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Sandoval-Castellanos E, Hare AJ, Lin AT, Dimopoulos EA, Daly KG, Geiger S, Mullin VE, Wiechmann I, Mattiangeli V, Lühken G, Zinovieva NA, Zidarov P, Çakırlar C, Stoddart S, Orton D, Bulatović J, Mashkour M, Sauer EW, Horwitz LK, Horejs B, Atici L, Özkaya V, Mullville J, Parker Pearson M, Mainland I, Card N, Brown L, Sharples N, Griffiths D, Allen D, Arbuckle B, Abell JT, Duru G, Mentzer SM, Munro ND, Uzdurum M, Gülçur S, Buitenhuis H, Gladyr E, Stiner MC, Pöllath N, Özbaşaran M, Krebs S, Burger J, Frantz L, Medugorac I, Bradley DG, Peters J. Ancient mitogenomes from Pre-Pottery Neolithic Central Anatolia and the effects of a Late Neolithic bottleneck in sheep ( Ovis aries). SCIENCE ADVANCES 2024; 10:eadj0954. [PMID: 38608027 PMCID: PMC11014441 DOI: 10.1126/sciadv.adj0954] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 03/11/2024] [Indexed: 04/14/2024]
Abstract
Occupied between ~10,300 and 9300 years ago, the Pre-Pottery Neolithic site of Aşıklı Höyük in Central Anatolia went through early phases of sheep domestication. Analysis of 629 mitochondrial genomes from this and numerous sites in Anatolia, southwest Asia, Europe, and Africa produced a phylogenetic tree with excessive coalescences (nodes) around the Neolithic, a potential signature of a domestication bottleneck. This is consistent with archeological evidence of sheep management at Aşıklı Höyük which transitioned from residential stabling to open pasturing over a millennium of site occupation. However, unexpectedly, we detected high genetic diversity throughout Aşıklı Höyük's occupation rather than a bottleneck. Instead, we detected a tenfold demographic bottleneck later in the Neolithic, which caused the fixation of mitochondrial haplogroup B in southwestern Anatolia. The mitochondrial genetic makeup that emerged was carried from the core region of early Neolithic sheep management into Europe and dominates the matrilineal diversity of both its ancient and the billion-strong modern sheep populations.
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Affiliation(s)
- Edson Sandoval-Castellanos
- Population Genomics Group, Department of Veterinary Sciences, LMU Munich, 82152 Martinsried, Germany
- Institute of Palaeoanatomy, Domestication Research and the History of Veterinary Medicine, LMU Munich, 80539 Munich, Germany
| | - Andrew J. Hare
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin D02 PN40, Ireland
| | - Audrey T. Lin
- The Palaeogenomics and Bio-archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford, UK
- Department of Anthropology, National Museum of Natural History, Smithsonian Institution, Washington, DC, 20560 USA
| | - Evangelos A. Dimopoulos
- The Palaeogenomics and Bio-archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford, UK
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Kevin G. Daly
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin D02 PN40, Ireland
- School of Agriculture and Food Science, University College Dublin, Dublin, Ireland
| | - Sheila Geiger
- Institute of Palaeoanatomy, Domestication Research and the History of Veterinary Medicine, LMU Munich, 80539 Munich, Germany
| | - Victoria E. Mullin
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin D02 PN40, Ireland
| | - Ingrid Wiechmann
- Institute of Palaeoanatomy, Domestication Research and the History of Veterinary Medicine, LMU Munich, 80539 Munich, Germany
| | - Valeria Mattiangeli
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin D02 PN40, Ireland
| | - Gesine Lühken
- Institute of Animal Breeding and Genetics, Justus Liebig University of Gießen, Ludwigstr. 21, 35390 Gießen, Germany
| | - Natalia A. Zinovieva
- L.K. Ernst Federal Research Centre for Animal Husbandry, Dubrovitsy, Podolsk, Moscow Region, Russia
| | - Petar Zidarov
- Institute of Prehistory, Early History and Medieval Archaeology, Tübingen University, Tübingen, Germany
| | - Canan Çakırlar
- Institute of Archaeology, University of Groningen, 9712 ER Groningen, Netherlands
| | - Simon Stoddart
- Magdalene College, University of Cambridge, Cambridge CB3 0AG, UK
| | - David Orton
- BioArCh, Department of Archaeology, University of York, York YO10 5NG, UK
| | - Jelena Bulatović
- Department of Historical Studies, University of Gothenburg, BOX 200, 40530 Gothenburg, Sweden
| | - Marjan Mashkour
- Unité Archéozoologie, Archéobotanique, Sociétés Pratiques et Environnements (AASPE), CNRS, Muséum National d’Histoire Naturelle, 75020 Paris, France
| | - Eberhard W. Sauer
- School of History, Classics and Archaeology, University of Edinburgh, Old Medical School, Teviot Place, Edinburgh EH8 9AG, UK
| | - Liora Kolska Horwitz
- National Natural History Collections, Faculty of Life Sciences, The Hebrew University, Jerusalem, Israel
| | - Barbara Horejs
