1
|
Lan X, Ao WL, Li J. Preimplantation genetic testing as a preventive strategy for the transmission of mitochondrial DNA disorders. Syst Biol Reprod Med 2024; 70:38-51. [PMID: 38323618 DOI: 10.1080/19396368.2024.2306389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Accepted: 01/07/2024] [Indexed: 02/08/2024]
Abstract
Mitochondrial diseases are distinct types of metabolic and/or neurologic abnormalities that occur as a consequence of dysfunction in oxidative phosphorylation, affecting several systems in the body. There is no effective treatment modality for mitochondrial disorders so far, emphasizing the clinical significance of preventing the inheritance of these disorders. Various reproductive options are available to reduce the probability of inheriting mitochondrial disorders, including in vitro fertilization (IVF) using donated oocytes, preimplantation genetic testing (PGT), and prenatal diagnosis (PND), among which PGT not only makes it possible for families to have genetically-owned children but also PGT has the advantage that couples do not have to decide to terminate the pregnancy if a mutation is detected in the fetus. PGT for mitochondrial diseases originating from nuclear DNA includes analyzing the nuclear genome for the presence or absence of corresponding mutations. However, PGT for mitochondrial disorders arising from mutations in mitochondrial DNA (mtDNA) is more intricate, due to the specific characteristics of mtDNA such as multicopy nature, heteroplasmy phenomenon, and exclusive maternal inheritance. Therefore, the present review aims to discuss the utility and challenges of PGT as a preventive approach to inherited mitochondrial diseases caused by mtDNA mutations.
Collapse
Affiliation(s)
- Xinpeng Lan
- College of Basic Medical Sciences, Heilongjiang University of Chinese Medicine, Harbin, Heilongjiang, China
| | - Wu Liji Ao
- College of Mongolian Medicine and Pharmacy, Inner Mongolia University for Nationalities, Tongliao, Inner Mongolia, China
| | - Ji Li
- College of Basic Medical Sciences, Heilongjiang University of Chinese Medicine, Harbin, China
| |
Collapse
|
2
|
Jain K, Panigrahi M, Nayak SS, Rajawat D, Sharma A, Sahoo SP, Bhushan B, Dutt T. The evolution of contemporary livestock species: Insights from mitochondrial genome. Gene 2024; 927:148728. [PMID: 38944163 DOI: 10.1016/j.gene.2024.148728] [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: 04/16/2024] [Revised: 06/05/2024] [Accepted: 06/24/2024] [Indexed: 07/01/2024]
Abstract
The domestication of animals marks a pivotal moment in human history, profoundly influencing our demographic and cultural progress. This process has led to significant genetic, behavioral, and physical changes in livestock species compared to their wild ancestors. Understanding the evolutionary history and genetic diversity of livestock species is crucial, and mitochondrial DNA (mtDNA) has emerged as a robust marker for investigating molecular diversity in animals. Its highly conserved gene content across animal species, minimal duplications, absence of introns, and short intergenic regions make mtDNA analysis ideal for such studies. Mitochondrial DNA analysis has uncovered distinct cattle domestication events dating back to 8000 years BC in Southwestern Asia. The sequencing of water buffalo mtDNA in 2004 provided important insights into their domestication history. Caprine mtDNA analysis identified three haplogroups, indicating varied maternal origins. Sheep, domesticated 12,000 years ago, exhibit diverse mtDNA lineages, suggesting multiple domestication events. Ovine mtDNA studies revealed clades A, B, C, and a fourth lineage, group D. The origins of domestic pigs were traced to separate European and Asian events followed by interbreeding. In camels, mtDNA elucidated the phylogeographic structure and genetic differentiation between wild and domesticated species. Horses, domesticated around 3500 BC, show significant mtDNA variability, highlighting their diverse origins. Yaks exhibit unique adaptations for high-altitude environments, with mtDNA analysis providing insights into their adaptation. Chicken mtDNA studies supported a monophyletic origin from Southeast Asia's red jungle fowl, with evidence of multiple origins. This review explores livestock evolution and diversity through mtDNA studies, focusing on cattle, water buffalo, goat, sheep, pig, camel, horse, yak and chicken. It highlights mtDNA's significance in unraveling maternal lineages, genetic diversity, and domestication histories, concluding with insights into its potential application in improving livestock production and reproduction dynamics.
Collapse
Affiliation(s)
- Karan Jain
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Manjit Panigrahi
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India.
| | - Sonali Sonejita Nayak
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Divya Rajawat
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Anurodh Sharma
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | | | - Bharat Bhushan
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Triveni Dutt
- Livestock Production and Management Section, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| |
Collapse
|
3
|
Sundar Panja A. The systematic codon usage bias has an important effect on genetic adaption in native species. Gene 2024; 926:148627. [PMID: 38823656 DOI: 10.1016/j.gene.2024.148627] [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: 02/06/2024] [Revised: 05/06/2024] [Accepted: 05/29/2024] [Indexed: 06/03/2024]
Abstract
Random mutations increase genetic variety and natural selection enhances adaption over generations. Codon usage biases (CUB) provide clues about the genome adaptation mechanisms of native species and extremophile species. Significant numbers of gene (CDS) of nine classes of endangered, native species, including extremophiles and mesophiles were utilised to compute CUB. Codon usage patterns differ among the lineages of endangered and extremophiles with native species. Polymorphic usage of nucleotides with codon burial suggests parallelism of native species within relatively confined taxonomic groups. Utilizing the deviation pattern of CUB of endangered and native species, I present a calculation parameter to estimate the extinction risk of endangered species. Species diversity and extinction risk are both positively associated with the propensity of random mutation in CDS (Coding DNA sequence). Codon bias tenet profoundly selected and it governs to adaptive evolution of native species.
Collapse
Affiliation(s)
- Anindya Sundar Panja
- Department of Biotechnology, Molecular Informatics Laboratory, Oriental Institute of Science and Technology, Vidyasagar University, Midnapore, West Bengal 721102, India.
| |
Collapse
|
4
|
Islam S, Peart C, Kehlmaier C, Sun YH, Lei F, Dahl A, Klemroth S, Alexopoulou D, Del Mar Delgado M, Laiolo P, Carlos Illera J, Dirren S, Hille S, Lkhagvasuren D, Töpfer T, Kaiser M, Gebauer A, Martens J, Paetzold C, Päckert M. Museomics help resolving the phylogeny of snowfinches (Aves, Passeridae, Montifringilla and allies). Mol Phylogenet Evol 2024; 198:108135. [PMID: 38925425 DOI: 10.1016/j.ympev.2024.108135] [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: 06/01/2023] [Revised: 03/25/2024] [Accepted: 06/16/2024] [Indexed: 06/28/2024]
Abstract
Historical specimens from museum collections provide a valuable source of material also from remote areas or regions of conflict that are not easily accessible to scientists today. With this study, we are providing a taxon-complete phylogeny of snowfinches using historical DNA from whole skins of an endemic species from Afghanistan, the Afghan snowfinch, Pyrgilauda theresae. To resolve the strong conflict between previous phylogenetic hypotheses, we generated novel mitogenome sequences for selected taxa and genome-wide SNP data using ddRAD sequencing for all extant snowfinch species endemic to the Qinghai-Tibet Plateau (QTP) and for an extended intraspecific sampling of the sole Central and Western Palearctic snowfinch species (Montifringilla nivalis). Our phylogenetic reconstructions unanimously refuted the previously suggested paraphyly of genus Pyrgilauda. Misplacement of one species-level taxon (Onychostruthus tazcanowskii) in previous snowfinch phylogenies was undoubtedly inferred from chimeric mitogenomes that included heterospecific sequence information. Furthermore, comparison of novel and previously generated sequence data showed that the presumed sister-group relationship between M. nivalis and the QTP endemic M. henrici was suggested based on flawed taxonomy. Our phylogenetic reconstructions based on genome-wide SNP data and on mitogenomes were largely congruent and supported reciprocal monophyly of genera Montifringilla and Pyrgilauda with monotypic Onychostruthus being sister to the latter. The Afghan endemic P. theresae likely originated from a rather ancient Pliocene out-of-Tibet dispersal probably from a common ancestor with P. ruficollis. Our extended trans-Palearctic sampling for the white-winged snowfinch, M. nivalis, confirmed strong lineage divergence between an Asian and a European clade dated to 1.5 - 2.7 million years ago (mya). Genome-wide SNP data suggested subtle divergence among European samples from the Alps and from the Cantabrian mountains.
Collapse
Affiliation(s)
- Safiqul Islam
- Senckenberg Natural History Collections, Museum of Zoology, Königsbrücker Landstraße 159, 01109 Dresden, Germany; Max Planck-Genome-Centre Cologne, Max Planck Institute for Plant Breeding Research, Carl-von-Linne-Weg 10, 50829 Köln, Germany; Division of Systematic Zoology, Faculty of Biology, LMU Munich, Biocenter, Großhaderner Str. 2, 82152 Planegg-Martinsried, Germany
| | - Claire Peart
- Division of Evolutionary Biology, Faculty of Biology, LMU Munich, Biocenter, Großhaderner Str. 2, 82152 Planegg-Martinsried, Germany
| | - Christian Kehlmaier
- Senckenberg Natural History Collections, Museum of Zoology, Königsbrücker Landstraße 159, 01109 Dresden, Germany
| | - Yue-Hua Sun
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Fumin Lei
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Andreas Dahl
- Dresden-Concept Genome Center, c/o Center for Molecular and Cellular Bioengineering (CMCB), Technische Universität Dresden, Fetscherstraße 105, 1307 Dresden, Germany
| | - Sylvia Klemroth
- Dresden-Concept Genome Center, c/o Center for Molecular and Cellular Bioengineering (CMCB), Technische Universität Dresden, Fetscherstraße 105, 1307 Dresden, Germany
| | - Dimitra Alexopoulou
- Dresden-Concept Genome Center, c/o Center for Molecular and Cellular Bioengineering (CMCB), Technische Universität Dresden, Fetscherstraße 105, 1307 Dresden, Germany
| | - Maria Del Mar Delgado
- Biodiversity Research Institute (IMIB, Universidad de Oviedo, CSIC, Principality of Asturias) - Campus de Mieres, Edificio de Investigación - 5ª planta, C. Gonzalo Gutiérrez Quirós s/n, 33600 Mieres, Spain
| | - Paola Laiolo
- Biodiversity Research Institute (IMIB, Universidad de Oviedo, CSIC, Principality of Asturias) - Campus de Mieres, Edificio de Investigación - 5ª planta, C. Gonzalo Gutiérrez Quirós s/n, 33600 Mieres, Spain
| | - Juan Carlos Illera
- Biodiversity Research Institute (IMIB, Universidad de Oviedo, CSIC, Principality of Asturias) - Campus de Mieres, Edificio de Investigación - 5ª planta, C. Gonzalo Gutiérrez Quirós s/n, 33600 Mieres, Spain
| | | | - Sabine Hille
- University of Natural Resources and Life Sciences, Vienna, Gregor Mendel-Strasse 33, 1180 Vienna, Austria
| | - Davaa Lkhagvasuren
- Department of Biology, School of Arts and Sciences, National University of Mongolia, P.O.Box 46A-546, Ulaanbaatar 210646, Mongolia
| | - Till Töpfer
- Leibniz Institute for the Analysis of Biodiversity Change, Zoologisches Forschungsmuseum Alexander Koenig, Adenauerallee, Bonn, Germany
| | | | | | - Jochen Martens
- Institute of Organismic and Molecular Evolution (iomE), Johannes Gutenberg University, 55099 Mainz, Germany
| | - Claudia Paetzold
- Senckenberg Natural History Collections, Museum of Zoology, Königsbrücker Landstraße 159, 01109 Dresden, Germany
| | - Martin Päckert
- Senckenberg Natural History Collections, Museum of Zoology, Königsbrücker Landstraße 159, 01109 Dresden, Germany.
| |
Collapse
|
5
|
Papila B, Karimova A, Onaran I. Altered lactate/pyruvate ratio may be responsible for aging-associated intestinal barrier dysfunction in male rats. Biogerontology 2024; 25:679-689. [PMID: 38619668 PMCID: PMC11217102 DOI: 10.1007/s10522-024-10102-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Accepted: 02/29/2024] [Indexed: 04/16/2024]
Abstract
Some evidence points to a link between aging-related increased intestinal permeability and mitochondrial dysfunction in in-vivo models. Several studies have also demonstrated age-related accumulation of the of specific deletion 4834-bp of "common" mitochondrial DNA (mtDNA) in various rat tissues and suggest that this deletion may disrupt mitochondrial metabolism. The present study aimed to investigate possible associations among the mitochondrial DNA (mtDNA) common deletion, mitochondrial function, intestinal permeability, and aging in rats. The study was performed on the intestinal tissue from (24 months) and young (4 months) rats. mtDNA4834 deletion, mtDNA copy number, mitochondrial membrane potential, and ATP, lactate and pyruvate levels were analyzed in tissue samples. Zonulin and intestinal fatty acid-binding protein (I-FABP) levels were also evaluated in serum. Serum zonulin and I-FABP levels were significantly higher in 24-month-old rats than 4-month-old rats (p = 0.04, p = 0.026, respectively). There is not significant difference in mtDNA4834 copy levels was observed between the old and young intestinal tissues (p > 0.05). The intestinal mitochondrial DNA copy number was similar between the two age groups (p > 0.05). No significant difference was observed in ATP levels in the intestinal tissue lysates between old and young rats (p > 0.05). ATP levels in isolated mitochondria from both groups were also similar. Analysis of MMP using JC-10 in intestinal tissue mitochondria showed that mitochondrial membrane potentials (red/green ratios) were similar between the two age groups (p > 0.05). Pyruvate tended to be higher in the 24-month-old rat group and the L/P ratio was found to be approximately threefold lower in the intestinal tissue of the older rats compared to the younger rats (p < 0.002). The tissue lactate/pyruvate ratio (L/P) was three times lower in old rats than in young rats. Additionally, there were significant negative correlations between intestinal permeability parameters and L/P ratios. The intestinal tissues of aged rats are not prone to accumulate mtDNA common deletion, we suggest that this mutation does not explain the age-related increase in intestinal permeability. It seems to be more likely that altered glycolytic capacity could be a link to increased intestinal permeability with age. This observation strengthens assertions that the balance between glycolysis and mitochondrial metabolism may play a critical role in intestinal barrier functions.
Collapse
Affiliation(s)
- Berrin Papila
- Department of General Surgery, Cerrahpasa Faculty of Medicine, Istanbul University-Cerrahpasa, Cerrahpasa, Fatih, 34098, Istanbul, Turkey.
| | - Ayla Karimova
- Department of Medical Biology and Genetics, Cerrahpasa Faculty of Medicine, Istanbul University-Cerrahpasa, Istanbul, Turkey
| | - Ilhan Onaran
- Department of Medical Biology and Genetics, Cerrahpasa Faculty of Medicine, Istanbul University-Cerrahpasa, Istanbul, Turkey
| |
Collapse
|
6
|
Yazdani M. Cellular and Molecular Responses to Mitochondrial DNA Deletions in Kearns-Sayre Syndrome: Some Underlying Mechanisms. Mol Neurobiol 2024; 61:5665-5679. [PMID: 38224444 DOI: 10.1007/s12035-024-03938-7] [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] [Indexed: 01/16/2024]
Abstract
Kearns-Sayre syndrome (KSS) is a rare multisystem mitochondrial disorder. It is caused by mitochondrial DNA (mtDNA) rearrangements, mostly large-scale deletions of 1.1-10 kb. These deletions primarily affect energy supply through impaired oxidative phosphorylation and reduced ATP production. This impairment gives rise to dysfunction of several tissues, in particular those with high energy demand like brain and muscles. Over the past decades, changes in respiratory chain complexes and energy metabolism have been emphasized, whereas little attention has been paid to other reports on ROS overproduction, protein synthesis inhibition, myelin vacuolation, demyelination, autophagy, apoptosis, and involvement of lipid raft and oligodendrocytes in KSS. Therefore, this paper draws attention towards these relatively underemphasized findings that might further clarify the pathologic cascades following deletions in the mtDNA.
Collapse
Affiliation(s)
- Mazyar Yazdani
- Department of Medical Biochemistry, Oslo University Hospital, Rikshospitalet, Oslo, 0027, Norway.
| |
Collapse
|
7
|
Liu J, Shang Y, Deng F, Feng Z, Hu M, Wang Y. Nano titanium dioxide alleviates the toxic effects of tris (2-chloropropyl) phosphate on the digestive gland and hemolymph of thick-shell mussel Mytilus coruscus. MARINE POLLUTION BULLETIN 2024; 205:116682. [PMID: 38981190 DOI: 10.1016/j.marpolbul.2024.116682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2024] [Revised: 06/28/2024] [Accepted: 07/03/2024] [Indexed: 07/11/2024]
Abstract
In the marine environment, nanoparticles play a role in adsorbing and catalytically degrading organic pollutants, thereby mitigating their toxic effects on aquatic organisms. This study aimed to investigate the impact of nano titanium dioxide (nTiO2) and tris (2-chloropropyl) phosphate (TCPP) on the hemolymph and digestive function of the thick-shell mussel Mytilus coruscus. Mussels were divided into a control group, a group exposed to TCPP alone, a group exposed to a combination of TCPP and 0.5 mg/L nTiO2, and a group exposed to a combination of TCPP and 1 mg/L nTiO2. After 14 days of exposure, oxidative stress responses, including superoxide dismutase (SOD) activity and malondialdehyde (MDA) content, immune defense responses, including acid phosphatase (ACP) and alkaline phosphatase (AKP) activities, and gene expression, including HSP70 expression, were measured in the hemolymph and digestive glands of the mussels. Compared to the control group, mussels solely exposed to 100 μg/L TCPP exhibited a significant reduction in SOD activity in the hemolymph. When TCPP was co-exposed with 0.5 mg/L nTiO2, there were significant increases in MDA content and AKP activity in both the digestive gland and hemolymph compared to the control group. Upon co-exposure of TCPP with 1 mg/L nTiO2, MDA content and AKP activity in the digestive gland significantly decreased, while SOD, ACP, and AKP activity in the hemolymph significantly increased and MDA content significantly decreased, returning to the control group levels. Furthermore, in the combined exposure, HSP70 gene expression significantly decreased as the nTiO2 concentration increased from 0.5 mg/L to 1 mg/L. In summary, TCPP impacted the hemolymph and digestive function of mussels, whereas a concentration of 1 mg/L nTiO2 effectively alleviated the toxic effects of TCPP. This study is crucial for assessing the ecological risks of nanoparticles and emerging organic pollutants in marine environments, and provides new insights into the interaction between nTiO2 and TCPP, as well as the influence of nTiO2 concentration on mitigating TCPP toxicity.
