
- Department of Biology, Carleton University, Ottawa, ON K1S5B6, Canada;
| | - Jiayong Zhang
- College of Life Sciences, Zhejiang Normal University, Jinhua 321004, China; (L.Z.)
| | - Danna Yu
- College of Life Sciences, Zhejiang Normal University, Jinhua 321004, China; (L.Z.)
- Key Lab of Wildlife Biotechnology, Conservation and Utilization of Zhejiang Province, Zhejiang Normal University, Jinhua 321004, China
| |
Collapse
|
32
|
Fernández MV, Beltramino AA, Vogler RE, Hamann MI. Morphological and molecular characterization of brown-banded broodsacs and metacercariae of Leucochloridium (Trematoda: Leucochloridiidae) parasitizing the semi-slug Omalonyx unguis (Succineidae) in Argentina. J Invertebr Pathol 2024; 204:108112. [PMID: 38631556 DOI: 10.1016/j.jip.2024.108112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2023] [Revised: 04/09/2024] [Accepted: 04/14/2024] [Indexed: 04/19/2024]
Abstract
Trematodes of the genus Leucochloridium exhibit an unusual transmission strategy among mollusks (intermediate host). The fully developed sporocyst, housing encysted metacercariae, displays vivid coloration and rhythmic activity in the snail's tentacle, mimicking insect larvae. These strategies attract insectivorous birds, their final hosts, thereby increasing the chances of completing their life cycle. In South America, the reports of adults and larval stages of Leucochloridium are scarce. Brown-banded broodsac of Leucochloridium sp. were obtained from Omalonyx unguis collected in a shallow lake from Corrientes Province, Argentina. Here, we morphologically characterized the larval stages (broodsac and metacercaria), identified the parasite through DNA sequences from nuclear 28S-rRNA (28S) and the mitochondrial cytochrome c oxidase I (COI) genes, and explored its evolutionary affinities with the Leucochloridium species available in GenBank. The present broodsac displays brown bands, with a yellowish background in the first two-thirds and yellowish-white in the last third. Based on morphological comparisons, the broodsac and metacercaria described in this study could not be conclusively categorized under any known South American species of Leucochloridium. In relation to the phylogenetic reconstructions, Leucochloridium sp. consistently clustered with L. perturbatum, and species delimitation analyses resulted in recognized Leucochloridium sp. from Argentina as a distinct species. The DNA sequences obtained in this study constitute the first genetic data generated for sporocyst broodsacs in South America. Future studies, incorporating morphology, genetic, and biological data, will be essential for both species identification and the elucidation of leucochloridiid diversity in the region.
Collapse
Affiliation(s)
- María V Fernández
- Centro de Ecología Aplicada del Litoral, Consejo Nacional de Investigaciones Científicas y Técnicas-Universidad Nacional del Nordeste, Corrientes, W 3400, Argentina.
| | - Ariel A Beltramino
- Instituto de Biología Subtropical, Consejo Nacional de Investigaciones Científicas y Técnicas-Universidad Nacional de Misiones, Posadas, N3300LDX, Argentina
| | - Roberto E Vogler
- Instituto de Biología Subtropical, Consejo Nacional de Investigaciones Científicas y Técnicas-Universidad Nacional de Misiones, Posadas, N3300LDX, Argentina
| | - Monika I Hamann
- Centro de Ecología Aplicada del Litoral, Consejo Nacional de Investigaciones Científicas y Técnicas-Universidad Nacional del Nordeste, Corrientes, W 3400, Argentina
| |
Collapse
|
33
|
Yue L, Chen J, Tuo Y, Qi Z, Liu Y, He XL, Zhang B, Hu J, Li Y. Taxonomy and phylogeny of Panus (Polyporales, Panaceae) in China and its relationship with allies. MycoKeys 2024; 105:267-294. [PMID: 38855321 PMCID: PMC11161681 DOI: 10.3897/mycokeys.105.121025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Accepted: 04/26/2024] [Indexed: 06/11/2024] Open
Abstract
Panus is a typical wood-rotting fungi, which plays considerable roles in ecosystems and has significant economic value. The genus Panus currently consists of more than 100 species; however, only eight species have been reported from China. This study aims to distinguish and describe two novel species from the Panussimilis complex, namely Panusminisporus and Panusbaishanzuensis, one new record species from Zhejiang Province, Panussimilis and three common species, Panusconchatus, Panusneostrigosus and Panusrudis, based on detailed morphological and phylogenetic studies, relying on Chinese specimens. Panusminisporus is characterised by its reddish-brown pileus, decurrent lamellae with cross-veins, slender stipe, smaller basidiospores, wider generative hyphae and absence of sclerocystidia. Panusbaishanzuensis is featured by its pileus with concentric and darker ring zone, decurrent lamellae with cross-veins, shorter stipe, longer basidiospores, diverse and shorter cheilocystidia and smaller sclerocystidia. Internal transcribed spacer (ITS) regions, large subunit nuclear ribosomal RNA gene (nLSU) and translation elongation factor 1-α gene (tef-1α) were employed to perform a thorough phylogenetic analysis for genus Panus and related genera, using Bayesian Inference and Maximum Likelihood analysis. The results indicate that Panusminisporus and Panusbaishanzuensis form two independent clades within the Panussimilis complex themselves. Detailed descriptions, taxonomic notes, illustrations etc. were provided. In addition, a key to the reported species of Panus from China is also provided.