- OeAI, Austrian Academy of Sciences and HEAS, University of Vienna, Vienna, Austria
| | - Levent Atici
- Department of Anthropology, University of Nevada, Las Vegas, NV 89154, USA
| | - Vecihi Özkaya
- Department of Archaeology, Dicle University, Diyarbakir, Türkiye
| | - Jacqui Mullville
- School of History, Archaeology and Religion, Cardiff University, Cardiff CF10 3EU, UK
| | | | - Ingrid Mainland
- The University of the Highlands and Islands Orkney, Kirkwall, UK
| | - Nick Card
- The University of the Highlands and Islands Orkney, Kirkwall, UK
| | | | - Niall Sharples
- School of History, Archaeology and Religion, Cardiff University, Cardiff CF10 3EU, UK
| | - David Griffiths
- University of Oxford, OUDCE, Rewley House, Oxford OX1 2JA, UK
| | - David Allen
- Hampshire Cultural Trust, Chilcomb House, Winchester, SO23 8RB, UK
| | - Benjamin Arbuckle
- Department of Anthropology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Jordan T. Abell
- Department of Geosciences, University of Arizona, Tucson, AZ 85721, USA
| | - Güneş Duru
- Department of Archaeology, Mimar Sinan Fine Arts University, 34381 Şişli/İstanbul, Türkiye
| | - Susan M. Mentzer
- Senckenberg Centre for Human Evolution and Palaeoenvironment, Institute for Archaeological Sciences, Department of Geosciences, Tübingen University, 72074 Tübingen, Germany
| | - Natalie D. Munro
- Department of Anthropology, University of Connecticut, Storrs, CT 06269, USA
| | - Melis Uzdurum
- Department of Archaeology, Ondokuz Mayıs University, 55270 Atakum/Samsun, Türkiye
| | - Sevil Gülçur
- Prehistory Department, Faculty of Letters, Istanbul University, 34134 Istanbul, Türkiye
| | | | - Elena Gladyr
- L.K. Ernst Federal Research Centre for Animal Husbandry, Dubrovitsy, Podolsk, Moscow Region, Russia
| | - Mary C. Stiner
- School of Anthropology, University of Arizona, Tucson, AZ 85721, USA
| | - Nadja Pöllath
- Bavarian Natural History Collections, State Collection of Palaeoanatomy Munich, 80333 Munich, Germany
- ArchaeoBioCenter, LMU Munich, 80539 Munich, Germany
| | - Mihriban Özbaşaran
- Prehistory Department, Faculty of Letters, Istanbul University, 34134 Istanbul, Türkiye
| | - Stefan Krebs
- Laboratory for Functional Genome Analysis (LAFUGA), Gene Center, LMU Munich, Feodor-Lynen-Straße 25, 81377 Munich, Germany
| | - Joachim Burger
- Institute of Organismic and Molecular Evolution (iomE), Johannes Gutenberg University Mainz, 55128 Mainz, Germany
| | - Laurent Frantz
- Palaeogenomics Group, Institute of Palaeoanatomy, Domestication Research and the History of Veterinary Medicine, LMU Munich, 80539 Munich, Germany
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK
| | - Ivica Medugorac
- Population Genomics Group, Department of Veterinary Sciences, LMU Munich, 82152 Martinsried, Germany
- ArchaeoBioCenter, LMU Munich, 80539 Munich, Germany
| | - Daniel G. Bradley
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin D02 PN40, Ireland
| | - Joris Peters
- Institute of Palaeoanatomy, Domestication Research and the History of Veterinary Medicine, LMU Munich, 80539 Munich, Germany
- Bavarian Natural History Collections, State Collection of Palaeoanatomy Munich, 80333 Munich, Germany
- ArchaeoBioCenter, LMU Munich, 80539 Munich, Germany
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202
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Zhao R, Li H, Wu G, Wang YF. Codon usage bias analysis in the mitochondrial genomes of five Rhingia Scopoli (Diptera, Syrphidae, Eristalinae) species. Gene 2024; 917:148466. [PMID: 38615984 DOI: 10.1016/j.gene.2024.148466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2024] [Revised: 03/26/2024] [Accepted: 04/11/2024] [Indexed: 04/16/2024]
Abstract
This study presents the sequencing and annotation of mitochondrial genomes from five Rhingia species of the family Syrphidae, focusing on codon bias. Each species possessed 22 tRNAs genes, 13 protein-coding genes, 2 rRNAs genes, and a control region, without any observed gene rearrangements. Nucleotide composition analysis revealed a higher AT content compared with GC content, indicating AT enrichment. Neutrality plot, Parity rule 2 bias, and effective number of codons plot analyses collectively indicated that natural selection primarily influences the codon usage bias in the five Rhingia species. Relative synonymous codon usage analysis identified the optimal codons for Rhingia binotata, R. fromosana, R. campestris, R. louguanensis, and R. xanthopoda as 10, 14, 10, 11, and 12, respectively, all ending with A/U and exhibiting AT preference. Phylogenetic analysis, based on maximum likelihood and Bayesian inference methods applied to three datasets, confirmed the monophyly of Rhingia. In conclusion, this research establishes a foundation for understanding the phylogenetic evolution and codon usage patterns in Rhingia, offering valuable for future studies.