Collapse
Affiliation(s)
- Jiani Liu
- International Research Center for Marine Biosciences, Ministry of Science and Technolgy, Shanghai Ocean University, Shanghai 201306, China; Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai 201306, China
| | - Yueyong Shang
- International Research Center for Marine Biosciences, Ministry of Science and Technolgy, Shanghai Ocean University, Shanghai 201306, China; Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai 201306, China
| | - Fujing Deng
- International Research Center for Marine Biosciences, Ministry of Science and Technolgy, Shanghai Ocean University, Shanghai 201306, China; Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai 201306, China
| | - Zhihua Feng
- Jiangsu Key Laboratory of Marine Bioresources and Environment, Jiangsu Ocean University, China
| | - Menghong Hu
- International Research Center for Marine Biosciences, Ministry of Science and Technolgy, Shanghai Ocean University, Shanghai 201306, China; Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai 201306, China
| | - Youji Wang
- International Research Center for Marine Biosciences, Ministry of Science and Technolgy, Shanghai Ocean University, Shanghai 201306, China; Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai 201306, China.
| |
Collapse
|
8
|
Feng J, Ren Q, Xie A, Jiang Z, Liu Y. High-resolution melting analysis to authenticate deer-derived materials in processed products in China using a cytochrome oxidase I mini-barcode. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2024. [PMID: 39051761 DOI: 10.1002/jsfa.13761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Revised: 06/29/2024] [Accepted: 07/09/2024] [Indexed: 07/27/2024]
Abstract
BACKGROUND Deer-derived materials (antler, venison, fetus, penis, bone, tail, and others) are some of the most valuable traditional animal-based medicinal and food materials in China. In production, processing, and trade, the quality of deer products varies. The market is confusing, and counterfeit and shoddy products are common. There is an urgent need to establish an accurate identification method. RESULTS Two pairs of primers suitable for identifying deer-derived medicinal materials were obtained by screening the cytochrome oxidase I (COI) sequences of 18 species from nine genera of the deer family. The two primers were used to identify the species and adulteration of 22 batches of commercially available deer-derived products with a mini-barcode combining high-resolution melting (HRM) technology and methodical investigation. Deer-derived materials (sika and red deer) were correctly identified by species using varying DNA amounts (1 to 500 ng). The two pairs of primers COI-1FR and COI-2FR yielded melting temperatures (Tm) of 80.55 to 81.00 °C and 82.00 to 82.50 °C for sika deer, and 81.00 to 82.00 °C and 81.40 to 82.00 °C for red deer. Twenty-two batches of commercially available samples were analyzed by HRM analysis and conventional amplification sequencing, and it was found that the species samples had an error rate of species labeling of 31.8%. Four batches of samples were identified as mixed (adulterated) in the HRM analysis. CONCLUSION The combination of DNA mini-barcode with HRM analysis facilitated the accurate identification of species of deer-derived materials, especially the identification of samples in an adulterated mixed state. © 2024 Society of Chemical Industry.
Collapse
Affiliation(s)
- Jian Feng
- Hainan Provincial Key Laboratory of Resources Conservation and Development of Southern Medicine & International Joint Research Center for Quality of Traditional Chinese Medicine, Hainan Branch of the Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Haikou, China
| | - Qiqi Ren
- Hainan Provincial Key Laboratory of Resources Conservation and Development of Southern Medicine & International Joint Research Center for Quality of Traditional Chinese Medicine, Hainan Branch of the Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Haikou, China
| | - Anzhen Xie
- Hainan Provincial Key Laboratory of Resources Conservation and Development of Southern Medicine & International Joint Research Center for Quality of Traditional Chinese Medicine, Hainan Branch of the Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Haikou, China
| | - Zixiao Jiang
- Hainan Provincial Key Laboratory of Resources Conservation and Development of Southern Medicine & International Joint Research Center for Quality of Traditional Chinese Medicine, Hainan Branch of the Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Haikou, China
| | - Yangyang Liu
- Hainan Provincial Key Laboratory of Resources Conservation and Development of Southern Medicine & International Joint Research Center for Quality of Traditional Chinese Medicine, Hainan Branch of the Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Haikou, China
| |
Collapse
|
9
|
Kamal SA, Baeza JA. Detailed characterization of the complete mitochondrial genome of the oceanic whitetip shark Carcharhinus longimanus (Poey, 1861). Mol Biol Rep 2024; 51:826. [PMID: 39030452 DOI: 10.1007/s11033-024-09780-3] [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: 04/29/2024] [Accepted: 07/04/2024] [Indexed: 07/21/2024]
Abstract
BACKGROUND The oceanic whitetip shark Carcharhinus longimanus (family Carcharhinidae) is one of the largest sharks inhabiting all tropical and subtropical oceanic regions. Due to their life history traits and mortality attributed to pelagic longline fishing practices, this species is experiencing substantial population decline. Currently, C. longimanus is considered by the IUCN Red List of Threatened Species as "vulnerable" throughout its range and "critically endangered" in the western north Atlantic. This study sequences and describes the complete mitochondrial genome of C. longimanus in detail. METHODS AND RESULTS The mitochondrial genome of C. longimanus was assembled through next-generation sequencing and then analyzed using specialized bioinformatics tools. The circular, double-stranded AT-rich mitogenome of C. longimanus is 16,704 bp long and contains 22 tRNA genes, 2 rRNA genes, 13 protein coding genes and a 1,065 bp long control region (CR). Out of the 22 tRNA genes, only one (tRNA-Ser1) lacked a typical 'cloverleaf' secondary structure. The prevalence of TTA (Leu), ATT (Ile) and CTA (Leu) codons in the PCGs likely contributes to the AT-rich nature of this mitogenome. In the CR, ten microsatellites were detected but no tandem repeats were found. Stem-and-loop secondary structures were common along the entire length of the CR. Ka/Ks values estimated for all PCGs were < 1, indicating that all the PCGs experience purifying selection. A phylomitogenomic analysis based on translated PCGs confirms the sister relationship between C. longimanus and C. obscurus. The analysis did not support the monophyly of the genus Carcharhinus. CONCLUSIONS The assembled mitochondrial genome of this pelagic shark can provide insight into the phylogenetic relationships in the genus Carcharhinus and aid conservation and management efforts in the Central Pacific Ocean.
Collapse
Affiliation(s)
- Sadia A Kamal
- Department of Fisheries Biology and Genetics, Sher-e-Bangla Agricultural University, Dhaka, Bangladesh
| | - J Antonio Baeza
- Department of Biological Sciences, Clemson University, Clemson, SC, USA.
- Smithsonian Marine Station at Fort Pierce, Smithsonian Institution, Fort Pierce, FL, USA.
- Departamento de Biología Marina, Universidad Catolica del Norte, Coquimbo, Chile.
| |
Collapse
|
10
|
Vahedi Raad M, Firouzabadi AM, Tofighi Niaki M, Henkel R, Fesahat F. The impact of mitochondrial impairments on sperm function and male fertility: a systematic review. Reprod Biol Endocrinol 2024; 22:83. [PMID: 39020374 PMCID: PMC11253428 DOI: 10.1186/s12958-024-01252-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/20/2024] [Accepted: 06/27/2024] [Indexed: 07/19/2024] Open
Abstract
BACKGROUND Besides adenine triphosphate (ATP) production for sustaining motility, the mitochondria of sperm also host other critical cellular functions during germ cell development and fertilization including calcium homeostasis, generation of reactive oxygen species (ROS), apoptosis, and in some cases steroid hormone biosynthesis. Normal mitochondrial membrane potential with optimal mitochondrial performance is essential for sperm motility, capacitation, acrosome reaction, and DNA integrity. RESULTS Defects in the sperm mitochondrial function can severely harm the fertility potential of males. The role of sperm mitochondria in fertilization and its final fate after fertilization is still controversial. Here, we review the current knowledge on human sperm mitochondria characteristics and their physiological and pathological conditions, paying special attention to improvements in assistant reproductive technology and available treatments to ameliorate male infertility. CONCLUSION Although mitochondrial variants associated with male infertility have potential clinical use, research is limited. Further understanding is needed to determine how these characteristics lead to adverse pregnancy outcomes and affect male fertility potential.
Collapse
Affiliation(s)
- Minoo Vahedi Raad
- Department of Biology & Anatomical Sciences, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Amir Masoud Firouzabadi
- Reproductive Immunology Research Center, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
- Department of Physiology, School of Medical Sciences, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
| | - Maryam Tofighi Niaki
- Health Reproductive Research Center, Sari Branch, Islamic Azad University, Sari, Iran
| | - Ralf Henkel
- LogixX Pharma, Theale, Berkshire, UK.
- Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK.
- Department of Medical Bioscience, University of the Western Cape, Bellville, South Africa.
| | - Farzaneh Fesahat
- Reproductive Immunology Research Center, Shahid Sadoughi University of Medical Sciences, Yazd, Iran.
| |
Collapse
|
11
|
Matos A, Gomes-dos-Santos A, Kebapçı Ü, Emre Gürlek M, Froufe E, Lopes-Lima M. The complete female mitogenome of Potomida semirugata (Lamarck, 1819). Mitochondrial DNA B Resour 2024; 9:892-896. [PMID: 39027116 PMCID: PMC11257011 DOI: 10.1080/23802359.2024.2378964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Accepted: 07/06/2024] [Indexed: 07/20/2024] Open
Abstract
Freshwater mussels perform important ecological functions in ecosystems, such as water filtration and energy cycling. Unlike marine bivalves, freshwater mussels have unique characteristics including internal fertilization and parental care. Some freshwater mussels are facing a high risk of extinction due to several factors such as climate change and habitat loss. Potomida semirugata (Lamarck, 1819) is one of the freshwater mussel species with a high risk of extinction and listed as Endangered in the Red List of the International Union for Conservation of Nature. Here, we present the first F-type mitogenome sequence of P. semirugata. The genome was sequenced on an Illumina high-throughput platform from a P. semirugata specimen collected from the Tersakan River (Turkey). The 16,093 bp mitochondrial genome sequence contains 13 protein-coding genes, 22 transfer RNAs, and two ribosomal RNAs. Phylogenetic analysis placed P. semirugata in the Lamprotulini clade with Potomida littoralis, as expected. Potomida semirugata is a poorly studied species and the genomic resource provided here will contribute to a better understanding of its biological characterization.
Collapse
Affiliation(s)
- Ana Matos
- CIIMAR/CIMAR – Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Matosinhos, Portugal
| | - André Gomes-dos-Santos
- CIIMAR/CIMAR – Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Matosinhos, Portugal
| | - Ümit Kebapçı
- Biology Department, Faculty of Science and Arts, Burdur Mehmet Akif Ersoy University, Burdur, Turkey
| | - Mustafa Emre Gürlek
- Burdur Vocational School of Food Agriculture and Livestock, Mehmet Akif Ersoy University, Burdur, Turkey
| | - Elsa Froufe
- CIIMAR/CIMAR – Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Matosinhos, Portugal
| | - Manuel Lopes-Lima
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, Portugal
| |
Collapse
|
12
|
Hua W, Qi J, Zhou M, Han S, Xu X, Su J, Pan T, Wu D, Han Y. Overexpression of REC8 induces aberrant gamete meiotic division and contributes to AML pathogenesis - a multiplexed microarray analysis and mendelian randomization study. Ann Hematol 2024:10.1007/s00277-024-05882-x. [PMID: 39012516 DOI: 10.1007/s00277-024-05882-x] [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: 03/08/2024] [Accepted: 07/04/2024] [Indexed: 07/17/2024]
Abstract
Acute myeloid leukemia (AML) is a notably lethal disease, characterized by malignant clonal proliferation of hematopoietic stem cells in the bone marrow. This study seeks to unveil potential therapeutic targets for AML, using a combined approach of microarray analysis and Mendelian randomization (MR). We collected data samples from the Gene Expression Omnibus (GEO) database and extracted pQTL data from genome-wide association studies (GWAS) to identify overlapping genes between the DEGs and GWAS data. Gene enrichment and pathway annotation analyses were performed on these genes. Furthermore, we validated gene expression levels and assessed their clinical relevance. By taking the intersection of these gene sets, we obtained a list of co-expressed genes, including four upregulated genes (REC8, TPM2, ZMIZ1, CD82) and two downregulated genes (IFNAR1, TMCO3). MR analysis demonstrated that genetically predicted protein levels of CD82, REC8, ZMIZ1, and TPM2 were significantly associated with increased odds of AML, while IFNAR1 and TMCO3 showed a protective effect. Gene ontology and KEGG pathway analyses revealed significant enrichment in functions related to female gamete generation, meiosis, p53 signaling pathway, and cardiac muscle contraction. Differences in immune cell profiles were observed between AML survivors and those with poor prognosis, including lower levels of neutrophils and higher levels of follicular helper T cells in the latter group. This study identifies a causal relationship between gene expression and AML and highlights the potential role of REC8 in leukemogenesis, possibly through its impact on gametocyte meiotic abnormalities. The findings provide new insights into the prevention and treatment of leukemia.
Collapse
Affiliation(s)
- Wenxi Hua
- National Clinical Research Center for Hematologic Diseases, Jiangsu Institute of Hematology, The First Affiliated Hospital of Soochow University, Suzhou, China
- Institute of Blood and Marrow Transplantation, Collaborative Innovation Center of Hematology, Soochow University, Suzhou, China
| | - Jiaqian Qi
- National Clinical Research Center for Hematologic Diseases, Jiangsu Institute of Hematology, The First Affiliated Hospital of Soochow University, Suzhou, China
- Institute of Blood and Marrow Transplantation, Collaborative Innovation Center of Hematology, Soochow University, Suzhou, China
- Key Laboratory of Thrombosis and Hemostasis of Ministry of Health, Suzhou, China
| | - Meng Zhou
- National Clinical Research Center for Hematologic Diseases, Jiangsu Institute of Hematology, The First Affiliated Hospital of Soochow University, Suzhou, China
- Institute of Blood and Marrow Transplantation, Collaborative Innovation Center of Hematology, Soochow University, Suzhou, China
- Key Laboratory of Thrombosis and Hemostasis of Ministry of Health, Suzhou, China
| | - Shiyu Han
- National Clinical Research Center for Hematologic Diseases, Jiangsu Institute of Hematology, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Xiaoyan Xu
- National Clinical Research Center for Hematologic Diseases, Jiangsu Institute of Hematology, The First Affiliated Hospital of Soochow University, Suzhou, China
- Institute of Blood and Marrow Transplantation, Collaborative Innovation Center of Hematology, Soochow University, Suzhou, China
- Key Laboratory of Thrombosis and Hemostasis of Ministry of Health, Suzhou, China
| | - Jinwen Su
- National Clinical Research Center for Hematologic Diseases, Jiangsu Institute of Hematology, The First Affiliated Hospital of Soochow University, Suzhou, China
- Institute of Blood and Marrow Transplantation, Collaborative Innovation Center of Hematology, Soochow University, Suzhou, China
| | - Tingting Pan
- National Clinical Research Center for Hematologic Diseases, Jiangsu Institute of Hematology, The First Affiliated Hospital of Soochow University, Suzhou, China
- Institute of Blood and Marrow Transplantation, Collaborative Innovation Center of Hematology, Soochow University, Suzhou, China
- Key Laboratory of Thrombosis and Hemostasis of Ministry of Health, Suzhou, China
| | - Depei Wu
- National Clinical Research Center for Hematologic Diseases, Jiangsu Institute of Hematology, The First Affiliated Hospital of Soochow University, Suzhou, China.
- Institute of Blood and Marrow Transplantation, Collaborative Innovation Center of Hematology, Soochow University, Suzhou, China.
- Key Laboratory of Thrombosis and Hemostasis of Ministry of Health, Suzhou, China.
- State Key Laboratory of Radiation Medicine and Protection, Soochow University, Suzhou, China.
| | - Yue Han
- National Clinical Research Center for Hematologic Diseases, Jiangsu Institute of Hematology, The First Affiliated Hospital of Soochow University, Suzhou, China.
- Institute of Blood and Marrow Transplantation, Collaborative Innovation Center of Hematology, Soochow University, Suzhou, China.
- Key Laboratory of Thrombosis and Hemostasis of Ministry of Health, Suzhou, China.