Collapse
Affiliation(s)
- Lei Yue
- Engineering Research Centre of Edible and Medicinal Fungi, Ministry of Education, Jilin Agricultural University, Changchun City, 130118, Jilin Province, China
| | - Junliang Chen
- College of Plant Protection, Jilin Agricultural University, Changchun City, 130118, Jilin Province, China
| | - Yonglan Tuo
- Engineering Research Centre of Edible and Medicinal Fungi, Ministry of Education, Jilin Agricultural University, Changchun City, 130118, Jilin Province, China
| | - Zhengxiang Qi
- Engineering Research Centre of Edible and Medicinal Fungi, Ministry of Education, Jilin Agricultural University, Changchun City, 130118, Jilin Province, China
| | - Yajie Liu
- Engineering Research Centre of Edible and Medicinal Fungi, Ministry of Education, Jilin Agricultural University, Changchun City, 130118, Jilin Province, China
| | - Xiao Lan He
- Science and Research Center for Edible Fungi of Qingyuan County, Lishui City, 323800, Zhejiang Province, China
| | - Bo Zhang
- Engineering Research Centre of Edible and Medicinal Fungi, Ministry of Education, Jilin Agricultural University, Changchun City, 130118, Jilin Province, China
| | - Jiajun Hu
- Engineering Research Centre of Edible and Medicinal Fungi, Ministry of Education, Jilin Agricultural University, Changchun City, 130118, Jilin Province, China
- Joint Laboratory of International Cooperation in Modern Agricultural Technology, Ministry of Education, Jilin Agricultural University, Changchun City, 130118, Jilin Province, China
| | - Yu Li
- Engineering Research Centre of Edible and Medicinal Fungi, Ministry of Education, Jilin Agricultural University, Changchun City, 130118, Jilin Province, China
| |
Collapse
|
34
|
Mu T, Lin Y, Keyhani NO, Pu H, Lv Z, Lan C, Xiong J, Chen X, Zhan X, Zhao Z, Lv H, Jibola-Shittu MY, Wu J, Jia P, Huang S, Qiu J, Guan X. Phylogenetic and Morphological Evidence for Three New Species of Diaporthales (Ascomycota) from Fujian Province, China. J Fungi (Basel) 2024; 10:383. [PMID: 38921368 PMCID: PMC11205210 DOI: 10.3390/jof10060383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2024] [Revised: 05/23/2024] [Accepted: 05/24/2024] [Indexed: 06/27/2024] Open
Abstract
Members of the fungal order Diaporthales are sac fungi that include plant pathogens (the notorious chestnut blight fungus), as well as saprobes and endophytes, and are capable of colonizing a wide variety of substrates in different ecosystems, habitats, and hosts worldwide. However, many Diaporthales species remain unidentified, and various inconsistencies within its taxonomic category remain to be resolved. Here, we aimed to identify and classify new species of Diaporthales by using combined morphological and molecular characterization and coupling this information to expand our current phylogenetic understanding of this order. Fungal samples were obtained from dead branches and diseasedleaves of Camellia (Theaceae) and Castanopsis (Fagaceae) in Fujian Province, China. Based on morphological characteristics and molecular phylogenetic analyses derived from the combined nucleotide sequences of loci of the internal transcribed spacer regions with the intervening 5.8S nrRNA gene (ITS), the 28S large subunit of nuclear ribosomal RNA gene (LSU), the translation elongation factor 1-α gene (tef1), the partial beta-tubulin gene (tub2), and partial RNA polymerase II second-largest subunit gene (rpb2), three new species of Diaporthales were identified and characterized. They are as follows: Chrysofolia camelliae sp. nov., Dendrostoma castanopsidis sp. nov., and Pseudoplagiostoma wuyishanense sp. nov. They are described and illustrated. This study extends our understanding of species diversity within the Diaporthales.
Collapse
Affiliation(s)
- Taichang Mu
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (T.M.); (Y.L.); (H.P.); (Z.L.); (C.L.); (X.C.); (X.Z.); (Z.Z.); (H.L.); (M.Y.J.-S.)
| | - Yongsheng Lin
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (T.M.); (Y.L.); (H.P.); (Z.L.); (C.L.); (X.C.); (X.Z.); (Z.Z.); (H.L.); (M.Y.J.-S.)
| | - Nemat O. Keyhani
- Department of Biological Sciences, University of Illinois, Chicago, IL 60607, USA;
| | - Huili Pu
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (T.M.); (Y.L.); (H.P.); (Z.L.); (C.L.); (X.C.); (X.Z.); (Z.Z.); (H.L.); (M.Y.J.-S.)
| | - Ziying Lv
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (T.M.); (Y.L.); (H.P.); (Z.L.); (C.L.); (X.C.); (X.Z.); (Z.Z.); (H.L.); (M.Y.J.-S.)
| | - Chenhui Lan
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (T.M.); (Y.L.); (H.P.); (Z.L.); (C.L.); (X.C.); (X.Z.); (Z.Z.); (H.L.); (M.Y.J.-S.)
| | - Jinming Xiong
- Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China;
| | - Xiaohao Chen
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (T.M.); (Y.L.); (H.P.); (Z.L.); (C.L.); (X.C.); (X.Z.); (Z.Z.); (H.L.); (M.Y.J.-S.)
| | - Xinyang Zhan
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (T.M.); (Y.L.); (H.P.); (Z.L.); (C.L.); (X.C.); (X.Z.); (Z.Z.); (H.L.); (M.Y.J.-S.)
| | - Zhiying Zhao
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (T.M.); (Y.L.); (H.P.); (Z.L.); (C.L.); (X.C.); (X.Z.); (Z.Z.); (H.L.); (M.Y.J.-S.)
| | - Huajun Lv
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (T.M.); (Y.L.); (H.P.); (Z.L.); (C.L.); (X.C.); (X.Z.); (Z.Z.); (H.L.); (M.Y.J.-S.)
| | - Motunrayo Yemisi Jibola-Shittu
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (T.M.); (Y.L.); (H.P.); (Z.L.); (C.L.); (X.C.); (X.Z.); (Z.Z.); (H.L.); (M.Y.J.-S.)
| | - Jianlong Wu
- Xiamen Botanical Garden, Xiamen 361004, China;
| | - Peisong Jia
- Institute of Plant Protection, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China;
| | - Shuaishuai Huang
- School of Ecology and Environment, Tibet University, Lhasa 850014, China;
| | - Junzhi Qiu
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (T.M.); (Y.L.); (H.P.); (Z.L.); (C.L.); (X.C.); (X.Z.); (Z.Z.); (H.L.); (M.Y.J.-S.)
| | - Xiayu Guan
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| |
Collapse
|
35
|
Iqbal Z, Azad R, Chen XS, Lin XL, Zhou Z, Wang XM, Nie RE. A New Species of Scymnus (Coleoptera, Coccinellidae) from Pakistan with Mitochondrial Genome and Its Phylogenetic Implications. INSECTS 2024; 15:371. [PMID: 38786927 PMCID: PMC11122443 DOI: 10.3390/insects15050371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2024] [Revised: 05/13/2024] [Accepted: 05/16/2024] [Indexed: 05/25/2024]
Abstract
In this study, a new species of the subgenus Pullus belonging to the Scymnus genus from Pakistan, Scymnus (Pullus) cardi sp. nov., was described and illustrated, with information on its distribution, host plants, and prey. Additionally, the completed mitochondrial genome (mitogenome) of the new species using high-throughput sequencing technology was obtained. The genome contains the typical 37 genes (13 protein-coding genes, two ribosomal RNAs, and 22 transfer RNAs) and a non-coding control region, and is arranged in the same order as that of the putative ancestor of beetles. The AT content of the mitogenome is approximately 85.1%, with AT skew and GC skew of 0.05 and -0.43, respectively. The calculated values of relative synonymous codon usage (RSCU) determine that the codon UUA (L) has the highest frequency. Furthermore, we explored the phylogenetic relationship among 59 representatives of the Coccinellidae using Bayesian inference and maximum likelihood methods, the results of which strongly support the monophyly of Coccinellinae. The phylogenetic results positioned Scymnus (Pullus) cardi in a well-supported clade with Scymnus (Pullus) loewii and Scymnus (Pullus) rubricaudus within the genus Scymnus and the tribe Scymnini. The mitochondrial sequence of S. (P.) cardi will contribute to the mitochondrial genome database and provide helpful information for the identification and phylogeny of Coccinellidae.