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Affiliation(s)
- Rui Zhao
- Shaanxi Key Laboratory of Bio-Resources, State Key Laboratory of Biological Resources and Ecological Environment of Qinling-Bashan, Qinling-Bashan Mountains Bioresources Comprehensive Development C.I.C., School of Biological Science & Engineering, Shaanxi University of Technology, Hanzhong, Shaanxi, China
| | - Hu Li
- Shaanxi Key Laboratory of Bio-Resources, State Key Laboratory of Biological Resources and Ecological Environment of Qinling-Bashan, Qinling-Bashan Mountains Bioresources Comprehensive Development C.I.C., School of Biological Science & Engineering, Shaanxi University of Technology, Hanzhong, Shaanxi, China.
| | - Gang Wu
- Shaanxi Key Laboratory of Bio-Resources, State Key Laboratory of Biological Resources and Ecological Environment of Qinling-Bashan, Qinling-Bashan Mountains Bioresources Comprehensive Development C.I.C., School of Biological Science & Engineering, Shaanxi University of Technology, Hanzhong, Shaanxi, China
| | - Yi-Fan Wang
- Shaanxi Key Laboratory of Bio-Resources, State Key Laboratory of Biological Resources and Ecological Environment of Qinling-Bashan, Qinling-Bashan Mountains Bioresources Comprehensive Development C.I.C., School of Biological Science & Engineering, Shaanxi University of Technology, Hanzhong, Shaanxi, China
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203
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Morris DR, McWhorter TJ, Boardman WSJ, Simpson G, Wentzel J, Coetzee J, Moodley Y. Unravelling the maternal evolutionary history of the African leopard ( Panthera pardus pardus). PeerJ 2024; 12:e17018. [PMID: 38618571 PMCID: PMC11016244 DOI: 10.7717/peerj.17018] [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: 09/18/2023] [Accepted: 02/06/2024] [Indexed: 04/16/2024] Open
Abstract
The African leopard (Panthera pardus pardus) has lost a significant proportion of its historical range, notably in north-western Africa and South Africa. Recent studies have explored the genetic diversity and population structure of African leopards across the continent. A notable genetic observation is the presence of two divergent mitochondrial lineages, PAR-I and PAR-II. Both lineages appeared to be distributed widely, with PAR-II frequently found in southern Africa. Until now, no study has attempted to date the emergence of either lineage, assess haplotype distribution, or explore their evolutionary histories in any detail. To investigate these underappreciated questions, we compiled the largest and most geographically representative leopard data set of the mitochondrial NADH-5 gene to date. We combined samples (n = 33) collected in an altitudinal transect across the Mpumalanga province of South Africa, where two populations of leopard are known to be in genetic contact, with previously published sequences of African leopard (n = 211). We estimate that the maternal PAR-I and PAR-II lineages diverged approximately 0.7051 (0.4477-0.9632) million years ago (Ma). Through spatial and demographic analyses, we show that while PAR-I underwent a mid-Pleistocene population expansion resulting in several closely related haplotypes with little geographic structure across much of its range, PAR-II remained at constant size and may even have declined slightly in the last 0.1 Ma. The higher genetic drift experienced within PAR-II drove a greater degree of structure with little haplotype sharing and unique haplotypes in central Africa, the Cape, KwaZulu-Natal and the South African Highveld. The phylogeographic structure of PAR-II, with its increasing frequency southward and its exclusive occurrence in south-eastern South Africa, suggests that this lineage may have been isolated in South Africa during the mid-Pleistocene. This hypothesis is supported by historical changes in paleoclimate that promoted intense aridification around the Limpopo Basin between 1.0-0.6 Ma, potentially reducing gene flow and promoting genetic drift. Interestingly, we ascertained that the two nuclear DNA populations identified by a previous study as East and West Mpumalanga correspond to PAR-I and PAR-II, respectively, and that they have come into secondary contact in the Lowveld region of South Africa. Our results suggest a subdivision of African leopard mtDNA into two clades, with one occurring almost exclusively in South Africa, and we identify the potential environmental drivers of this observed structure. We caution that our results are based on a single mtDNA locus, but it nevertheless provides a hypothesis that can be further tested with a dense sample of nuclear DNA data, preferably whole genomes. If our interpretation holds true, it would provide the first genetic explanation for the smaller observed size of leopards at the southernmost end of their range in Africa.