- State Key Laboratory of Radiation Medicine and Protection, Soochow University, Suzhou, China.
| |
Collapse
|
13
|
Bashir NH, Li W, Wang Z, Gao Y, Chen H. The chloroplast genome of a subtropical tree Sassafras randaiense (Hayata) Rehder, 1920 (Lauraceae). Mitochondrial DNA B Resour 2024; 9:876-880. [PMID: 39021391 PMCID: PMC467100 DOI: 10.1080/23802359.2024.2378967] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2024] [Accepted: 07/07/2024] [Indexed: 07/20/2024] Open
Abstract
The complete chloroplast genome sequence of Sassafras randaiense (Hayata) Rehder, 1920, a subtropical tree in the family Lauraceae, was determined. For a better understanding of the differences between S. randaiense and S. tzumu, the complete chloroplast genome of S. randaiense was sequenced and analyzed. The complete chloroplast genome is 151,781 bp in length, consisting of a pair of inverted repeat (IR) regions of 20,114 bp, one large single-copy (LSC) region of 92,740 bp, and one small single-copy (SSC) region of 18,813 bp. The overall GC content of the complete chloroplast genome is 39.2%. Further, maximum-likelihood phylogenetic analysis was conducted using 31 complete plastome sequences, which support that S. randaiense and S. tzumu are nested among the members of Cinnamomum, suggesting that Sassafras belongs to Cinnamomum.
Collapse
Affiliation(s)
- Nawaz Haider Bashir
- College of Biological Resource and Food Engineering, Qujing Normal University, Qujing, China
| | - Wenbo Li
- College of Biological Resource and Food Engineering, Qujing Normal University, Qujing, China
| | - Zijie Wang
- Heilongjiang Academy of Agricultural Science, Jiamusi, China
| | - Yong Gao
- College of Biological Resource and Food Engineering, Qujing Normal University, Qujing, China
| | - Huanhuan Chen
- College of Biological Resource and Food Engineering, Qujing Normal University, Qujing, China
| |
Collapse
|
14
|
Takagui FH, Viana P, Haerter CAG, Zuanon J, Birindelli JLO, Lui RL, Feldberg E, Margarido VP. Chromosomal analysis of two Acanthodoras species (Doradidae, Siluriformes): Insights into the oldest thorny catfish clade and its karyotype evolution. JOURNAL OF FISH BIOLOGY 2024. [PMID: 39007200 DOI: 10.1111/jfb.15863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 05/29/2024] [Accepted: 06/18/2024] [Indexed: 07/16/2024]
Abstract
The Doradidae fishes constitute one of the most diverse groups of Neotropical freshwater environments. Acanthodoradinae is the oldest lineage and the sister group to all other thorny catfishes, and it includes only the genus Acanthodoras. The diversity of Acanthodoras remains underestimated, and the use of complementary approaches, including genetic studies, is an important step to better characterize this diversity and the relationships among the species within the genus. Therefore, we conducted a comprehensive analysis using conventional cytogenetic techniques and physical mapping of three multigene families (18S and 5S ribosomal DNA [rDNA], U2 small nuclear DNA [snDNA]) and four microsatellite motifs, namely (AC)n, (AT)n, (GA)n, and (GATA)n, in two sympatric species from the Negro River: Acanthodoras cataphractus and Acanthodoras cf. polygrammus. We found significant differences in constitutive heterochromatin (CH) content, distribution of the microsatellite (AT)n, and the number of 5S rDNA and U2 snDNA sites. These differences may result from chromosome rearrangements and repetitive DNA dispersal mechanisms. Furthermore, the characterization of the diploid number (2n) of these Acanthodoras species enables us to propose 2n = 58 chromosomes as the plesiomorphic 2n state in Doradidae based on ancestral state reconstruction. Acanthodoradinae is the oldest lineage of the thorny catfishes, and knowledge about its cytogenetic patterns is crucial for disentangling the karyotype evolution of the whole group. Thus, this study contributes to the understanding of the mechanisms behind chromosome diversification of Doradidae and highlights the importance of Acanthodoradinae in the evolutionary history of thorny catfishes.
Collapse
Affiliation(s)
- Fábio Hiroshi Takagui
- Coordenação de Biodiversidade, Instituto Nacional de Pesquisas da Amazônia, Manaus, Brazil
| | - Patrik Viana
- Coordenação de Biodiversidade, Instituto Nacional de Pesquisas da Amazônia, Manaus, Brazil
| | | | - Jansen Zuanon
- Coordenação de Biodiversidade, Instituto Nacional de Pesquisas da Amazônia, Manaus, Brazil
| | - José Luís Olivan Birindelli
- Museu de Zoologia, Departamento de Biologia Animal e Vegetal, Universidade Estadual de Londrina, Londrina, Brazil
| | - Roberto Laridondo Lui
- Laboratório de Citogenética, Centro de Ciĉncias Biológicas e da Saúde, Cascavel, Brazil
| | - Eliana Feldberg
- Coordenação de Biodiversidade, Instituto Nacional de Pesquisas da Amazônia, Manaus, Brazil
| | | |
Collapse
|
15
|
He Y, Zhao H, Wang Y, Qu C, Gao X, Miao J. A novel deep-benthic sea cucumber species of Benthodytes (Holothuroidea, Elasipodida, Psychropotidae) and its comprehensive mitochondrial genome sequencing and evolutionary analysis. BMC Genomics 2024; 25:689. [PMID: 39003448 PMCID: PMC11245801 DOI: 10.1186/s12864-024-10607-5] [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: 04/12/2024] [Accepted: 07/09/2024] [Indexed: 07/15/2024] Open
Abstract
BACKGROUND The holothurians, commonly known as sea cucumbers, are marine organisms that possess significant dietary, nutritional, and medicinal value. However, the National Center for Biotechnology Information (NCBI) currently possesses only approximately 70 complete mitochondrial genome datasets of Holothurioidea, which poses limitations on conducting comprehensive research on their genetic resources and evolutionary patterns. In this study, a novel species of sea cucumber belonging to the genus Benthodytes, was discovered in the western Pacific Ocean. The genomic DNA of the novel sea cucumber was extracted, sequenced, assembled and subjected to thorough analysis. RESULTS The mtDNA of Benthodytes sp. Gxx-2023 (GenBank No. OR992091) exhibits a circular structure spanning 17,386 bp, comprising of 13 protein-coding genes (PCGs), 24 non-coding RNAs (2 rRNA genes and 22 tRNA genes), along with two putative control regions measuring 882 bp and 1153 bp, respectively. It exhibits a high AT% content and negative AT-skew, which distinguishing it from the majority of sea cucumbers in terms of environmental adaptability evolution. The mitochondrial gene homology between Gxx-2023 and other sea cucumbers is significantly low, with less than 91% similarity to Benthodytes marianensis, which exhibits the highest level of homology. Additionally, its homology with other sea cucumbers is below 80%. The mitogenome of this species exhibits a unique pattern in terms of start and stop codons, featuring only two types of start codons (ATG and ATT) and three types of stop codons including the incomplete T. Notably, the abundance of AT in the Second position of the codons surpasses that of the First and Third position. The gene arrangement of PCGs exhibits a relatively conserved pattern, while there exists substantial variability in tRNA. Evolutionary analysis revealed that it formed a distinct cluster with B. marianensis and exhibited relatively distant phylogenetic relationships with other sea cucumbers. CONCLUSIONS These findings contribute to the taxonomic diversity of sea cucumbers in the Elasipodida order, thereby holding significant implications for the conservation of biological genetic resources, evolutionary advancements, and the exploration of novel sea cucumber resources.
Collapse
Affiliation(s)
- Yingying He
- Marine Natural Products Research and Development Laboratory, First Institute of Oceanography, Ministry of Natural Resources, Qingdao, 266061, China
- Marine Functional Food Technology Innovation Center of Shandong Province, Rongcheng, 264306, China
| | - Hancheng Zhao
- Marine Natural Products Research and Development Laboratory, First Institute of Oceanography, Ministry of Natural Resources, Qingdao, 266061, China
| | - Yongxin Wang
- College of Chemistry and Chemical Engineering, Qingdao University, Qingdao, 266071, China
| | - Changfeng Qu
- Marine Natural Products Research and Development Laboratory, First Institute of Oceanography, Ministry of Natural Resources, Qingdao, 266061, China
- Laboratory for Marine Drugs and Bioproducts, Qingdao Marine Science and Technology Center, Qingdao, 266237, China
- Marine Functional Food Technology Innovation Center of Shandong Province, Rongcheng, 264306, China
| | | | - Jinlai Miao
- Marine Natural Products Research and Development Laboratory, First Institute of Oceanography, Ministry of Natural Resources, Qingdao, 266061, China.
- Laboratory for Marine Drugs and Bioproducts, Qingdao Marine Science and Technology Center, Qingdao, 266237, China.
- Marine Functional Food Technology Innovation Center of Shandong Province, Rongcheng, 264306, China.
| |
Collapse
|
16
|
Li L, Yang M, Qi Y, Yu Y, Gao P, Yang S, Zhao Y, Guo J, Liu J, Huang F, Yu L. Complete chloroplast genome and phylogenetic analysis of Amorphophallus paeoniifolius (Araceae). Mitochondrial DNA B Resour 2024; 9:865-870. [PMID: 39010881 PMCID: PMC11249165 DOI: 10.1080/23802359.2024.2378966] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Accepted: 07/07/2024] [Indexed: 07/17/2024] Open
Abstract
Amorphophallus paeoniifolius (Dennst.) Nicolson, 1885, often known as elephant foot yam, is a tropical tuber crop that originates from south-east Asia and belongs to the Araceae family. It is known for its high production potential and popularity as a medicinal plant. However, the phylogeny and genes for this species are still unavailable. In this study, the first complete chloroplast genome of A. paeoniifolius was reported and phylogenetic analysis was conducted with Araceae species. The chloroplast genome was 176,258 bp in length with 34.80% overall GC content and includes a large single-copy (LSC) region (93,951 bp), a small single-copy (SSC) region (15,013 bp), and a pair of inverted repeat (IRs) regions (33,647 bp). The chloroplast genome has 130 genes, which include 85 protein-coding genes, 37 tRNA genes, and eight rRNA genes. A maximum-likelihood (ML) phylogenetic analysis indicated that all Amorphophallus species formed a single monophyletic clade with a high bootstrap value and A. paeoniifolius was closely related to A. konjac, A. albus, A. krausei, and A. titanum. The chloroplast genome reported in this study will be useful for further taxonomic and evolutionary studies of Amorphophallus.
Collapse
Affiliation(s)
- Lifang Li
- College of Agronomy, Yunnan Urban Agricultural Engineering and Technological Research Center, Kunming University, Kunming, China
| | - Min Yang
- College of Agronomy, Yunnan Urban Agricultural Engineering and Technological Research Center, Kunming University, Kunming, China
| | - Ying Qi
- College of Agronomy, Yunnan Urban Agricultural Engineering and Technological Research Center, Kunming University, Kunming, China
| | - Yajun Yu
- College of Agronomy, Yunnan Urban Agricultural Engineering and Technological Research Center, Kunming University, Kunming, China
| | - Penghua Gao
- College of Agronomy, Yunnan Urban Agricultural Engineering and Technological Research Center, Kunming University, Kunming, China
| | - Shaowu Yang
- College of Agronomy, Yunnan Urban Agricultural Engineering and Technological Research Center, Kunming University, Kunming, China
| | - Yongteng Zhao
- College of Agronomy, Yunnan Urban Agricultural Engineering and Technological Research Center, Kunming University, Kunming, China
| | - Jianwei Guo
- College of Agronomy, Yunnan Urban Agricultural Engineering and Technological Research Center, Kunming University, Kunming, China
| | - Jiani Liu
- College of Agronomy, Yunnan Urban Agricultural Engineering and Technological Research Center, Kunming University, Kunming, China
| | - Feiyan Huang
- College of Agronomy, Yunnan Urban Agricultural Engineering and Technological Research Center, Kunming University, Kunming, China
| | - Lei Yu
- College of Agronomy, Yunnan Urban Agricultural Engineering and Technological Research Center, Kunming University, Kunming, China
| |
Collapse
|
17
|
Woravatin W, Wongkomonched R, Tassaneeyakul W, Stoneking M, Makarawate P, Kutanan W. Complete mitochondrial genomes of patients from Thailand with cardiovascular diseases. PLoS One 2024; 19:e0307036. [PMID: 38990956 PMCID: PMC11239017 DOI: 10.1371/journal.pone.0307036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2024] [Accepted: 06/27/2024] [Indexed: 07/13/2024] Open
Abstract
Several previous studies have reported that both variation and haplogroups of mitochondrial (mt) DNA were associated with various kinds of diseases, including cardiovascular diseases, in different populations, but such studies have not been carried out in Thailand. Here, we sequenced complete mtDNA genomes from 82 patients diagnosed with three types of cardiovascular disease, i.e., Hypertrophic Cardiomyopathy (HCM) (n = 26), Long Q-T Syndrome (LQTS) (n = 7) and Brugada Syndrome (BrS) (n = 49) and compared these with 750 previously published mitogenome sequences from interviewed normal individuals as a control group. Both patient and control groups are from the same geographic region of northeastern Thailand. We found 9, 2, and 5 novel mutations that were not both damaging and deleterious in HCM, LQTS, and BrS patients, respectively. Haplogroup R9c was significantly associated with HCM (P = 0.0032; OR = 62.42; 95%CI = 6.892-903.4) while haplogroup M12b was significantly associated with LQTS (P = 0.0039; OR = 32.93; 95% CI = 5.784-199.6). None of the haplogroups was found to be significantly associated with BrS. A significantly higher density of mtDNA variants in the rRNA genes was found in patients with HCM and BrS (P < 0.001) than in those with LQTS or the control group. Effects of detected SNPs in either protein coding or tRNA genes of all the mitogenome sequences were also predicted. Interestingly, three SNPs in two tRNA genes (MT-TA m.5618T>C and m.5631G>A heteroplasmic variants in two BrS patients and MT-TQ m.4392C>T novel homoplasmic variant in a HCM patient) were predicted to alter tRNA secondary structure, possibly leading to abnormal tRNA function.
Collapse
Affiliation(s)
- Wipada Woravatin
- Department of Biology, Faculty of Science, Khon Kaen University, Khon Kaen, Thailand
| | | | | | - Mark Stoneking
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Biométrie et Biologie Évolutive, UMR 5558, CNRS & Université de Lyon, Lyon, France
| | | | - Wibhu Kutanan
- Department of Biology, Faculty of Science, Khon Kaen University, Khon Kaen, Thailand
- Department of Biology, Faculty of Science, Naresuan University, Phitsanulok, Thailand
| |
Collapse
|
18
|
Sun D, Wang S, Wang C, Zou J. Transcriptomics reveals that NAD(P)H affects the development of the Zig-zag eel (Mastacembelus armatus ♀) × Spiny eel (Sinobdella sinensis ♂) hybrid offspring leading to low hatching rates. Anim Reprod Sci 2024; 268:107561. [PMID: 39004014 DOI: 10.1016/j.anireprosci.2024.107561] [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: 04/20/2024] [Revised: 06/17/2024] [Accepted: 07/07/2024] [Indexed: 07/16/2024]
Abstract
Zig-zag eel (Mastacembelus armatus (2 n = 48)) and Spiny eel (Sinobdella sinensis (2 n = 48)) are two species of the Mastacembelidae family commonly found in southern China. Hybridization between the two has a very high deformity rate and a very low hatching rate. In order to investigate the reasons for this, the first hybridization between M. armatus and S. sinensis was carried out using artificial insemination, and the embryonic development of the hybrid offspring was examined using microphotography, and the malformations of the hybrid offspring were investigated by transcriptomics. The experiments showed that the average egg production was 4265.7 ± 322.94 (Mean ± SD), the average fertilization rate of hybrid offspring was 98.67 ± 0.58 % (Mean ± SD), the hatching rate was 12.06 ± 3.44 % (Mean ± SD), the deformity rate was 98.15 ± 3.21 % (Mean ± SD), and the embryonic development successively went through the five main stages of fertilized egg, egg cleavage, embryo formation, organogenesis, and exertion of membranes. Transcriptomics showed that the expression of NAD(P)H-related enzyme activity DEGs was increased, and many DEGs related to cell signaling molecule transmission and metabolic regulation are enriched in KEGG pathways, such as IL-17 signaling pathway, Osteoclast differentiation, TNF signaling pathway and MAPK signaling pathway. etc. The major types of DEGs corresponded to those coding for proteins. This study suggests that the high malformation rate in hybrid offspring may be caused by impaired synthesis of proteins during embryonic development.
Collapse
Affiliation(s)
- Di Sun
- College of Marine Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Shaodan Wang
- College of Marine Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Chong Wang
- College of Marine Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Jixing Zou
- College of Marine Sciences, South China Agricultural University, Guangzhou 510642, China.
| |
Collapse
|
19
|
Liu Q, Naganuma T. Metabolomics in sturgeon research: a mini-review. FISH PHYSIOLOGY AND BIOCHEMISTRY 2024:10.1007/s10695-024-01377-8. [PMID: 38980504 DOI: 10.1007/s10695-024-01377-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Accepted: 07/02/2024] [Indexed: 07/10/2024]
Abstract
Sturgeons are ancient fish, with 27 species distributed in the Northern Hemisphere. This review first touches upon the significance of sturgeons in the context of their biological, ecological, and economic importance, highlighting their status as "living fossils" and the challenges they face in genomic research due to their diverse chromosome numbers. This review then discusses how omics technologies (genomics, transcriptomics, proteomics, and metabolomics) have been used in sturgeon research, which so far has only been done on Acipenser species. It focuses on metabolomics as a way to better understand how sturgeons work and how they react to their environment. Specific studies in sturgeon metabolomics are cited, showing how metabolomics has been used to investigate various aspects of sturgeon biology, such as growth, reproduction, stress responses, and nutrition. These studies demonstrate the potential of metabolomics in improving sturgeon aquaculture practices and conservation efforts. Overall, the review suggests that metabolomics, as a relatively new scientific tool, has the potential to enhance our understanding of sturgeon biology and aid in their conservation and sustainable aquaculture, contributing to global food security efforts.