Collapse
Affiliation(s)
- Zafar Iqbal
- Key Laboratory of the Conservation and Exploitation of Biological Resources, College of Life Sciences, Anhui Normal University, Wuhu 241000, China; (Z.I.); (X.-L.L.)
| | - Rashid Azad
- Department of Entomology, The University of Haripur, Haripur 22620, Pakistan;
- Department of Entomology, South China Agricultural University, Guangzhou 510640, China
| | - Xiao-Sheng Chen
- Engineering Research Center of Biological Control, Ministry of Education, Guangzhou 510642, China;
- Department of Forest Protection, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China
| | - Xiao-Ling Lin
- Key Laboratory of the Conservation and Exploitation of Biological Resources, College of Life Sciences, Anhui Normal University, Wuhu 241000, China; (Z.I.); (X.-L.L.)
| | - Zichen Zhou
- Department of Life Sciences, Imperial College London, Exhibition Road, London SW7 2BX, UK;
- Department of Life Sciences, Natural History Museum, Cromwell Road, London SW7 5BD, UK
| | - Xing-Min Wang
- Department of Entomology, South China Agricultural University, Guangzhou 510640, China
- Engineering Technology Research Center of Agricultural Pest Biocontrol of Guangdong Province, Guangzhou 510640, China
| | - Rui-E Nie
- Key Laboratory of the Conservation and Exploitation of Biological Resources, College of Life Sciences, Anhui Normal University, Wuhu 241000, China; (Z.I.); (X.-L.L.)
| |
Collapse
|
36
|
Wu M, Chen T, Shen W. New camaenid genus and species from Zhejiang, East China (Eupulmonata, Helicoidea). Zookeys 2024; 1202:135-154. [PMID: 38800562 PMCID: PMC11112161 DOI: 10.3897/zookeys.1202.118964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Accepted: 04/17/2024] [Indexed: 05/29/2024] Open
Abstract
We report a new land snail species representing a new genus from the mountainous area of Zhejiang, China. The snail has a depressed shell with granules all over the surface. The soft part of the new taxon is characterized by the presence of a mantle lobe whose form is reviewed herein across a wide range of helicoid snails, the presence of a developed epiphallic papilla, and the absence of a penial sheath, a dart sac apparatus and a flagellum. As indicated by a molecular-based phylogeny (16S + ITS2), the new taxon is deeply nested in the eastern Asian camaenid genera and shows a close relationship with the camaenids distributed in Central China.
Collapse
Affiliation(s)
- Min Wu
- School of Life Sciences, Nanjing University, Xianlindadao 163, Qixia, Nanjing 210023, ChinaNanjing UniversityNanjingChina
| | - Tian Chen
- Southern University of Science and Technology, Xueyandadao 1088, Nanshan, Shenzhen 518055, ChinaSouthern University of Science and TechnologyShenzhenChina
| | - Wang Shen
- School of Life Sciences, Nanjing University, Xianlindadao 163, Qixia, Nanjing 210023, ChinaNanjing UniversityNanjingChina
| |
Collapse
|
37
|
Zou Y, Zhang Z, Zeng Y, Hu H, Hao Y, Huang S, Li B. Common Methods for Phylogenetic Tree Construction and Their Implementation in R. Bioengineering (Basel) 2024; 11:480. [PMID: 38790347 PMCID: PMC11117635 DOI: 10.3390/bioengineering11050480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2024] [Revised: 05/04/2024] [Accepted: 05/07/2024] [Indexed: 05/26/2024] Open
Abstract
A phylogenetic tree can reflect the evolutionary relationships between species or gene families, and they play a critical role in modern biological research. In this review, we summarize common methods for constructing phylogenetic trees, including distance methods, maximum parsimony, maximum likelihood, Bayesian inference, and tree-integration methods (supermatrix and supertree). Here we discuss the advantages, shortcomings, and applications of each method and offer relevant codes to construct phylogenetic trees from molecular data using packages and algorithms in R. This review aims to provide comprehensive guidance and reference for researchers seeking to construct phylogenetic trees while also promoting further development and innovation in this field. By offering a clear and concise overview of the different methods available, we hope to enable researchers to select the most appropriate approach for their specific research questions and datasets.
Collapse
Affiliation(s)
- Yue Zou
- College of Life Sciences, Chongqing Normal University, Chongqing 401331, China; (Y.Z.); (Z.Z.); (Y.Z.); (H.H.); (Y.H.)
| | - Zixuan Zhang
- College of Life Sciences, Chongqing Normal University, Chongqing 401331, China; (Y.Z.); (Z.Z.); (Y.Z.); (H.H.); (Y.H.)
| | - Yujie Zeng
- College of Life Sciences, Chongqing Normal University, Chongqing 401331, China; (Y.Z.); (Z.Z.); (Y.Z.); (H.H.); (Y.H.)
| | - Hanyue Hu
- College of Life Sciences, Chongqing Normal University, Chongqing 401331, China; (Y.Z.); (Z.Z.); (Y.Z.); (H.H.); (Y.H.)
| | - Youjin Hao
- College of Life Sciences, Chongqing Normal University, Chongqing 401331, China; (Y.Z.); (Z.Z.); (Y.Z.); (H.H.); (Y.H.)
| | - Sheng Huang
- Animal Nutrition Institute, Chongqing Academy of Animal Science, Chongqing 402460, China
| | - Bo Li
- College of Life Sciences, Chongqing Normal University, Chongqing 401331, China; (Y.Z.); (Z.Z.); (Y.Z.); (H.H.); (Y.H.)
| |
Collapse
|
38
|
Song WL, Chen SL. Arcyria similaris: A new myxomycete species from China. Mycologia 2024; 116:409-417. [PMID: 38442243 DOI: 10.1080/00275514.2024.2312077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Accepted: 01/26/2024] [Indexed: 03/07/2024]
Abstract
A new myxomycete species, Arcyria similaris, was reported herein. The specimens were found and collected in the field on dead bark from Jingangtai National Geopark in Henan Province of China. This species has distinct and unique morphological characteristics, including dark grayish olive sporothecae that fade to smoke gray with age, shallow saucer-shaped cups with marked reticulations and thick papillae on the inner surface, a netted capillitium with many bulges, uniformly marked with low, dense, and irregular reticulations, and spores (8.0-)9.3-10.1(-10.9) μm in diameter, marked with sparse small warts and grouped prominent warts. Apart from a comprehensive morphological study, partial sequences of the nuclear 18S rDNA and elongation factor-1 alpha (EF-1α) genes were also provided in this study. This new species was described and illustrated morphologically. The specimens are deposited in the Herbarium of Fungi of Nanjing Normal University (HFNNU).