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Affiliation(s)
- Declan R. Morris
- School of Animal and Veterinary Sciences, The University of Adelaide, Roseworthy, South Australia, Australia
| | - Todd J. McWhorter
- School of Animal and Veterinary Sciences, The University of Adelaide, Roseworthy, South Australia, Australia
| | - Wayne S. J. Boardman
- School of Animal and Veterinary Sciences, The University of Adelaide, Roseworthy, South Australia, Australia
| | - Gregory Simpson
- Department of Wildlife Studies, Faculty of Veterinary of Science, University of Pretoria, Onderstepoort, Gauteng, South Africa
| | - Jeanette Wentzel
- Department of Wildlife Studies, Faculty of Veterinary of Science, University of Pretoria, Onderstepoort, Gauteng, South Africa
- Department of Veterinary Tropical Diseases, Hans Hoheisen Wildlife Research Station, University of Pretoria, Onderstepoort, Gauteng, South Africa
| | - Jannie Coetzee
- Mpumalanga Tourism and Parks Agency, Nelspruit, Mpumalanga, South Africa
| | - Yoshan Moodley
- Department of Biological Sciences, University of Venda, Thohoyandou, Limpopo, South Africa
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204
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Li Y, Ru B, Zhang Y, Wan D. The complete mitochondrial genome of Hypsipetes amaurotis (Passeriformes: Pycnonotidae). Mitochondrial DNA B Resour 2024; 9:483-487. [PMID: 38617815 PMCID: PMC11011232 DOI: 10.1080/23802359.2024.2338266] [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: 11/27/2023] [Accepted: 03/28/2024] [Indexed: 04/16/2024] Open
Abstract
The brown-eared bulbul (Hypsipetes amaurotis) is a medium-sized songbird native to East Asia and characterized by its prominent reddish-brown ear-coverts. Previous studies on it have primarily been from the taxonomic and morphological aspects, with limited research in the realm of molecular biology. In this study, we sequenced and annotated the complete mitochondrial genome of H. amaurotis, which was the first reported complete mitogenome of the genus Hypsipetes. The mitogenome of H. amaurotis is 17,871 bp in length and was predicted to encode 37 typical mitochondrial genes, including 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), two ribosomal RNA genes (rRNAs). Specifically, this mitogenome contains two D-loop control regions that are of similar length and sequencing pattern. A total of 8 Pycnonotidae and six outgroup taxa were used to determine the phylogenetic placement with two methods: Maximum Likelihood Approximation (IQ-TREE) and Bayesian inference (MrBayes). Our findings reveal that H. amaurotis is phylogenetically closely related to Ixos mcclellandii. The outcomes are generally consistent with the phylogenetic trees constructed in previous studies. The data gathered from this research provides valuable insights for future genomic investigations into the evolution, ecology, and conservation of this species.