Collapse
Affiliation(s)
- Qi Liu
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, 739-8528, Japan
| | - Takeshi Naganuma
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, 739-8528, Japan.
| |
Collapse
|
20
|
Arya V, Narayana S, Sinha T, Kandan A, Satyanarayana Raju SV. A simple PCR-based quick detection of the economically important oriental fruit fly, Bactrocera dorsalis (Hendel) from India. FRONTIERS IN PLANT SCIENCE 2024; 15:1399718. [PMID: 39045589 PMCID: PMC11263087 DOI: 10.3389/fpls.2024.1399718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Accepted: 06/25/2024] [Indexed: 07/25/2024]
Abstract
The oriental fruit fly, Bactrocera dorsalis (Hendel), is a significant economic and quarantine pest due to its polyphagous nature. The accurate identification of B. dorsalis is challenging at the egg, maggot, and pupal stages, due to lack of distinct morphological characters and its similarity to other fruit flies. Adult identification requires specialized taxonomist. Existing identification methods are laborious, time consuming, and expensive. Rapid and precise identification is crucial for timely management. By analyzing the variations in the mitochondrial cytochrome oxidase-1 gene sequence (Insect barcoding gene), we developed a species-specific primer (SSP), DorFP1/DorRP1, for accurate identification of B. dorsalis. The optimal annealing temperature for the SSP was determined to be 66°C, with no cross-amplification or primer-dimer formation observed. The SSP was validated with B. dorsalis specimens from various locations in northern and eastern India and tested for cross-specificity with six other economically significant fruit fly species in India. The primer specificity was further confirmed by the analysis of critical threshold (Ct) value from a qPCR assay. Sensitivity analysis showed the primer could detect template DNA concentrations as low as 1 pg/µl, though sensitivity decreased at lower concentrations. Sequencing of the SSP-amplified product revealed over >99% similarity with existing B. dorsalis sequences in the NCBI GenBank. The developed SSP reliably identifies B. dorsalis across all developmental stages and sexes. This assay is expected to significantly impact pest identification, phytosanitary measures, and eradication programs for B. dorsalis.
Collapse
Affiliation(s)
- Varun Arya
- Insects Molecular Biology Laboratory, Institute of Agricultural Sciences, Department of Entomology and Agricultural Zoology, Banaras Hindu University, Varanasi, Uttar Pradesh, India
| | - Srinivasa Narayana
- Insects Molecular Biology Laboratory, Institute of Agricultural Sciences, Department of Entomology and Agricultural Zoology, Banaras Hindu University, Varanasi, Uttar Pradesh, India
| | - Twinke Sinha
- Insects Molecular Biology Laboratory, Institute of Agricultural Sciences, Department of Entomology and Agricultural Zoology, Banaras Hindu University, Varanasi, Uttar Pradesh, India
| | - Aravindaram Kandan
- Indian Council of Agricultural Research-National Bureau of Agricultural Insect Resources, Bengaluru, Karnataka, India
| | - Samantapudi Venkata Satyanarayana Raju
- Insect Physiology and Toxicology Laboratory, Institute of Agricultural Sciences, Department of Entomology and Agricultural Zoology, Banaras Hindu University, Varanasi, Uttar Pradesh, India
| |
Collapse
|
21
|
Ghosh A, Tyagi K, Dubey AK, Sweet AD, Singha D, Goswami P, Kumar V. Purifying selection drove the adaptation of mitochondrial genes along with correlation of gene rearrangements and evolutionary rates in two subfamilies of Whitefly (Insecta: Hemiptera). Funct Integr Genomics 2024; 24:121. [PMID: 38976062 DOI: 10.1007/s10142-024-01400-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Revised: 05/06/2024] [Accepted: 06/27/2024] [Indexed: 07/09/2024]
Abstract
Insect mitochondrial genomes (mitogenomes) are usually represented by a conserved gene order. Whiteflies exhibit gene rearrangement in their mitogenomes; however, understanding how nucleotide substitution rates shape gene rearrangement in whiteflies is unclear due to the limited number of mitogenomes. Additionally, the mechanisms by which selection pressure drives adaptations in mitochondrial genes in the two subfamilies of whiteflies are not yet known. Here, we analyzed 18 whitefly mitogenomes, including one newly generated mitogenome, to compare nucleotide substitution rates, selection pressure, and gene arrangements. The newly generated mitogenome is reported along with reannotation of Pealius mori and comparisons to other whitefly mitogenomes. Comparative studies on nucleotide composition of 18 whiteflies revealed the positive GC skewness, confirming the reversal of strand asymmetry. We found 11 rearranged gene orders within two subfamilies of whiteflies with 8-18 breakpoints of gene rearrangements. Members of the subfamily Aleyrodinae exhibit more complex pathways in the evolution of gene order as compared to the subfamily Aleurodicinae. Our findings also revealed that the increase or reduction of nucleotide substitution rates does not have an impact on any of the gene rearrangement scenarios depicting neutral correlation. Selection pressure analysis revealed that the mitogenomes from members of both the subfamilies Aleurodicinae and Aleyrodinae are characterized by intense purifying selection pressure.
Collapse
Affiliation(s)
- Abhishek Ghosh
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, Kolkata, West Bengal, India
- Department of Zoology, University of Calcutta, Kolkata, West Bengal, India
| | - Kaomud Tyagi
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, Kolkata, West Bengal, India.
| | - Anil Kumar Dubey
- Hemiptera Section, Zoological Survey of India, West Bengal, Kolkata, India
| | | | - Devkant Singha
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, Kolkata, West Bengal, India
| | - Prathana Goswami
- Lepidoptera Section, Zoological Survey of India, Kolkata, West Bengal, India
- Department of Zoology, Gauhati University, Guwahati, Assam, India
| | - Vikas Kumar
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, Kolkata, West Bengal, India.
| |
Collapse
|
22
|
Sangster G, Luksenburg JA. The published complete mitochondrial genome of Blue-fronted Redstart ( Phoenicurus frontalis) is a chimera and includes DNA from Pink-rumped Rosefinch Carpodacus waltoni eos (Aves: Passeriformes). Mitochondrial DNA B Resour 2024; 9:861-864. [PMID: 38983844 PMCID: PMC11232634 DOI: 10.1080/23802359.2024.2377170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2024] [Accepted: 07/02/2024] [Indexed: 07/11/2024] Open
Abstract
The complete mitochondrial genome of Blue-fronted Redstart (Phoenicurus frontalis), GenBank accession number MT360379 (NC_053917), was published by Li and colleages in 2020. Here we show that this mitogenome is actually a chimera containing DNA fragments of both P. frontalis (15,518 bp, 92.5%) and Pink-rumped Rosefinch (Carpodacus waltoni eos, 1258 bp, 7.5%). This mitogenome has been re-used in at least three phylogenies. Our study confirms that mitogenomes are best verified with multiple gene trees, and that any anomalies should be investigated by direct comparison of sequences.
Collapse
Affiliation(s)
| | - Jolanda A. Luksenburg
- Institute of Environmental Sciences, Leiden University, Leiden, The Netherlands
- Department of Environmental Science and Policy, George Mason University, Fairfax, VA, USA
| |
Collapse
|
23
|
Waneka G, Stewart J, Anderson JR, Li W, Wilusz J, Argueso JL, Sloan DB. UV damage induces production of mitochondrial DNA fragments with specific length profiles. Genetics 2024; 227:iyae070. [PMID: 38722894 PMCID: PMC11228841 DOI: 10.1093/genetics/iyae070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Revised: 02/08/2024] [Accepted: 04/22/2024] [Indexed: 05/21/2024] Open
Abstract
UV light is a potent mutagen that induces bulky DNA damage in the form of cyclobutane pyrimidine dimers (CPDs). Photodamage and other bulky lesions occurring in nuclear genomes can be repaired through nucleotide excision repair (NER), where incisions on both sides of a damaged site precede the removal of a single-stranded oligonucleotide containing the damage. Mitochondrial genomes (mtDNAs) are also susceptible to damage from UV light, but current evidence suggests that the only way to eliminate bulky mtDNA damage is through mtDNA degradation. Damage-containing oligonucleotides excised during NER can be captured with antidamage antibodies and sequenced (XR-seq) to produce high-resolution maps of active repair locations following UV exposure. We analyzed previously published datasets from Arabidopsis thaliana, Saccharomyces cerevisiae, and Drosophila melanogaster to identify reads originating from the mtDNA (and plastid genome in A. thaliana). In A. thaliana and S. cerevisiae, the mtDNA-mapping reads have unique length distributions compared to the nuclear-mapping reads. The dominant fragment size was 26 nt in S. cerevisiae and 28 nt in A. thaliana with distinct secondary peaks occurring in regular intervals. These reads also show a nonrandom distribution of di-pyrimidines (the substrate for CPD formation) with TT enrichment at positions 7-8 of the reads. Therefore, UV damage to mtDNA appears to result in production of DNA fragments of characteristic lengths and positions relative to the damaged location. The mechanisms producing these fragments are unclear, but we hypothesize that they result from a previously uncharacterized DNA degradation pathway or repair mechanism in mitochondria.
Collapse
Affiliation(s)
- Gus Waneka
- Department of Biology, Colorado State University, Fort Collins 80521, CO, USA
| | - Joseph Stewart
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins 80521, CO, USA
- Cell and Molecular Biology Graduate Program, Colorado State University, Fort Collins 80521, CO, USA
| | - John R Anderson
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins 80521, CO, USA
| | - Wentao Li
- Department of Environmental Health Science, University of Georgia, Athens 30602, GA, USA
| | - Jeffrey Wilusz
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins 80521, CO, USA
| | - Juan Lucas Argueso
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins 80521, CO, USA
- Cell and Molecular Biology Graduate Program, Colorado State University, Fort Collins 80521, CO, USA
| | - Daniel B Sloan
- Department of Biology, Colorado State University, Fort Collins 80521, CO, USA
- Cell and Molecular Biology Graduate Program, Colorado State University, Fort Collins 80521, CO, USA
| |
Collapse
|
24
|
Zhao H, Cheng H, Wang N, Bai L, Chen X, Liu X, Qiao B. Identifying climate refugia for wild yaks (Bos mutus) on the Tibetan Plateau. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2024; 366:121655. [PMID: 38981271 DOI: 10.1016/j.jenvman.2024.121655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Revised: 06/20/2024] [Accepted: 06/29/2024] [Indexed: 07/11/2024]
Abstract
Climate change is threatening fragile alpine ecosystems and their resident ungulates, particularly the wild yak (Bos mutus) that inhabits alpine areas between the tree line and glaciers on the Tibetan Plateau. Although wild yaks tend to shift habitats in response to changes in climatic factors, the precise impacts of climate change on their habitat distribution and climate refugia remain unclear. Based on over 1000 occurrence records, the maximum entropy (MaxEnt) algorithm was applied to simulate habitat ranges in the last glacial maximum (LGM), Mid-Holocene, current stage, and three greenhouse gas emission scenarios in 2070. Three habitat patches were identified as climate refugia for wild yaks that have persisted from the LGM to the present and are projected to persist until 2070. These stable areas account for approximately 64% of the current wild yak habitat extent and are sufficiently large to support viable populations. The long-term persistence of these climate refugia areas is primarily attributed to the unique alpine environmental features of the Tibetan Plateau, where relatively stable arid or semi-arid climates are maintained, and a wide range of forage resource supplies are available. However, habitat loss by 2070 caused by insufficient protection is predicted to lead to severe fragmentation in the southeastern and northwestern Kunlun, Hengduan, central-western Qilian, and southern Tanggula-northern Himalaya Mountains. Habitat disturbance has also been caused by increasing anthropogenic effects in the southern Tanggula and northern Himalaya Mountains. We suggest that sufficient protection, transboundary cooperation, and community involvement are required to improve wild yak conservation efforts. Our combined modeling method (MaxEnt-Zonation-Linkage Mapper-FRAGSTAT) can be utilized to identify priority areas and linkages between habitat patches while assessing the conservation efficiency of protected areas and analyzing the coupled relationship between climate change and anthropogenic impacts on the habitat distribution of endangered species.
Collapse
Affiliation(s)
- Hang Zhao
- College of Earth and Environmental Sciences, Center for Glacier and Desert Research, Scientific Observing Station for Desert and Glacier, Lanzhou University, Lanzhou, 730000, China.
| | - Hongyi Cheng
- College of Earth and Environmental Sciences, Center for Glacier and Desert Research, Scientific Observing Station for Desert and Glacier, Lanzhou University, Lanzhou, 730000, China.
| | - Nai'ang Wang
- College of Earth and Environmental Sciences, Center for Glacier and Desert Research, Scientific Observing Station for Desert and Glacier, Lanzhou University, Lanzhou, 730000, China.
| | - Liqiong Bai
- College of Earth and Environmental Sciences, Center for Glacier and Desert Research, Scientific Observing Station for Desert and Glacier, Lanzhou University, Lanzhou, 730000, China.
| | - Xiaowen Chen
- College of Earth and Environmental Sciences, Center for Glacier and Desert Research, Scientific Observing Station for Desert and Glacier, Lanzhou University, Lanzhou, 730000, China.
| | - Xiao Liu
- College of Earth and Environmental Sciences, Center for Glacier and Desert Research, Scientific Observing Station for Desert and Glacier, Lanzhou University, Lanzhou, 730000, China.
| | - Bin Qiao
- College of Earth and Environmental Sciences, Center for Glacier and Desert Research, Scientific Observing Station for Desert and Glacier, Lanzhou University, Lanzhou, 730000, China.
| |
Collapse
|
25
|
Ehemann NR, Hernández S, Siccha-Ramírez R, García-Rodríguez FJ, De La Cruz-Agüero J. Alike but genetically divergent: The resurrection of Urotrygon asterias (Jordan & Gilbert, 1883) from its closest relatives, the Munda and the Blotched stingray. JOURNAL OF FISH BIOLOGY 2024. [PMID: 38978288 DOI: 10.1111/jfb.15864] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 06/13/2024] [Accepted: 06/18/2024] [Indexed: 07/10/2024]
Abstract
The genus Urotrygon comprises small- to medium-sized endemic round rays on the American continent and has undergone several synonymization processes. Here, we used an integrative taxonomic approach, including meristic, morphometric, and mtDNA analyses, to resolve the particularly intricate relationship among Urotrygon munda Gill, 1863, Urotrygon chilensis (Günther, 1872), and Urotrygon asterias (Jordan & Gilbert, 1883). The latter species is currently a synonym of U. munda but is also considered the U. chilensis "northern morphotype." These taxonomic entities have historically been confounded, mainly due to their phenotypical resemblance along their geographic distribution in the eastern Pacific. We assessed 78 specimens (43 "northern" and 30 "southern morphotypes" of U. chilensis, as well as 5 U. munda) using 19 external variables for taxonomic and morphometric analysis. Distinct meristic patterns, including pectoral and pelvic ceratotrichia, vertebrae number, and thorn distribution along the dorsal midline, were observed in the series-type specimens of the three taxonomic entities. Our multivariate morphometric analyses consistently differentiated the three groups as distinct taxonomic entities, with an overall classification accuracy of 66.7%. The meristic results also provided reliable information distinguishing the three entities. Based on the nicotinamide adenine dinucleotide (NADH2) and cytochrome oxidase subunit I (COI) genes, our phylogenetic analysis were consistent with the morphometric and meristic data, supporting these three entities as distinct species having their own evolutionary lineages. Our comprehensive approach confidently demonstrated that the northern U. chilensis morphotype matched and corresponded to the description of the Starry round ray, U. asterias, confirming its taxonomic resurrection as a valid species distinct from U. chilensis and U. munda. The geographic distribution of U. asterias spans from the tropical west coast of Mexico (including the Gulf of California) to Costa Rica, revealing that microevolutionary processes have well-defined population clades within this range. Furthermore, U. chilensis is unequivocally established as the sole Urotrygon species occurring south of the Guayaquil marine ecoregion. In addition, the public COI and NADH2 sequences available for Urotrygon hosted in the ad hoc online databases were found to be misidentified, emphasizing the need for rigorous taxonomic scrutiny in this group. Finally, our research underscores the significance of an integrative approach that combines morphometric, meristic, and molecular techniques with historical data to disentangle the complexities of closely related taxa.
