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Zhou G, Zhang H, Chen W, Li Z, Zhang X, Fu Y. Morphological observation, molecular identification and evolutionary analysis of Hydatigera kamiyai found in Neodon fuscus from the Qinghai-Tibetan plateau. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2024; 123:105629. [PMID: 38936527 DOI: 10.1016/j.meegid.2024.105629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Revised: 06/10/2024] [Accepted: 06/23/2024] [Indexed: 06/29/2024]
Abstract
Hydatigera kamiyai (H. kamiyai) is a new species within Hydatigera that has recently been resurrected. Voles and cats are hosts of H. kamiyai and have a certain impact on its health and economy. Moreover, the Qinghai-Tibetan plateau (QTP) is a research hotspot representing Earth's biodiversity, as its unique geographical environment and climatic conditions support the growth of a variety of mammals and provide favorable conditions for various parasites to complete their life history. The aim of this study was to reveal the phylogenetic relationships and divergence times of H. kamiyai strains isolated from Neodon fuscus on the QTP using morphological and molecular methods. In this study, we morphologically observed H. kamiyai and sequenced the whole mitochondrial genome. Then, we constructed phylogenetic trees with the maximum likelihood (ML) and Bayesian inference (BI) methods. The GTR alternative model was selected for divergence time analysis. These data demonstrated that the results were consistent with the general morphological characteristics of Hydatigera. The whole genome of H. kamiyai was 13,822 bp in size, and the A + T content (73%) was greater than the G + C content (27%). The Ka/Ks values were all <1, indicating that all 13 protein-coding genes (13 PCGs) underwent purifying selection during the process of evolution. The phylogenetic tree generated based on the 13 PCGs, cytochrom oxidase subunit I (COI), 18S rRNA and 28S rRNA revealed close phylogenetic relationships between H. kamiyai and Hydatigera, with high node support for the relationship. The divergence time based on 13 PCGs indicated that H. kamiyai diverged approximately 11.3 million years ago (Mya) in the Miocene. Interestingly, it diverged later than the period of rapid uplift in the QTP. We also speculated that H. kamiyai differentiation was caused by host differentiation due to the favorable living conditions brought about by the uplift of the QTP. As there have been relatively few investigations on the mitochondrial genome of H. kamiyai, our study could provide factual support for further studies of H. kamiyai on the QTP. We also emphasized the importance of further studies of its hosts, Neodon fuscus and cats, which will be important for further understanding the life cycle of H. kamiyai.
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Affiliation(s)
- Guoyan Zhou
- Academy of Animal Sciences and Veterinary Medicine, Qinghai University, Xining, People's Republic of China; Qinghai Provincial Key Laboratory of Pathogen Diagnosis for Animal Diseases and Green Technical Research for Prevention and Control, Xining, People's Republic of China
| | - Haining Zhang
- Academy of Animal Sciences and Veterinary Medicine, Qinghai University, Xining, People's Republic of China; Qinghai Provincial Key Laboratory of Pathogen Diagnosis for Animal Diseases and Green Technical Research for Prevention and Control, Xining, People's Republic of China
| | - Wangkai Chen
- Academy of Animal Sciences and Veterinary Medicine, Qinghai University, Xining, People's Republic of China; Qinghai Provincial Key Laboratory of Pathogen Diagnosis for Animal Diseases and Green Technical Research for Prevention and Control, Xining, People's Republic of China
| | - Zhi Li
- Academy of Animal Sciences and Veterinary Medicine, Qinghai University, Xining, People's Republic of China; Qinghai Provincial Key Laboratory of Pathogen Diagnosis for Animal Diseases and Green Technical Research for Prevention and Control, Xining, People's Republic of China
| | - Xueyong Zhang
- Academy of Animal Sciences and Veterinary Medicine, Qinghai University, Xining, People's Republic of China; Qinghai Provincial Key Laboratory of Pathogen Diagnosis for Animal Diseases and Green Technical Research for Prevention and Control, Xining, People's Republic of China
| | - Yong Fu
- Academy of Animal Sciences and Veterinary Medicine, Qinghai University, Xining, People's Republic of China; Qinghai Provincial Key Laboratory of Pathogen Diagnosis for Animal Diseases and Green Technical Research for Prevention and Control, Xining, People's Republic of China.
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Chen W, Zhang H, Meng R, Zhang X, Duo H, Guo Z, Shen X, Chen C, Li Z, Fu Y. Genome-wide phylogenetic and genetic evolutionary analyses of mitochondria in Hypoderma bovis and H. sinense on the Qinghai-Tibetan Plateau. Parasitol Res 2023; 123:43. [PMID: 38095728 DOI: 10.1007/s00436-023-08060-6] [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: 07/26/2023] [Accepted: 10/27/2023] [Indexed: 12/18/2023]
Abstract
Hypoderma bovis (H. bovis) and Hypoderma sinense (H. sinense) are insects that cause hypodermosis in yaks and Bos taurus. Hypodermosis is a severe skin condition that not only impairs the development of local animal husbandry but also poses threats to human health as a zoonosis. The Qinghai-Tibetan Plateau (QTP) is known as the "Roof of the World." Its unique geographical environment and climate conditions have supported the growth of a wide range of mammals, providing favorable conditions for Hypoderma spp. to complete their life cycles. In this study, the whole mitochondrial genomes of H. bovis and H. sinense collected from the QTP were sequenced and phylogenetically analyzed. We found that the whole genomes of H. bovis and H. sinense are 16,283 bp and 16,300 bp in length, respectively. Both the H. bovis and H. sinense genomes have 37 mitochondrial genes, which include two rRNA genes (16S rRNA and 12S rRNA), 22 tRNA genes, the control region (D-loop region), the light chain replication initiation region, and 13 protein-coding genes (PCGs). The phylogenetic tree generated based on the 13 PCGs revealed close phylogenetic relationships between H. sinense, H. bovis, and Hypoderma lineatum. A similar result was also found in our phylogenetic analysis based on 18S rRNA and 28S rRNA. However, analysis of cytochrome oxidase subunit I (COI) showed cluster of H. bovis, H. sinense, and Cuterebra spp. on the same branch, all belonging to Oestridae. The differentiation time generated based on 13 PCGs indicates that H. bovis and H. sinense differentiated and formed ~4.69 million years ago (Mya) and ~4.06 Mya, respectively. This timing coincides with the differentiation and appearance of yak and Bos taurus in the Pliocene (~4.7 Mya), indicating that the parasites and mammals diverged in close temporal proximity. Of note, this period also witnessed a rapid uplift of the QTP, causing significant climate and environmental changes. Thus, we conjecture that the differentiation of Hypoderma spp. is potentially related to the differentiation of their host species, as well as climate changes caused by the uplift of the QTP. Overall, our study can provide valuable data to support further studies on the phylogeny and differentiation of Hypoderma spp. on the QTP.
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Affiliation(s)
- Wangkai Chen
- Qinghai Academy of Animal Sciences and Veterinary Medicine, Qinghai University, Xining, People's Republic of China
- Qinghai Provincial Key Laboratory of Pathogen Diagnosis for Animal Diseases and Green Technical Research for Prevention and Control, Xining, People's Republic of China
| | - Haining Zhang
- Qinghai Academy of Animal Sciences and Veterinary Medicine, Qinghai University, Xining, People's Republic of China
- Qinghai Provincial Key Laboratory of Pathogen Diagnosis for Animal Diseases and Green Technical Research for Prevention and Control, Xining, People's Republic of China
| | - Ru Meng
- Xining Animal Disease Control Center, Xining, People's Republic of China
| | - Xueyong Zhang
- Qinghai Academy of Animal Sciences and Veterinary Medicine, Qinghai University, Xining, People's Republic of China
- Qinghai Provincial Key Laboratory of Pathogen Diagnosis for Animal Diseases and Green Technical Research for Prevention and Control, Xining, People's Republic of China
| | - Hong Duo
- Qinghai Academy of Animal Sciences and Veterinary Medicine, Qinghai University, Xining, People's Republic of China
- Qinghai Provincial Key Laboratory of Pathogen Diagnosis for Animal Diseases and Green Technical Research for Prevention and Control, Xining, People's Republic of China
| | - Zhihong Guo
- Qinghai Academy of Animal Sciences and Veterinary Medicine, Qinghai University, Xining, People's Republic of China
- Qinghai Provincial Key Laboratory of Pathogen Diagnosis for Animal Diseases and Green Technical Research for Prevention and Control, Xining, People's Republic of China
| | - Xiuying Shen
- Qinghai Academy of Animal Sciences and Veterinary Medicine, Qinghai University, Xining, People's Republic of China
- Qinghai Provincial Key Laboratory of Pathogen Diagnosis for Animal Diseases and Green Technical Research for Prevention and Control, Xining, People's Republic of China
| | - Changjiang Chen
- Animal Husbandry and Veterinary Station of Huangyuan County, Xining, People's Republic of China
| | - Zhi Li
- Qinghai Academy of Animal Sciences and Veterinary Medicine, Qinghai University, Xining, People's Republic of China.
- Qinghai Provincial Key Laboratory of Pathogen Diagnosis for Animal Diseases and Green Technical Research for Prevention and Control, Xining, People's Republic of China.
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, People's Republic of China.
| | - Yong Fu
- Qinghai Academy of Animal Sciences and Veterinary Medicine, Qinghai University, Xining, People's Republic of China.
- Qinghai Provincial Key Laboratory of Pathogen Diagnosis for Animal Diseases and Green Technical Research for Prevention and Control, Xining, People's Republic of China.
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Pava-Ripoll M, Miller AK, Ziobro GC. Development of A Multiplex Polymerase Chain Reaction (PCR) Assay for the Potential Detection of Insect Contaminants in Food. J Food Prot 2023:100120. [PMID: 37348561 DOI: 10.1016/j.jfp.2023.100120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 05/01/2023] [Accepted: 06/15/2023] [Indexed: 06/24/2023]
Abstract
Molecular methods can potentially be used to detect insect contaminants of food products. In this study, we used three sets of group-specific primers, two of them targeting the amplification of two regions of the insect's mitochondrial cytochrome c oxidase subunit I (COI-Fa and COI-Fb) and the other targeting a region of the nuclear protein-coding wingless (wg) gene. Using singleplex and multiplex polymerase chain reaction (PCR), we evaluated the three set of primers using genomic DNA (gDNA) from 48 insect species including food-storage insect pests and known vectors of foodborne pathogens. Seven plant-based food matrices were also evaluated for exclusivity testing. Additionally, we spiked fragments from five insect species in a selected food matrix (whole wheat flour). Singleplex and multiplex PCR amplified single specific bands (401-449 bp), corresponding to the wg gene, from insect species belonging to families Blattidae and Formicidae, and in Plodia interpunctella (Hübner) (Lepidoptera: Pyralidae). The COI-Fa primers amplified specific bands (171-188 bp) in all Dipteran species and the COI-Fb primers amplified a specific band (∼140 bp) in DNA from Tribolium castaneum (Herbst) (Coleoptera: Tenebrionidae) and P. interpunctella. However, the presence of specific bands in most Coleopterans was not consistent. No amplicon bands were observed in any of the food matrixes tested and the expected pattern of amplicon bands was seen in multiplex reactions using gDNA from spiked food samples. Our multiplex PCR assay targeted specific groups of insects that commonly contaminate foods without amplifying bands from the food matrixes tested; thus, molecular methods may be suitable for detecting insects or their fragments in foods.
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Affiliation(s)
- Monica Pava-Ripoll
- U.S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, Office of Food Safety, Division of Dairy, Egg and Meat Products, College Park, MD.
| | - Amy K Miller
- U.S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, Office of Food Safety, Division of Dairy, Egg and Meat Products, College Park, MD
| | - George C Ziobro
- U.S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, Office of Food Safety, Division of Dairy, Egg and Meat Products, College Park, MD
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Tokareva A, Koszela K, Ferreira VS, Yamamoto S, Żyła D. The oldest case of paedomorphosis in rove beetles and description of a new genus of Paederinae from Cretaceous amber (Coleoptera: Staphylinidae). Sci Rep 2023; 13:5317. [PMID: 37002406 PMCID: PMC10066364 DOI: 10.1038/s41598-023-32446-2] [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: 10/26/2022] [Accepted: 03/28/2023] [Indexed: 04/03/2023] Open
Abstract
The ecology of extinct species from the Cretaceous is largely unknown. Morphological features of specimens preserved in amber can help to reveal habitats and evolutionary strategies that occurred in fossil lineages. An unusually small rove beetle (Staphylinidae) from the subfamily Paederinae with a Y-shaped suture on the head and modified tarsi and antennae is newly described here as Midinudon juvenis Tokareva & Żyła gen. et sp. nov. We hypothesise that such a combination of characters represents the earliest example of paedomorphosis in Staphylinidae and discuss other possible reasons that could explain the small size and morphological modifications of the new species. We provide the results of total-evidence phylogenetic analysis and discuss the relationships of Midinudon juvenis Tokareva & Żyła gen. et sp. nov. within Paederinae.
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Affiliation(s)
- Alexandra Tokareva
- Museum and Institute of Zoology, Polish Academy of Sciences, Wilcza 64, 00-679, Warsaw, Poland.
| | - Katarzyna Koszela
- Museum and Institute of Zoology, Polish Academy of Sciences, Wilcza 64, 00-679, Warsaw, Poland
| | - Vinicius S Ferreira
- Natural History Museum of Denmark, Universitetsparken 15, 2100, Copenhagen, Denmark
| | - Shûhei Yamamoto
- The Hokkaido University Museum, Hokkaido University, Kita 10, Nishi 8, Kita-Ku, Sapporo, Hokkaido, 060-0810, Japan
| | - Dagmara Żyła
- Museum and Institute of Zoology, Polish Academy of Sciences, Wilcza 64, 00-679, Warsaw, Poland.
- Leibniz Institute for the Analysis of Biodiversity Change, Martin-Luther-King-Platz 3, 20146, Hamburg, Germany.
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Zhou X, Wang L, Zhu P, Yang Z, Wang Z, Chen Y, Gu X, He R, Xu J, Jing B, Yang G, Chen S, Wu S, Xie Y. Comprehensive molecular characterization of complete mitogenome assemblies of 33 Eimeria isolates infecting domestic chickens. Parasit Vectors 2023; 16:109. [PMID: 36935516 PMCID: PMC10026407 DOI: 10.1186/s13071-023-05712-5] [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: 12/29/2022] [Accepted: 02/22/2023] [Indexed: 03/21/2023] Open
Abstract
BACKGROUND Coccidiosis caused by Eimeria is one of the most severe chicken diseases and poses a great economic threat to the poultry industry. Understanding the evolutionary biology of chicken Eimeria parasites underpins development of new interactions toward the improved prevention and control of this poultry disease. METHODS We presented an evolutionary blueprint of chicken coccidia by genetically characterizing complete mitogenome assemblies of 33 isolates representing all seven known Eimeria species infecting chickens in China. Further genome- and gene-level phylogenies were also achieved to better understand the evolutionary relationships of these chicken Eimeria at the species level. RESULTS 33 mitogenomes of chicken eimerian parasites ranged from 6148 bp to 6480 bp in size and encoded typical mitochondrial compositions of apicomplexan parasites including three protein-coding genes (PCGs), seven fragmented small subunit (SSU) and 12/13 fragmented large subunit (LSU) rRNAs. Comparative genomics provided an evolutionary scenario for the genetic diversity of PCGs-cytochrome c oxidase subunits 1 and 3 (cox1 and cox3) and cytochrome b (cytb); all were under purifying selection with cox1 and cox3 being the lowest and highest evolutionary rates, respectively. Genome-wide phylogenies classified the 33 Eimeria isolates into seven subgroups, and furthermore Eimeria tenella and Eimeria necatrix were determined to be more closely related to each other than to the other eight congenic species. Single/concatenated mitochondrial protein gene-based phylogenies supported cox1 as the genetic marker for evolutionary and phylogenetic studies for avain coccidia. CONCLUSIONS To our knowledge, these are the first population-level mitogenomic data on the genus Eimeria, and its comprehensive molecular characterization provides valuable resources for systematic, population genetic and evolutionary biological studies of apicomplexan parasites in poultry.