Collapse
Affiliation(s)
- Wen-Long Song
- School of Life Sciences, Nanjing Normal University, No.1 Wenyuan Road Qixia District, Nanjing 210023, Jiangsu Province, China
| | - Shuang-Lin Chen
- School of Life Sciences, Nanjing Normal University, No.1 Wenyuan Road Qixia District, Nanjing 210023, Jiangsu Province, China
| |
Collapse
|
39
|
Guo X, Wang H, Fu K, Ding X, Deng J, Guo W, Rao Q. First report of the complete mitochondrial genome of Carpomya pardalina (Bigot) (Diptera: Tephritidae) and phylogenetic relationships with other Tephritidae. Heliyon 2024; 10:e29233. [PMID: 38681631 PMCID: PMC11053197 DOI: 10.1016/j.heliyon.2024.e29233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 03/31/2024] [Accepted: 04/03/2024] [Indexed: 05/01/2024] Open
Abstract
Carpomya pardalina is known for its potential invasiveness, which poses a significant and alarming threat to Cucurbitaceae crops. It is considered a highly perilous pest species that requires immediate attention for quarantine and prevention. Due to the challenges in distinguishing pests of the Tephritidae family based on morphological characteristics, it is imperative to elucidate the mitochondrial genomic information of C. pardalina. In this study, the mitochondrial genome sequence of C. pardalina was determined and analyzed using next-generation sequencing. The results revealed that the mitogenome sequence had a total length of 16,257 bp, representing a typical circular molecule. It consisted of 13 PCGs, two rRNA genes, 22 tRNA genes and a non-coding region. The structure and organization of the mitochondrial genome of C. pardalina were found to be typical and similar to the published homologous sequences of other fruit flies in the Tephritidae family. Phylogenetic analysis confirmed that C. pardalina belongs to the Carpomya genus, which is consistent with traditional morphological taxonomy. Additionally, Carpomya and Rhagoletis were identified as sister groups. This study presents the first report of the complete mitochondrial genome of C. pardalina, which can serve as a valuable resource for future investigations in species diagnosis, evolutionary biology, prevention and control measures.
Collapse
Affiliation(s)
- Xianting Guo
- Key Lab for Biology of Crop Pathogens and Insect Pests and Their Ecological Regulation of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang A & F University, Hangzhou, 311300, China
| | - Hualing Wang
- College of Forestry, Hebei Agricultural University, Baoding, 071000, Hebei, China
| | - Kaiyun Fu
- Key Laboratory of Integrated Pest Management on Crops in Northwestern Oasis, Ministry of Agriculture and Rural Affairs, Xinjiang Key Laboratory of Agricultural Bio-safety, Institute of Plant Protection, Xinjiang Academy of Agricultural Sciences, Urumqi, Xinjiang, 830091, China
| | - Xinhua Ding
- Key Laboratory of Integrated Pest Management on Crops in Northwestern Oasis, Ministry of Agriculture and Rural Affairs, Xinjiang Key Laboratory of Agricultural Bio-safety, Institute of Plant Protection, Xinjiang Academy of Agricultural Sciences, Urumqi, Xinjiang, 830091, China
| | - Jianyu Deng
- Key Lab for Biology of Crop Pathogens and Insect Pests and Their Ecological Regulation of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang A & F University, Hangzhou, 311300, China
| | - Wenchao Guo
- Key Laboratory of Integrated Pest Management on Crops in Northwestern Oasis, Ministry of Agriculture and Rural Affairs, Xinjiang Key Laboratory of Agricultural Bio-safety, Institute of Plant Protection, Xinjiang Academy of Agricultural Sciences, Urumqi, Xinjiang, 830091, China
| | - Qiong Rao
- Key Lab for Biology of Crop Pathogens and Insect Pests and Their Ecological Regulation of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang A & F University, Hangzhou, 311300, China
| |
Collapse
|
40
|
Hua CJ, Huang Y, Li HQ, Feng JM, Qiao JL, Hu S, Liu W, Shu XJ. Characterization of the complete mitochondrial genome of Ergasilus anchoratus Markevich, 1946 (Ergasilidae) and phylogeny of Copepoda. Syst Parasitol 2024; 101:33. [PMID: 38647718 DOI: 10.1007/s11230-023-10140-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Accepted: 12/11/2023] [Indexed: 04/25/2024]
Abstract
The mitochondrial (mt) genome can provide data for phylogenetic analyses and evolutionary biology. Herein, we sequenced and annotated the complete mt genome of Ergasilus anchoratus. This mt genome was 13852 bp long and comprised 13 protein-coding genes (PCGs), 22 tRNAs and 2 rRNAs. All PCGs used the standard ATN start codons and complete TAA/TAG termination codons. A majority of tRNA genes exhibited standard cloverleaf secondary structures, with the exception of one tRNA that lacked the TψC arm (trnC), and three tRNAs that lacked the DHU arm (trnR, trnS1 and trnS2). Phylogenetic analyses conducted using Bayesian inference (BI) and maximum likelihood (ML) methods both supported Ergasilidae as a monophyletic family forming a sister group to Lernaea cyprinacea and Paracyclopina nana. It also supported the monophyly of orders Calanoida, Cyclopoida, and Siphonostomatoida; and the monophyly of families Harpacticidae, Ergasilidae, Diaptomidae, and Calanidae. The gene orders of E. anchoratus and Sinergasilus undulatus were identical, which represents the first instance of two identical gene orders in copepods. More mt genomes are needed to better understand the phylogenetic relationships within Copepoda in the future.