Collapse
Affiliation(s)
- Nicolás Roberto Ehemann
- Instituto Politécnico Nacional-Centro Interdisciplinario de Ciencias Marinas (CICIMAR-IPN), Colección Ictiológica, La Paz, Mexico
- Biology Department, University of Konstanz, Konstanz, Germany
| | - Sebastían Hernández
- Biomolecular Laboratory, Center for International Programs and Sustainability Studies, Universidad Veritas, San José, Costa Rica
- Sala de Colecciones, Facultad de Ciencias del Mar, Universidad Católica del Norte, Coquimbo, Chile
| | - Raquel Siccha-Ramírez
- Facultad de Ciencias Biológicas, Universidad Nacional Mayor de San Marcos, Lima, Peru
| | | | - José De La Cruz-Agüero
- Instituto Politécnico Nacional-Centro Interdisciplinario de Ciencias Marinas (CICIMAR-IPN), Colección Ictiológica, La Paz, Mexico
| |
Collapse
|
26
|
Lee S, Hwang S, Lee M, Seung J, Choi W, Bai M. DNA barcoding reveals a taxonomic fraud: Note on validity of Propomacrusmuramotoae (Coleoptera, Scarabaeidae). Zookeys 2024; 1206:181-190. [PMID: 39015529 PMCID: PMC11249845 DOI: 10.3897/zookeys.1206.124932] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Accepted: 05/28/2024] [Indexed: 07/18/2024] Open
Abstract
Until the early 2000s, the genus Propomacrus was known to comprise two species, occurring in the Eastern Mediterranean and Southeast China. The discovery of Propomacrusmuramotoae Fujioka in Tibet and subsequently in Bhutan and Nepal, might play a crucial role in bridging the geographical distribution gap of the Euchirini tribe between the Mediterranean and Central China, offering profound insights into its evolution and biogeography. However, all specimens, including the holotype specimen, were sourced from a single insect vendor, with no further specimens found or catalogued in museum collections thereafter. During our examination of a P.muramotoae specimen from a private collection in South Korea, we found its COI gene sequence to be identical to that of P.bimucronatus (Pallas) from Turkey, a species known for its wide distribution and genetic variability across regional populations. This overlap in genetic identity raised significant doubts, further compounded by our detection of deliberate modifications in essential diagnostic features during morphological examination. All three specimens we examined showed crude modifications, including staining and artificial grinding. Despite our inability to access the P.muramotoae type specimens for direct examination-a challenge we attempted to overcome through various means-it is evident that significant fraudulent tampering has occurred with the P.muramotoae specimens. Therefore, a new synonymy is proposed: Propomacrusbimucronatus Pallas, 1781 = P.muramotoae Fujioka, 2007 (syn. nov.). We also advocate for a straightforward verification of the type specimen through molecular analysis of the COI barcode region and morphological re-examination under a microscope for those who have access to the type specimens.
Collapse
Affiliation(s)
- Seunghyun Lee
- Key Laboratory of Animal Biodiversity Conservation and Integrated Pest Management, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, ChinaInstitute of Zoology, Chinese Academy of SciencesBeijingChina
- Department of Life Sciences, Natural History Museum, London, UKNatural History MuseumLondonUnited Kingdom
| | - Seulmaro Hwang
- Department of Science Contents, Visang Education, Gwacheon, Republic of KoreaVisang EducationGwacheonRepublic of Korea
| | - Minhyeuk Lee
- National Institute of Agricultural Sciences, Wanju, Republic of KoreaSeoul National UniversitySeoulRepublic of Korea
- Insect Biosystematics Laboratory, Department of Agricultural Biotechnology, Seoul National University, Seoul, Republic of KoreaNational Institute of Agricultural SciencesWanjuRepublic of Korea
| | - Jinbae Seung
- Insect Biosystematics Laboratory, Department of Agricultural Biotechnology, Seoul National University, Seoul, Republic of KoreaNational Institute of Agricultural SciencesWanjuRepublic of Korea
| | - Woong Choi
- 305-403, Sechangnamsunhwan-ro, Namdong-gu, Incheon, Republic of KoreaUnaffiliatedIncheonRepublic of Korea
| | - Ming Bai
- Key Laboratory of Animal Biodiversity Conservation and Integrated Pest Management, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, ChinaInstitute of Zoology, Chinese Academy of SciencesBeijingChina
- University of Chinese Academy of Sciences, Beijing, ChinaUniversity of Chinese Academy of SciencesBeijingChina
| |
Collapse
|
27
|
Huang Y, Jin XJ, Zhang CY, Li P, Meng HH, Zhang YH. Plastome evolution of Engelhardia facilitates phylogeny of Juglandaceae. BMC PLANT BIOLOGY 2024; 24:634. [PMID: 38971744 PMCID: PMC11227234 DOI: 10.1186/s12870-024-05293-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Accepted: 06/12/2024] [Indexed: 07/08/2024]
Abstract
BACKGROUND Engelhardia (Juglandaceae) is a genus of significant ecological and economic importance, prevalent in the tropics and subtropics of East Asia. Although previous efforts based on multiple molecular markers providing profound insights into species delimitation and phylogeography of Engelhardia, the maternal genome evolution and phylogeny of Engelhardia in Juglandaceae still need to be comprehensively evaluated. In this study, we sequenced plastomes from 14 samples of eight Engelhardia species and the outgroup Rhoiptelea chiliantha, and incorporated published data from 36 Juglandaceae and six outgroup species to test phylogenetic resolution. Moreover, comparative analyses of the plastomes were conducted to investigate the plastomes evolution of Engelhardia and the whole Juglandaceae family. RESULTS The 13 Engelhardia plastomes were highly similar in genome size, gene content, and order. They exhibited a typical quadripartite structure, with lengths from 161,069 bp to 162,336 bp. Three mutation hotspot regions (TrnK-rps16, ndhF-rpl32, and ycf1) could be used as effective molecular markers for further phylogenetic analyses and species identification. Insertion and deletion (InDels) may be an important driving factor for the evolution of plastomes in Juglandoideae and Engelhardioideae. A total of ten codons were identified as the optimal codons in Juglandaceae. The mutation pressure mostly contributed to shaping codon usage. Seventy-eight protein-coding genes in Juglandaceae experienced relaxed purifying selection, only rpl22 and psaI genes showed positive selection (Ka/Ks > 1). Phylogenetic results fully supported Engelhardia as a monophyletic group including two sects and the division of Juglandaceae into three subfamilies. The Engelhardia originated in the Late Cretaceous and diversified in the Late Eocene, and Juglandaceae originated in the Early Cretaceous and differentiated in Middle Cretaceous. The phylogeny and divergence times didn't support rapid radiation occurred in the evolution history of Engelhardia. CONCLUSION Our study fully supported the taxonomic treatment of at the section for Engelhardia species and three subfamilies for Juglandaceae and confirmed the power of phylogenetic resolution using plastome sequences. Moreover, our results also laid the foundation for further studying the course, tempo and mode of plastome evolution of Engelhardia and the whole Juglandaceae family.
Collapse
Affiliation(s)
- Yue Huang
- College of Life and Environmental Science, Wenzhou University, Wenzhou, 325035, China
| | - Xin-Jie Jin
- College of Life and Environmental Science, Wenzhou University, Wenzhou, 325035, China
- Zhejiang Provincial Key Laboratory for Water Environment and Marine Biological Resources Protection, Wenzhou University, Wenzhou, 325035, China
| | - Can-Yu Zhang
- Yunnan Normal University, Kunming, 650500, Yunnan, China
| | - Pan Li
- Laboratory of Systematic & Evolutionary Botany and Biodiversity, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Hong-Hu Meng
- Plant Phylogenetics and Conservation Group, Center for Integrative Conservation & Yunnan Key Laboratory for Conservation of Tropical Rainforests and Asian Elephants, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, 666303, China.
| | - Yong-Hua Zhang
- College of Life and Environmental Science, Wenzhou University, Wenzhou, 325035, China.
- Zhejiang Provincial Key Laboratory for Water Environment and Marine Biological Resources Protection, Wenzhou University, Wenzhou, 325035, China.
| |
Collapse
|
28
|
Wu XF, Xu Q, Wang A, Wang BZ, Lan XY, Li WY, Liu Y. Relationship between Indel Variants within the JAK2 Gene and Growth Traits in Goats. Animals (Basel) 2024; 14:1994. [PMID: 38998106 PMCID: PMC11240706 DOI: 10.3390/ani14131994] [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: 05/29/2024] [Revised: 06/28/2024] [Accepted: 07/05/2024] [Indexed: 07/14/2024] Open
Abstract
Janus kinase 2 (JAK2) plays a critical role in myoblast proliferation and fat deposition in animals. Our previous RNA-Seq analyses identified a close association between the JAK2 gene and muscle development. To date, research delving into the relationship between the JAK2 gene and growth traits has been sparse. In this study, we sought to investigate the relationship between novel mutations within the JAK2 gene and goat growth traits. Herein, two novel InDel (Insertion/Deletion) polymorphisms within the JAK2 gene were detected in 548 goats, and only two genotypes were designated as ID (Insertion/Deletion) and DD (Deletion/Deletion). The results indicate that the two InDels, the del19008 locus in intron 2 and del72416 InDel in intron 6, showed significant associations with growth traits (p < 0.05). Compared to Nubian and Jianzhou Daer goats, the del72416 locus displayed a more pronounced effect in the Fuqing breed group. In the Nubian breed (NB) group, both InDels showed a marked influence on body height (BH). There were strong linkages observed for these two InDels between the Fuqing (FQ) and Jianzhou (JZ) populations. The DD-ID diplotype was associated with inferior growth traits in chest width (ChW) and cannon circumference (CaC) in the FQ goats compared to the other diplotypes. In the NB population, the DD-DD diplotype exhibited a marked negative impact on BH and HuWI (hucklebone width index), in contrast to the other diplotypes. In summary, our findings suggest that the two InDel polymorphisms within the JAK2 gene could serve as valuable molecular markers for enhancing goat growth traits in breeding programs.
Collapse
Affiliation(s)
- Xian-Feng Wu
- Fujian Provincial Key Laboratory of Animal Genetics and Breeding/Institute of Animal Husbandry and Veterinary, Fujian Academy of Agricultural Sciences, Fuzhou 350013, China
| | - Qian Xu
- Fujian Provincial Key Laboratory of Animal Genetics and Breeding/Institute of Animal Husbandry and Veterinary, Fujian Academy of Agricultural Sciences, Fuzhou 350013, China
| | - Ao Wang
- College of Animal Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Ben-Zhi Wang
- College of Animal Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Xian-Yong Lan
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A&F University, Yangling, Xianyang 712100, China
| | - Wen-Yang Li
- Fujian Provincial Key Laboratory of Animal Genetics and Breeding/Institute of Animal Husbandry and Veterinary, Fujian Academy of Agricultural Sciences, Fuzhou 350013, China
| | - Yuan Liu
- Fujian Provincial Key Laboratory of Animal Genetics and Breeding/Institute of Animal Husbandry and Veterinary, Fujian Academy of Agricultural Sciences, Fuzhou 350013, China
| |
Collapse
|
29
|
Sun CH, Lu CH, Wang ZJ. Comparison and phylogenetic analysis of the mitochondrial genomes of Synodontis eupterus and Synodontis polli. Sci Rep 2024; 14:15393. [PMID: 38965284 PMCID: PMC11224264 DOI: 10.1038/s41598-024-65809-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2024] [Accepted: 06/24/2024] [Indexed: 07/06/2024] Open
Abstract
We aimed to distinguish Synodontis eupterus and Synodontis polli. We performed sequencing and bioinformatic analysis of their mitochondrial genomes and constructed a phylogenetic tree of Mochokidae fish using maximum likelihood and Bayesian methods based on protein-coding gene (PCG) sequences of 14 Mochokidae species. The total length of the S. eupterus mitochondrial genome was 16,579 bp, including 13 (PCGs), 22 tRNA genes, two rRNA genes, and one D-loop, with an AT-biased nucleotide composition (56.0%). The total length of the S. polli mitochondrial genome was 16,544 bp, including 13 PCGs, 22 tRNA genes, two rRNA genes, and one D-loop, with an AT-biased nucleotide composition (55.0%). In both species, except for COI, PCGs use ATG as the starting codon, the vast majority use TAG or TAA as the ending codon, and a few use incomplete codons (T - or TA -) as the ending codon. Phylogenetic analysis showed that S. eupterus and Synodontis clarias converged into one branch, S. polli and Synodontis petricola converged into one branch, Mochokiella paynei, Mochokus brevis, and nine species of the genus Synodontis converged into one branch, and M. paynei clustered with the genus Synodontis. This study lays a foundation for rebuilding a clearer Mochokidae fish classification system.
Collapse
Affiliation(s)
- Cheng-He Sun
- The Co-Innovation Center for Sustainable Forestry in Southern China, College of Life Sciences, Nanjing Forestry University, Nanjing, 210037, China.
| | - Chang-Hu Lu
- The Co-Innovation Center for Sustainable Forestry in Southern China, College of Life Sciences, Nanjing Forestry University, Nanjing, 210037, China.
| | - Zi-Jian Wang
- Agriculture and Rural Bureau of Gaochun District, Nanjing, 211300, China
| |
Collapse
|
30
|
Doorenweerd C, San Jose M, Leblanc L, Barr N, Geib SM, Chung AYC, Dupuis JR, Ekayanti A, Fiegalan E, Hemachandra KS, Hossain MA, Huang CL, Hsu YF, Morris KY, Maryani A Mustapeng A, Niogret J, Pham TH, Thi Nguyen N, Sirisena UGAI, Todd T, Rubinoff D. Towards a better future for DNA barcoding: Evaluating monophyly- and distance-based species identification using COI gene fragments of Dacini fruit flies. Mol Ecol Resour 2024:e13987. [PMID: 38956928 DOI: 10.1111/1755-0998.13987] [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: 03/07/2024] [Revised: 05/14/2024] [Accepted: 06/17/2024] [Indexed: 07/04/2024]
Abstract
The utility of a universal DNA 'barcode' fragment (658 base pairs of the Cytochrome C Oxidase I [COI] gene) has been established as a useful tool for species identification, and widely criticized as one for understanding the evolutionary history of a group. Large amounts of COI sequence data have been produced that hold promise for rapid species identification, for example, for biosecurity. The fruit fly tribe Dacini holds about a thousand species, of which 80 are pests of economic concern. We generated a COI reference library for 265 species of Dacini containing 5601 sequences that span most of the COI gene using circular consensus sequencing. We compared distance metrics versus monophyly assessments for species identification and although we found a 'soft' barcode gap around 2% pairwise distance, the exceptions to this rule dictate that a monophyly assessment is the only reliable method for species identification. We found that all fragments regularly used for Dacini fruit fly identification >450 base pairs long provide similar resolution. 11.3% of the species in our dataset were non-monophyletic in a COI tree, which is mostly due to species complexes. We conclude with recommendations for the future generation and use of COI libraries. We revise the generic assignment of Dacus transversus stat. rev. Hardy 1982, and Dacus perpusillus stat. rev. Drew 1971 and we establish Dacus maculipterus White 1998 syn. nov. as a junior synonym of Dacus satanas Liang et al. 1993.
Collapse
Affiliation(s)
- Camiel Doorenweerd
- Entomology Section, Department of Plant and Environmental Protection Sciences, College of Tropical Agriculture and Human Resources, University of Hawai'i at Mānoa, Honolulu, Hawaii, USA
| | - Michael San Jose
- Entomology Section, Department of Plant and Environmental Protection Sciences, College of Tropical Agriculture and Human Resources, University of Hawai'i at Mānoa, Honolulu, Hawaii, USA
| | - Luc Leblanc
- Department of Entomology, Plant Pathology and Nematology, University of Idaho, Moscow, Idaho, USA
| | - Norman Barr
- United States Department of Agriculture, Animal and Plant Health Inspection Service, Plant Protection and Quarantine, Science & Technology, Insect Management and Molecular Diagnostics Laboratory, Edinburg, Texas, USA
| | - Scott M Geib
- Tropical Pest Genetics and Molecular Biology Research Unit, Daniel K. Inouye U.S. Pacific Basin Agricultural Center, USDA Agricultural Research Services, Hilo, Hawaii, USA
| | - Arthur Y C Chung
- Forest Research Centre, Sabah Forestry Department, Sandakan, Sabah, Malaysia
| | - Julian R Dupuis
- Department of Entomology, University of Kentucky, Lexington, Kentucky, USA
| | - Arni Ekayanti
- Niogret Ecology Consulting LLC, Wotu, Luwu Timor, Sulawesi Seleaton, Indonesia
| | - Elaida Fiegalan
- Department of Crop Protection, College of Agriculture, Central Luzon State University, Science City of Muñoz, Nueva Ecija, Philippines
| | | | - Mohammad A Hossain
- Insect Biotechnology Division, Institute of Food and Radiation Biology, Bangladesh Atomic Energy Commission, Dhaka, Bangladesh
| | - Chia-Lung Huang
- Institute of Oceanography, Minjiang University, Fuzhou, Fujian, China
| | - Yu-Feng Hsu
- Department of Life Science, National Taiwan Normal University, Taipei, Taiwan, ROC
| | - Kimberly Y Morris
- Tropical Pest Genetics and Molecular Biology Research Unit, Daniel K. Inouye U.S. Pacific Basin Agricultural Center, USDA Agricultural Research Services, Hilo, Hawaii, USA
| | | | - Jerome Niogret
- Centre for Tropical Environmental & Sustainability Science, Nguma-Bada Campus, James Cook University, Smithfield, Queensland, Australia
| | - Thai Hong Pham
- Mientrung Institute for Scientific Research, Vietnam Academy of Science and Technology (VAST), Hue, Vietnam
- Vietnam National Museum of Nature & Graduate School of Science and Technology, VAST, Hanoi, Vietnam
| | - Nhien Thi Nguyen
- Faculty of Biotechnology, Vietnam National University of Agriculture, Hanoi, Vietnam
| | - Uda G A I Sirisena
- Department of Plant Sciences, Faculty of Agriculture, Rajarata University of Sri Lanka, Mihintale, Sri Lanka
| | - Terrence Todd
- United States Department of Agriculture, Animal and Plant Health Inspection Service, Plant Protection and Quarantine, Science & Technology, Insect Management and Molecular Diagnostics Laboratory, Edinburg, Texas, USA
| | - Daniel Rubinoff
- Entomology Section, Department of Plant and Environmental Protection Sciences, College of Tropical Agriculture and Human Resources, University of Hawai'i at Mānoa, Honolulu, Hawaii, USA
| |
Collapse
|
31
|
Doré G, Barloy D, Barloy-Hubler F. De Novo Hybrid Assembly Unveils Multi-Chromosomal Mitochondrial Genomes in Ludwigia Species, Highlighting Genomic Recombination, Gene Transfer, and RNA Editing Events. Int J Mol Sci 2024; 25:7283. [PMID: 39000388 PMCID: PMC11242644 DOI: 10.3390/ijms25137283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2024] [Revised: 06/28/2024] [Accepted: 06/29/2024] [Indexed: 07/16/2024] Open
Abstract
Biological invasions have been identified as the fifth cause of biodiversity loss, and their subsequent dispersal represents a major ecological challenge. The aquatic invasive species Ludwigia grandiflora subsp. hexapetala (Lgh) and Ludwigia peploides subsp. montevidensis (Lpm) are largely distributed in aquatic environments in North America and in Europe. However, they also present worrying terrestrial forms that are able to colonize wet meadows. To comprehend the mechanisms of the terrestrial adaptation of Lgh and Lpm, it is necessary to develop their genomic resources, which are currently poorly documented. We performed de novo assembly of the mitogenomes of Lgh and Lpm through hybrid assemblies, combining short reads (SR) and/or long reads (LR) before annotating both mitogenomes. We successfully assembled the mitogenomes of Lgh and Lpm into two circular molecules each, resulting in a combined total length of 711,578 bp and 722,518 bp, respectively. Notably, both the Lgh and Lpm molecules contained plastome-origin sequences, comprising 7.8% of the mitochondrial genome length. Additionally, we identified recombinations that were mediated by large repeats, suggesting the presence of multiple alternative conformations. In conclusion, our study presents the first high-quality mitogenomes of Lpm and Lgh, which are the only ones in the Myrtales order found as two circular molecules.