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Affiliation(s)
- Yanze Li
- School of Life Sciences, Liaoning University, Liaoning, China
| | - Bingyi Ru
- School of Life Sciences, Liaoning University, Liaoning, China
| | - Yuan Zhang
- School of Life Sciences, Liaoning University, Liaoning, China
| | - Dongmei Wan
- School of Life Sciences, Liaoning University, Liaoning, China
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205
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Shah B, Hassan MA, Xie B, Wu K, Naveed H, Yan M, Dietrich CH, Duan Y. Mitogenomic Analysis and Phylogenetic Implications for the Deltocephaline Tribe Chiasmini (Hemiptera: Cicadellidae: Deltocephalinae). INSECTS 2024; 15:253. [PMID: 38667383 PMCID: PMC11050438 DOI: 10.3390/insects15040253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 03/26/2024] [Accepted: 04/02/2024] [Indexed: 04/28/2024]
Abstract
The grassland leafhopper tribe Chiasmini (Cicadellidae: Deltocephalinae) presently comprises 324 described species worldwide, with the highest species diversity occurring in the Nearctic region but a greater diversity of genera occurring in the Old World. In China, this tribe comprises 39 described species in 11 genera, but the fauna remains understudied. The complete mitogenomes of three species of this tribe have been sequenced previously. In order to better understand the phylogenetic position of Chiasmini within the subfamily Deltocephalinae and to investigate relationships among Chiasmini genera and species, we sequenced and analyzed the complete mitogenomes of 13 species belonging to seven genera from China. Comparison of the newly sequenced mitogenomes reveals a closed circular double-stranded structure containing 37 genes with a total length of 14,805 to 16,269 bp and a variable number of non-coding A + T-rich regions. The gene size, gene order, gene arrangement, base composition, codon usage, and secondary structure of tRNAs of the newly sequenced mitogenomes of these 13 species are highly conserved in Chiasmini. The ATN codon is commonly used as the start codon in protein-coding genes (PCGs), except for ND5 in Doratura sp. and ATP6 in Nephotettix nigropictus, which use the rare GTG start codon. Most protein-coding genes have TAA or TAG as the stop codon, but some genes have an incomplete T stop codon. Except for the tRNA for serine (trnS1(AGN)), the secondary structure of the other 21 tRNAs is a typical cloverleaf structure. In addition to the primary type of G-U mismatch, five other types of tRNA mismatches were observed: A-A, A-C, A-G, U-C, and U-U. Chiasmini mitochondrial genomes exhibit gene overlaps with three relatively stable regions: the overlapping sequence between trnW and trnC is AAGTCTTA, the overlapping sequence between ATP8 and ATP6 is generally ATGATTA, and the overlapping sequence between ND4 and ND4L is generally TTATCAT. The largest non-coding region is the control region, which exhibits significant length and compositional variation among species. Some Chiasmini have tandem repeat structures within their control regions. Unlike some other deltocephaline leafhoppers, the sequenced Chiasmini lack mitochondrial gene rearrangements. Phylogenetic analyses of different combinations of protein-coding and ribosomal genes using maximum likelihood and Bayesian methods under different models, using either amino acid or nucleotide sequences, are generally consistent and also agree with results of prior analyses of nuclear and partial mitochondrial gene sequence data, indicating that complete mitochondrial genomes are phylogenetically informative at different levels of divergence within Chiasmini and among leafhoppers in general. Apart from Athysanini and Opsiini, most of the deltocephaline tribes are recovered as monophyletic. The results of ML and BI analyses show that Chiasmini is a monophyletic group with seven monophyletic genera arranged as follows: ((Zahniserius + (Gurawa + (Doratura + Aconurella))) + (Leofa + (Exitianus + Nephotettix))).
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Affiliation(s)
- Bismillah Shah
- Anhui Province Key Laboratory of Integrated Pest Management on Crops, Key Laboratory of Biology and Sustainable Management of Plant Diseases and Pests of Anhui Higher Education Institutes, School of Plant Protection, Anhui Agricultural University, Hefei 230036, China; (B.S.); (B.X.); (K.W.); (M.Y.)
- Department of Forestry Protection, School of Forestry and Biotechnology, Zhejiang A&F University, 666 Wusu Street, Linan, Hangzhou 311300, China
| | - Muhammad Asghar Hassan
- The Provincial Special Key Laboratory for Development and Utilization of Insect Resources, Institute of Entomology, Guizhou University, Guiyang 550025, China;
| | - Bingqing Xie
- Anhui Province Key Laboratory of Integrated Pest Management on Crops, Key Laboratory of Biology and Sustainable Management of Plant Diseases and Pests of Anhui Higher Education Institutes, School of Plant Protection, Anhui Agricultural University, Hefei 230036, China; (B.S.); (B.X.); (K.W.); (M.Y.)
| | - Kaiqi Wu
- Anhui Province Key Laboratory of Integrated Pest Management on Crops, Key Laboratory of Biology and Sustainable Management of Plant Diseases and Pests of Anhui Higher Education Institutes, School of Plant Protection, Anhui Agricultural University, Hefei 230036, China; (B.S.); (B.X.); (K.W.); (M.Y.)