Collapse
Affiliation(s)
- Cong-Jie Hua
- Hubei Key Laboratory of Cognitive and Affective Disorders, Institute of Biomedical Sciences, School of Medicine, Jianghan University, Wuhan, 430056, China
- Department of Pathogenic Biology, School of Medicine, Jianghan University, Wuhan, 430056, China
| | - Yan Huang
- Hubei Key Laboratory of Cognitive and Affective Disorders, Institute of Biomedical Sciences, School of Medicine, Jianghan University, Wuhan, 430056, China
| | - Hui-Quan Li
- Hubei Key Laboratory of Cognitive and Affective Disorders, Institute of Biomedical Sciences, School of Medicine, Jianghan University, Wuhan, 430056, China
| | - Jin-Mei Feng
- Department of Pathogenic Biology, School of Medicine, Jianghan University, Wuhan, 430056, China
| | - Jia-Lu Qiao
- Hubei Key Laboratory of Cognitive and Affective Disorders, Institute of Biomedical Sciences, School of Medicine, Jianghan University, Wuhan, 430056, China
| | - Song Hu
- Hubei Key Laboratory of Cognitive and Affective Disorders, Institute of Biomedical Sciences, School of Medicine, Jianghan University, Wuhan, 430056, China
| | - Wei Liu
- Hubei Key Laboratory of Cognitive and Affective Disorders, Institute of Biomedical Sciences, School of Medicine, Jianghan University, Wuhan, 430056, China
| | - Xi-Ji Shu
- Hubei Key Laboratory of Cognitive and Affective Disorders, Institute of Biomedical Sciences, School of Medicine, Jianghan University, Wuhan, 430056, China.
| |
Collapse
|
41
|
Zhang Y, Lu Y, Jin Z, Li B, Wu L, He Y. Antifungal mechanism of cell-free supernatant produced by Trichoderma virens and its efficacy for the control of pear Valsa canker. Front Microbiol 2024; 15:1377683. [PMID: 38694806 PMCID: PMC11061385 DOI: 10.3389/fmicb.2024.1377683] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2024] [Accepted: 03/13/2024] [Indexed: 05/04/2024] Open
Abstract
Introduction Pear Valsa canker, caused by Valsa pyri (V. pyri), poses a major threat to pear production. We aimed to assess the effectiveness of the cell-free supernatant (CFS) produced by Trichoderma virens (T. virens) to control the development of pear Valsa canker and reveal the inhibitory mechanism against the pathogenic fungi. Results Using morphological characteristics and phylogenetic analysis, the pathogen G1H was identified as V. pyri, and the biocontrol fungus WJ561 was identified as Trichoderma virens. CFS derived from WJ561 exhibited strong inhibition of mycelial growth and was capable of reducing the pathogenicity of V. pyri on pear leaves and twigs. Scanning electron microscopy (SEM) observations revealed deformations and shrinkages in the fungal hyphae treated with CFS. The CFS also destroyed the hyphal membranes leading to the leakage of cellular contents and an increase in the malondialdehyde (MDA) content. Additionally, CFS significantly inhibited the activities of catalase (CAT) and superoxide dismutase (SOD), and downregulated the expression of antioxidant defense-related genes in V. pyri, causing the accumulation of reactive oxygen species (ROS). Artesunate, identified as the main component in CFS by liquid chromatograph-mass spectrometry (LC-MS), exhibited antifungal activity against V. pyri. Conclusion Our findings demonstrate the promising potential of T. virens and its CFS in controlling pear Valsa canker. The primary inhibitory mechanism of CFS involves multiple processes, including membrane damage and negatively affecting enzymatic detoxification pathways, consequently leading to hyphal oxidative damage of V. pyri. This study lays a theoretical foundation for the utilization of T. virens to control V. pyri in practical production.
Collapse
Affiliation(s)
- Yang Zhang
- School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Ying Lu
- School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Zhaoyang Jin
- School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Bo Li
- School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Li Wu
- School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Yujian He
- School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing, China
- School of Future Technology, University of Chinese Academy of Sciences, Beijing, China
- Institute of Farmland Water Conservancy and Soil Fertilizer, Xinjiang Academy of Agricultural and Reclamation Science, Shihezi City, China
| |
Collapse
|
42
|
Zhou H, Li S, Shen Z, Liu S, Rao D. A new species of Hemiphyllodactylus (Squamata, Gekkonidae) from southwest Yunnan, China. Zookeys 2024; 1197:197-213. [PMID: 38666072 PMCID: PMC11043650 DOI: 10.3897/zookeys.1197.117359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Accepted: 03/27/2024] [Indexed: 04/28/2024] Open
Abstract
A new species of gekkonid, Hemiphyllodactylusgengmaensissp. nov., is described based on six specimens from Gengma Dai and Wa Autonomous County, Yunnan, China. The new species can be distinguished from its congeners by a significant genetic divergence of greater than 9.7% in the mitochondrial ND2 gene and a combination of the following characters: a maximum SVL of 43.24mm; 8 or 9 chin scales; six circumnasal scales; 2 or 3 internasal scales; 9-11 supralabial scales; 8 or 9 infralabial scales; 11-18 dorsal scales; 8-10 ventral scales; a manual lamellar formula of 5-5-5-4 or 5-6-5-4 and a pedal lamellar formula of 5-5-6-5; 20-25 precloacal and femoral pore-bearing scales contiguous in males; dark postorbital stripes or striping on body; dark dorsal transverse blotches present; and a brown postsacral mark bearing anteriorly projecting arms. The discovery of this new species brings the number of Hemiphyllodactylus species in China to 15.
Collapse
Affiliation(s)
- Hongxin Zhou
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education Faculty of Biodiversity and Conservation, Southwest Forestry University, Kunming, Yunnan 650224, ChinaKunming Institute of Zoology, Chinese Academy of SciencesKunmingChina
- Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650201, ChinaSouthwest Forestry UniversityKunmingChina
| | - Shimin Li
- Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650201, ChinaSouthwest Forestry UniversityKunmingChina
- Anhui Normal University, Wuhu, Anhui 241000, ChinaAnhui Normal UniversityWuhuChina
| | - Ziqi Shen
- Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650201, ChinaSouthwest Forestry UniversityKunmingChina
| | - Shuo Liu
- Kunming Natural History Museum of Zoology, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, ChinaKunming Natural History Museum of Zoology, Chinese Academy of ScienceKunmingChina
| | - Dingqi Rao
- Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650201, ChinaSouthwest Forestry UniversityKunmingChina
| |
Collapse
|
43
|
Liu X, Liu Y, Liu J, Zhang H, Shan C, Guo Y, Gong X, Cui M, Li X, Tang M. Correlation between the gut microbiome and neurodegenerative diseases: a review of metagenomics evidence. Neural Regen Res 2024; 19:833-845. [PMID: 37843219 PMCID: PMC10664138 DOI: 10.4103/1673-5374.382223] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 04/19/2023] [Accepted: 06/17/2023] [Indexed: 10/17/2023] Open
Abstract
A growing body of evidence suggests that the gut microbiota contributes to the development of neurodegenerative diseases via the microbiota-gut-brain axis. As a contributing factor, microbiota dysbiosis always occurs in pathological changes of neurodegenerative diseases, such as Alzheimer's disease, Parkinson's disease, and amyotrophic lateral sclerosis. High-throughput sequencing technology has helped to reveal that the bidirectional communication between the central nervous system and the enteric nervous system is facilitated by the microbiota's diverse microorganisms, and for both neuroimmune and neuroendocrine systems. Here, we summarize the bioinformatics analysis and wet-biology validation for the gut metagenomics in neurodegenerative diseases, with an emphasis on multi-omics studies and the gut virome. The pathogen-associated signaling biomarkers for identifying brain disorders and potential therapeutic targets are also elucidated. Finally, we discuss the role of diet, prebiotics, probiotics, postbiotics and exercise interventions in remodeling the microbiome and reducing the symptoms of neurodegenerative diseases.