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Affiliation(s)
- Xuan Zhou
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Sichuan, 611130, China
| | - Lidan Wang
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Sichuan, 611130, China
| | - Pengchen Zhu
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Sichuan, 611130, China
| | - Zijiang Yang
- Tokyo University of Marine Science and Technology, Konan Minato-Ku, Tokyo, 1088477, Japan
| | - Zhao Wang
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Sichuan, 611130, China
| | - Yijun Chen
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Sichuan, 611130, China
| | - Xiaobin Gu
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Sichuan, 611130, China
| | - Ran He
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Sichuan, 611130, China
| | - Jing Xu
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Sichuan, 611130, China
| | - Bo Jing
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Sichuan, 611130, China
| | - Guangyou Yang
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Sichuan, 611130, China
| | - Shun Chen
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Sichuan, 611130, China.
| | - Shuangyang Wu
- Gregor Mendel Institute, Austrian Academy of Sciences, 1030, Vienna, Austria.
| | - Yue Xie
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Sichuan, 611130, China.
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Li S, Zhu Y, Xu Z, Chen L, Wang W, Cheng Z. The phylogeny and divergence time of Ophiocordyceps sinensis and its host insects based on elongation factor 1 alpha. Arch Microbiol 2023; 205:98. [PMID: 36853446 DOI: 10.1007/s00203-023-03444-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 09/18/2022] [Accepted: 02/16/2023] [Indexed: 03/01/2023]
Abstract
Ophiocordyceps sinensis Berk. is a fungal parasite that parasitizes the larvae of Hepialidae and is endemic to the Qinghai-Tibet Plateau (QTP). The phylogeny and divergence time of O. sinensis and its host insects were analyzed for 137 individuals from 48 O. sinensis populations based on the elongation factor 1 alpha (EF-1α) gene. Lower nucleotide variation, with only 7 and 16 EF-1α haplotypes, was detected in O. sinensis and its host insects, respectively. The isolated and broad distribution patterns coexisted in both O. sinensis and its host insects on the QTP. The divergence time estimates show that O. sinensis and its host insects originated later than 14.33 million years (Myr) and earlier than 23.60 Myr in the Miocene period, and the major differentiation occurred later than 4 Myr. Their origin and differentiation match well with the second and third uplifts of the QTP, respectively. The host insects from the O. sinensis populations distributed around Qinghai Lake are inferred as an ancient and relict species that has survived various geological events of the QTP. It is suitable to estimate the divergence times of both O. sinensis and its host insects from the same individuals using one gene: EF-1α. Our findings of the origin, phylogeny, and evolution of the endemic species also support the epoch of geological events on the QTP.
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Affiliation(s)
- Shan Li
- School of Life Science and Technology, Tongji University, 1239, Siping Road, Shanghai, 200092, People's Republic of China
| | - Yunguo Zhu
- School of Life Science and Technology, Tongji University, 1239, Siping Road, Shanghai, 200092, People's Republic of China
| | - Zixian Xu
- School of Life Science and Technology, Tongji University, 1239, Siping Road, Shanghai, 200092, People's Republic of China
| | - Lingling Chen
- School of Life Science and Technology, Tongji University, 1239, Siping Road, Shanghai, 200092, People's Republic of China
| | - Wenqian Wang
- School of Life Science and Technology, Tongji University, 1239, Siping Road, Shanghai, 200092, People's Republic of China
| | - Zhou Cheng
- School of Life Science and Technology, Tongji University, 1239, Siping Road, Shanghai, 200092, People's Republic of China.
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Bondareva O, Petrova T, Bodrov S, Gavrilo M, Smorkatcheva A, Abramson N. How voles adapt to subterranean lifestyle: Insights from RNA-seq. Front Ecol Evol 2023. [DOI: 10.3389/fevo.2023.1085993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/19/2023] Open
Abstract
Life under the earth surface is highly challenging and associated with a number of morphological, physiological and behavioral modifications. Subterranean niche protects animals from predators, fluctuations in environmental parameters, but is characterized by high levels of carbon dioxide and low levels of oxygen and implies high energy requirements associated with burrowing. Moreover, it lacks most of the sensory inputs available above ground. The current study describes results from RNA-seq analysis of four subterranean voles from subfamily Arvicolinae: Prometheomys schaposchnikowi, Ellobius lutescens, Terricola subterraneus, and Lasiopodomys mandarinus. Original RNA-seq data were obtained for eight species, for nine species, SRA data were downloaded from the NCBI SRA database. Additionally assembled transcriptomes of Mynomes ochrogaster and Cricetulus griseus were included in the analysis. We searched for the selection signatures and parallel amino acid substitutions in a total of 19 species. Even within this limited data set, we found significant changes of dN/dS ratio by free-ratio model analysis for subterranean Arvicolinae. Parallel substitutions were detected in genes RAD23B and PYCR2. These genes are associated with DNA repair processes and response to oxidative stress. Similar substitutions were discovered in the RAD23 genes for highly specialized subterranean Heterocephalus glaber and Fukomys damarensis. The most pronounced signatures of adaptive evolution related to subterranean niche within species of Arvicolinae subfamily were detected for Ellobius lutescens. Our results suggest that genomic adaptations can occur very quickly so far as the amount of selection signatures was found to be compliant with the degree of specialization to the subterranean niche and independent from the evolutionary age of the taxon. We found that the number of genomic signatures of selection does not depend on the age of the taxon, but is positively correlated with the degree of specialization to the subterranean niche.
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Xia J, Chang L, Xu D, Jia Y, Ding Y, Cao C, Geng Z, Jin S. Next-Generation Sequencing of the Complete Huaibei Grey Donkey Mitogenome and Mitogenomic Phylogeny of the Equidae Family. Animals (Basel) 2023; 13:ani13030531. [PMID: 36766420 PMCID: PMC9913526 DOI: 10.3390/ani13030531] [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: 11/11/2022] [Revised: 01/26/2023] [Accepted: 01/28/2023] [Indexed: 02/05/2023] Open
Abstract
The Huaibei grey donkey (HGD) is an endangered species and a vital native breed in Anhui Province, China. However, its complete mitogenome, phylogeny, and maternal origin remain unclear. The objectives of this study were to detect the genetic diversity of the HGD and investigate its phylogenetic relationship with other breeds to inform conservation management. The complete mitogenome of the HGD was sequenced through next-generation sequencing, and the most variable region in the mitochondrial DNA displacement-loop (D-loop) was amplified via a polymerase chain reaction (PCR). Next, we used the median-joining network (MJN) to calculate the genetic relationships among populations and the neighbor-jointing method to build a phylogenetic tree and speculate as to its origin. The results showed that the mitogenome contains 22 tRNAs, 2 rRNAs, 13 PCGs, and 1 D-loop region. Analyzing the D-loop region of the HGDs, we identified 23 polymorphic sites and 11 haplotypes. The haplotype and nucleotide diversity were 0.87000 (Hd) and 0.02115 (Pi), respectively. The MJN analysis indicated that the HGD potentially has two maternal lineages, and phylogenetic analysis indicated that the Somali lineage could be the most probable domestication center for this breed. Therefore, our mitogenome analysis highlights the high genetic diversity of the HGD, which may have originated from the Somali wild ass, as opposed to the Asian wild ass. This study will provide a useful resource for HGD conservation and breeding.
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Affiliation(s)
- Jingjing Xia
- College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China
| | - Liang Chang
- College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China
| | - Dashuang Xu
- Anhui Livestock and Poultry Genetic Resources Protection Center, Hefei 231283, China
| | - Yuqing Jia
- College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China
| | - Yuanfei Ding
- College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China
| | - Chengcheng Cao
- College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China
| | - Zhaoyu Geng
- College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China
| | - Sihua Jin
- College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China
- Correspondence: ; Tel.:+86-551-6578-6328; Fax:+86-551-6578-6326
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Spatio-Temporal Evolutionary Patterns of the Pieridae Butterflies (Lepidoptera: Papilionoidea) Inferred from Mitogenomic Data. Genes (Basel) 2022; 14:genes14010072. [PMID: 36672814 PMCID: PMC9858963 DOI: 10.3390/genes14010072] [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: 11/23/2022] [Revised: 12/17/2022] [Accepted: 12/23/2022] [Indexed: 12/28/2022] Open
Abstract
Pieridae is one of the largest and almost cosmopolitan groups of butterflies, which plays an important role in natural ecosystems; however, to date, its phylogeny and evolutionary history have not been fully resolved. In this study, we obtained the complete or nearly complete mitochondrial genomes of 100 pierid taxa (six newly sequenced, sixty extracted from the whole-genome data, and thirty-four directly available from GenBank). At the same time, for the first time, we conducted comparative mitogenomic and phylogenetic analyses based on these mitogenomic data, to further clarify their spatio-temporal evolutionary patterns. Comparative mitogenomic analysis showed that, except for cox2, the GC content of each of the 13 protein-coding genes (PCGs) in the rapidly diverging subfamily Pierinae was higher than in its sister group Coliadinae. Moreover, the dN/dS values of nine genes (atp6, atp8, cox1, cox3, cob, nad1, nad3, nad5, and nad6) in Pierinae were also relatively higher than those in its sister group, Coliadinae. Phylogenetic analysis showed that all the resultant phylogenetic trees were generally in agreement with those of previous studies. The Pierinae family contained six clades in total with the relationship of (Leptosiaini + (((Nepheroniini + Arthocharidini) + Teracolini) + (Pierini + Elodini))). The Pieridae originated in the Palearctic region approximately 72.3 million years ago in the late Cretaceous, and the subfamily Pierinae diverged from this family around 57.9 million years ago in the Oriental region, shortly after the K-Pg mass extinction event; in addition, the spatio-temporal evolutionary patterns of Pierinae were closely correlated with geological events and environmental changes, as well as the host plant coevolutionary scenario in Earth's history. However, some incongruencies were observed between our results and those of previous studies in terms of shallow phylogenies for a few taxa, and should be further investigated.
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Zheng X, Zhang R, Yue B, Wu Y, Yang N, Zhou C. Enhanced Resolution of Evolution and Phylogeny of the Moths Inferred from Nineteen Mitochondrial Genomes. Genes (Basel) 2022; 13:genes13091634. [PMID: 36140802 PMCID: PMC9498458 DOI: 10.3390/genes13091634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Revised: 09/03/2022] [Accepted: 09/06/2022] [Indexed: 11/21/2022] Open
Abstract
The vast majority (approximately 90%) of Lepidoptera species belong to moths whose phylogeny has been widely discussed and highly controversial. For the further understanding of phylogenetic relationships of moths, nineteen nearly complete mitochondrial genomes (mitogenomes) of moths involved in six major lineages were sequenced and characterized. These mitogenomes ranged from 15,177 bp (Cyclidia fractifasciata) to 15,749 bp (Ophthalmitis albosignaria) in length, comprising of the core 37 mitochondrial genes (13 protein-coding genes (PCGs) + 22 tRNAs + two rRNAs) and an incomplete control region. The order and orientation of genes showed the same pattern and the gene order of trnM-trnI-trnQ showed a typical rearrangement of Lepidoptera compared with the ancestral order of trnI-trnQ-trnM. Among these 13 PCGs, ATP8 exhibited the fastest evolutionary rate, and Drepanidae showed the highest average evolutionary rate among six families involved in 66 species. The phylogenetic analyses based on the dataset of 13 PCGs suggested the relationship of (Notodontidae + (Noctuidae + Erebidae)) + (Geometridae + (Sphingidae + Drepanidae)), which suggested a slightly different pattern from previous studies. Most groups were well defined in the subfamily level except Erebidae, which was not fully consistent across bayesian and maximum likelihood methods. Several formerly unassigned tribes of Geometridae were suggested based on mitogenome sequences despite a not very strong support in partial nodes. The study of mitogenomes of these moths can provide fundamental information of mitogenome architecture, and the phylogenetic position of moths, and contributes to further phylogeographical studies and the biological control of pests.
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Affiliation(s)
- Xiaofeng Zheng
- Key Laboratory of Bioresources and Ecoenvironment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu 610064, China
| | - Rusong Zhang
- Key Laboratory of Bioresources and Ecoenvironment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu 610064, China
| | - Bisong Yue
- Key Laboratory of Bioresources and Ecoenvironment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu 610064, China
| | - Yongjie Wu
- Key Laboratory of Bioresources and Ecoenvironment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu 610064, China
| | - Nan Yang
- Institute of Qinghai-Tibetan Plateau, Southwest Minzu University, Chengdu 610064, China
- Collaborative Innovation Center for Ecological Animal Husbandry of Qinghai-Tibetan Plateau, Southwest Minzu University, Chengdu 610064, China
- Correspondence: (N.Y.); (C.Z.)
| | - Chuang Zhou
- Key Laboratory of Bioresources and Ecoenvironment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu 610064, China
- Correspondence: (N.Y.); (C.Z.)
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11
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Bargues MD, Halajian A, Artigas P, Luus-Powell WJ, Valero MA, Mas-Coma S. Paleobiogeographical origins of Fasciola hepatica and F. gigantica in light of new DNA sequence characteristics of F. nyanzae from hippopotamus. Front Vet Sci 2022; 9:990872. [PMID: 36157179 PMCID: PMC9500510 DOI: 10.3389/fvets.2022.990872] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2022] [Accepted: 08/08/2022] [Indexed: 11/13/2022] Open
Abstract
Fascioliasis is a highly pathogenic disease affecting humans and livestock worldwide. It is caused by the liver flukes Fasciola hepatica transmitted by Galba/Fossaria lymnaeid snails in Europe, Asia, Africa, the Americas and Oceania, and F. gigantica transmitted by Radix lymnaeids in Africa and Asia. An evident founder effect appears in genetic studies as the consequence of their spread by human-guided movements of domestic ruminants, equines and Old World camelids in the post-domestication period from the beginning of the Neolithic. Establishing the geographical origins of fasciolid expansion is multidisciplinary crucial for disease assessment. Sequencing of selected nuclear ribosomal and mitochondrial DNA markers of F. nyanzae infecting hippopotamuses (Hippopotamus amphibius) in South Africa and their comparative analyses with F. hepatica and F. gigantica, and the two Fascioloides species, Fs. jacksoni from Asian elephants and Fs. magna from Holarctic cervids, allow to draw a tuned-up evolutionary scenario during the pre-domestication period. Close sequence similarities indicate a direct derivation of F. hepatica and F. gigantica from F. nyanzae by speciation after host capture phenomena. Phylogenetic reconstruction, genetic distances and divergence estimates fully fit fossil knowledge, past interconnecting bridges between continents, present fasciolid infection in the wild fauna, and lymnaeid distribution. The paleobiogeographical analyses suggest an origin for F. gigantica by transfer from primitive hippopotamuses to grazing bovid ancestors of Reduncinae, Bovinae and Alcelaphinae, by keeping the same vector Radix natalensis in warm lowlands of southeastern Africa in the mid-Miocene, around 13.5 mya. The origin of F. hepatica should have occurred after capture from primitive, less amphibious Hexaprotodon hippopotamuses to mid-sized ovicaprines as the wild bezoar Capra aegagrus and the wild mouflon Ovis gmelini, and from R. natalensis to Galba truncatula in cooler areas and mountainous foothills of Asian Near East in the latest Miocene to Early Pliocene, around 6.0 to 4.0 mya and perhaps shortly afterwards.