Collapse
Affiliation(s)
- Guillaume Doré
- DECOD (Ecosystem Dynamics and Sustainability), Institut Agro, INRAE, IFREMER, 35042 Rennes, France
| | - Dominique Barloy
- DECOD (Ecosystem Dynamics and Sustainability), Institut Agro, INRAE, IFREMER, 35042 Rennes, France
| | | |
Collapse
|
32
|
Song Y, Wang W, Wang B, Shi Q. The Protective Mechanism of TFAM on Mitochondrial DNA and its Role in Neurodegenerative Diseases. Mol Neurobiol 2024; 61:4381-4390. [PMID: 38087167 DOI: 10.1007/s12035-023-03841-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Accepted: 11/28/2023] [Indexed: 07/11/2024]
Abstract
Mitochondrial transcription factor A (TFAM) is a mitochondrial protein encoded by nuclear genes and transported from the cytoplasm to the mitochondria. TFAM is essential for the maintenance, expression, and delivery of mitochondrial DNA (mtDNA) and can regulate the replication and transcription of mtDNA. TFAM is associated with the formation of mtDNA nucleomimetic structures, mtDNA repair, and mtDNA stability. However, the mechanism by which TFAM protects mtDNA is still being studied. This review provides a summary of the protective mechanism of TFAM on mtDNA including the discrete regulatory effects of TFAM acetylation and phosphorylation on mtDNA, the regulation of Ca2+ levels by TFAM to activate transcription in mitochondria, and the increased binding of TFAM to mtDNA damage hot spots. This review also discusses the association between TFAM and some neurodegenerative diseases.
Collapse
Affiliation(s)
- Ying Song
- Department of Pharmacology, Zhejiang University of Technology, Hangzhou, Zhejiang, 310014, People's Republic of China.
- Hangzhou King's Bio-Pharmaceutical Technology Co., Ltd., Hangzhou, 310007, Zhejiang, China.
| | - Wenjun Wang
- Department of Pharmacology, Zhejiang University of Technology, Hangzhou, Zhejiang, 310014, People's Republic of China
| | - Beibei Wang
- Department of Pharmacology, Zhejiang University of Technology, Hangzhou, Zhejiang, 310014, People's Republic of China
| | - Qiwen Shi
- Department of Pharmacology, Zhejiang University of Technology, Hangzhou, Zhejiang, 310014, People's Republic of China
| |
Collapse
|
33
|
Mejia E, Buckup PA. Species boundaries of the whiptail catfish Rineloricaria (Siluriformes: Loricariidae) from the Paraíba do Sul River drainage, southeastern Brazil, with species redescriptions and description of a new species. JOURNAL OF FISH BIOLOGY 2024; 105:288-313. [PMID: 38747127 DOI: 10.1111/jfb.15780] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 04/13/2024] [Accepted: 04/17/2024] [Indexed: 07/19/2024]
Abstract
Species of the catfish genus Rineloricaria are common in the Paraíba do Sul River basin, in southeastern Brazil; here we present a revision of the taxonomic diversity and geographic distribution of the species of the genus inhabiting the basin, based on novel morphologic and molecular data. Five species delimitation methods based on cytochrome C oxidase subunit 1 nucleotide sequences yielded comparable molecular operational taxonomic units. The automatic barcode gap discovery, assemble species by automatic partitioning, barcode index number, and Bayesian implementation of the Poisson tree process methods supported the recognition of five evolutionary lineages. These taxonomic units were assigned to the previously described Rineloricaria nigricauda, Rineloricaria steindachneri, Rineloricaria zawadzkii, and Rineloricaria nudipectoris, and an additional undescribed species. R. zawadzkii was further divided into two intraspecific geographically structured lineages using the generalized mixed Yule coalescent delimitation method. A maximum likelihood phylogenetic analysis revealed that the five lineages from the Paraíba do Sul have closer relationships to different species from southern and southeastern Brazil (Ribeira de Iguape, Lagoa dos Patos, Uruguay, Paraguay, and Parana river basins) than to each other. Based on the analysis of lectotypes, recently collected material, and specimens from ichthyological collections, the poorly described R. nigricauda and R. steindachneri are redescribed following current descriptive standards. The undescribed species from the middle and upper Paraíba do Sul River basin is formally described. The description of a new species, along with the description of species boundaries in R. nigricauda and R. steindachneri, contributes to the knowledge of the ichthyofauna of the Paraíba do Sul River basin and adjacent coastal drainages of southeastern Brazil. An identification key for the species of Rineloricaria occurring in the Paraíba do Sul River basin is provided.
Collapse
Affiliation(s)
- Eduardo Mejia
- Programa de Pós-graduação em Ciências Biológicas (Zoologia), Museu Nacional, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Paulo A Buckup
- Programa de Pós-graduação em Ciências Biológicas (Zoologia), Museu Nacional, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| |
Collapse
|
34
|
Xiang H, Zhou Q, Li W, Shu J, Gu Z, Jiang W. Insights into phylogenetic positions and distribution patterns: Complete mitogenomes of two sympatric Asian horned toads in Boulenophrys (Anura: Megophryidae). Ecol Evol 2024; 14:e11687. [PMID: 38994208 PMCID: PMC11237341 DOI: 10.1002/ece3.11687] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Revised: 06/06/2024] [Accepted: 06/20/2024] [Indexed: 07/13/2024] Open
Abstract
Boulenophrys sangzhiensis and Boulenophrys tuberogranulata, two narrow-distributed toad species within the Megophryidae family in southern China, are experiencing population declines due to habitat loss and degradation. Despite their critical conservation status, the two species remain largely overlooked in public and scientific spheres. This study presented the first sequencing, assembly, and annotation of the complete mitogenomes of both species using next-generation sequencing. The mitogenome of B. sangzhiensis was 16,950 bp, while that of B. tuberogranulata was 16,841 bp, each comprising 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), two ribosomal RNA genes (rRNAs), and a noncoding control region (D-loop). The gene content, nucleotide composition, and evolutionary rates of each mitogenome were analyzed. Both mitogenomes exhibited negative AT skew and GC skew with high A + T content. ATP8 exhibited the highest evolutionary rate, while COI had the lowest. A phylogenetic analysis based on 28 mitogenomes revealed two major clades of Megophryidae, supporting the classification of two subfamilies, Megophryinae and Leptobrachiinae. Within the subfamily Megophryinae, the genus Boulenophrys was divided into two species groups. Intriguingly, despite coexisting in Zhangjiajie City, B. sangzhiensis and B. tuberogranulata exhibited distinct origins from the two different species groups, underscoring the unique role of the coexisting area Zhangjiajie in driving their speciation and preserving their current populations. A parallel pattern was also identified in the Leptobrachiinae genus Leptobrachium within the same region. This study provided valuable data references and enhanced our understanding of the molecular characteristics of these threatened amphibian species.
Collapse
Affiliation(s)
- Hongmei Xiang
- Key Laboratory of Hunan Forest Products and Chemical Industry Engineering, National and Local United Engineering Laboratory of Integrative Utilization Technology of Eucommia ulmoidesJishou UniversityZhangjiajieChina
| | - Qiang Zhou
- Key Laboratory of Hunan Forest Products and Chemical Industry Engineering, National and Local United Engineering Laboratory of Integrative Utilization Technology of Eucommia ulmoidesJishou UniversityZhangjiajieChina
- College of Biology and Environmental SciencesJishou UniversityJishouChina
| | - Wei Li
- Zhangjiajie National Forest ParkZhangjiajieChina
| | - Juan Shu
- Zhangjiajie National Forest ParkZhangjiajieChina
| | - Zhirong Gu
- National Nature Reserve of BadagongshanZhangjiajieChina
| | - Wansheng Jiang
- Key Laboratory of Hunan Forest Products and Chemical Industry Engineering, National and Local United Engineering Laboratory of Integrative Utilization Technology of Eucommia ulmoidesJishou UniversityZhangjiajieChina
- College of Biology and Environmental SciencesJishou UniversityJishouChina
| |
Collapse
|
35
|
Saranholi BH, França FM, Vogler AP, Barlow J, Vaz de Mello FZ, Maldaner ME, Carvalho E, Gestich CC, Howes B, Banks-Leite C, Galetti PM. Testing and optimizing metabarcoding of iDNA from dung beetles to sample mammals in the hyperdiverse Neotropics. Mol Ecol Resour 2024; 24:e13961. [PMID: 38646932 DOI: 10.1111/1755-0998.13961] [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: 10/31/2023] [Revised: 03/16/2024] [Accepted: 04/08/2024] [Indexed: 04/25/2024]
Abstract
Over the past few years, insects have been used as samplers of vertebrate diversity by assessing the ingested-derived DNA (iDNA), and dung beetles have been shown to be a good mammal sampler given their broad feeding preference, wide distribution and easy sampling. Here, we tested and optimized the use of iDNA from dung beetles to assess the mammal community by evaluating if some biological and methodological aspects affect the use of dung beetles as mammal species samplers. We collected 403 dung beetles from 60 pitfall traps. iDNA from each dung beetle was sequenced by metabarcoding using two mini-barcodes (12SrRNA and 16SrRNA). We assessed whether dung beetles with different traits related to feeding, nesting and body size differed in the number of mammal species found in their iDNA. We also tested differences among four killing solutions in preserving the iDNA and compared the effectiveness of each mini barcode to recover mammals. We identified a total of 50 mammal OTUs (operational taxonomic unit), including terrestrial and arboreal species from 10 different orders. We found that at least one mammal-matching sequence was obtained from 70% of the dung beetle specimens. The number of mammal OTUs obtained did not vary with dung beetle traits as well as between the killing solutions. The 16SrRNA mini-barcode recovered a higher number of mammal OTUs than 12SrRNA, although both sets were partly non-overlapping. Thus, the complete mammal diversity may not be achieved by using only one of them. This study refines the methodology for routine assessment of tropical mammal communities via dung beetle 'samplers' and its universal applicability independently of the species traits of local beetle communities.
Collapse
Affiliation(s)
- Bruno H Saranholi
- Department of Life Sciences, Imperial College London, Ascot, UK
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, Brazil
| | - Filipe M França
- School of Biological Sciences, University of Bristol, Bristol, UK
- Graduate Program in Ecology, Biological Sciences Institute, Federal University of Pará, Belém, Pará, Brazil
| | - Alfried P Vogler
- Department of Life Sciences, Imperial College London, Ascot, UK
- Department of Life Sciences, Natural History Museum, London, UK
| | - Jos Barlow
- Lancaster Environment Centre, Lancaster University, Lancaster, UK
| | - Fernando Z Vaz de Mello
- Departamento de Biologia e Zoologia, Universidade Federal de Mato Grosso, Instituto de Biociências, Cuiabá, MT, Brazil
| | - Maria E Maldaner
- Programa de Pós-Graduação Em Ecologia e Conservação da Biodiversidade (PPGECB), Universidade Federal de Mato Grosso (UFMT), Cuiabá, Brazil
| | - Edrielly Carvalho
- Programa de Pós-Graduação Em Entomologia, Instituto Nacional de Pesquisas da Amazônia, INPA, Manaus, Amazonas, Brazil
| | - Carla C Gestich
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, Brazil
| | - Benjamin Howes
- Department of Life Sciences, Imperial College London, Ascot, UK
| | | | - Pedro M Galetti
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, Brazil
| |
Collapse
|
36
|
Chiba M, Chiba S. Hidden invasiveness of non-native Schlegel's Japanese gecko (Reptilia: Squamata: Gekkonidae) and three-way competition among natives and non-natives in Japan. Mol Ecol 2024; 33:e17420. [PMID: 38837546 DOI: 10.1111/mec.17420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Revised: 04/18/2024] [Accepted: 04/25/2024] [Indexed: 06/07/2024]
Abstract
In this study, we investigated the invasiveness of Gekko japonicus, a prevalent gecko species in Japan and an ancient non-native species, focusing on its competition with both the undescribed endemic Gekko species (referred to as Nishiyamori in Japanese) and G. hokouensis. These species are co-distributed with G. japonicus, leading us to hypothesize that G. japonicus was invasive upon its initial introduction. We employed niche analysis and population genetics through ddRAD-seq to assess the historical invasiveness of G. japonicus by comparing regions with and without interspecies competition. Our niche analysis across the Goto Islands, Hiradojima Island (colonized by G. japonicus) and the Koshikishima Islands (not colonized by G. japonicus) indicated that endemic Gekko sp. alter their microhabitat usage in response to invasions by other gecko species, despite having similar suitable habitats and microhabitat preferences. Population genetic analysis revealed significant population declines in Gekko sp. within areas of introduced competition, in contrast to stable populations in areas without such competition. These findings suggest a tripartite competitive relationship among the gecko species, with G. japonicus and G. hokouensis invasions restricting the distribution of the endemic Gekko sp. Consequently, G. japonicus may have historically acted as an invasive species. Acknowledging the historical dynamics of current biodiversity is crucial for addressing complex ecological issues and making informed conservation decisions.
Collapse
Affiliation(s)
- Minoru Chiba
- Graduate School of Life Sciences, Tohoku University, Sendai, Japan
- Doctoral Institute for Evidence Based Policy, Inc., Tokyo, Japan
| | - Satoshi Chiba
- Graduate School of Life Sciences, Tohoku University, Sendai, Japan
- Center for Northeast Asian Studies, Tohoku University, Sendai, Japan
| |
Collapse
|
37
|
Josić D, Çoraman E, Waurick I, Franzenburg S, Ancillotto L, Bajić B, Budinski I, Dietz C, Görföl T, Hayden Bofill SI, Presetnik P, Russo D, Spada M, Zrnčić V, Blom MPK, Mayer F. Cryptic hybridization between the ancient lineages of Natterer's bat (Myotis nattereri). Mol Ecol 2024; 33:e17411. [PMID: 38785347 DOI: 10.1111/mec.17411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 04/16/2024] [Accepted: 05/08/2024] [Indexed: 05/25/2024]
Abstract
Studying hybrid zones that form between morphologically cryptic taxa offers valuable insights into the mechanisms of cryptic speciation and the evolution of reproductive barriers. Although hybrid zones have long been the focus of evolutionary studies, the awareness of cryptic hybrid zones increased recently due to rapidly growing evidence of biological diversity lacking obvious phenotypic differentiation. The characterization of cryptic hybrid zones with genome-wide analysis is in its early stages and offers new perspectives for studying population admixture and thus the impact of gene flow. In this study, we investigate the population genomics of the Myotis nattereri complex in one of its secondary contact zones, where a putative hybrid zone is formed between two of its cryptic lineages. By utilizing a whole-genome shotgun sequencing approach, we aim to characterize this cryptic hybrid zone in detail. Demographic analysis suggests that the cryptic lineages diverged during the Pliocene, c. 3.6 million years ago. Despite this ancient separation, the populations in the contact zone exhibit mitochondrial introgression and a considerable amount of mixing in nuclear genomes. The genomic structure of the populations corresponds to geographic locations and the genomic admixture changes along a geographic gradient. These findings suggest that there is no effective hybridization barrier between both lineages, nevertheless, their population structure is shaped by dispersal barriers. Our findings highlight how such deeply diverged cryptic lineages can still readily hybridize in secondary contact.