Collapse
Affiliation(s)
- Xiaoyan Liu
- School of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu Province, China
| | - Yi Liu
- School of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu Province, China
- Institute of Animal Husbandry, Jiangsu Academy of Agricultural Sciences, Nanjing, Jiangsu Province, China
| | - Junlin Liu
- School of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu Province, China
| | - Hantao Zhang
- School of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu Province, China
| | - Chaofan Shan
- School of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu Province, China
| | - Yinglu Guo
- School of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu Province, China
| | - Xun Gong
- Department of Rheumatology & Immunology, Affiliated Hospital of Jiangsu University, Zhenjiang, Jiangsu Province, China
| | - Mengmeng Cui
- Department of Neurology, The Second Affiliated Hospital of Shandong First Medical University, Taian, Shandong Province, China
| | - Xiubin Li
- Department of Neurology, The Second Affiliated Hospital of Shandong First Medical University, Taian, Shandong Province, China
| | - Min Tang
- School of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu Province, China
| |
Collapse
|
44
|
Cai Y, Yin A. The complete mitochondrial genome of Chibiraga houshuaii (Lepidoptera, Limacodidae) and its phylogenetic implications. Sci Rep 2024; 14:7009. [PMID: 38528107 DOI: 10.1038/s41598-024-57709-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Accepted: 03/21/2024] [Indexed: 03/27/2024] Open
Abstract
Chibiraga is a mall East Asian genus in the family Limacodidae (slug-moths). The latter includes many agricultural pests. Mitochondrial genome analysis is an important tool for studying insect molecular identification and phylogenetics. However, there are very few mitogenome sequences available for Limacodidae species, and none for the genus Chibiraga at all. To explore the mitogenome features of Chibiraga and verify its phylogenetic position, the complete mitogenome of Chibiraga houshuaii was sequenced and annotated. The complete 15,487 bp genome encoded 37 mitochondrial genes, including 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, two ribosomal RNA (rRNA) genes, and a control region (CR). Most of the PCGs had typical ATN start codons and terminated with TAA or a single T residue. UUA (Leu2), AUU (Ile), UUU (Phe), AUA (Met) and AAU (Asn) were the five most frequently used codons. All tRNAs were folded into cloverleaf secondary structure, except for trnS1, which lacked the DHU arm. Phylogenetic analyses within the superfamily Zygaenoidea were performed based on multiple datasets from mitochondrial genes. The results showed that the families Phaudidae, Limacodidae and Zygaenidae were respectively recovered as monophyly; C. houshuaii was clustered in a clade with nettle type larvae in Limacodidae.
Collapse
Affiliation(s)
- Yanpeng Cai
- Molecular Diagnostic Research Center, Guizhou University of Traditional Chinese Medicine, Guiyang, 550025, China
| | - Aihui Yin
- Molecular Diagnostic Research Center, Guizhou University of Traditional Chinese Medicine, Guiyang, 550025, China.
| |
Collapse
|
45
|
Liu J, Chen J, Cai X, Yang D, Li X, Liu X. Comparative Analysis of the Mitochondrial Genomes of Chloropidae and Their Implications for the Phylogeny of the Family. Int J Mol Sci 2024; 25:2920. [PMID: 38474171 DOI: 10.3390/ijms25052920] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 02/27/2024] [Accepted: 02/29/2024] [Indexed: 03/14/2024] Open
Abstract
Chloropidae, commonly known as grass flies, represent the most taxonomically diverse family of Diptera Carnoidea, comprising over 3000 described species worldwide. Previous phylogenetic studies of this family have predominantly relied on morphological characters, with mitochondrial genomes being reported in a few species. This study presents 11 newly sequenced mitochondrial genomes (10 Chloropidae and 1 Milichiidae) and provides the first comprehensive comparative analysis of mitochondrial genomes for Chloropidae. Apart from 37 standard genes and the control region, three conserved intergenic sequences across Diptera Cyclorrhapha were identified in all available chloropid mitochondrial genomes. Evolutionary rates within Chloropidae exhibit significant variation across subfamilies, with Chloropinae displaying higher rates than the other three subfamilies. Phylogenetic relationships based on mitochondrial genomes were inferred using maximum likelihood and Bayesian methods. The monophyly of Chloropidae and all four subfamilies is consistently strongly supported, while subfamily relationships within Chloropidae remain poorly resolved, possibly due to rapid evolution.
Collapse
Affiliation(s)
- Jiuzhou Liu
- Hubei Insect Resources Utilization and Sustainable Pest Management Key Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
- College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Jiajia Chen
- Hubei Insect Resources Utilization and Sustainable Pest Management Key Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Xiaodong Cai
- College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Ding Yang
- College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Xuankun Li
- College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Xiaoyan Liu
- Hubei Insect Resources Utilization and Sustainable Pest Management Key Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| |
Collapse
|
46
|
Cadorna CAE, Pahayo DG, Rey JD. The first mitochondrial genome of Calophyllum soulattri Burm.f. Sci Rep 2024; 14:5112. [PMID: 38429360 PMCID: PMC10907642 DOI: 10.1038/s41598-024-55016-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 02/19/2024] [Indexed: 03/03/2024] Open
Abstract
Calophyllum soulattri Burm.f. is traditionally used to treat skin infections and reduce rheumatic pain, yet genetic and genomic studies are still limited. Here, we present the first complete mitochondrial genome of C. soulattri. It is 378,262 bp long with 43.97% GC content, containing 55 genes (30 protein-coding, 5 rRNA, and 20 tRNA). Repeat analysis of the mitochondrial genome revealed 194 SSRs, mostly mononucleotides, and 266 pairs of dispersed repeats ( ≥ 30 bp) that were predominantly palindromic. There were 23 homologous fragments found between the mitochondrial and plastome genomes. We also predicted 345 C-to-U RNA editing sites from 30 protein-coding genes (PCGs) of the C. soulatrii mitochondrial genome. These RNA editing events created the start codon of nad1 and the stop codon of ccmFc. Most PCGs of the C. soulattri mitochondrial genome underwent negative selection, but atp4 and ccmB experienced positive selection. Phylogenetic analyses showed C. soulattri is a sister taxon of Garcinia mangostana. This study has shed light on C. soulattri's evolution and Malpighiales' phylogeny. As the first complete mitochondrial genome in Calophyllaceae, it can be used as a reference genome for other medicinal plant species within the family for future genetic studies.