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Affiliation(s)
- María Dolores Bargues
- Departamento de Parasitologia, Facultad de Farmacia, Universidad de Valencia, Valencia, Spain
- Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Infecciosas, Instituto de Salud Carlos IIII, Madrid, Spain
- *Correspondence: María Dolores Bargues
| | - Ali Halajian
- DSI-NRF SARChi Chair (Ecosystem Health), Department of Biodiversity, University of Limpopo, Sovenga, South Africa
- Research Administration and Development, University of Limpopo, Sovenga, South Africa
| | - Patricio Artigas
- Departamento de Parasitologia, Facultad de Farmacia, Universidad de Valencia, Valencia, Spain
- Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Infecciosas, Instituto de Salud Carlos IIII, Madrid, Spain
| | - Wilmien J. Luus-Powell
- DSI-NRF SARChi Chair (Ecosystem Health), Department of Biodiversity, University of Limpopo, Sovenga, South Africa
| | - M. Adela Valero
- Departamento de Parasitologia, Facultad de Farmacia, Universidad de Valencia, Valencia, Spain
- Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Infecciosas, Instituto de Salud Carlos IIII, Madrid, Spain
| | - Santiago Mas-Coma
- Departamento de Parasitologia, Facultad de Farmacia, Universidad de Valencia, Valencia, Spain
- Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Infecciosas, Instituto de Salud Carlos IIII, Madrid, Spain
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12
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Scarpassa VM, Batista ET, Ferreira VDC, Alvesdos Santos Neto V, Roque RA, Ferreira FADS, da Costa FM. DNA barcoding suggests new species for the Mansonia subgenus (Mansonia, Mansoniini, Culicidae, Diptera) in the area surrounding the Jirau hydroelectric dam, Porto Velho municipality, Rondônia state, Brazil. Acta Trop 2022; 233:106574. [DOI: 10.1016/j.actatropica.2022.106574] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 06/24/2022] [Accepted: 06/25/2022] [Indexed: 11/16/2022]
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13
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Salabao L, Plevoets T, Frédérich B, Lepoint G, Kochzius M, Schön I. Describing novel mitochondrial genomes of Antarctic amphipods. Mitochondrial DNA B Resour 2022; 7:810-818. [PMID: 35573593 PMCID: PMC9103263 DOI: 10.1080/23802359.2022.2073837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Abstract
To date, only one mitogenome from an Antarctic amphipod has been published. Here, novel complete mitochondrial genomes (mitogenomes) of two morphospecies are assembled, namely, Charcotia amundseni and Eusirus giganteus. For the latter species, we have assembled two mitogenomes from different genetic clades of this species. The lengths of Eusirus and Charcotia mitogenomes range from 15,534 to 15,619 base pairs and their mitogenomes are composed of 13 protein coding genes, 22 transfer RNAs, 2 ribosomal RNAs, and 1 putative control region CR. Some tRNAs display aberrant structures suggesting that minimalization is also ongoing in amphipod mitogenomes. The novel mitogenomes of the two Antarctic species have features distinguishing them from other amphipod mitogenomes such as a lower AT-richness in the whole mitogenomes and a negative GC- skew in both strands of protein coding genes. The genetically most variable mitochondrial regions of amphipods are nad6 and atp8, while cox1 shows low nucleotide diversity among closely and more distantly related species. In comparison to the pancrustacean mitochondrial ground pattern, E. giganteus shows a translocation of the nad1 gene, while cytb and nad6 genes are translocated in C. amundseni. Phylogenetic analysis based on mitogenomes illustrates that Eusirus and Charcotia cluster together with other species belonging to the same amphipod superfamilies. In the absence of reference nuclear genomes, mitogenomes can be useful to develop markers for studying population genetics or evolutionary relationships at higher taxonomic levels.
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Affiliation(s)
- Louraine Salabao
- Laboratory of Functional and Evolutionary Morphology, FOCUS, University of Liège, Liège, Belgium
- Centre for Environmental Sciences, Zoology: Toxicology and Biodiversity, Diepenbeek, Belgium
| | - Tim Plevoets
- Unit Animal Sciences - ILVO Marine Research, Flanders Research Institute for Agriculture, Fisheries and Food, Oostende, Belgium
| | - Bruno Frédérich
- Laboratory of Functional and Evolutionary Morphology, FOCUS, University of Liège, Liège, Belgium
| | - Gilles Lepoint
- Laboratory of Trophic and Isotopes Ecology, FOCUS, University of Liège, Liège, Belgium
| | - Marc Kochzius
- Marine Biology, Vrije Universiteit Brussel (VUB), Brussels, Belgium
| | - Isa Schön
- Centre for Environmental Sciences, Zoology: Toxicology and Biodiversity, Diepenbeek, Belgium
- OD Nature, Freshwater Biology, Royal Belgian Institute of Natural Sciences, Brussels, Belgium
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Żyła D, Bogri A, Hansen AK, Jenkins Shaw J, Kypke J, Solodovnikov A. A New Termitophilous Genus of Paederinae Rove Beetles (Coleoptera, Staphylinidae) from the Neotropics and Its Phylogenetic Position. NEOTROPICAL ENTOMOLOGY 2022; 51:282-291. [PMID: 35175510 PMCID: PMC8967768 DOI: 10.1007/s13744-022-00946-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 01/24/2022] [Indexed: 06/14/2023]
Abstract
We describe a new genus and species of Paederinae rove beetles, Ruptor cordatus gen. et sp. nov., which lives in the arboreal nests of the termite Labiotermes labralis (Holmgren, 1906) in the Amazon lowlands of Peru. The morphology of Ruptor gen. nov. is highly derived, apparently due to its close association with the termite host, and thus, morphologically, the genus cannot be classified further than Lathrobiini incertae sedis. In order to address the sister-group relationships of Ruptor gen. nov., we conducted a molecular phylogenetic analysis based on seven gene fragments. The analysis indeed resolved the genus as a member of the tribe Lathrobiini and placed it nested within the informal clade of 'Medonina and allied taxa'. We provide a morphological comparison of the new genus with all known myrmeco- and termitophilous representatives of the subfamily, and to the extent possible, we illustrate other relevant and poorly known Neotropical Paederinae inquilines.
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Affiliation(s)
- Dagmara Żyła
- Museum and Institute of Zoology, Polish Academy of Sciences, Warsaw, Poland.
- Leibniz Institute for the Analysis of Biodiversity Change, Zoological Museum, Hamburg, Germany.
| | - Amalia Bogri
- Natural History Museum of Denmark, Univ of Copenhagen, Copenhagen, Denmark
| | | | - Josh Jenkins Shaw
- Natural History Museum of Denmark, Univ of Copenhagen, Copenhagen, Denmark
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Janina Kypke
- Natural History Museum of Denmark, Univ of Copenhagen, Copenhagen, Denmark
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15
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Insights into the Divergence of Chinese Ips Bark Beetles during Evolutionary Adaptation. BIOLOGY 2022; 11:biology11030384. [PMID: 35336758 PMCID: PMC8945085 DOI: 10.3390/biology11030384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 02/25/2022] [Accepted: 02/26/2022] [Indexed: 12/02/2022]
Abstract
Simple Summary Bark beetle species of the genus Ips are among the major pests of Chinese conifer forests. Based on mitochondrial genome and SNP, we investigated the phylogenetic relationships and evolutionary trends of 19 populations of six Ips species that had serious outbreaks in recent years. Our results demonstrated the relationships between Ips evolution and host plants, pheromones, and altitudinal differences, and provided new insights into the mechanism of adaptive evolution of Ips bark beetles. Abstract Many bark beetles of the genus Ips are economically important insect pests that cause severe damage to conifer forests worldwide. In this study, sequencing the mitochondrial genome and restriction site-associated DNA of Ips bark beetles helps us understand their phylogenetic relationships, biogeographic history, and evolution of ecological traits (e.g., pheromones and host plants). Our results show that the same topology in phylogenetic trees constructed in different ways (ML/MP/BI) and with different data (mtDNA/SNP) helps us to clarify the phylogenetic relationships between Chinese Ips bark beetle populations and Euramerican species and their higher order clades; Ips bark beetles are polyphyletic. The structure of the mitochondrial genome of Ips bark beetles is similar and conserved to some extent, especially in the sibling species Ips typographus and Ips nitidus. Genetic differences among Ips species are mainly related to their geographic distribution and different hosts. The evolutionary pattern of aggregation pheromones of Ips species reflects their adaptations to the environment and differences among hosts in their evolutionary process. The evolution of Ips species is closely related to the uplift of the Qinghai-Tibet Plateau and host switching. Our study addresses the evolutionary trend and phylogenetic relationships of Ips bark beetles in China, and also provides a new perspective on the evolution of bark beetles and their relationships with host plants and pheromones.
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Zheng B, Han Y, Yuan R, Liu J, van Achterberg C, Tang P, Chen X. Comparative Mitochondrial Genomics of 104 Darwin Wasps (Hymenoptera: Ichneumonidae) and Its Implication for Phylogeny. INSECTS 2022; 13:insects13020124. [PMID: 35206698 PMCID: PMC8874624 DOI: 10.3390/insects13020124] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/26/2021] [Revised: 01/17/2022] [Accepted: 01/21/2022] [Indexed: 02/04/2023]
Abstract
Simple Summary Nearly a hundred mitochondrial genomes of ichneumonid wasps are newly reported. Comparative mitogenomics of 104 mitochondrial genomes representing 33 subfamilies of Ichneumonidae, as well as its implications for phylogeny, were studied. We found that the mitochondrial genomes of ichneumonid wasps were highly conserved in their base composition and had low evolutionary rates, but were diverse in gene order. There are 38 types of gene rearrangement events in 104 ichneumonid mitochondrial genomes, of which 30 novel rearrangement types (R3-6, R8-R10, R12-R15, R17-R18, R20-R35 and R38) and a hot spot rearrangement around R1, with a shuffled tRNA cluster trnW-trnY-trnC and trnI-trnQ-trnM, were detected. The relationships among these subfamilies are firstly discussed based on mitochondrial genomes at a large scale. We suggest five subfamily groupings of Ichneumonidae: Brachycyrtiformes, Ichneumoniformes, Ophioniformes, Pimpliformes and Xoridiformes. Two formerly unplaced subfamilies, Eucerotinae and Microleptinae, were placed in Brachycyrtiformes and Ichneumoniformes, respectively. Abstract Ichneumonidae is one of the largest families of insects with a mega-diversity of specialized morphological and biological characteristics. We newly sequenced 92 mitochondrial genomes of ichneumonid wasps and found that they have a conserved base composition and a lower evolutionary rate than that of other families of parasitic Hymenoptera. There are 38 types of gene order in the ichneumonid mitochondrial genome, with 30 novel types identified in 104 ichneumonids. We also found that the rearrangement events occur more frequently in Ophioniformes than in Ichneumoniformes and Pimpliformes. Furthermore, the higher Ophioniformes and their relative lineages shared the transposition of trnL2 to trnI-trnQ-trnM tRNA cluster. We confirmed five higher-level groupings of Ichneumonidae: Brachycyrtiformes, Ichneumoniformes, Ophioniformes, Pimpliformes and Xoridiformes. Two formerly unplaced subfamilies, Eucerotinae and Microleptinae, were placed in Brachycyrtiformes and Ichneumoniformes, respectively. The results will improve our understanding of the diversity and evolution of Ichneumonidae.
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Affiliation(s)
- Boying Zheng
- State Key Laboratory of Rice Biology, Zhejiang University, Hangzhou 310058, China; (B.Z.); (Y.H.); (R.Y.); (C.v.A.); (X.C.)
- Institute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Yuanyuan Han
- State Key Laboratory of Rice Biology, Zhejiang University, Hangzhou 310058, China; (B.Z.); (Y.H.); (R.Y.); (C.v.A.); (X.C.)
- Institute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Ruizhong Yuan
- State Key Laboratory of Rice Biology, Zhejiang University, Hangzhou 310058, China; (B.Z.); (Y.H.); (R.Y.); (C.v.A.); (X.C.)
- Institute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Jingxian Liu
- Department of Entomology, College of Plant Protection, South China Agricultural University, Guangzhou 510642, China;
| | - Cornelis van Achterberg
- State Key Laboratory of Rice Biology, Zhejiang University, Hangzhou 310058, China; (B.Z.); (Y.H.); (R.Y.); (C.v.A.); (X.C.)
- Institute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Pu Tang
- State Key Laboratory of Rice Biology, Zhejiang University, Hangzhou 310058, China; (B.Z.); (Y.H.); (R.Y.); (C.v.A.); (X.C.)
- Institute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
- Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou 310058, China
- Zhejiang Provincial Key Laboratory of Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou 310058, China
- Correspondence:
| | - Xuexin Chen
- State Key Laboratory of Rice Biology, Zhejiang University, Hangzhou 310058, China; (B.Z.); (Y.H.); (R.Y.); (C.v.A.); (X.C.)
- Institute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
- Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou 310058, China
- Zhejiang Provincial Key Laboratory of Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou 310058, China
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17
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Filée J, Merle M, Bastide H, Mougel F, Bérenger JM, Folly-Ramos E, Almeida CE, Harry M. Phylogenomics for Chagas Disease Vectors of the Rhodnius Genus (Hemiptera, Triatominae): What We Learn From Mito-Nuclear Conflicts and Recommendations. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2021.750317] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
We provide in this study a very large DNA dataset on Rhodnius species including 36 samples representing 16 valid species of the three Rhodnius groups, pictipes, prolixus and pallescens. Samples were sequenced at low-depth with whole-genome shotgun sequencing (Illumina technology). Using phylogenomics including 15 mitochondrial genes (13.3 kb), partial nuclear rDNA (5.2 kb) and 51 nuclear protein-coding genes (36.3 kb), we resolve sticking points in the Rhodnius phylogeny. At the species level, we confirmed the species-specific status of R. montenegrensis and R. marabaensis and we agree with the synonymy of R. taquarussuensis with R. neglectus. We also invite to revisit the species-specific status of R. milesi that is more likely R. nasutus. We proposed to define a robustus species complex that comprises the four close relative species: R. marabaensis, R. montenegrensis, R. prolixus and R. robustus. As Psammolestes tertius was included in the Rhodnius clade, we strongly recommend reclassifying this species as R. tertius. At the Rhodnius group level, molecular data consistently supports the clustering of the pictipes and pallescens groups, more related to each other than they are to the prolixus group. Moreover, comparing mitochondrial and nuclear tree topologies, our results demonstrated that various introgression events occurred in all the three Rhodnius groups, in laboratory strains but also in wild specimens. We demonstrated that introgressions occurred frequently in the prolixus group, involving the related species of the robustus complex but also the pairwise R. nasutus and R. neglectus. A genome wide analysis highlighted an introgression event in the pictipes group between R. stali and R. brethesi and suggested a complex gene flow between the three species of the pallescens group, R. colombiensis, R. pallescens and R. ecuadoriensis. The molecular data supports also a sylvatic distribution of R. prolixus in Brazil (Pará state) and the monophyly of R. robustus. As we detected extensive introgression events and selective pressure on mitochondrial genes, we strongly recommend performing separate mitochondrial and nuclear phylogenies and to take advantages of mito-nuclear conflicts in order to have a comprehensive evolutionary vision of this genus.