Collapse
Affiliation(s)
- Darija Josić
- Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Berlin, Germany
| | - Emrah Çoraman
- Department of Ecology and Evolution, Eurasia Institute of Earth Sciences, Istanbul Technical University, İstanbul, Türkiye
| | - Isabelle Waurick
- Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Berlin, Germany
| | - Sören Franzenburg
- IKMB, Institute of Clinical Molecular Biology, University of Kiel, Kiel, Germany
| | - Leonardo Ancillotto
- Laboratory of Animal Ecology and Evolution (AnEcoEvo), Dipartimento di Agraria, Universita degli Studi di Napoli Federico II, Portici, Italy
| | - Branka Bajić
- Department of Genetic Research, Institute for Biological Research 'Siniša Stanković' - National Institute of Republic of Serbia, University of Belgrade, Belgrade, Serbia
| | - Ivana Budinski
- Department of Genetic Research, Institute for Biological Research 'Siniša Stanković' - National Institute of Republic of Serbia, University of Belgrade, Belgrade, Serbia
| | | | - Tamás Görföl
- Department of Zoology, Hungarian Natural History Museum, Budapest, Hungary
- National Laboratory of Virology, University of Pécs, Pécs, Hungary
| | - Sofia I Hayden Bofill
- Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Berlin, Germany
| | - Primož Presetnik
- Centre for Cartography of Fauna and Flora, Miklavž na Dravskem Polju, Slovenia
| | - Danilo Russo
- Laboratory of Animal Ecology and Evolution (AnEcoEvo), Dipartimento di Agraria, Universita degli Studi di Napoli Federico II, Portici, Italy
| | - Martina Spada
- Dipartimento Ambiente-Salute-Sicurezza, Universita degli Studi dell'Insubria, Varese, Italy
| | - Vida Zrnčić
- Croatian Biospeleogical Society Zagreb, Zagreb, Croatia
| | - Mozes P K Blom
- Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Berlin, Germany
| | - Frieder Mayer
- Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Berlin, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Berlin, Germany
| |
Collapse
|
38
|
Allison PF, Pickich ET, Barnett ZC, Garrick RC. DNA barcoding is currently unreliable for species identification in most crayfishes. Ecol Evol 2024; 14:e70050. [PMID: 39041008 PMCID: PMC11260883 DOI: 10.1002/ece3.70050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Revised: 07/06/2024] [Accepted: 07/08/2024] [Indexed: 07/24/2024] Open
Abstract
DNA barcoding is commonly used for species identification. Despite this, there has not been a comprehensive assessment of the utility of DNA barcoding in crayfishes (Decapoda: Astacidea). Here we examined the extent to which local barcoding gaps (used for species identification) and global barcoding gaps (used for species discovery) exist among crayfishes, and whether global gaps met a previously suggested 10× threshold (mean interspecific difference being 10× larger than mean intra specific difference). We examined barcoding gaps using publicly available mitochondrial COI sequence data from the National Center for Biotechnology Information's nucleotide database. We created two versions of the COI datasets used for downstream analyses: one focused on the number of unique haplotypes (N H) per species, and another that focused on total number of sequences (N S; i.e., including redundant haplotypes) per species. A total of 81 species were included, with 58 species and five genera from the family Cambaridae and 23 species from three genera from the family Parastacidae. Local barcoding gaps were present in only 30 species (20 Cambaridae and 10 Parastacidae species). We detected global barcoding gaps in only four genera (Cambarus, Cherax, Euastacus, and Tenuibranchiurus), which were all below (4.2× to 5.2×) the previously suggested 10× threshold. We propose that a ~5× threshold would be a more appropriate working hypothesis for species discovery. While the N H and N S datasets yielded largely similar results, there were some discrepant inferences. To understand why some species lacked a local barcoding gap, we performed species delimitation analyses for each genus using the N H dataset. These results suggest that current taxonomy in crayfishes may be inadequate for the majority of examined species, and that even species with local barcoding gaps present may be in need of taxonomic revisions. Currently, the utility of DNA barcoding for species identification and discovery in crayfish is quite limited, and caution should be exercised when mitochondrial-based approaches are used in place of taxonomic expertise. Assessment of the evidence for local and global barcoding gaps is important for understanding the reliability of molecular species identification and discovery, but outcomes are dependent on the current state of taxonomy. As this improves (e.g., via resolving species complexes, possibly elevating some subspecies to the species-level status, and redressing specimen misidentifications in natural history and other collections), so too will the utility of DNA barcoding.
Collapse
Affiliation(s)
| | - Emily T. Pickich
- Department of BiologyUniversity of MississippiUniversityMississippiUSA
| | - Zanethia C. Barnett
- Southern Research StationUSDA Forest Service, Center for Bottomland Hardwoods ResearchClemsonSouth CarolinaUSA
| | - Ryan C. Garrick
- Department of BiologyUniversity of MississippiUniversityMississippiUSA
| |
Collapse
|
39
|
Loeslakwiboon K, Li HH, Tsai S, Wen ZH, Lin C. Effects of chilling and cryoprotectants on glycans in shrimp embryos. Cryobiology 2024; 116:104930. [PMID: 38871207 DOI: 10.1016/j.cryobiol.2024.104930] [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: 03/04/2024] [Revised: 05/30/2024] [Accepted: 06/10/2024] [Indexed: 06/15/2024]
Abstract
Glycans are carbohydrates present in every organism that bind to specific molecules such as lectins, a diverse group of proteins. Glycans are vital to cell proliferation and protein trafficking. In addition, embryogenesis is a critical phase in the development of marine organisms. This study investigated the effects of chilling and cryoprotective agents (CPAs) on glycans in the embryos of Stenopus hispidus. The glycan profiles of embryos of S. hispidus at the heartbeat stage were analyzed using lectin arrays. The results of analyses revealed that mannose was the most abundant glycan in the S. hispidus embryos; mannose is crucial to cell proliferation, providing the energy required for embryonic growth. Additionally, the results reveled that chilling altered the content of several glycans, including fucose and Gla-GlcNAc. Chilling may promote monosaccharide accumulation, facilitating osmotic regulation of cells and signal molecules to aid S. hispidus embryos in adapting to cold conditions. Changes were also observed in the lectins NPA, orysata, PALa, ASA, discoidin II, discoidin I, UDA, PA-IIL, and PHA-P after the samples were treated with different CPAs. DMSO may minimize cell damage during exposure to chilling by preserving cell structures, membrane properties, and functions. The present study is the first to investigate the profiles and functions of glycans in shrimp embryos subjected to low-temperature injuries. This study enhances the understanding of cell reproduction during embryogenesis and provides valuable information for the study of glycans in embryos.
Collapse
Affiliation(s)
- Kanokpron Loeslakwiboon
- Department of Marine Biotechnology and Resources, National Sun Yat-sen University, Kaohsiung, Taiwan; National Museum of Marine Biology & Aquarium, Pingtung, Taiwan; Graduate Institute of Marine Biology, National Dong Hwa University, Pingtung, Taiwan
| | - Hsing-Hui Li
- Department of Marine Biotechnology and Resources, National Sun Yat-sen University, Kaohsiung, Taiwan; National Museum of Marine Biology & Aquarium, Pingtung, Taiwan
| | - Sujune Tsai
- Department of Post Modern Agriculture, Mingdao University, Chang Hua, Taiwan
| | - Zhi-Hong Wen
- Department of Marine Biotechnology and Resources, National Sun Yat-sen University, Kaohsiung, Taiwan
| | - Chiahsin Lin
- National Museum of Marine Biology & Aquarium, Pingtung, Taiwan; Graduate Institute of Marine Biology, National Dong Hwa University, Pingtung, Taiwan.
| |
Collapse
|
40
|
Hao Z, Jiang X, Pan L, Guo J, Chen Y, Li J, Liu B, Guo A, Luo L, Jia R. The complete mitochondrial genome of Pontederia crassipes: using HiFi reads to investigate genome recombination and gene transfer from chloroplast genome. FRONTIERS IN PLANT SCIENCE 2024; 15:1407309. [PMID: 39006960 PMCID: PMC11240117 DOI: 10.3389/fpls.2024.1407309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Accepted: 06/12/2024] [Indexed: 07/16/2024]
Abstract
Water hyacinth (Pontederia crassipes Mart.) is a monocotyledonous aquatic plant renowned for its rapid growth, extensive proliferation, biological invasiveness, and ecological resilience to variations in pH, nutrients, and temperature. The International Union for Conservation of Nature (IUCN) has listed P. crassipes among the top 100 invasive species. However, comprehensive genomic information, particularly concerning its mitochondrial genome (mitogenome), remains surprisingly limited. In this study, the complete mitogenome of P. crassipes was analyzed using bioinformatics approaches. The mitogenome is 399,263 bp long and contains 38 protein-coding genes (PCGs), 24 tRNA genes, and 3 rRNA genes. Sequence analysis revealed that the complete mitogenome of the species contains 3,289 dispersed repeats, and 765 RNA editing sites in protein-coding genes. The P. crassipes mitogenome possessed un-conserved structures, including extensive sequence transfer between its chloroplasts and mitochondria. Our study on the mitogenome of P. crassipes offers critical insights into its evolutionary patterns and phylogenetic relationships with related taxa. This research enhances our understanding of this invasive species, known for its significant biomass and rapid overgrowth in aquatic environments.
Collapse
Affiliation(s)
- Zhigang Hao
- Sanya Research Institution, Chinese Academy of Tropical Agriculture Sciences/Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Sanya, Hainan, China
- Hainan Seed Industry Laboratory, Sanya, Hainan, China
- Department of Plant Pathology, China Agricultural University, Beijing, China
- Sanya Institute of China Agricultural University, Sanya, China
| | - Xiaoqi Jiang
- Sanya Research Institution, Chinese Academy of Tropical Agriculture Sciences/Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Sanya, Hainan, China
| | - Lei Pan
- CAIQ Center for Biosafety in Sanya, Sanya, Hainan, China
| | - Jingyuan Guo
- Sanya Research Institution, Chinese Academy of Tropical Agriculture Sciences/Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Sanya, Hainan, China
| | - Yi Chen
- Sanya Research Institution, Chinese Academy of Tropical Agriculture Sciences/Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Sanya, Hainan, China
| | - Jianqiang Li
- Department of Plant Pathology, China Agricultural University, Beijing, China
- Sanya Institute of China Agricultural University, Sanya, China
| | - Biao Liu
- Ministry of Ecology and Environment, Nanjing Institute of Environmental Sciences, Nanjing, China
| | - Anping Guo
- Sanya Research Institution, Chinese Academy of Tropical Agriculture Sciences/Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Sanya, Hainan, China
| | - Laixin Luo
- Department of Plant Pathology, China Agricultural University, Beijing, China
- Sanya Institute of China Agricultural University, Sanya, China
| | - Ruizong Jia
- Sanya Research Institution, Chinese Academy of Tropical Agriculture Sciences/Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Sanya, Hainan, China
| |
Collapse
|
41
|
Kartavtsev YP, Masalkova NA. Structure, Evolution, and Mitochondrial Genome Analysis of Mussel Species (Bivalvia, Mytilidae). Int J Mol Sci 2024; 25:6902. [PMID: 39000014 PMCID: PMC11241113 DOI: 10.3390/ijms25136902] [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: 04/30/2024] [Revised: 06/13/2024] [Accepted: 06/17/2024] [Indexed: 07/14/2024] Open
Abstract
Based on the nucleotide sequences of the mitochondrial genome (mitogenome) of specimens taken from two mussel species (Arcuatula senhousia and Mytilus coruscus), an investigation was performed by means of the complex approaches of the genomics, molecular phylogenetics, and evolutionary genetics. The mitogenome structure of studied mussels, like in many other invertebrates, appears to be much more variable than in vertebrates and includes changing gene order, duplications, and deletions, which were most frequent for tRNA genes; the mussel species' mitogenomes also have variable sizes. The results demonstrate some of the very important properties of protein polypeptides, such as hydrophobicity and its determination by the purine and pyrimidine nucleotide ratio. This fact might indirectly indicate the necessity of purifying natural selection for the support of polypeptide functionality. However, in accordance with the widely accepted and logical concept of natural cutoff selection for organisms living in nature, which explains its action against deleterious nucleotide substitutions in the nonsynonymous codons (mutations) and its holding of the active (effective) macromolecules of the polypeptides in a population, we were unable to get unambiguous evidence in favor of this concept in the current paper. Here, the phylogeny and systematics of mussel species from one of the largest taxons of bivalve mollusks are studied, the family known as Mytilidae. The phylogeny for Mytilidae (order Mytilida), which currently has no consensus in terms of systematics, is reconstructed using a data matrix of 26-27 mitogenomes. Initially, a set of 100 sequences from GenBank were downloaded and checked for their gender: whether they were female (F) or male (M) in origin. Our analysis of the new data confirms the known drastic differences between the F/M mitogenome lines in mussels. Phylogenetic reconstructions of the F-lines were performed using the combined set of genetic markers, reconstructing only protein-coding genes (PCGs), only rRNA + tRNA genes, and all genes. Additionally, the analysis includes the usage of nucleotide sequences composed of other data matrices, such as 20-68 mitogenome sequences. The time of divergence from MRCA, estimated via BEAST2, for Mytilidae is close to 293 Mya, suggesting that they originate in the Silurian Period. From all these data, a consensus for the phylogeny of the subfamily of Mytilinae and its systematics is suggested. In particular, the long-debated argument on mussel systematics was resolved as to whether Mytilidae, and the subfamily of Mytilinae, are monophyletic. The topology signal, which was strongly resolved in this paper and in the literature, has refuted the theory regarding the monophyly of Mytilinae.
Collapse
Affiliation(s)
- Yuri Phedorovich Kartavtsev
- A.V. Zhirmunsky National Scientific Center of Marine Biology (NSCMB), Far Eastern Branch, Russian Academy of Sciences, 690041 Vladivostok, Russia
| | | |
Collapse
|
42
|
Yao Y, Shi Y, Feng K, Du J, Chang Y, Xue Y, Li W. The mitochondrial genome of Homoneura picta (Diptera: Lauxaniidae) and its phylogenetic analysis. Mitochondrial DNA B Resour 2024; 9:828-831. [PMID: 38919812 PMCID: PMC11198121 DOI: 10.1080/23802359.2024.2333560] [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: 09/15/2023] [Accepted: 03/15/2024] [Indexed: 06/27/2024] Open
Abstract
Homoneura picta belongs to the Homoneurinae subfamily of Lauxaniidae, and it is widely distributed and common in China. This study reports the newly sequenced mitochondrial genome of H. picta. The sequence is 15,469 bp long and contains 37 genes (13 protein-coding, 22 tRNA, and 2 rRNA genes) and a control region. The overall base composition is 38.4% for A, 37.7% for T, 14.1% for C, and 9.8% for G, with a bias toward A + T (76.1%). Phylogenetic analysis show that Homoneura is a sister genus of Cestrotus. We have successfully sequenced the mitochondrial genome of H. picta, which can be useful in investigating the phylogenetic status of Homoneurinae. Our results provide data for further studies of phylogeny in Diptera.
Collapse
Affiliation(s)
- Yao Yao
- College of Horticulture and Plant Protection, Henan University of Science and Technology, Luoyang, China
| | - Yedi Shi
- College of Horticulture and Plant Protection, Henan University of Science and Technology, Luoyang, China
| | - Keli Feng
- College of Horticulture and Plant Protection, Henan University of Science and Technology, Luoyang, China
| | - Jiaoyi Du
- College of Horticulture and Plant Protection, Henan University of Science and Technology, Luoyang, China
| | - Yiming Chang
- College of Horticulture and Plant Protection, Henan University of Science and Technology, Luoyang, China
| | - Yaoyao Xue
- College of Horticulture and Plant Protection, Henan University of Science and Technology, Luoyang, China
| | - Wenliang Li
- College of Horticulture and Plant Protection, Henan University of Science and Technology, Luoyang, China
| |
Collapse
|
43
|
Wei XL, Zhai YY, Wang K, Li Y, Hong B. The complete mitochondrial genome of a jujube geometrid, Sucra jujuba (Lepidoptera: Geometridae) and its phylogenetic analysis. Mitochondrial DNA B Resour 2024; 9:832-836. [PMID: 38919810 PMCID: PMC11198131 DOI: 10.1080/23802359.2024.2368219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Accepted: 06/10/2024] [Indexed: 06/27/2024] Open
Abstract
Sucra jujuba Chu, 1979 (Lepidoptera: Geometridae) is a major insect pest in jujube plantation. In this study, we have sequenced the complete mitochondrial genome of S. jujuba. The circular genome was 15,557 bp in length and contained 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), two ribosomal RNA genes (rRNAs), and one AT-rich region (GenBank accession no. MZ507574). The nucleotide composition was significantly biased (A, T, C, and G were 41.85%, 39.65%, 10.97%, and 7.53%, respectively) with A + T contents of 81.50%. The Bayesian phylogenetic analysis of the concatenated nucleotide sequences of 13 PCGs from 30 species in the subfamily Ennominae and two outgroup species was performed. The results indicated that S. jujuba was closely related to Amraica recursaria in the subfamily Ennominae.
Collapse
Affiliation(s)
- Xue-Lian Wei
- Department of Information Engineering, Xi’an Technology and Business College, Xi’an, China
| | - Ying-Yan Zhai
- Shaanxi Key Laboratory of Qinling Ecological Security, Bio-Agriculture Institute of Shaanxi, Shaanxi Academy of Sciences, Xi’an, China
| | - Kai Wang
- Shenmu Agricultural Technology and Promotion Center, Yulin, China
| | - Yang Li
- Chang’an University Journal Center, Chang’an University, Xi’an, China
| | - Bo Hong
- Shaanxi Key Laboratory of Qinling Ecological Security, Bio-Agriculture Institute of Shaanxi, Shaanxi Academy of Sciences, Xi’an, China
| |
Collapse
|
44
|
Nagao N, Hiraoka S, Mori T, Shimizu N, Kurabayashi A, Kambayashi C. The complete mitochondrial genome of a Biwa goby, Gymnogobius isaza (Tanaka, 1916). Mitochondrial DNA B Resour 2024; 9:837-840. [PMID: 38919808 PMCID: PMC11198123 DOI: 10.1080/23802359.2024.2368732] [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: 10/19/2023] [Accepted: 06/11/2024] [Indexed: 06/27/2024] Open
Abstract
We determined the complete mitochondrial DNA sequence of a Biwa goby, Gymnogobius isaza (Tanaka, 1916) using next-generation sequencing methods. The composition of its mitogenome is the same as that observed in most other vertebrates, comprising of 13 protein-coding genes, 22 tRNA genes, two rRNA genes, and two control regions. Our molecular phylogenetic analysis confirmed the close phylogenetic relationship between G. isaza and G. petschiliensis. This mitogenome information will be useful for distribution surveys using environmental DNA and the development of conservation strategies for this species.