Collapse
Affiliation(s)
- Charles Anthon E Cadorna
- Plant Molecular Phylogenetics Laboratory, Institute of Biology, College of Science, University of the Philippines, Diliman, 1101, Quezon City, Philippines
| | - Dexter G Pahayo
- Plant Molecular Phylogenetics Laboratory, Institute of Biology, College of Science, University of the Philippines, Diliman, 1101, Quezon City, Philippines
| | - Jessica D Rey
- Plant Molecular Phylogenetics Laboratory, Institute of Biology, College of Science, University of the Philippines, Diliman, 1101, Quezon City, Philippines.
| |
Collapse
|
47
|
Arya M, Ghosh A, Tyagi K, Tyagi I, Bisht SS, Kumar V. Characterization of Complete Mitochondrial Genome of Badri Breed of Bos indicus (Bovidae: Bovinae): Selection Pressure and Comparative Analysis. Biochem Genet 2024:10.1007/s10528-024-10691-y. [PMID: 38407767 DOI: 10.1007/s10528-024-10691-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 01/05/2024] [Indexed: 02/27/2024]
Abstract
High-altitude mammals are often subject to specific environmental obstacles, which exert selective pressure on their physiological and morphological traits, hence driving their evolutionary processes. It is anticipated that these circumstances will lead to the adaptive evolution of protein-coding genes (PCGs) in the mitochondrial genome, which play a crucial role in the oxidative phosphorylation system. In this study, we have generated the complete mitochondrial genome of the Badri breed of Bos indicus inhabiting a high-altitude environment to test the signatures of adaptive evolution on PCGs and their phylogenetic relationships. The complete mitogenome of the Badri breed is 16,339 bp and most tRNAs showed typical clover-leaf secondary structure with a few exceptions, like trnS1 and trnS2 without DHU arm and trnK without DHU loop. Comparative analysis of PCGs indicated that cox1 is the most conserved, while atp6 is the most variable gene. Moreover, the ratios of non-synonymous to synonymous substitution rates indicated the purifying selection (Ka/Ks < 1) in the protein-coding genes that shape the diversity in mitogenome of Bos indicus. Furthermore, Branch-site model (BSM) suggested that cox1, cox2, nad3, nad4L, and nad6 underwent stronger purifying selection (ω < 1) than other PCGs in 15 breeds of 4 species, including Badri. BSM also detected 10 positive sites in PCGs and one in 13 PCGs concatenated dataset. Additional analyses in Datamonkey indicated 11 positive sites and 23 purifying sites in the concatenated dataset, a relaxation of selection strength in nad3, and no evidence of episodic diversifying selection in any PCGs. Phylogeny revealed the sister relationship of the Badri with other breeds of Bos indicus as well as Bos frontalis (Gayal-2). The mitogenome of the Badri breed is an important genomic resource for conservation genetics of this species and also contributes to the understanding of the adaptive evolution of mitochondrial protein coding genes.
Collapse
Affiliation(s)
- Mansi Arya
- Department of Zoology, Kumaun University, Nainital, Uttarakhand, India
| | - Abhishek Ghosh
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, Kolkata, West Bengal, India
- Department of Zoology, University of Calcutta, Kolkata, West Bengal, India
| | - Kaomud Tyagi
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, Kolkata, West Bengal, India.
| | - Inderjeet Tyagi
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, Kolkata, West Bengal, India
| | - Satpal Singh Bisht
- Department of Zoology, Kumaun University, Nainital, Uttarakhand, India
- Vice Chancellor, Soban Singh Jeena University, Almora, Uttarakahand, India
| | - Vikas Kumar
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, Kolkata, West Bengal, India.
| |
Collapse
|
48
|
Qin Q, Chen L, Zhang F, Xu J, Zeng Y. Characterization of the Complete Mitochondrial Genome of Schizothorax kozlovi (Cypriniformes, Cyprinidae, Schizothorax) and Insights into the Phylogenetic Relationships of Schizothorax. Animals (Basel) 2024; 14:721. [PMID: 38473106 DOI: 10.3390/ani14050721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2024] [Revised: 02/20/2024] [Accepted: 02/23/2024] [Indexed: 03/14/2024] Open
Abstract
Schizothorax kozlovi is an endemic and vulnerable fish species found in the upper Yangtze River in China. Over the past few years, the population resources of S. kozlovi have been nearly completely depleted owing to multiple contributing threats. While the complete mitochondrial genomes serve as important molecular markers for phylogenetic and genetic studies, the mitochondrial genome of S. kozlovi has still received little attention. In this study, we analyzed the characterization of the mitochondrial genome of S. kozlovi and investigated the phylogenetic relationships of Schizothorax. The complete mitochondrial genome of S. kozlovi was 16,585 bp in length, which contained thirty-seven genes (thirteen protein-coding genes (PCGs), two ribosomal RNA genes (rRNAs), twenty-two transfer RNA genes (tRNAs)) and two non-coding regions for the origin of light strand (OL) and the control region (CR). There were nine overlapping regions and seventeen intergenic spacers regions in the mitochondrial genome. The genome also showed a bias towards A + T content (55.01%) and had a positive AT-skew (0.08) and a negative GC-skew (-0.20). All the PCGs employed the ATG or GTG as the start codon and TAA, TAG, or single T as the stop codon. Additionally, all of the tRNAs displayed a typical cloverleaf secondary structure, except trnS1 which lacked the D arm. The phylogenetic analysis, based on the maximum likelihood (ML) and Bayesian inference (BI) methods, revealed that the topologies of the phylogenetic tree divided the Schizothorax into four clades and did not support the classification of Schizothorax based on morphology. The phylogenetic status of S. kozlovi was closely related to that of S. chongi. The present study provides valuable genomic information for S. kozlovi and new insights in phylogenetic relationships of Schizothorax. These data could also offer fundamental references and guidelines for the management and conservation of S. kozlovi and other species of Schizothorax.