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Lue CH, Buffington ML, Scheffer S, Lewis M, Elliott TA, Lindsey ARI, Driskell A, Jandova A, Kimura MT, Carton Y, Kula RR, Schlenke TA, Mateos M, Govind S, Varaldi J, Guerrieri E, Giorgini M, Wang X, Hoelmer K, Daane KM, Abram PK, Pardikes NA, Brown JJ, Thierry M, Poirié M, Goldstein P, Miller SE, Tracey WD, Davis JS, Jiggins FM, Wertheim B, Lewis OT, Leips J, Staniczenko PPA, Hrcek J. DROP: Molecular voucher database for identification of Drosophila parasitoids. Mol Ecol Resour 2021; 21:2437-2454. [PMID: 34051038 DOI: 10.1111/1755-0998.13435] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 05/11/2021] [Accepted: 05/20/2021] [Indexed: 01/03/2023]
Abstract
Molecular identification is increasingly used to speed up biodiversity surveys and laboratory experiments. However, many groups of organisms cannot be reliably identified using standard databases such as GenBank or BOLD due to lack of sequenced voucher specimens identified by experts. Sometimes a large number of sequences are available, but with too many errors to allow identification. Here, we address this problem for parasitoids of Drosophila by introducing a curated open-access molecular reference database, DROP (Drosophila parasitoids). Identifying Drosophila parasitoids is challenging and poses a major impediment to realize the full potential of this model system in studies ranging from molecular mechanisms to food webs, and in biological control of Drosophila suzukii. In DROP, genetic data are linked to voucher specimens and, where possible, the voucher specimens are identified by taxonomists and vetted through direct comparison with primary type material. To initiate DROP, we curated 154 laboratory strains, 856 vouchers, 554 DNA sequences, 16 genomes, 14 transcriptomes, and six proteomes drawn from a total of 183 operational taxonomic units (OTUs): 114 described Drosophila parasitoid species and 69 provisional species. We found species richness of Drosophila parasitoids to be heavily underestimated and provide an updated taxonomic catalogue for the community. DROP offers accurate molecular identification and improves cross-referencing between individual studies that we hope will catalyse research on this diverse and fascinating model system. Our effort should also serve as an example for researchers facing similar molecular identification problems in other groups of organisms.
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Affiliation(s)
- Chia-Hua Lue
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, Ceske Budejovice, Czech Republic
- Department of Biology, Brooklyn College, City University of New York (CUNY), Brooklyn, NY, USA
| | - Matthew L Buffington
- Systematic Entomology Laboratory, ARS/USDA c/o Smithsonian Institution, National Museum of Natural History, Washington, DC, USA
| | - Sonja Scheffer
- Systematic Entomology Laboratory, ARS/USDA c/o Smithsonian Institution, National Museum of Natural History, Washington, DC, USA
| | - Matthew Lewis
- Systematic Entomology Laboratory, ARS/USDA c/o Smithsonian Institution, National Museum of Natural History, Washington, DC, USA
| | - Tyler A Elliott
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | | | - Amy Driskell
- Laboratories of Analytical Biology, Smithsonian Institution, National Museum of Natural History, Washington, DC, USA
| | - Anna Jandova
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, Ceske Budejovice, Czech Republic
| | | | - Yves Carton
- "Évolution, Génomes, Comportement, Écologie", CNRS et Université Paris-Saclay, Paris, France
| | - Robert R Kula
- Systematic Entomology Laboratory, ARS/USDA c/o Smithsonian Institution, National Museum of Natural History, Washington, DC, USA
| | - Todd A Schlenke
- Department of Entomology, University of Arizona, Tucson, AZ, USA
| | - Mariana Mateos
- Wildlife and Fisheries Sciences Department, Texas A&M University, College Station, TX, USA
| | - Shubha Govind
- The Graduate Center of the City University of New York, New York, NY, USA
| | - Julien Varaldi
- CNRS, Laboratoire de Biométrie et Biologie Evolutive, UMR 5558, Université de Lyon, Université Lyon 1, Villeurbanne, France
| | - Emilio Guerrieri
- CNR-Institute for Sustainable Plant Protection (CNR-IPSP), National Research Council of Italy, Portici, Italy
| | - Massimo Giorgini
- CNR-Institute for Sustainable Plant Protection (CNR-IPSP), National Research Council of Italy, Portici, Italy
| | - Xingeng Wang
- United States Department of Agriculture, Agricultural Research Services, Beneficial Insects Introduction Research Unit, Newark, DE, USA
| | - Kim Hoelmer
- United States Department of Agriculture, Agricultural Research Services, Beneficial Insects Introduction Research Unit, Newark, DE, USA
| | - Kent M Daane
- Department of Environmental Science, Policy and Management, University of California, Berkeley, CA, USA
| | - Paul K Abram
- Agriculture and Agri-Food Canada, Agassiz Research and Development Centre, Agassiz, BC, Canada
| | - Nicholas A Pardikes
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, Ceske Budejovice, Czech Republic
| | - Joel J Brown
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, Ceske Budejovice, Czech Republic
- Faculty of Science, University of South Bohemia, Branisovska 31, Czech Republic
| | - Melanie Thierry
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, Ceske Budejovice, Czech Republic
- Faculty of Science, University of South Bohemia, Branisovska 31, Czech Republic
| | - Marylène Poirié
- INRAE, CNRS. and Evolution and Specificity of Multitrophic Interactions (ESIM) Sophia Agrobiotech Institute, Université "Côte d'Azur", Sophia Antipolis, France
| | - Paul Goldstein
- Systematic Entomology Laboratory, ARS/USDA c/o Smithsonian Institution, National Museum of Natural History, Washington, DC, USA
| | - Scott E Miller
- Smithsonian Institution, National Museum of Natural History, Washington, DC, USA
| | - W Daniel Tracey
- Department of Biology, Indiana University Bloomington, Bloomington, IN, USA
- Gill Center for Biomolecular Science, Indiana University Bloomington, Bloomington, IN, USA
| | - Jeremy S Davis
- Department of Biology, Indiana University Bloomington, Bloomington, IN, USA
- Biology Department, University of Kentucky, Lexington, KY, USA
| | | | - Bregje Wertheim
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, the Netherlands
| | - Owen T Lewis
- Department of Zoology, University of Oxford, Oxford, UK
| | - Jeff Leips
- Department of Biological Sciences, University of Maryland Baltimore County, Baltimore, MD, USA
| | - Phillip P A Staniczenko
- Department of Biology, Brooklyn College, City University of New York (CUNY), Brooklyn, NY, USA
| | - Jan Hrcek
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, Ceske Budejovice, Czech Republic
- Faculty of Science, University of South Bohemia, Branisovska 31, Czech Republic
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19
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Orlov I, Leschen RAB, Żyła D, Solodovnikov A. Total-evidence backbone phylogeny of Aleocharinae (Coleoptera: Staphylinidae). Cladistics 2021; 37:343-374. [PMID: 34478192 DOI: 10.1111/cla.12444] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/14/2020] [Indexed: 11/29/2022] Open
Abstract
Phylogenetic studies of Aleocharinae rove beetles, arguably one of the least known and the largest insect lineages, are compromised by its enormous taxonomic diversity. DNA, a powerful resource for phylogenetics, is not available for numerous extant aleocharine species. We provide a broad comparative morphological study of Aleocharinae to frame molecular datasets for total-evidence analyses. Using full-body dissections and slide-mounting techniques for light microscopy supplemented by scanning electron microscopy, we constructed a morphological matrix across all major taxa focused on non-inquiline tribes of Aleocharinae and outgroups. Phylogenetic analyses of this matrix concatenated with earlier published DNA loci and including exemplar taxa lacking molecular data, resolved outstanding controversies and, among other novelties, showed that: the Habrocerinae + Trichophyinae clade is sister group to Aleocharinae; Hypocyphtini are sister to the rest of the "higher Aleocharinae"; Taxicerini are sister to Aleocharini; Hoplandriini and Placusini are nested within a polyphyletic Oxypodini; Hoplandriini are sister to Meoticina; and Actocharini are nested within Liparocephalini. For the first time, morphological synapomorphies are identified for some large clades of Aleocharinae. In addition, 1252 high-resolution microphotographs of aleocharine structures are made available online with the entire matrix for future research.
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Affiliation(s)
- Igor Orlov
- Natural History Museum of Denmark, Zoological Museum, University of Copenhagen, Universitetsparken 15, Copenhagen, 2100, Denmark.,X-BIO Institute, University of Tyumen, 6 Volodarskogo Str., Tyumen, 625003, Russian Federation.,Zoological Institute, Russian Academy of Science, Universitetskaja nab. 1, St. Petersburg, 199034, Russian Federation
| | - Richard A B Leschen
- Manaaki Whenua - Landcare Research, New Zealand Arthropod Collection, 231 Morrin Road, St Johns, Auckland, 1072, New Zealand
| | - Dagmara Żyła
- Department of Ecology, Evolution, & Organismal Biology, Iowa State University, 2200 Osborn Dr., 228 Bessey Hall, Ames, IA, 50011, USA.,Department of Invertebrate Zoology and Parasitology, University of Gdańsk, Wita Stwosza 59, Gdańsk, 80-308, Poland
| | - Alexey Solodovnikov
- Natural History Museum of Denmark, Zoological Museum, University of Copenhagen, Universitetsparken 15, Copenhagen, 2100, Denmark.,Zoological Institute, Russian Academy of Science, Universitetskaja nab. 1, St. Petersburg, 199034, Russian Federation
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20
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DNA barcodes enable higher taxonomic assignments in the Acari. Sci Rep 2021; 11:15922. [PMID: 34354125 PMCID: PMC8342613 DOI: 10.1038/s41598-021-95147-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 07/09/2021] [Indexed: 11/09/2022] Open
Abstract
Although mites (Acari) are abundant in many terrestrial and freshwater ecosystems, their diversity is poorly understood. Since most mite species can be distinguished by variation in the DNA barcode region of cytochrome c oxidase I, the Barcode Index Number (BIN) system provides a reliable species proxy that facilitates large-scale surveys. Such analysis reveals many new BINs that can only be identified as Acari until they are examined by a taxonomic specialist. This study demonstrates that the Barcode of Life Datasystem's identification engine (BOLD ID) generally delivers correct ordinal and family assignments from both full-length DNA barcodes and their truncated versions gathered in metabarcoding studies. This result was demonstrated by examining BOLD ID's capacity to assign 7021 mite BINs to their correct order (4) and family (189). Identification success improved with sequence length and taxon coverage but varied among orders indicating the need for lineage-specific thresholds. A strict sequence similarity threshold (86.6%) prevented all ordinal misassignments and allowed the identification of 78.6% of the 7021 BINs. However, higher thresholds were required to eliminate family misassignments for Sarcoptiformes (89.9%), and Trombidiformes (91.4%), consequently reducing the proportion of BINs identified to 68.6%. Lineages with low barcode coverage in the reference library should be prioritized for barcode library expansion to improve assignment success.
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21
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Uengwetwanit T, Pootakham W, Nookaew I, Sonthirod C, Angthong P, Sittikankaew K, Rungrassamee W, Arayamethakorn S, Wongsurawat T, Jenjaroenpun P, Sangsrakru D, Leelatanawit R, Khudet J, Koehorst JJ, Schaap PJ, Martins dos Santos V, Tangy F, Karoonuthaisiri N. A chromosome-level assembly of the black tiger shrimp (Penaeus monodon) genome facilitates the identification of growth-associated genes. Mol Ecol Resour 2021; 21:1620-1640. [PMID: 33586292 PMCID: PMC8197738 DOI: 10.1111/1755-0998.13357] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Revised: 01/31/2021] [Accepted: 02/10/2021] [Indexed: 12/13/2022]
Abstract
To salvage marine ecosystems from fishery overexploitation, sustainable and efficient aquaculture must be emphasized. The knowledge obtained from available genome sequence of marine organisms has accelerated marine aquaculture in many cases. The black tiger shrimp (Penaeus monodon) is one of the most prominent cultured penaeid shrimps (Crustacean) with an average annual global production of half a million tons in the last decade. However, its currently available genome assemblies lack the contiguity and completeness required for accurate genome annotation due to the highly repetitive nature of the genome and technical difficulty in extracting high-quality, high-molecular weight DNA. Here, we report the first chromosome-level whole-genome assembly of P. monodon. The combination of long-read Pacific Biosciences (PacBio) and long-range Chicago and Hi-C technologies enabled a successful assembly of this first high-quality genome sequence. The final assembly covered 2.39 Gb (92.3% of the estimated genome size) and contained 44 pseudomolecules, corresponding to the haploid chromosome number. Repetitive elements occupied a substantial portion of the assembly (62.5%), the highest of the figures reported among crustacean species. The availability of this high-quality genome assembly enabled the identification of genes associated with rapid growth in the black tiger shrimp through the comparison of hepatopancreas transcriptome of slow-growing and fast-growing shrimps. The results highlighted several growth-associated genes. Our high-quality genome assembly provides an invaluable resource for genetic improvement and breeding penaeid shrimp in aquaculture. The availability of P. monodon genome enables analyses of ecological impact, environment adaptation and evolution, as well as the role of the genome to protect the ecological resources by promoting sustainable shrimp farming.