| | - Hassan Naveed
- School of Life Sciences, Jiangsu University, Zhenjiang 212013, China;
| | - Minhui Yan
- Anhui Province Key Laboratory of Integrated Pest Management on Crops, Key Laboratory of Biology and Sustainable Management of Plant Diseases and Pests of Anhui Higher Education Institutes, School of Plant Protection, Anhui Agricultural University, Hefei 230036, China; (B.S.); (B.X.); (K.W.); (M.Y.)
| | - Christopher H. Dietrich
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois, Champaign, IL 61820, USA;
| | - Yani Duan
- Anhui Province Key Laboratory of Integrated Pest Management on Crops, Key Laboratory of Biology and Sustainable Management of Plant Diseases and Pests of Anhui Higher Education Institutes, School of Plant Protection, Anhui Agricultural University, Hefei 230036, China; (B.S.); (B.X.); (K.W.); (M.Y.)
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206
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Yılmaz E, Mann DG, Gastineau R, Trobajo R, Solak CN, Górecka E, Turmel M, Lemieux C, Ertorun N, Witkowski A. Description of Naviculavanseea sp. nov. (Naviculales, Naviculaceae), a new species of diatom from the highly alkaline Lake Van (Republic of Türkiye) with complete characterisation of its organellar genomes and multigene phylogeny. PHYTOKEYS 2024; 241:27-48. [PMID: 38628637 PMCID: PMC11019260 DOI: 10.3897/phytokeys.241.118903] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Accepted: 02/19/2024] [Indexed: 04/19/2024]
Abstract
The current article describes Naviculavanseeasp. nov., a new species of diatom from Lake Van, a highly alkaline lake in Eastern Anatolia (Türkiye). The description is based on light and scanning electron microscopy performed on two monoclonal cultures. The complete nuclear rRNA clusters and plastid genomes have been sequenced for these two strains and the complete mitogenome for one of them. The plastome of both strains shows the probable loss of a functional ycf35 gene. They also exhibit two IB4 group I introns in their rrl, each encoding for a putative LAGLIDADG homing endonuclease, with the first L1917 IB4 intron reported amongst diatoms. The Maximum Likelihood phylogeny inferred from a concatenated alignment of 18S, rbcL and psbC distinguishes N.vanseea sp. nov. from the morphologically similar species Naviculacincta and Naviculamicrodigitoradiata.
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Affiliation(s)
- Elif Yılmaz
- Institute of Marine and Environmental Sciences, University of Szczecin, Mickiewicza 16A, PL70–383 Poland
| | - David G. Mann
- Royal Botanic Garden Edinburgh, Edinburgh EH3 5LR, Scotland, UK
| | - Romain Gastineau
- Institute of Marine and Environmental Sciences, University of Szczecin, Mickiewicza 16A, PL70–383 Poland
| | - Rosa Trobajo
- Marine and Continental Waters, Institute for Food and Agricultural Research and Technology (IRTA), Crta de Poble Nou Km 5.5, E-43540 La Ràpita, Catalunya, Spain
| | - Cüneyt Nadir Solak
- Department of Biology, Faculty of Science & Art, Dumlupınar University, 43000 Kütahya, Türkiye
| | - Ewa Górecka
- Institute of Marine and Environmental Sciences, University of Szczecin, Mickiewicza 16A, PL70–383 Poland
| | - Monique Turmel
- Département de biochimie, de microbiologie et de bio-Informatique, Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, QC, Canada
| | - Claude Lemieux
- Département de biochimie, de microbiologie et de bio-Informatique, Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, QC, Canada
| | - Nesil Ertorun
- Department of Biology, Science Faculty, Eskişehir Technical University, 26000 Eskişehir, Türkiye
| | - Andrzej Witkowski
- Institute of Marine and Environmental Sciences, University of Szczecin, Mickiewicza 16A, PL70–383 Poland
- Deceased
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207
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Itoigawa A, Toda Y, Kuraku S, Ishimaru Y. Evolutionary origins of bitter taste receptors in jawed vertebrates. Curr Biol 2024; 34:R271-R272. [PMID: 38593768 DOI: 10.1016/j.cub.2024.02.024] [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: 10/25/2023] [Revised: 02/08/2024] [Accepted: 02/13/2024] [Indexed: 04/11/2024]
Abstract
Taste is a sense that detects information about nutrients and toxins in foods. Of the five basic taste qualities, bitterness is associated with the detection of potentially harmful substances like plant alkaloids. In bony vertebrates, type 2 taste receptors (T2Rs), which are G-protein-coupled receptors (GPCRs), act as bitter taste receptors1,2. In vertebrates, six GPCR gene families are described as chemosensory receptor genes, encoding taste receptor families (T1Rs and T2Rs) and olfactory receptor families (ORs, V1Rs, V2Rs, and TAARs). These families of receptors have been found in all major jawed vertebrate lineages, except for the T2Rs, which are confined to bony vertebrates3. Therefore, T2Rs are believed to have emerged later than the other chemosensory receptor genes in the bony vertebrate lineage. So far, only the genomes of two cartilaginous fish species have been mined for TAS2R genes, which encode T2Rs4. Here, we identified novel T2Rs in elasmobranchs, namely selachimorphs (sharks) and batoids (rays, skates, and their close relatives) by an exhaustive search covering diverse cartilaginous fishes. Using functional and mRNA expression analyses, we demonstrate that their T2Rs are expressed in the oral taste buds and contribute to the detection of bitter compounds. This finding indicates the early origin of T2Rs in the common ancestor of jawed vertebrates.