Collapse
Affiliation(s)
- Qiang Qin
- College of Environmental Science and Engineering, China West Normal University, Nanchong 637009, China
| | - Lin Chen
- Powerchina Chengdu Engineering Corporation Limited, Chengdu 611130, China
| | - Fubin Zhang
- College of Environmental Science and Engineering, China West Normal University, Nanchong 637009, China
| | - Jianghaoyue Xu
- College of Environmental Science and Engineering, China West Normal University, Nanchong 637009, China
| | - Yu Zeng
- College of Life Science, China West Normal University, Nanchong 637009, China
| |
Collapse
|
49
|
Huang Y, Feng JM, Liu W, Sun BL, Shu XJ, Li WX, Wang GT, Hua CJ. Comprehensive molecular characterisation of the complete mitogenome of Ergasilus tumidus and phylogenetic relationships of Copepoda inferred from mitogenomes. Folia Parasitol (Praha) 2024; 71:2024.002. [PMID: 38440897 DOI: 10.14411/fp.2024.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Accepted: 01/05/2024] [Indexed: 03/06/2024]
Abstract
Although parasitic copepods of the genus Ergasilus von Nordmann, 1832 are globally distributed parasites of fish, their phylogenetic relationships with other Copepoda are not clear, and the characteristics of their mitochondrial genomes (mitogenomes) are not thoroughly understood. The objective of this study was to address these knowledge gaps by sequencing the complete mitogenome of Ergasilus tumidus Markevich, 1940. The complete mitogenome (GenBank Acc. No. OQ596537) was 14,431 bp long and it comprised 13 protein-coding genes (PCGs), 22 tRNAs, two tRNAs, and two control regions (CRs). Phylogenetic analyses, conducted using concatenated nucleotide and amino acid sequences of 13 protein-coding genes, produced two partially incongruent topologies. While the order Calanoida was consistently resolved as the sister lineage to the other three orders, topological instability was observed in the relationships of the orders Cyclopoida, Siphonostomatoida and Harpacticoida. Siphonostomatoida clustered with Cyclopoida in the nucleotide-based phylogeny, but with Harpacticoida in the amino acid-based phylogeny. The latter topology conforms to the widely accepted relationships, but we speculate that the former topology is more likely to be the correct one. Our study provides a complete mitogenome sequence of E. tumidus, which helps us better understand the molecular evolution of the genus Ergasilus. Additionally, we suggest a different perspective on the controversial phylogenetic relationships among Siphonostomatoida, Cyclopoida and Harpacticoida, diverging from previously accepted views.
Collapse
Affiliation(s)
- Yan Huang
- Hubei Key Laboratory of Cognitive and Affective Disorders, Institute of Biomedical Sciences, School of Medicine, Jianghan University, Wuhan, China
| | - Jin-Mei Feng
- Department of Pathogenic Biology, School of Medicine, Jianghan University, Wuhan, China
| | - Wei Liu
- Hubei Key Laboratory of Cognitive and Affective Disorders, Institute of Biomedical Sciences, School of Medicine, Jianghan University, Wuhan, China
| | - Bin-Lian Sun
- Hubei Key Laboratory of Cognitive and Affective Disorders, Institute of Biomedical Sciences, School of Medicine, Jianghan University, Wuhan, China
| | - Xi-Ji Shu
- Hubei Key Laboratory of Cognitive and Affective Disorders, Institute of Biomedical Sciences, School of Medicine, Jianghan University, Wuhan, China
| | - Wen-Xiang Li
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan China
| | - Gui-Tang Wang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan China
| | - Cong-Jie Hua
- Hubei Key Laboratory of Cognitive and Affective Disorders, Institute of Biomedical Sciences, School of Medicine, Jianghan University, Wuhan, China
- Department of Pathogenic Biology, School of Medicine, Jianghan University, Wuhan, China
| |
Collapse
|
50
|
Zhang L, Wang F, Wu J, Ye S, Xu Y, Liu Y. Fine-Scale Genetic Structure of Curculio chinensis (Coleoptera: Curculionidae) Based on Mitochondrial COI: The Role of Host Specificity and Spatial Distance. INSECTS 2024; 15:116. [PMID: 38392535 PMCID: PMC10888635 DOI: 10.3390/insects15020116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Revised: 01/30/2024] [Accepted: 02/04/2024] [Indexed: 02/24/2024]
Abstract
The Camellia weevil, Curculio chinensis (Chevrolat, 1978), is a dominant oligophagous pest that bores into the fruit of oil-tea Camellia. Genetic differentiation among populations in various hosts can easily occur, which hinders research on pest management. In this study, the genetic structure, genetic diversity, and phylogenetic structure of local C. chinensis populations were examined using 147 individuals (from 6 localities in Jiangxi), based on 2 mitochondrial COI markers. Results indicated that the C. chinensis population in Jiangxi exhibits a high haplotype diversity, especially for the populations from Cam. meiocarpa plantations. Structural differentiation was observed between Haplogroup 1 (73 individuals from Ganzhou, Jian, and Pingxiang) in the monoculture plantations of Cam. meiocarpa and Haplogroup 2 (75 individuals from Pingxiang and Jiujiang) in Cam. oleifera. Two haplogroups have recently undergone a demographic expansion, and Haplogroup 1 has shown a higher number of effective migrants than Haplogroup 2. This suggests that C. chinensis has been spreading from Cam. meiocarpa plantations to other oil-tea Camellia, such as Cam. oleifera. The increased cultivation of oil-tea Camellia in Jiangxi has contributed to a unique genetic structure within the C. chinensis population. This has, in turn, expanded the distribution of C. chinensis and increased migration between populations.
Collapse
Affiliation(s)
- Li Zhang
- Institute of Jiangxi Oil-Tea Camellia, Jiujiang University, Jiujiang 332005, China
| | - Fuping Wang
- Institute of Jiangxi Oil-Tea Camellia, Jiujiang University, Jiujiang 332005, China
| | - Jiaxi Wu
- Institute of Jiangxi Oil-Tea Camellia, Jiujiang University, Jiujiang 332005, China
| | - Sicheng Ye
- Institute of Jiangxi Oil-Tea Camellia, Jiujiang University, Jiujiang 332005, China
| | - Ye Xu
- School of Agricultural Science, Jiangxi Agricultural University, Nanchang 330045, China
| | - Yanan Liu
- Institute of Jiangxi Oil-Tea Camellia, Jiujiang University, Jiujiang 332005, China
| |
Collapse
|