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Affiliation(s)
- Tanaporn Uengwetwanit
- National Center for Genetic Engineering and Biotechnology (BIOTEC)National Science and Technology Development Agency (NSTDA)Pathum Thani12120Thailand
| | - Wirulda Pootakham
- National Omics CenterNational Science and Technology Development AgencyPathum ThaniThailand
| | - Intawat Nookaew
- Department of Biomedical Informatics, College of MedicineUniversity of Arkansas for Medical SciencesLittle RockArkansasUSA
| | - Chutima Sonthirod
- National Omics CenterNational Science and Technology Development AgencyPathum ThaniThailand
| | - Pacharaporn Angthong
- National Center for Genetic Engineering and Biotechnology (BIOTEC)National Science and Technology Development Agency (NSTDA)Pathum Thani12120Thailand
| | - Kanchana Sittikankaew
- National Center for Genetic Engineering and Biotechnology (BIOTEC)National Science and Technology Development Agency (NSTDA)Pathum Thani12120Thailand
| | - Wanilada Rungrassamee
- National Center for Genetic Engineering and Biotechnology (BIOTEC)National Science and Technology Development Agency (NSTDA)Pathum Thani12120Thailand
| | - Sopacha Arayamethakorn
- National Center for Genetic Engineering and Biotechnology (BIOTEC)National Science and Technology Development Agency (NSTDA)Pathum Thani12120Thailand
| | - Thidathip Wongsurawat
- Department of Biomedical Informatics, College of MedicineUniversity of Arkansas for Medical SciencesLittle RockArkansasUSA
- Division of Bioinformatics and Data Management for ResearchDepartment of Research and DevelopmentFaculty of MedicineSiriraj HospitalMahidol UniversityBangkokThailand
| | - Piroon Jenjaroenpun
- Department of Biomedical Informatics, College of MedicineUniversity of Arkansas for Medical SciencesLittle RockArkansasUSA
- Division of Bioinformatics and Data Management for ResearchDepartment of Research and DevelopmentFaculty of MedicineSiriraj HospitalMahidol UniversityBangkokThailand
| | - Duangjai Sangsrakru
- National Omics CenterNational Science and Technology Development AgencyPathum ThaniThailand
| | - Rungnapa Leelatanawit
- National Center for Genetic Engineering and Biotechnology (BIOTEC)National Science and Technology Development Agency (NSTDA)Pathum Thani12120Thailand
| | - Jutatip Khudet
- Shrimp Genetic Improvement CenterIntegrative Aquaculture Biotechnology Research GroupSurat ThaniThailand
| | - Jasper J. Koehorst
- Laboratory of Systems and Synthetic BiologyDepartment of Agrotechnology and Food SciencesWageningen University and ResearchWageningenThe Netherlands
| | - Peter J. Schaap
- Laboratory of Systems and Synthetic BiologyDepartment of Agrotechnology and Food SciencesWageningen University and ResearchWageningenThe Netherlands
| | - Vitor Martins dos Santos
- Laboratory of Systems and Synthetic BiologyDepartment of Agrotechnology and Food SciencesWageningen University and ResearchWageningenThe Netherlands
| | - Frédéric Tangy
- Viral Genomics and Vaccination UnitUMR3569 CNRSVirology DepartmentInstitut PasteurParisFrance
| | - Nitsara Karoonuthaisiri
- National Center for Genetic Engineering and Biotechnology (BIOTEC)National Science and Technology Development Agency (NSTDA)Pathum Thani12120Thailand
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22
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Karagozlu MZ, Do TD, Kim JI, Choi TJ, Kim SG, Kim CB. An Investigation of the Variations in Complete Mitochondrial Genomes of Lingula anatina in the Western Pacific Region. BIOLOGY 2021; 10:biology10050367. [PMID: 33922950 PMCID: PMC8146825 DOI: 10.3390/biology10050367] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 04/04/2021] [Accepted: 04/23/2021] [Indexed: 06/12/2023]
Abstract
Lingula anatina is a brachiopod widely distributed in the western Pacific region. Even though L. anatina has been targeted for a number of biological studies, there is still limited information on intraspecific genetic variations of L. anatina. In this study, L. anatina specimens were collected from Korea and Vietnam, and complete mitochondrial genome (mitogenome) sequences were analyzed and compared with previous records. The total mitogenomes of L. anatina were 24,875 bp and 25,305 bp in size for Korean and Vietnamese specimens, respectively. Those mitogenomes are extraordinarily longer than the typical mitogenome size for an animal but shorter than the previous record from Yanagawa (Japan) for this species. The gene orders and the sizes of the protein-coding genes are also different from those for the Japanese specimen. Furthermore, the nonsynonymous (Ka) and synonymous (Ks) substitution rates in protein-coding genes (PCGs) were calculated to test the idea of evolutionary rate differences in mitochondrial genomes. The analyses showed relatively low Ka and Ks for the complete mitogenomes from Buan (Korea), Doson (Vietnam) and Yanagawa (Japan). The Ka/Ks ratio was less than 1 in comparisons of three localities, indicating the existence of purifying selection in this species. The phylogenetic analyses showed that L. anatina diverged among localities in the western Pacific region.
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Affiliation(s)
- Mustafa Zafer Karagozlu
- Department of Biotechnology, Sangmyung University, Seoul 03016, Korea; (M.Z.K.); (T.D.D.); (J.-I.K.); (T.-J.C.); (S.-G.K.)
- 3Billion Inc., Seoul 06193, Korea
| | - Thinh Dinh Do
- Department of Biotechnology, Sangmyung University, Seoul 03016, Korea; (M.Z.K.); (T.D.D.); (J.-I.K.); (T.-J.C.); (S.-G.K.)
- Institute of Marine Environment and Resources, Vietnam Academy of Science and Technology, Haiphong 04000, Vietnam
| | - Jung-Il Kim
- Department of Biotechnology, Sangmyung University, Seoul 03016, Korea; (M.Z.K.); (T.D.D.); (J.-I.K.); (T.-J.C.); (S.-G.K.)
| | - Tae-June Choi
- Department of Biotechnology, Sangmyung University, Seoul 03016, Korea; (M.Z.K.); (T.D.D.); (J.-I.K.); (T.-J.C.); (S.-G.K.)
| | - Seong-Geun Kim
- Department of Biotechnology, Sangmyung University, Seoul 03016, Korea; (M.Z.K.); (T.D.D.); (J.-I.K.); (T.-J.C.); (S.-G.K.)
| | - Chang-Bae Kim
- Department of Biotechnology, Sangmyung University, Seoul 03016, Korea; (M.Z.K.); (T.D.D.); (J.-I.K.); (T.-J.C.); (S.-G.K.)
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23
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Jiang Y, Li HX, Yu XF, Yang MF. Characterization of Two Complete Mitochondrial Genomes of Atkinsoniella (Hemiptera: Cicadellidae: Cicadellinae) and the Phylogenetic Implications. INSECTS 2021; 12:insects12040338. [PMID: 33920412 PMCID: PMC8070250 DOI: 10.3390/insects12040338] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 04/05/2021] [Accepted: 04/08/2021] [Indexed: 01/18/2023]
Abstract
Simple Summary Atkinsoniella is a large genus of almost 99 species across the world within the subfamily Cicadellinae, which is a large subfamily, comprising more than 2400 species of approximately 330 genera. Some of the Cicadellinae distributed worldwide are known as important agricultural pests. To better understand the mitogenomic characteristics of the genus Atkinsoniella and reveal phylogenetic relationships, the complete mitochondrial genomes of Atkinsoniella grahami and Atkinsoniella xanthonota were sequenced and comparatively analyzed in this study. The mitogenomes of these two Atkinsoniella species were found to be highly conserved, similarly to other Cicadellidae, except for the secondary structure of trnaS1, which formed a loop with the dihydrouridine (DHC) arm. This phenomenon has also been observed in other insect mitogenomes. Phylogenetic analyses, based on mitogenomes using both the maximum likelihood (ML) and Bayesian inference (BI) methods of three datasets, supported the monophyly of Cicadellinae, as well as the other subfamilies, and produced a well-resolved framework of Cicadellidae and valuable data for the phylogenetic study of Cicadellinae. Abstract The complete mitochondrial genomes of Atkinsoniella grahami and Atkinsoniella xanthonota were sequenced. The results showed that the mitogenomes of these two species are 15,621 and 15,895 bp in length, with A+T contents of 78.6% and 78.4%, respectively. Both mitogenomes contain 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), 2 ribosomal RNA genes (rRNAs), and a control region (CR). For all PCGs, a standard start ATN codon (ATT, ATG, or ATA) was found at the initiation site, except for ATP8, for which translation is initiated with a TTG codon. All PCGs terminate with a complete TAA or TAG stop codon, except for COX2, which terminates with an incomplete stop codon T. All tRNAs have the typical cloverleaf secondary structure, except for trnS, which has a reduced dihydrouridine arm. Furthermore, these phylogenetic analyses were reconstructed based on 13 PCGs and two rRNA genes of 73 mitochondrial genome sequences, with both the maximum likelihood (ML) and Bayesian inference (BI) methods. The obtained mitogenome sequences in this study will promote research into the classification, population genetics, and evolution of Cicadellinae insects in the future.
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Affiliation(s)
- Yan Jiang
- Institute of Entomology, Guizhou University, Guiyang 550025, China;
- Guizhou Provincial Key Laboratory for Agricultural Pest Management of the Mountainous Region, Guiyang 550025, China; (H.-X.L.); (X.-F.Y.)
| | - Hao-Xi Li
- Guizhou Provincial Key Laboratory for Agricultural Pest Management of the Mountainous Region, Guiyang 550025, China; (H.-X.L.); (X.-F.Y.)
- College of Tobacco Sciences, Guizhou University, Guiyang 550025, China
| | - Xiao-Fei Yu
- Guizhou Provincial Key Laboratory for Agricultural Pest Management of the Mountainous Region, Guiyang 550025, China; (H.-X.L.); (X.-F.Y.)
- College of Tobacco Sciences, Guizhou University, Guiyang 550025, China
| | - Mao-Fa Yang
- Institute of Entomology, Guizhou University, Guiyang 550025, China;
- Guizhou Provincial Key Laboratory for Agricultural Pest Management of the Mountainous Region, Guiyang 550025, China; (H.-X.L.); (X.-F.Y.)
- College of Tobacco Sciences, Guizhou University, Guiyang 550025, China
- Correspondence: ; Tel.: +86-13984073566
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24
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First complete mitogenomes of three mayflies in the genus Afronurus (Ephemeroptera: Heptageniidae) and their implications for phylogenetic reconstruction. Biologia (Bratisl) 2021. [DOI: 10.1007/s11756-021-00729-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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25
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Organization and phylogenetic relationships of the mitochondrial genomes of Speiredonia retorta and other lepidopteran insects. Sci Rep 2021; 11:2957. [PMID: 33536496 PMCID: PMC7859238 DOI: 10.1038/s41598-021-82561-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Accepted: 01/21/2021] [Indexed: 11/08/2022] Open
Abstract
In this study, we analyzed the complete mitochondrial genome (mitogenome) of Speiredonia retorta, which is a pest and a member of the Lepidoptera order. In total, the S. retorta mitogenome was found to contain 15,652 base pairs encoding 13 protein-coding genes (PCGs), 22 tRNAs, 2 rRNAs, as well as an adenine (A) + thymine (T)-rich region. These findings were consistent with the mitogenome composition of other lepidopterans, as we identified all 13 PCGs beginning at ATN codons. We also found that 11 PCGs terminated with canonical stop codons, whereas cox2 and nad4 exhibited incomplete termination codons. By analyzing the mitogenome of S. retorta using Bayesian inference (BI) and maximum likelihood (ML) models, we were able to further confirm that this species is a member of the Erebidae family.
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26
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Li R, Ying X, Deng W, Rong W, Li X. Mitochondrial genomes of eight Scelimeninae species (Orthoptera) and their phylogenetic implications within Tetrigoidea. PeerJ 2021; 9:e10523. [PMID: 33604160 PMCID: PMC7863789 DOI: 10.7717/peerj.10523] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Accepted: 11/17/2020] [Indexed: 11/20/2022] Open
Abstract
Scelimeninae is a key member of the pygmy grasshopper community, and an important ecological indicator. No mitochondrial genomes of Scelimeninae have been reported to date, and the monophyly of Scelimeninae and its phylogenetic relationship within Tetrigidae is still unclear. We sequenced and analyzed eight nearly complete mitochondrial genomes representing eight genera of Scelimeninae. These mitogenomes ranged in size from 13,112 to 16,380 bp and the order of tRNA genes between COII and ATP8 was reversed compared with the ancestral order of insects. The protein-coding genes (PCGs) of tetrigid species mainly with the typical ATN codons and most terminated with complete (TAA or TAG) stop codons. Analyses of pairwise genetic distances showed that ATP8 was the least conserved gene within Tetrigidae, while COI was the most conserved. The longest intergenic spacer (IGS) region in the mitogenomes was always found between tRNASer(UCN) and ND1. Additionally, tandem repeat units were identified in the longest IGS of three mitogenomes. Maximum likelihood (ML) and Bayesian Inference (BI) analyses based on the two datasets supported the monophyly of Tetriginae. Scelimeninae was classified as a non-monophyletic subfamily.
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Affiliation(s)
- Ran Li
- College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Xiaoli Ying
- College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Weian Deng
- School of Chemistry and Bioengineering, Hechi University, Yizhou, China
| | - Wantao Rong
- School of Chemistry and Bioengineering, Hechi University, Yizhou, China
| | - Xiaodong Li
- School of Chemistry and Bioengineering, Hechi University, Yizhou, China
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27
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Wang LH, Liu S, Tang YJ, Chen YP, Wu J, Li JL. Using the combined gene approach and multiple analytical methods to improve the phylogeny and classification of Bombus (Hymenoptera, Apidae) in China. Zookeys 2021; 1007:1-21. [PMID: 33505180 PMCID: PMC7788072 DOI: 10.3897/zookeys.1007.34105] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Accepted: 01/21/2020] [Indexed: 11/12/2022] Open
Abstract
Bumble bees are vital to our agro-ecological system, with approximately 250 species reported around the world in the single genus Bombus. However, the health of bumble bees is threatened by multiple factors: habitat loss, climate change, pesticide use, and disease caused by pathogens and parasites. It is therefore vitally important to have a fully developed phylogeny for bumble bee species as part of our conservation efforts. The purpose of this study was to explore the phylogenetic relationships of the dominant bumble bees on the Tibetan plateau and in northern China as well as their placement and classification within the genus Bombus. The study used combined gene analysis consisting of sequence fragments from six genes, 16S rRNA, COI, EF-1α, Argk, Opsin and PEPCK, and the phylogenetic relationships of 209 Bombus species were explored. Twenty-six species, including 152 gene sequences, were collected from different regions throughout China, and 1037 gene sequences representing 183 species were obtained from GenBank or BOLD. The results suggest that the 209 analyzed species belong to fifteen subgenera and that most of the subgenera in Bombus are monophyletic, which is in accordance with conventional morphology-based classifications. The phylogenetic trees also show that nearly all subgenera easily fall into two distinct clades: short-faced and long-faced. The study is the first to investigate the phylogenetic placement of Bombus turneri (Richards), Bombus opulentus Smith, Bombus pyrosoma Morawitz, Bombus longipennis Friese, Bombus minshanensis Bischoff, and Bombus lantschouensis Vogt, all of which are widely distributed throughout different regions of China. The knowledge and understanding gained from the findings can provide a molecular basis to accurately classify Bombus in China and to define strategies to conserve biodiversity and promote pollinator populations.
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Affiliation(s)
- Liu-Hao Wang
- Key Laboratory of Pollinating Insect Biology of the Ministry of Agriculture, Institute of Apicultural Research, Chinese Academy of Agricultural Science, Xiangshan, Beijing 100093, China Institute of Apicultural Research, Chinese Academy of Agricultural Science Beijing China.,College of Resources and Environmental Sciences, Henan Institute of Science and Technology, Xinxiang, Henan 453003, China Henan Institute of Science and Technology Xinxiang China
| | - Shan Liu
- Key Laboratory of Pollinating Insect Biology of the Ministry of Agriculture, Institute of Apicultural Research, Chinese Academy of Agricultural Science, Xiangshan, Beijing 100093, China Institute of Apicultural Research, Chinese Academy of Agricultural Science Beijing China
| | - Yu-Jie Tang
- Key Laboratory of Pollinating Insect Biology of the Ministry of Agriculture, Institute of Apicultural Research, Chinese Academy of Agricultural Science, Xiangshan, Beijing 100093, China Institute of Apicultural Research, Chinese Academy of Agricultural Science Beijing China
| | - Yan-Ping Chen
- United States Department of Agriculture (USDA) - Agricultural Research Service (ARS) Bee Research Laboratory, Beltsville, Maryland, USA Agricultural Research Service, United States Department of Agriculture Beltsville United States of America
| | - Jie Wu
- Key Laboratory of Pollinating Insect Biology of the Ministry of Agriculture, Institute of Apicultural Research, Chinese Academy of Agricultural Science, Xiangshan, Beijing 100093, China Institute of Apicultural Research, Chinese Academy of Agricultural Science Beijing China
| | - Ji-Lian Li
- Key Laboratory of Pollinating Insect Biology of the Ministry of Agriculture, Institute of Apicultural Research, Chinese Academy of Agricultural Science, Xiangshan, Beijing 100093, China Institute of Apicultural Research, Chinese Academy of Agricultural Science Beijing China
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28
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Yu P, Zhou L, Yang WT, Miao LJ, Li Z, Zhang XJ, Wang Y, Gui JF. Comparative mitogenome analyses uncover mitogenome features and phylogenetic implications of the subfamily Cobitinae. BMC Genomics 2021; 22:50. [PMID: 33446100 PMCID: PMC7809818 DOI: 10.1186/s12864-020-07360-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Accepted: 12/29/2020] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Loaches of Cobitinae, widely distributed in Eurasian continent, have high economic, ornamental and scientific value. However, the phylogeny of Cobitinae fishes within genera or family level remains complex and controversial. Up to now, about 60 Cobitinae mitogenomes had been deposited in GenBank, but their integrated characteristics were not elaborated. RESULTS In this study, we sequenced and analyzed the complete mitogenomes of a female Cobits macrostigma. Then we conducted a comparative mitogenome analysis and revealed the conserved and unique characteristics of 58 Cobitinae mitogenomes, including C. macrostigma. Cobitinae mitogenomes display highly conserved tRNA secondary structure, overlaps and non-coding intergenic spacers. In addition, distinct base compositions were observed among different genus and significantly negative linear correlation between AT% and AT-skew were found among Cobitinae, genus Cobitis and Pangio mitogenomes, respectively. A specific 3 bp insertion (GCA) in the atp8-atp6 overlap was identified as a unique feature of loaches, compared to other Cypriniformes fish. Additionally, all protein coding genes underwent a strong purifying selection. Phylogenetic analysis strongly supported the paraphyly of Cobitis and polyphyly of Misgurnus. The strict molecular clock predicted that Cobitinae might have split into northern and southern lineages in the late Eocene (42.11 Ma), furthermore, mtDNA introgression might occur (14.40 Ma) between ancestral species of Cobitis and ancestral species of Misgurnus. CONCLUSIONS The current study represents the first comparative mitogenomic and phylogenetic analyses within Cobitinae and provides new insights into the mitogenome features and evolution of fishes belonging to the cobitinae family.