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Affiliation(s)
- Akihiro Itoigawa
- Department of Agricultural Chemistry, School of Agriculture, Meiji University, Kawasaki, Kanagawa 214-8571, Japan; Japan Society for the Promotion of Science, Chiyoda-ku, Tokyo 102-0083, Japan
| | - Yasuka Toda
- Department of Agricultural Chemistry, School of Agriculture, Meiji University, Kawasaki, Kanagawa 214-8571, Japan
| | - Shigehiro Kuraku
- Molecular Life History Laboratory, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan; Department of Genetics, SOKENDAI (Graduate University for Advanced Studies), Mishima, Shizuoka 411-8540, Japan
| | - Yoshiro Ishimaru
- Department of Agricultural Chemistry, School of Agriculture, Meiji University, Kawasaki, Kanagawa 214-8571, Japan.
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208
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Li CL, Liu JF, Liu SF. Mitochondrial Dysfunction in Chronic Obstructive Pulmonary Disease: Unraveling the Molecular Nexus. Biomedicines 2024; 12:814. [PMID: 38672169 PMCID: PMC11048013 DOI: 10.3390/biomedicines12040814] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2024] [Revised: 04/04/2024] [Accepted: 04/05/2024] [Indexed: 04/28/2024] Open
Abstract
Chronic obstructive pulmonary disease (COPD) is a prevalent and debilitating respiratory disorder characterized by persistent airflow limitation and chronic inflammation. In recent years, the role of mitochondrial dysfunction in COPD pathogenesis has emerged as a focal point of investigation. This review endeavors to unravel the molecular nexus between mitochondrial dysfunction and COPD, delving into the intricate interplay of oxidative stress, bioenergetic impairment, mitochondrial genetics, and downstream cellular consequences. Oxidative stress, a consequence of mitochondrial dysfunction, is explored as a driving force behind inflammation, exacerbating the intricate cascade of events leading to COPD progression. Bioenergetic impairment sheds light on the systemic consequences of mitochondrial dysfunction, impacting cellular functions and contributing to the overall energy imbalance observed in COPD patients. This review navigates through the genetic landscape, elucidating the role of mitochondrial DNA mutations, variations, and haplogroups in COPD susceptibility and severity. Cellular consequences, including apoptosis, autophagy, and cellular senescence, are examined, providing insights into the intricate mechanisms by which mitochondrial dysfunction influences COPD pathology. Therapeutic implications, spanning antioxidant strategies, mitochondria-targeted compounds, and lifestyle modifications, are discussed in the context of translational research. Important future directions include identifying novel biomarkers, advancing mitochondria-targeted therapies, and embracing patient-centric approaches to redefine COPD management. This abstract provides a comprehensive overview of our review, offering a roadmap for understanding and addressing the molecular nexus between mitochondrial dysfunction and COPD, with potential implications for precision medicine and improved patient outcomes.