Collapse
Affiliation(s)
- Nao Nagao
- Faculty of Bio-Science, Nagahama Institute of Bio-Science and Technology, Shiga, Japan
| | - Saki Hiraoka
- Faculty of Bio-Science, Nagahama Institute of Bio-Science and Technology, Shiga, Japan
| | - Tsuyoshi Mori
- Faculty of Bio-Science, Nagahama Institute of Bio-Science and Technology, Shiga, Japan
| | - Norio Shimizu
- Hiroshima University Museum, Higashihiroshima, Hiroshima, Japan
| | - Atsushi Kurabayashi
- Faculty of Bio-Science, Nagahama Institute of Bio-Science and Technology, Shiga, Japan
| | - Chiaki Kambayashi
- Faculty of Bio-Science, Nagahama Institute of Bio-Science and Technology, Shiga, Japan
- Graduate School of Science, Kyoto University, Kyoto, Japan
| |
Collapse
|
45
|
Zhao Y, Chen Z, Hu M, Liu H, Zhao H, Huang Y, Jiang M, Li S, Li G, Zhu C, Hu W, Luo D. Integrating Iso-seq and RNA-seq data for the reannotation of the greater amberjack genome. Sci Data 2024; 11:675. [PMID: 38909036 PMCID: PMC11193819 DOI: 10.1038/s41597-024-03495-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Accepted: 06/07/2024] [Indexed: 06/24/2024] Open
Abstract
The greater amberjack is a very important fishery species with high commercial value, and it is distributed worldwide. Transcriptome-based studies on S. dumerili have been limited by an inadequate reference genome and a lack of well-annotated full-length transcripts. In this study, a total of 12 tissues from juvenile and adult fish both sexes were collected for next-generation RNA sequencing (RNA-seq) and full-length isoform sequencing (Iso-seq). For Iso-seq, a total of 163,218, 149,716, and 189,169 high-quality unique transcript sequences were obtained, with an N50 of 5,441, 5,255, and 5,939, from juvenile, adult male and adult female S. dumerili, respectively. We integrated the Iso-seq and RNA-seq data to construct a comprehensive gene annotation and systematically profiled the dynamics of gene expression across the 12 tissues. Our gene models had greater detail and accuracy than those from NCBI and Ensembl, with more precise polyA locations. These resources serve as a foundation for functional genomic studies and provide valuable insights into the molecular mechanisms underlying the development, reproduction and commercial traits of amberjack.
Collapse
Affiliation(s)
- Yuanli Zhao
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Institute of Hydrobiology, The Innovative Academy of Seed Design, Hubei Hongshan Laboratory, Guangdong Laboratory for Lingnan Modern Agriculture, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Zonggui Chen
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Institute of Hydrobiology, The Innovative Academy of Seed Design, Hubei Hongshan Laboratory, Guangdong Laboratory for Lingnan Modern Agriculture, Chinese Academy of Sciences, Wuhan, 430072, China
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871, China
| | - Meidi Hu
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Institute of Hydrobiology, The Innovative Academy of Seed Design, Hubei Hongshan Laboratory, Guangdong Laboratory for Lingnan Modern Agriculture, Chinese Academy of Sciences, Wuhan, 430072, China
- Fisheries College, Ocean University of China, Qingdao, 266001, China
| | - Hairong Liu
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Institute of Hydrobiology, The Innovative Academy of Seed Design, Hubei Hongshan Laboratory, Guangdong Laboratory for Lingnan Modern Agriculture, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Haiping Zhao
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Institute of Hydrobiology, The Innovative Academy of Seed Design, Hubei Hongshan Laboratory, Guangdong Laboratory for Lingnan Modern Agriculture, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Yang Huang
- China Southern Marine Science and Engineering Guangdong Laboratory (Zhanjiang), Zhanjiang, 524025, China
- Fisheries College of Guangdong Ocean University, Guangdong Research Center on Reproductive Control and Breeding Technology of Indigenous Valuable Fish Species, Guangdong Provincial Key Laboratory of Aquatic Animal Disease Control and Healthy Culture, Zhanjiang, 524088, China
| | - Mouyan Jiang
- Fisheries College of Guangdong Ocean University, Guangdong Research Center on Reproductive Control and Breeding Technology of Indigenous Valuable Fish Species, Guangdong Provincial Key Laboratory of Aquatic Animal Disease Control and Healthy Culture, Zhanjiang, 524088, China
| | - Shengkang Li
- Guangdong Provincial Key Laboratory of Marine Biology, Shantou University, Shantou, 515063, China
| | - Guangli Li
- Fisheries College of Guangdong Ocean University, Guangdong Research Center on Reproductive Control and Breeding Technology of Indigenous Valuable Fish Species, Guangdong Provincial Key Laboratory of Aquatic Animal Disease Control and Healthy Culture, Zhanjiang, 524088, China
| | - Chunhua Zhu
- China Southern Marine Science and Engineering Guangdong Laboratory (Zhanjiang), Zhanjiang, 524025, China.
- Fisheries College of Guangdong Ocean University, Guangdong Research Center on Reproductive Control and Breeding Technology of Indigenous Valuable Fish Species, Guangdong Provincial Key Laboratory of Aquatic Animal Disease Control and Healthy Culture, Zhanjiang, 524088, China.
| | - Wei Hu
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Institute of Hydrobiology, The Innovative Academy of Seed Design, Hubei Hongshan Laboratory, Guangdong Laboratory for Lingnan Modern Agriculture, Chinese Academy of Sciences, Wuhan, 430072, China.
| | - Daji Luo
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Institute of Hydrobiology, The Innovative Academy of Seed Design, Hubei Hongshan Laboratory, Guangdong Laboratory for Lingnan Modern Agriculture, Chinese Academy of Sciences, Wuhan, 430072, China.
- Fisheries College, Ocean University of China, Qingdao, 266001, China.
| |
Collapse
|
46
|
He R, Wang S, Li Q, Wang Z, Mei Y, Li F. Phylogenomic analysis and molecular identification of true fruit flies. Front Genet 2024; 15:1414074. [PMID: 38974385 PMCID: PMC11224437 DOI: 10.3389/fgene.2024.1414074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Accepted: 05/30/2024] [Indexed: 07/09/2024] Open
Abstract
The family Tephritidae in the order Diptera, known as true fruit flies, are agriculturally important insect pests. However, the phylogenetic relationships of true fruit flies, remain controversial. Moreover, rapid identification of important invasive true fruit flies is essential for plant quarantine but is still challenging. To this end, we sequenced the genome of 16 true fruit fly species at coverage of 47-228×. Together with the previously reported genomes of nine species, we reconstructed phylogenetic trees of the Tephritidae using benchmarking universal single-copy ortholog (BUSCO), ultraconserved element (UCE) and anchored hybrid enrichment (AHE) gene sets, respectively. The resulting trees of 50% taxon-occupancy dataset for each marker type were generally congruent at 88% nodes for both concatenation and coalescent analyses. At the subfamily level, both Dacinae and Trypetinae are monophyletic. At the species level, Bactrocera dorsalis is more closely related to Bactrocera latifrons than Bactrocera tryoni. This is inconsistent with previous conclusions based on mitochondrial genes but consistent with recent studies based on nuclear data. By analyzing these genome data, we screened ten pairs of species-specific primers for molecular identification of ten invasive fruit flies, which PCR validated. In summary, our work provides draft genome data of 16 true fruit fly species, addressing the long-standing taxonomic controversies and providing species-specific primers for molecular identification of invasive fruit flies.
Collapse
Affiliation(s)
- Rong He
- State Key Laboratory of Rice Biology and Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Shuping Wang
- Technical Centre for Animal, Plant and Food Inspection and Quarantine, Shanghai Customs, Shanghai, China
| | - Qiang Li
- State Key Laboratory of Rice Biology and Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Zuoqi Wang
- State Key Laboratory of Rice Biology and Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Yang Mei
- State Key Laboratory of Rice Biology and Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Fei Li
- State Key Laboratory of Rice Biology and Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| |
Collapse
|
47
|
Zhang SY, Yan Q, Zhao J, Liu Y, Yao M. Distinct multitrophic biodiversity composition and community organization in a freshwater lake and a hypersaline lake on the Tibetan Plateau. iScience 2024; 27:110124. [PMID: 38957787 PMCID: PMC11217615 DOI: 10.1016/j.isci.2024.110124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Revised: 04/07/2024] [Accepted: 05/24/2024] [Indexed: 07/04/2024] Open
Abstract
Alpine lakes play pivotal roles in plateau hydrological processes but are highly sensitive to climate change, yet we lack comprehensive knowledge of their multitrophic biodiversity patterns. Here, we compared the biodiversity characteristics of diverse taxonomic groups across water depths and in surface sediments from a freshwater lake and a hypersaline lake on the northwestern Tibetan Plateau. Using multi-marker environmental DNA metabarcoding, we detected 134 cyanobacteria, 443 diatom, 1,519 invertebrate, and 28 vertebrate taxa. Each group had a substantially different community composition in the two lakes, and differences were also found between water and sediments within each lake. Cooccurrence network analysis revealed higher network complexity, lower modularity, and fewer negative cohesions in the hypersaline lake, suggesting that high salinity may destabilize ecological networks. Our results provide the first holistic view of Tibetan lake biodiversity under contrasting salinity levels and reveal structural differences in the ecological networks that may impact ecosystem resilience.
Collapse
Affiliation(s)
- Si-Yu Zhang
- School of Life Sciences, Peking University, Beijing 100871, China
- Institute of Ecology, College of Urban and Environmental Sciences, Peking University, Beijing 100871, China
| | - Qi Yan
- Center for Pan-Third Pole Environment, Lanzhou University, Lanzhou 730000, China
| | - Jindong Zhao
- School of Life Sciences, Peking University, Beijing 100871, China
- Institute of Ecology, College of Urban and Environmental Sciences, Peking University, Beijing 100871, China
| | - Yongqin Liu
- Center for Pan-Third Pole Environment, Lanzhou University, Lanzhou 730000, China
- State Key Laboratory of Tibetan Plateau Earth System, Resources and Environment (TPESRE), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 101408, China
| | - Meng Yao
- School of Life Sciences, Peking University, Beijing 100871, China
- Institute of Ecology, College of Urban and Environmental Sciences, Peking University, Beijing 100871, China
| |
Collapse
|
48
|
Jeong JS, Kim HK, Park JS, Hwang HS, Kim I. Complete mitochondrial genome of the European common barnacle Perforatus perforatus Bruguière, 1789 (balanomorpha: balanidae). Mitochondrial DNA B Resour 2024; 9:823-827. [PMID: 38911522 PMCID: PMC11191835 DOI: 10.1080/23802359.2024.2368727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Accepted: 06/11/2024] [Indexed: 06/25/2024] Open
Abstract
This study is the first to sequence the complete mitochondrial genome (mitogenome) of Perforatus perforatus Bruguière, 1789 (Balanomorpha: Balanidae). The 15,536-bp long P. perforatus mitogenome contained a typical set of animal mitochondrial genes, along with one control region. The P. perforatus mitogenome had an inverted gene block (trnP-ND4L-ND4-trnH-ND5-trnF) between trnS(gct) and trnT. This inverted gene block had been detected six species in three subfamilies of the Balanidae family (Balaninae, Acastinae and Megabalaninae), but our results show that it is also present in Concavinae, in which P. perforatus is included. The phylogenetic tree based on the concatenated sequences of the 13 protein-coding genes and two rRNA genes showed that P. perforatus is closely associated with Acasta sulcate and Balanus trigonus within Balanidae.
Collapse
Affiliation(s)
- Jun Seong Jeong
- Division of Genetic Resources, Honam National Institute of Biological Resources, Mokpo, Republic of Korea
| | - Hyun Kyong Kim
- Division of Zoology, Honam National Institute of Biological Resources, Mokpo, Republic of Korea
| | - Jeong Sun Park
- Department of Applied Biology, College of Agriculture and Life Sciences, Chonnam National University, Gwangju, Republic of Korea
| | - Hee-Seung Hwang
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Iksoo Kim
- Department of Applied Biology, College of Agriculture and Life Sciences, Chonnam National University, Gwangju, Republic of Korea
| |
Collapse
|
49
|
Hu Q, Luo Y, Li Q, Deng Z, Liu J. The complete chloroplast genome sequence of Ampelopsis delavayana Planchon. ex Franch 1886 (Vitaceae). Mitochondrial DNA B Resour 2024; 9:777-781. [PMID: 38911520 PMCID: PMC11191827 DOI: 10.1080/23802359.2024.2364753] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Accepted: 05/31/2024] [Indexed: 06/25/2024] Open
Abstract
Ampelopsis delavayana Planchon. ex Franch 1886 is a plant with significant pharmacological effects and ornamental importance. This research unveiled the complete chloroplast (cp) genome sequence of A. delavayana. The study highlights that the cp genome of A. delavayana possesses a distinct tetrameric structure spanning 162,497 base pairs, comprising a small single-copy (SSC) region of 18,902 base pairs, a large single-copy (LSC) region of 90,441 base pairs, and two inverted-repeat regions (IRs), each 26,577 base pairs in length. The GC content of the SSC, LSC, and IR regions of the genome was 31.80%, 35.16%, and 42.82%, respectively, culminating in an overall GC content of 37.27%. The genome comprised 130 genes, which included eight rRNAs, 36 tRNAs, and 86 protein-coding genes. Through phylogenetic analysis utilizing the maximum-likelihood method, it was established that A. delavayana was closely related to Ampelopsis glandulosa var. brevipedunculata, positioning it as a sister species. This report not only provides a scientific reference for understanding the phylogeny of the family Vitaceae but also enriches our genetic information of Ampelopsis.
Collapse
Affiliation(s)
- Qun Hu
- Hubei Key Laboratory of Biologic Resources Protection and Utilization (Hubei Minzu University), Enshi, PR China
- Guangdong Key Laboratory for Crop Germplasm Resources Preservation and Utilization, Agro-biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou, PR China
- Research Center for Germplasm Engineering of Characteristic Plant Resources in Enshi Prefecture (Hubei Minzu University), Enshi, PR China
| | - Yongjian Luo
- Guangdong Key Laboratory for Crop Germplasm Resources Preservation and Utilization, Agro-biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou, PR China
| | - Qing Li
- Guangdong Key Laboratory for Crop Germplasm Resources Preservation and Utilization, Agro-biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou, PR China
| | - Zhijun Deng
- Hubei Key Laboratory of Biologic Resources Protection and Utilization (Hubei Minzu University), Enshi, PR China
- Research Center for Germplasm Engineering of Characteristic Plant Resources in Enshi Prefecture (Hubei Minzu University), Enshi, PR China
| | - Jun Liu
- Guangdong Key Laboratory for Crop Germplasm Resources Preservation and Utilization, Agro-biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou, PR China
| |
Collapse
|
50
|
Rabbani G, Rasool F, Fatima M, Majeed MBB. Morphometric and molecular characterization of Channa marulius from Riverine system of Punjab, Pakistan. Mol Biol Rep 2024; 51:771. [PMID: 38900353 DOI: 10.1007/s11033-024-09689-x] [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: 02/16/2024] [Accepted: 05/30/2024] [Indexed: 06/21/2024]
Abstract
OBJECTIVE Channidae family, are major freshwater fish species amongst the local aquatic fauna of Pakistan, while, there is limited availability of local data on their molecular identification and phylogenetic analysis. METHODS Channa species were collected from four different geographical sites in the tertiary of Punjab province on the Indus and Chenab rivers of Pakistan. Morphometric records and molecular techniques were used to determine the intraspecific variations among populations of Channa marulius. Mitochondrial DNA was extracted from the flesh of C. marulius, while, COI gene was used for molecular identification and variation levels were estimated by using Principal Component Analysis. RESULTS Data recorded on the basis of morphometric parameters clearly divided the C. marulius of different locations into two distinct categories, which accounted for a cumulative variability of 97.6%. Non-significance (P < 0.05) among the C. marulius showed that it contains a unique control haplotype localized within the sub-population. The intra-species distance ranged from 0.000 to 0.001 for four different populations, in contrast, the sequences retrieved from the NCBI database exhibited a range span of 0.000-0.003, while, sequence diversity ranged from 0.000 to 0.006 for this intra-specific comparison. The cladogram was also constructed for C. marulius of different geographical locations for observation of phylogenetic relationship. The conclusion drawn from the phylogenetic analysis of C. marulius populations used in this study, contributes significantly to the understanding of genetic variations within populations of this species. The findings provide valuable insight to devise conservation strategies in fisheries management programs in Pakistan.
Collapse
Affiliation(s)
- Ghulam Rabbani
- Department of Fisheries and Aquaculture, University of Veterinary and Animal Sciences, Lahore, 54600, Pakistan
| | - Fayyaz Rasool
- Department of Zoology, University of Education Lahore, Faisalabad Campus, Lahore, 54600, Pakistan.
| | - Mahroze Fatima
- Department of Fisheries and Aquaculture, University of Veterinary and Animal Sciences, Lahore, 54600, Pakistan
| | - Muhammad Bilal Bin Majeed
- Department of Animal Breeding and Genetics, University of Veterinary and Animal Sciences, Lahore, 54600, Pakistan
| |
Collapse
|