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Affiliation(s)
- Peng Yu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, the Innovation Academy of Seed Design, Chinese Academy of Sciences, Wuhan, 430072, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Li Zhou
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, the Innovation Academy of Seed Design, Chinese Academy of Sciences, Wuhan, 430072, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Wen-Tao Yang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, the Innovation Academy of Seed Design, Chinese Academy of Sciences, Wuhan, 430072, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Li-Jun Miao
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, the Innovation Academy of Seed Design, Chinese Academy of Sciences, Wuhan, 430072, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhi Li
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, the Innovation Academy of Seed Design, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Xiao-Juan Zhang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, the Innovation Academy of Seed Design, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Yang Wang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, the Innovation Academy of Seed Design, Chinese Academy of Sciences, Wuhan, 430072, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Jian-Fang Gui
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, the Innovation Academy of Seed Design, Chinese Academy of Sciences, Wuhan, 430072, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
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Żyła D, Bogri A, Heath TA, Solodovnikov A. Total-evidence analysis resolves the phylogenetic position of an enigmatic group of Paederinae rove beetles (Coleoptera: Staphylinidae). Mol Phylogenet Evol 2020; 157:107059. [PMID: 33383175 DOI: 10.1016/j.ympev.2020.107059] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 12/10/2020] [Accepted: 12/24/2020] [Indexed: 11/29/2022]
Abstract
Paederinae is one of the most diverse subfamilies among rove beetles, yet their evolutionary history remains poorly understood. This is attributed to the limited number of phylogenetic studies, which either sought answers at a shallower taxonomic level or included limited taxon sampling. Especially problematic is the position of the rare Neotropical tribe Cylindroxystini, morphologically one of the most puzzling groups of Paederinae. The phylogenetic position of this group within Paederinae was never understood, though its rank in the classification has already been shifted twice. We assembled molecular and morphological data matrices sampled from all currently recognized Paederinae subtribes, including both genera of Cylindroxystini, and used these data to estimate phylogenetic relationships using Bayesian inference. A total of 123 morphological characters and 4,631 bp of nuclear (28S, TP, Wg, CADA, CADC, ArgK) and mitochondrial (COI) sequences were analyzed for 76 taxa. The current tribe Cylindroxystini was resolved as a monophylum within the tribe Lathrobiini as sister to the genus Pseudolathra, and together they are sister to the so-called 'Medonina and allied taxa' clade. Based on these results, we downgraded Cylindroxystini back to the subtribal level, Cylindroxystina status reinstated, now with a known sister group. The resulting phylogeny is the largest of the subfamily Paederinae to date and lays the foundation for establishing a natural classification of the group.
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Affiliation(s)
- Dagmara Żyła
- Iowa State University, Department of Ecology, Evolution, & Organismal Biology, 2200 Osborn Dr, Ames, IA 50011, USA; University of Gdańsk, Department of Invertebrate Zoology and Parasitology, Wita Stwosza 59, 80-308 Gdańsk, Poland.
| | - Amalia Bogri
- Natural History Museum of Denmark, University of Copenhagen, Universitetsparken 15, DK-2100 Copenhagen, Denmark
| | - Tracy A Heath
- Iowa State University, Department of Ecology, Evolution, & Organismal Biology, 2200 Osborn Dr, Ames, IA 50011, USA
| | - Alexey Solodovnikov
- Natural History Museum of Denmark, University of Copenhagen, Universitetsparken 15, DK-2100 Copenhagen, Denmark; Zoological Institute, Russian Academy of Sciences, Universitetskaja emb. 1, 199034 St. Petersburg, Russia
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30
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Li R, Zhang W, Ma Z, Zhou C. Novel gene rearrangement pattern in the mitochondrial genomes of Torleya mikhaili and Cincticostella fusca (Ephemeroptera: Ephemerellidae). Int J Biol Macromol 2020; 165:3106-3114. [PMID: 33098898 DOI: 10.1016/j.ijbiomac.2020.10.124] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 10/12/2020] [Accepted: 10/14/2020] [Indexed: 10/23/2022]
Abstract
The mayfly family Ephemerellidae (Insecta: Ephemeroptera) is distributed around the world and has very high species diversity. However, its evolution pattern of mitogenome and phylogenetic relationships within Ephemeroptera remain unclear. In this study, the complete mitochondrial genomes (mitogenomes) of Torleya mikhaili (15,042 bp) and Cincticostella fusca (15,135 bp) were firstly determined and analyzed. Two ephemerellid mitogenomes shared similar gene organization with 37 typical genes as well as a putative control region. Compared with other reported mitogenomes of mayflies, the unique gene order (I'-CR-Q-M) was found in these two mitogenomes. Although the observed rearrangement pattern is novel within ephemeropteran mitogenomes, it could be explained presumably by the mechanisms of tandem duplication-random loss and recombination. The phylogenetic analyses using both Bayesian inference (BI) and maximum likelihood (ML) methods based on four nucleotide datasets placed three ephemerellid species together. Furthermore, the phylogenetic relationships of the three genera were recovered as ((Ephemerella + Cincticostella) + Torleya).
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Affiliation(s)
- Ran Li
- The Key Laboratory of Jiangsu Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu 210023, PR China
| | - Wei Zhang
- The Key Laboratory of Jiangsu Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu 210023, PR China
| | - Zhenxing Ma
- The Key Laboratory of Jiangsu Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu 210023, PR China
| | - Changfa Zhou
- The Key Laboratory of Jiangsu Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu 210023, PR China.
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31
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Kelava S, Mans BJ, Shao R, Moustafa MAM, Matsuno K, Takano A, Kawabata H, Sato K, Fujita H, Ze C, Plantard O, Hornok S, Gao S, Barker D, Barker SC, Nakao R. Phylogenies from mitochondrial genomes of 120 species of ticks: Insights into the evolution of the families of ticks and of the genus Amblyomma. Ticks Tick Borne Dis 2020; 12:101577. [PMID: 33120251 DOI: 10.1016/j.ttbdis.2020.101577] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Accepted: 08/19/2020] [Indexed: 11/28/2022]
Abstract
The evolution and phylogenetic relationships of the ticks at both the family and genus levels are contested. The genus Amblyomma and its subgenera are in a state of flux; moreover, the relationships among the three tick families are controversial due to conflicting phylogenetic support for different arrangements of the three families of living ticks. With 18 newly sequenced mitochondrial (mt) genomes of ticks included, we executed the largest mt genome phylogenetic study of ticks so far. Phylogenetic trees were inferred from one sea spider mt genome, one horseshoe crab, five mite mt genomes and 146 tick mt genomes from 120 species: 153 mt genomes in total. Sixteen phylogenetic trees were inferred from 10 datasets using both maximum likelihood and Bayesian inference methods. We describe the first novel mt gene-arrangement for the metastriate Ixodidae in Amblyomma (Africaniella) transversale. Also, three unusual partial 16S rRNA gene inserts were found in the mt genome of Haemaphysalis (Alloceraea) kitaokai: we consider the possible role of past genome translocation events in the formation of these inserts. Our phylogenies revealed evidence that: (i) the genus Amblyomma is polyphyletic with respect to Amblyomma (Africaniella) transversale; (ii) the subgenus Aponomma is apparently embedded in the genus Amblyomma; (iii) Haemaphysalis (Segalia) parva and Haemaphysalis (Alloceraea) kitaokai form a clade to the exclusion of other Haemaphysalis species; and (iv) the phylogenetic position of the family Nuttalliellidae is unstable among phylogenies from different datasets.
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Affiliation(s)
- Samuel Kelava
- Department of Parasitology, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, 4072, Australia
| | - Ben J Mans
- Epidemiology, Parasites and Vectors, Agricultural Research Council - Onderstepoort Veterinary Research, Onderstepoort, 0110, South Africa; The Department of Veterinary Tropical Diseases, University of Pretoria, Pretoria, 0110, South Africa; The Department of Life and Consumer Sciences, University of South Africa, Florida, 1709, South Africa
| | - Renfu Shao
- School of Science and Engineering, GeneCology Research Centre, University of the Sunshine Coast, Sippy Downs, Queensland, 4558, Australia
| | | | - Keita Matsuno
- Department of Disease Control, Graduate School of Veterinary Medicine, Hokkaido University, Hokkaido, 060-0818, Japan
| | - Ai Takano
- Department of Bacteriology, National Institute of Infectious Diseases, Tokyo, 162-8640, Japan
| | - Hiroki Kawabata
- Department of Bacteriology, National Institute of Infectious Diseases, Tokyo, 162-8640, Japan
| | - Kozue Sato
- Department of Bacteriology, National Institute of Infectious Diseases, Tokyo, 162-8640, Japan
| | - Hiromi Fujita
- Mahara Institute of Medical Acarology, 56-3 Aratano, Anan-shi, Tokushima, 779-1510, Japan
| | - Chen Ze
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, Hebei, 050024, China
| | | | - Sandor Hornok
- Department of Parasitology and Zoology, University of Veterinary Medicine, Budapest, 1078, Hungary
| | - Shan Gao
- College of Life Sciences, Nankai University, Tianjin, PR China
| | - Dayana Barker
- School of Veterinary Science, The University of Queensland, Gatton, Queensland 4343, Australia
| | - Stephen C Barker
- Department of Parasitology, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, 4072, Australia.
| | - Ryo Nakao
- Department of Disease Control, Graduate School of Veterinary Medicine, Hokkaido University, Hokkaido, 060-0818, Japan
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32
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Mir RA, Bhat KA, Rashid G, Ebinezer LB, Masi A, Rakwal R, Shah AA, Zargar SM. DNA barcoding: a way forward to obtain deep insights about the realistic diversity of living organisms. THE NUCLEUS 2020. [DOI: 10.1007/s13237-020-00330-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
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33
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Huang W, Xie X, Peng F, Liang X, Wang X, Chen X. Optimizing the widely used nuclear protein-coding gene primers in beetle phylogenies and their application in the genus Sasajiscymnus Vandenberg (Coleoptera: Coccinellidae). Ecol Evol 2020; 10:7731-7738. [PMID: 32760560 PMCID: PMC7391345 DOI: 10.1002/ece3.6497] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2020] [Revised: 05/10/2020] [Accepted: 06/02/2020] [Indexed: 11/26/2022] Open
Abstract
Advances in genomic biology and the increasing availability of genomic resources allow developing hundreds of nuclear protein-coding (NPC) markers, which can be used in phylogenetic research. However, for low taxonomic levels, it may be more practical to select a handful of suitable molecular loci for phylogenetic inference. Unfortunately, the presence of degenerate primers of NPC markers can be a major impediment, as the amplification success rate is low and they tend to amplify nontargeted regions. In this study, we optimized five NPC fragments widely used in beetle phylogenetics (i.e., two parts of carbamoyl-phosphate synthetase: CADXM and CADMC, Topoisomerase, Wingless and Pepck) by reducing the degenerate site of primers and the length of target genes slightly. These five NPC fragments and 6 other molecular loci were amplified to test the monophyly of the coccinellid genus Sasajiscymnus Vandenberg. The analysis of our molecular data set clearly supported the genus Sasajiscymnus may be monophyletic but confirmation with an extended sampling is required. A fossil-calibrated chronogram was generated by BEAST, indicating an origin of the genus at the end of the Cretaceous (77.87 Myr). Furthermore, a phylogenetic informativeness profile was generated to compare the phylogenetic properties of each gene more explicitly. The results showed that COI provides the strongest phylogenetic signal among all the genes, but Pepck, Topoisomerase, CADXM and CADMC are also relatively informative. Our results provide insight into the evolution of the genus Sasajiscymnus, and also enrich the molecular data resources for further study.
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Affiliation(s)
- Weidong Huang
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant GermplasmDepartment of Forest ProtectionCollege of Forestry and Landscape ArchitectureSouth China Agricultural UniversityGuangzhouChina
- Key Laboratory of Bio‐Pesticide Innovation and Application, Guangdong ProvinceEngineering Research Center of BiocontrolMinistry of Education and Guangdong ProvinceGuangzhouChina
| | - Xiufeng Xie
- Guangdong Agriculture Industry Business Polytechnic CollegeGuangzhouChina
| | - Feng Peng
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant GermplasmDepartment of Forest ProtectionCollege of Forestry and Landscape ArchitectureSouth China Agricultural UniversityGuangzhouChina
| | - Xinyue Liang
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant GermplasmDepartment of Forest ProtectionCollege of Forestry and Landscape ArchitectureSouth China Agricultural UniversityGuangzhouChina
- Key Laboratory of Bio‐Pesticide Innovation and Application, Guangdong ProvinceEngineering Research Center of BiocontrolMinistry of Education and Guangdong ProvinceGuangzhouChina
| | - Xingmin Wang
- Key Laboratory of Bio‐Pesticide Innovation and Application, Guangdong ProvinceEngineering Research Center of BiocontrolMinistry of Education and Guangdong ProvinceGuangzhouChina
| | - Xiaosheng Chen
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant GermplasmDepartment of Forest ProtectionCollege of Forestry and Landscape ArchitectureSouth China Agricultural UniversityGuangzhouChina
- Key Laboratory of Bio‐Pesticide Innovation and Application, Guangdong ProvinceEngineering Research Center of BiocontrolMinistry of Education and Guangdong ProvinceGuangzhouChina
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34
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Hurzaid A, Chan T, Mohd Nor SA, Muchlisin ZA, Chen W. Molecular phylogeny and diversity of penaeid shrimps (Crustacea: Decapoda) from South‐East Asian waters. ZOOL SCR 2020. [DOI: 10.1111/zsc.12428] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Amirah Hurzaid
- Institute of Oceanography National Taiwan University Taipei Taiwan
- Biological Sciences Department School of Distance Education Universiti Sains Malaysia Penang Malaysia
| | - Tin‐Yam Chan
- Institute of Marine Biology and Center of Excellence for the Oceans National Taiwan Ocean University Keelung Taiwan
| | - Siti Azizah Mohd Nor
- Institute of Marine Biotechnology Universiti Malaysia Terengganu Kuala Terengganu Malaysia
| | | | - Wei‐Jen Chen
- Institute of Oceanography National Taiwan University Taipei Taiwan
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35
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Sabadini CP, Machado CB, Vilhena PDS, Garófalo CA, Del Lama MA. Species delimitation and phylogenetic relationships in the genusTrypoxylon(Hymenoptera: Crabronidae) using molecular markers: an alternative to taxonomic impediment. SYST BIODIVERS 2020. [DOI: 10.1080/14772000.2020.1758824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
- Camila Pereira Sabadini
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, Rodovia Washington Luís, Km 235, São Carlos, 13565-905, SP, Brazil
| | - Carolina Barros Machado
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, Rodovia Washington Luís, Km 235, São Carlos, 13565-905, SP, Brazil
| | - Patrícia Dos Santos Vilhena
- Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Avenida Bandeirantes, 3900, Ribeirão Preto, 14040-900, SP, Brazil
| | - Carlos Alberto Garófalo
- Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Avenida Bandeirantes, 3900, Ribeirão Preto, 14040-900, SP, Brazil
| | - Marco Antonio Del Lama
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, Rodovia Washington Luís, Km 235, São Carlos, 13565-905, SP, Brazil
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36
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Song N, Geng Y, Li X. The Mitochondrial Genome of the Phytopathogenic Fungus Bipolaris sorokiniana and the Utility of Mitochondrial Genome to Infer Phylogeny of Dothideomycetes. Front Microbiol 2020; 11:863. [PMID: 32457727 PMCID: PMC7225605 DOI: 10.3389/fmicb.2020.00863] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Accepted: 04/09/2020] [Indexed: 12/01/2022] Open
Abstract
A number of species in Bipolaris are important plant pathogens. Due to a limited number of synapomorphic characters, it is difficult to perform species identification and to estimate phylogeny of Bipolaris based solely on morphology. In this study, we sequenced the complete mitochondrial genome of Bipolaris sorokiniana, and presented the detailed annotation of the genome. The B. sorokiniana mitochondrial genome is 137,775 bp long, and contains two ribosomal RNA genes, 12 core protein-coding genes, 38 tRNA genes. In addition, two ribosomal protein genes (rps3 gene and rps5 gene) and the fungal mitochondrial RNase P gene (rnpB) are identified. The large genome size is mostly determined by the presence of numerous intronic and intergenic regions. A total of 28 introns are inserted in eight core protein-coding genes. Together with the published mitochondrial genome sequences, we conducted a preliminary phylogenetic inference of Dothideomycetes under various datasets and substitution models. The monophyly of Capnodiales, Botryosphaeriales and Pleosporales are consistently supported in all analyses. The Venturiaceae forms an independent lineage, with a distant phylogenetic relationship to Pleosporales. At the family level, the Mycosphaerellaceae, Botryosphaeriaceae. Phaeosphaeriaceae, and Pleosporaceae are recognized in the majority of trees.
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Affiliation(s)
- Nan Song
- College of Plant Protection, Henan Agricultural University, Zhengzhou, China
| | - Yuehua Geng
- College of Plant Protection, Henan Agricultural University, Zhengzhou, China
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37
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Jensen AR, Jenkins Shaw J, Żyła D, Solodovnikov A. A total-evidence approach resolves phylogenetic placement of ‘Cafius’ gigas, a unique recently extinct rove beetle from Lord Howe Island. Zool J Linn Soc 2020. [DOI: 10.1093/zoolinnean/zlaa020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
Cafius gigas Lea, 1929 (Coleoptera: Staphylinidae) was a large rove beetle endemic to Lord Howe Island (LHI) resembling Cafius and the LHI flightless endemic Hesperus dolichoderes (Lea, 1925). Like several other LHI endemics, C. gigas became extinct due to human-introduced rats. It is a legacy species valuable for understanding the LHI biota in terms of evolutionary biology and historical biogeography. Whether C. gigas was a member of Cafius Curtis, 1829, restricted to oceanic shores and prone to trans-oceanic dispersal, or related to H. dolichoderes, would have different implications. We subjected C. gigas to a total-evidence phylogenetic analyses of morphological and molecular data using model-based and parsimony methods. As a result, it is transferred to Hesperus Fauvel, 1874 with the new combination Hesperus gigas (Lea, 1929) comb. nov. Our analysis indicates that the montane leaf litter inhabitant H. gigas evolved neither in situ nor from a seashore Cafius-ancestor, or from an ancestor shared by two other LHI endemic congeners, Hesperus pacificus Olliff, 1887 and H. dolichoderes. It also suggests that all three Hesperus species that currently occur on LHI could have evolved on various seamounts at various times before reaching LHI.
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Affiliation(s)
- Arn Rytter Jensen
- Natural History Museum of Denmark, Universitetsparken, Copenhagen, Denmark
- Department of Biology and Biotechnology “Charles Darwin”, Sapienza University of Rome, Rome Italy
| | - Josh Jenkins Shaw
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Dagmara Żyła
- Department of Ecology, Evolution, & Organismal Biology, Iowa State University, Osborn Dr, Ames, IA, USA
- Department of Invertebrate Zoology and Parasitology, University of Gdańsk, Wita Stwosza, Gdańsk, Poland
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38
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Tihelka E, Thayer MK, Newton AF, Cai C. New Data, Old Story: Molecular Data Illuminate the Tribal Relationships among Rove Beetles of the Subfamily Staphylininae (Coleoptera: Staphylinidae). INSECTS 2020; 11:E164. [PMID: 32143338 PMCID: PMC7143346 DOI: 10.3390/insects11030164] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 02/28/2020] [Accepted: 03/02/2020] [Indexed: 11/17/2022]
Abstract
The megadiverse subfamily Staphylininae traditionally belonged to the best-defined rove beetle taxa, but the advent of molecular phylogenetics in the last decade has brought turbulent changes to the group's classification. Here, we reevaluate the internal relationships among the tribes of Staphylininae by implementing tree inference methods that suppress common sources of systematic error. In congruence with morphological data, and in contrast to some previous phylogenetic studies, we unambiguously recover Staphylininae and Paederinae as monophyletic in the traditional sense. We show that the recently proposed subfamily Platyprosopinae (Arrowinus and Platyprosopus) is a phylogenetic artefact and reinstate Arrowinus as a member of Arrowinini stat. res. and Platyprosopus as a member of Platyprosopini stat. res. We show that several recent changes to the internal classification of the subfamily are phylogenetically unjustified and systematically unnecessary. We, therefore, reestablish Platyprosopini, Staphylinini, and Xantholinini as tribes within Staphylininae (all stat. res.) and recognize Coomaniini as a tribe (stat. nov.) rather than subfamily. Consequently, the traditional ranks of the subtribes Acylophorina, Afroquediina, Amblyopinina, Antimerina, †Baltognathina, Cyrtoquediina, Erichsoniina, Hyptiomina, Indoquediina, Quediina, and Tanygnathinina are restored (all stat. res.). We review the current classification of Staphylininae and discuss sources of incongruence in multigene phylogenies.
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Affiliation(s)
- Erik Tihelka
- Department of Animal Science, Hartpury College, Hartpury GL19 3BE, UK;
| | - Margaret K. Thayer
- Negaunee Integrative Research Center, Field Museum of Natural History, Chicago, IL 60605, USA; (M.K.T.); (A.F.N.)
| | - Alfred F. Newton
- Negaunee Integrative Research Center, Field Museum of Natural History, Chicago, IL 60605, USA; (M.K.T.); (A.F.N.)
| | - Chenyang Cai
- State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Palaeontology, and Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Nanjing 210008, China
- School of Earth Sciences, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, UK
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39
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Gamboa M, Arrivillaga-HenrÍQuez J. Biochemical and molecular differentiation of Anacroneuria species (Plecoptera, Insecta) in Andean National Park, Venezuela. SYST BIODIVERS 2019. [DOI: 10.1080/14772000.2019.1687604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- Maribet Gamboa
- Faculty of Engineering, Department of Civil and Environmental Engineering, Ehime University, Bunkyo-cho 3, Matsuyama 790-8577, Japan
| | - Jazzmin Arrivillaga-HenrÍQuez
- FACSO-Turismo THC, Área Ambiente y Territorio, Línea Salud y Calidad Ambiental, Grupo de Investigación Biodiversidad, Zoonosis y Salud Pública (GIBCIZ), Instituto de Investigación en Salud Pública y Zoonosis, Universidad Central del Ecuador, Quito, Ecuador
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40
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Ma J, Liu J, Shen Y, Fan Z, Yue B, Zhang X. Population genetic structure and intraspecific genetic distance of Periplaneta americana (Blattodea: Blattidae) based on mitochondrial and nuclear DNA markers. Ecol Evol 2019; 9:12928-12939. [PMID: 31788226 PMCID: PMC6876684 DOI: 10.1002/ece3.5777] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 10/01/2019] [Accepted: 10/02/2019] [Indexed: 11/06/2022] Open
Abstract
The American cockroach (Periplaneta americana) is a globally invasive pest that can cause significant economic loss and threaten human health. Although it is abundant and lives in close proximity to humans, few studies have investigated the genetic diversity of P. americana. Our study analyzed 1,053 P. americana and other Periplaneta species' samples from different locations in China and the United States. A traditional tree-based method using 17 unique mitochondrial COI haplotypes of P. americana and 20 haplotypes of the other Periplaneta species accurately identified P. americana with a barcoding threshold of 5.1%. To identify the population genetic structure of P. americana, we investigated wingless gene and pooled them with obtained mtDNA data for a combined analysis. Although the genetic diversity of the USA group was relatively higher than the China group, the number of haplotypes and alleles of both groups was small. The analysis of molecular variance (AMOVA), intraspecific phylogeny, and haplotype networks indicated that P. americana had very little global genetic differentiation. The weak geographic genetic structure might reflect the human-mediated dispersal of P. americana. Despite no apparent phylogeographic assignment of mtDNA and nuclear lineages was observed in both BI trees, the integrated COI sequence data identified four distinct P. americana haplotype groups, showing four ancient maternal lineages of P. americana in China and the United States.
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Affiliation(s)
- Jinnan Ma
- Key Laboratory of Bio‐resources and Eco‐environmentMinistry of EducationCollege of Life SciencesSichuan UniversityChengduChina
| | - Jinhua Liu
- Sichuan Key Laboratory of Conservation Biology on Endangered WildlifeCollege of Life SciencesSichuan UniversityChengduChina
| | - Yongmei Shen
- Sichuan Key Laboratory of Medicinal American CockroachSichuan Gooddoctor Pharmaceutical GroupChengduChina
| | - Zhenxin Fan
- Key Laboratory of Bio‐resources and Eco‐environmentMinistry of EducationCollege of Life SciencesSichuan UniversityChengduChina
- Sichuan Key Laboratory of Conservation Biology on Endangered WildlifeCollege of Life SciencesSichuan UniversityChengduChina
| | - Bisong Yue
- Key Laboratory of Bio‐resources and Eco‐environmentMinistry of EducationCollege of Life SciencesSichuan UniversityChengduChina
- Sichuan Key Laboratory of Conservation Biology on Endangered WildlifeCollege of Life SciencesSichuan UniversityChengduChina
| | - Xiuyue Zhang
- Key Laboratory of Bio‐resources and Eco‐environmentMinistry of EducationCollege of Life SciencesSichuan UniversityChengduChina
- Sichuan Key Laboratory of Conservation Biology on Endangered WildlifeCollege of Life SciencesSichuan UniversityChengduChina
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41
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Chen J, Cao J, Li W, Wang Y. Characterization of the complete mitochondrial genome of a stonefly species, Kamimuria klapaleki (Plecoptera: Pelidae). Mitochondrial DNA B Resour 2019; 4:3416-3417. [PMID: 33366019 PMCID: PMC7710318 DOI: 10.1080/23802359.2019.1674722] [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] [Indexed: 10/25/2022] Open
Abstract
We have sequenced and analyzed complete mitochondrial genome (mitogenomes) of the Kamimuria klapaleki, the third mitochondrial genome in the genus Kamimuria, which belongs to the family Pelidae in this paper. The mitogenome of K. klapaleki is circular with the length of 16,077 bp, which possessed 37 genes and a control region like other stonefly. The A + T content of the whole mitogenome was 67.1%. All PCGs were 11,217 bp in length, accounting for 65.3% of the content of A + T. The A + T content of lrRNA and srRNA were 72.3% and 66.4%. The highest A + T content was in the control region (76.2%). There are 15 gene overlaps and 9 gene intergenic spacers in this mitochondrial genome. In addition, we performed phylogenetic analysis by using the Bayesian (BI) and Maximum Likelihood (ML) methods based on the concatenated data set of PCGs from 11 species in Pelidae and two species in Styloperlidae (outgroups). The clade K. chungnanshana + K. wangi was a sister group to K. klapaleki, which is consistent with the traditional morphological classification.
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Affiliation(s)
- Jiajia Chen
- Department of Plant Protection, Henan Institute of Science and Technology, Xinxiang, China
| | - Jinjun Cao
- Department of Plant Protection, Henan Institute of Science and Technology, Xinxiang, China
| | - Weihai Li
- Department of Plant Protection, Henan Institute of Science and Technology, Xinxiang, China
| | - Ying Wang
- Department of Plant Protection, Henan Institute of Science and Technology, Xinxiang, China,CONTACT Ying Wang Department of Plant Protection, Henan Institute of Science and Technology, Xinxiang453003, China
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Chen M, Wang Y, Chen J, Cao J. The complete mitochondrial genome of a stonefly species, Indonemoura auriformis (Plecoptera: Nemouridae). MITOCHONDRIAL DNA PART B-RESOURCES 2019; 4:3392-3393. [PMID: 33366008 PMCID: PMC7707255 DOI: 10.1080/23802359.2019.1674723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
One new mitochondrial genome of Indonemoura auriformis from the family Nemouridae (Insecta: Plecoptera) was sequenced in the study. The mitochondrial genome has the length of 15,718 bp, encoding 37 genes: 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, and 2 ribosomal RNA (rRNA) genes. The whole nucleotide composition biased adenine and thymine with A + T accounting for 69.9%. Nine PCGs and 14 tRNA genes are encoded in the J chain, the other four PCGs, eight tRNAs, and two rRNA genes are encoded in the chain of N. The mitochondrial genome includes 13 gene overlaps and 12 intergenic spacers. Most PCGs strictly use the ATN as start codon, and terminate with traditional stop codon (TAA and TAG). Except the tRNASer(AGN) seems to lack dihydrogen glycine arm, all tRNA genes of the mitochondrial genome are the typical clover secondary structure. The phylogenetic tree of PCGs dataset based on bayesian inference (BI) and maximum likelihood (ML) analysis show the same tree topology. Both ML and BI analysis support the sister-group relationship between Amphinemuria and Nemoura. Meanwhile, Capniidae is closely related to Taeniopterygidae.
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Affiliation(s)
- Mengdan Chen
- Department of Plant Protection, Henan Institute of Science and Technology, Xinxiang, China
| | - Ying Wang
- Department of Plant Protection, Henan Institute of Science and Technology, Xinxiang, China
| | - Jiajia Chen
- Department of Plant Protection, Henan Institute of Science and Technology, Xinxiang, China
| | - Jinjun Cao
- Department of Plant Protection, Henan Institute of Science and Technology, Xinxiang, China
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The conserved mitochondrial genomes of Drosophila mercatorum (Diptera: Drosophilidae) with different reproductive modes and phylogenetic implications. Int J Biol Macromol 2019; 138:912-918. [PMID: 31362022 DOI: 10.1016/j.ijbiomac.2019.07.184] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Revised: 07/26/2019] [Accepted: 07/26/2019] [Indexed: 11/23/2022]
Abstract
Fruit flies (Drosophilidae: Drosophila) are commonly found in daily life and have long been used as model organisms in biology researches. Drosophila mercatorum is one important member of the Drosophila genus and has been used to study centrosome assembly of cells. In this study, we sequenced and analyzed the mitochondrial genome (mitogenome) of D. mercatorum, finding that it contains the typical structure of 37 genes and a control region. The arrangement of mitochondrial genes is in accordance with that in other Drosophila species, which is considered the ancestral organization of insects' mitogenomes. Phylogenetic analyses were performed based on 23 species of Drosophila. Our results supported two monophyletic subgenera, Drosophila and Sophophora, except for D. willistoni which was presented as an early offshoot of Drosophila. The topology ((D. yakuba + D. erecta) + D. melanogaster) was supported. We further compared the mitogenomes of parthenogenesis and sexual reproduction strains of D. mercatorum. However, only one synonymous mutation in COI gene was identified, indicating mitogenomic evolution is not strongly correlated with the different reproductive modes of this species. Taken together, our results demonstrate that mitogenome is an effective molecular marker that can be further used in phylogenetic studies of Drosophila and other organisms.
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Yu X, Tan W, Zhang H, Jiang W, Gao H, Wang W, Liu Y, Wang Y, Tian X. Characterization of the Complete Mitochondrial Genome of Harpalus sinicus and Its Implications for Phylogenetic Analyses. Genes (Basel) 2019; 10:E724. [PMID: 31540431 PMCID: PMC6771156 DOI: 10.3390/genes10090724] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Revised: 09/12/2019] [Accepted: 09/13/2019] [Indexed: 01/13/2023] Open
Abstract
In this study, we report the complete mitochondrial genome of Harpalus sinicus (occasionally named as the Chinese ground beetle) which is the first mitochondrial genome for Harpalus. The mitogenome is 16,521 bp in length, comprising 37 genes, and a control region. The A + T content of the mitogenome is as high as 80.6%. A mitochondrial origins of light-strand replication (OL)-like region is found firstly in the insect mitogenome, which can form a stem-loop hairpin structure. Thirteen protein-coding genes (PCGs) share high homology, and all of them are under purifying selection. All tRNA genes (tRNAs) can be folded into the classic cloverleaf secondary structures except tRNA-Ser (GCU), which lacks a dihydrouridine (DHU) stem. The secondary structure of two ribosomal RNA genes (rRNAs) is predicted based on previous insect models. Twelve types of tandem repeats and two stem-loop structures are detected in the control region, and two stem-loop structures may be involved in the initiation of replication and transcription. Additionally, phylogenetic analyses based on mitogenomes suggest that Harpalus is an independent lineage in Carabidae, and is closely related to four genera (Abax, Amara, Stomis, and Pterostichus). In general, this study provides meaningful genetic information for Harpalus sinicus and new insights into the phylogenetic relationships within the Carabidae.
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Affiliation(s)
- Xiaolei Yu
- Tianjin State Key Laboratory of Modern Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Wei Tan
- Tianjin State Key Laboratory of Modern Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Huanyu Zhang
- Tianjin State Key Laboratory of Modern Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Weiling Jiang
- Tianjin State Key Laboratory of Modern Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Han Gao
- Tianjin State Key Laboratory of Modern Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Wenxiu Wang
- Tianjin State Key Laboratory of Modern Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Yuxia Liu
- Tianjin State Key Laboratory of Modern Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Yu Wang
- School of Integrative Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Xiaoxuan Tian
- Tianjin State Key Laboratory of Modern Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China.
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Li JY, Song ZL, Yan GY, He LS. The complete mitochondrial genome of the largest amphipod, Alicella gigantea: Insight into its phylogenetic relationships and deep sea adaptive characters. Int J Biol Macromol 2019; 141:570-577. [PMID: 31505211 DOI: 10.1016/j.ijbiomac.2019.09.050] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 08/23/2019] [Accepted: 09/06/2019] [Indexed: 10/26/2022]
Abstract
Alicella gigantea (Alicelloidae) is a scavenger with the largest body size among amphipods. It is a participant in the foodweb of deepsea ecosystem and distributed with vast bathymetric and geographic ranges. In this study, the mitochondrial genome of A. gigantea was completely assembled and characterized. The complete sequence has a total length of 16,851 bp, comprising the usual eukaryotic components, with 13 protein-coding genes (PCGs), 2 ribosomal RNA genes (rRNAs), 22 transfer RNA genes (tRNAs), and 2 noncoding control regions (CRs). The gene rearrangement and reverse nucleotide strand bias of its mitochondrial genome are similar to those observed in the deepsea amphipod Eurythenes maldoror (Eurytheneidae), but different from the characters of Halice sp. MT-2017 (Dexaminoidea), an inhabitant of a deeper environment. Phylogenetic analysis indicates that A. gigantea occupies the basal branch of deepsea species-E. maldoror and Hirondellea gigas. This phylogeny supports the hypothesis that the evolution of hadal amphipods has undergone a transition from the abyssal depth. Compared to 41 available shallow water equivalents, the four accessible mitochondrial genomes from the deep sea, including the one produced in this study, show significantly fewer charged amino acids in the 13 PCGs, which suggests an adaption to the deepsea environment.
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Affiliation(s)
- Jun-Yuan Li
- Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, Hainan 572000, PR China
| | - Zeng-Lei Song
- Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, Hainan 572000, PR China
| | - Guo-Yong Yan
- Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, Hainan 572000, PR China
| | - Li-Sheng He
- Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, Hainan 572000, PR China.
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Wang W, Huang Y, Bartlett CR, Zhou F, Meng R, Qin D. Characterization of the complete mitochondrial genomes of two species of the genus Aphaena Guérin-Méneville (Hemiptera: Fulgoridae) and its phylogenetic implications. Int J Biol Macromol 2019; 141:29-40. [PMID: 31470055 DOI: 10.1016/j.ijbiomac.2019.08.222] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Revised: 08/19/2019] [Accepted: 08/26/2019] [Indexed: 12/27/2022]
Abstract
The complete mitochondrial genomes (mitogenomes) of Aphaena (Callidepsa) amabilis and Aphaena (Aphaena) discolor nigrotibiata were sequenced. The mitogenomes of these two species are 16,237 bp and 16,116 bp in length with an A + T content of 77.9% and 77.0%, respectively. Each contains 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), two ribosomal RNA genes (rRNAs) and a control region (A + T-rich region). All PCGs initiate with the standard start codon of ATN and terminate with the complete stop codon of TAA or TAG except for atp6, where nad1 ends with an incomplete T codon. All tRNAs have the typical clover-leaf structure except for trnS1 and trnV which have a reduced DHU arm. Moreover, these two mitogenomes have trnL2, trnR and trnT with an unpaired base in the acceptor stem. The putative A + T-rich region includes multiple types of tandem repeat regions. These phylogenetic analyses are reconstructed based on 13 protein-coding genes of 25 auchenorrhynchan mitogenomes, with both maximum likelihood and Bayesian analyses yielding robust identical phylogenetic trees. These results support a monophyletic Auchenorrhyncha and the relationship (Pyrops + (Lycorma + Aphaena)) within Fulgoridae.
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Affiliation(s)
- Wenqian Wang
- Key Laboratory of Plant Protection Resources and Pest Management of the Ministry of Education, Entomological Museum, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yixin Huang
- Key Laboratory of Biotic Environment and Ecological Safety in Anhui Province, College of Life Sciences, Anhui Normal University, Wuhu, Anhui 241000, China
| | - Charles R Bartlett
- Department of Entomology and Wildlife Ecology, University of Delaware, Newark, DE 19716, USA
| | - Fanmei Zhou
- Wuzhishan National Nature Reserve, Zhou Fanmei Photographic Art Gallery, Wuzhishan, Hainan 572200, China
| | - Rui Meng
- Post-Entry Quarantine Station for Tropical Plant, Haikou Customs District, Haikou, Hainan 570105, China
| | - Daozheng Qin
- Key Laboratory of Plant Protection Resources and Pest Management of the Ministry of Education, Entomological Museum, Northwest A&F University, Yangling, Shaanxi 712100, China.
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Wang T, Zhang S, Pei T, Yu Z, Liu J. The Complete Mitochondrial Genome and Expression Profile of Mitochondrial Protein-Coding Genes in the Bisexual and Parthenogenetic Haemaphysalis longicornis. Front Physiol 2019; 10:982. [PMID: 31417433 PMCID: PMC6682753 DOI: 10.3389/fphys.2019.00982] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Accepted: 07/15/2019] [Indexed: 11/13/2022] Open
Abstract
The tick Haemaphysalis longicornis is widely distributed in eastern Asia, New Zealand and Australia, and is well-known as a vector of multiple zoonotic pathogens. This species exhibits two reproductive strategies, bisexual and obligate parthenogenetic reproduction. Hence, in the current study, the complete mitochondrial genomes of the bisexual and parthenogenetic populations were assembled and analyzed, and the expression of the mitochondrial protein-coding genes was evaluated and compared between the two reproductive populations. The results indicated that the length of the mitochondrial genomes of the two reproductive populations is 14,694 and 14,693 bp in the bisexual and parthenogenetic populations, respectively. The AT content in the mitochondrial genome of the bisexual and obligate parthenogenetic population reached 77.22 and 77.34%, respectively. The phylogenetic tree was constructed combining 13 protein-coding genes, which showed that the genetic distance between the bisexual and parthenogenetic populations was less than that between the subspecies. The expression of the mitochondrial protein-coding genes was quantitatively analyzed at different feeding status for the bisexual and parthenogenetic populations, and the results showed significant differences in the expression patterns of these genes, suggesting that they might trigger specific energy utilization mechanisms due to their different reproductive strategies and environmental pressures.
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Affiliation(s)
- Tianhong Wang
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
| | - Shiqi Zhang
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
| | - Tingwei Pei
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
| | - Zhijun Yu
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
| | - Jingze Liu
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
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Comparative mitogenomic analysis of species in the subfamily Amphinemurinae (Plecoptera: Nemouridae) reveal conserved mitochondrial genome organization. Int J Biol Macromol 2019; 138:292-301. [PMID: 31319083 DOI: 10.1016/j.ijbiomac.2019.07.087] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Revised: 07/11/2019] [Accepted: 07/11/2019] [Indexed: 11/21/2022]
Abstract
The subfamily Amphinemurinae has five genera in China, with each genus of similar morphology. To gain a better understanding of architecture and evolution of mitogenome in Amphinemurinae, mitogenomes of eight species representing four genera (Amphinemura, Indonemoura, Protonemura and Sphaeronemoura) in the subfamily Amphinemurinae were sequenced, and a comparative mitogenomic analysis of five genera (including a published stonefly genus, Mesonemoura) was carried out. By comparative analysis, we found highly conserved genome organization of ten Amphinemurinae species including genome contents, gene order, nucleotide composition, codon usage, amino acid composition, as well as genome asymmetry. GC content was the most significant factor in determining codon bias among organisms. The Ka/Ks values for all PCGs were far lower than 1, indicating that these genes were evolving under purifying selection. We also found some important conserved stem and loop in the cloverleaf structure of tRNAs, and found conserved helices and loops in each domain of the secondary structure of rRNAs. The presence of structural elements in the control region is also discussed. The phylogenetic analyses indicated that within Amphinemurinae, Sphaeronemoura was assigned the sister group of Mesonemoura. Our analyses inferred a relationship within Euholognatha: ((Nemouridae + Notonemouridae) + (Taeniopterygidae + Capniidae) + Scopuridae) + Leuctridae.
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Muñoz-Tobar SI, Caterino MS. The role of dispersal for shaping phylogeographical structure of flightless beetles from the Andes. PeerJ 2019; 7:e7226. [PMID: 31304068 PMCID: PMC6611450 DOI: 10.7717/peerj.7226] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Accepted: 05/31/2019] [Indexed: 11/20/2022] Open
Abstract
Background Páramo is a tropical alpine ecosystem present in the northern Andes. Its patchy distribution imposes limits and barriers to specialist inhabitants. We aim to assess the effects of this habitat distribution on divergence across two independently flightless ground beetle lineages, in the genera Dyscolus and Dercylus. Methods One nuclear and one mitochondrial gene from 110 individuals from 10 sites across the two lineages were sequenced and analyzed using a combination of phylogenetics, population genetic analyses, and niche modeling methods. Results The two lineages show different degrees of population subdivision. Low levels of gene flow were found in Dyscolus alpinus, where one dominant haplotype is found in four out of the six populations analyzed for both molecular markers. However, complete population isolation was revealed in species of the genus Dercylus, where high levels of differentiation exist at species and population level for both genes. Maximum entropy models of species in the Dercylus lineage show overlapping distributions. Still, species distributions appear to be restricted to small areas across the Andes. Conclusion Even though both beetle lineages are flightless, the dispersal ability of each beetle lineage appears to influence the genetic diversity across fragmented páramo populations, where Dyscolus alpinus appears to be a better disperser than species in the genus Dercylus.
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Affiliation(s)
- Sofia I Muñoz-Tobar
- Department of Plant & Environmental Sciences, Clemson University, Clemson, SC, USA.,Escuela de Ciencias Biológicas, Pontificia Universidad Católica del Ecuador, Quito, Pichincha, Ecuador
| | - Michael S Caterino
- Department of Plant & Environmental Sciences, Clemson University, Clemson, SC, USA
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50
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Yan Z, Ye G, Werren JH. Evolutionary Rate Correlation between Mitochondrial-Encoded and Mitochondria-Associated Nuclear-Encoded Proteins in Insects. Mol Biol Evol 2019; 36:1022-1036. [PMID: 30785203 DOI: 10.1093/molbev/msz036] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The mitochondrion is a pivotal organelle for energy production, and includes components encoded by both the mitochondrial and nuclear genomes. Functional and evolutionary interactions are expected between the nuclear- and mitochondrial-encoded components. The topic is of broad interest in biology, with implications to genetics, evolution, and medicine. Here, we compare the evolutionary rates of mitochondrial proteins and ribosomal RNAs to rates of mitochondria-associated nuclear-encoded proteins, across the major orders of holometabolous insects. There are significant evolutionary rate correlations (ERCs) between mitochondrial-encoded and mitochondria-associated nuclear-encoded proteins, which are likely driven by different rates of mitochondrial sequence evolution and correlated changes in the interacting nuclear-encoded proteins. The pattern holds after correction for phylogenetic relationships and considering protein conservation levels. Correlations are stronger for both nuclear-encoded OXPHOS proteins that are in contact with mitochondrial OXPHOS proteins and for nuclear-encoded mitochondrial ribosomal amino acids directly contacting the mitochondrial rRNAs. We find that ERC between mitochondrial- and nuclear-encoded proteins is a strong predictor of nuclear-encoded proteins known to interact with mitochondria, and ERC shows promise for identifying new candidate proteins with mitochondrial function. Twenty-three additional candidate nuclear-encoded proteins warrant further study for mitochondrial function based on this approach, including proteins in the minichromosome maintenance helicase complex.
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Affiliation(s)
- Zhichao Yan
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China.,Department of Biology, University of Rochester, Rochester, NY
| | - Gongyin Ye
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - John H Werren
- Department of Biology, University of Rochester, Rochester, NY
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