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Affiliation(s)
- Chin-Ling Li
- Department of Respiratory Therapy, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung 833, Taiwan
| | - Jui-Fang Liu
- Department of Respiratory Care, Chang Gung University of Science and Technology, Chiayi 600, Taiwan
- Chronic Diseases and Health Promotion Research Center, Chang Gung University of Science and Technology, Chiayi 600, Taiwan
| | - Shih-Feng Liu
- Department of Respiratory Therapy, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung 833, Taiwan
- Department of Respiratory Care, Chang Gung University of Science and Technology, Chiayi 600, Taiwan
- Chronic Diseases and Health Promotion Research Center, Chang Gung University of Science and Technology, Chiayi 600, Taiwan
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung 833, Taiwan
- College of Medicine, Chang Gung University, Taoyuan 333, Taiwan
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209
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Tian L, Xu R, Chen D, Ananjeva NB, Brown RM, Min MS, Cai B, Mijidsuren B, Zhang B, Guo X. Range-Wide Phylogeography and Ecological Niche Modeling Provide Insights into the Evolutionary History of the Mongolian Racerunner ( Eremias argus) in Northeast Asia. Animals (Basel) 2024; 14:1124. [PMID: 38612363 PMCID: PMC11011046 DOI: 10.3390/ani14071124] [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: 03/06/2024] [Revised: 04/03/2024] [Accepted: 04/04/2024] [Indexed: 04/14/2024] Open
Abstract
The Mongolian racerunner, Eremias argus, is a small lizard endemic to Northeast Asia that can serve as an excellent model for investigating how geography and past climate change have jointly influenced the evolution of biodiversity in this region. To elucidate the processes underlying its diversification and demography, we reconstructed the range-wide phylogeographic pattern and evolutionary trajectory, using phylogenetic, population genetic, landscape genetic, Bayesian phylogeographic reconstruction and ecological niche modeling approaches. Phylogenetic analyses of the mtDNA cyt b gene revealed eight lineages that were unbounded by geographic region. The genetic structure of E. argus was mainly determined by geographic distance. Divergence dating indicated that E. argus and E. brenchleyi diverged during the Mid-Pliocene Warm Period. E. argus was estimated to have coalesced at~0.4351 Ma (Marine Isotope Stage 19). Bayesian phylogeographic diffusion analysis revealed out-of-Inner Mongolia and rapid colonization events from the end of the Last Interglacial to the Last Glacial Maximum, which is consistent with the expanded suitable range of the Last Glacial Maximum. Pre-Last Glacial Maximum growth of population is presented for most lineages of E. argus. The Glacial Maximum contraction model and the previous multiple glacial refugia hypotheses are rejected. This may be due to an increase in the amount of climatically favorable habitats in Northeast Asia. Furthermore, E. argus barbouri most likely represents an invalid taxon. The present study is the first to report a range-wide phylogeography of reptiles over such a large region in Northeast Asia. Our results make a significant contribution towards understanding the biogeography of the entire Northeast Asia.
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Affiliation(s)
- Lili Tian
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610223, China; (L.T.); (R.X.); (B.C.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Rui Xu
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610223, China; (L.T.); (R.X.); (B.C.)
| | - Dali Chen
- Department of Pathogenic Biology, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu 610041, China;
| | - Natalia B. Ananjeva
- Zoological Institute, Russian Academy of Sciences, St. Petersburg 199034, Russia;
| | - Rafe M. Brown
- Biodiversity Institute, Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS 66045, USA;
| | - Mi-Sook Min
- Conservation Genome Resource Bank for Korean Wildlife, Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul 151-742, Republic of Korea;
| | - Bo Cai
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610223, China; (L.T.); (R.X.); (B.C.)
| | - Byambasuren Mijidsuren
- Plant Protection Research Institute, Mongolian University of Life Sciences, Ulaanbaatar 210153, Mongolia;
| | - Bin Zhang
- College of Life Sciences and Technology, Inner Mongolia Normal University, Hohhot 010022, China;
| | - Xianguang Guo
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610223, China; (L.T.); (R.X.); (B.C.)
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210
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de la Cruz-Huervana JJ, Miyamoto N, Kano Y, Onikura N, Kurita Y. The complete mitochondrial genome of freshwater gammarid Gammarus nipponensis (Crustacea: Amphipoda: Gammaridae). Mitochondrial DNA B Resour 2024; 9:447-451. [PMID: 38586505 PMCID: PMC10993753 DOI: 10.1080/23802359.2024.2335990] [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: 09/11/2023] [Accepted: 03/23/2024] [Indexed: 04/09/2024] Open
Abstract
This study presents the complete mitochondrial genome sequence of Gammarus nipponensis, a freshwater crustacean found in the western regions of Honshu, Shikoku and Kyushu in Japan. The entire genome is 16,429 bp in length, encoding a standard set of 13 protein-coding genes, two ribosomal RNA genes and 22 transfer RNA genes, as well as the putative control regions. The mitochondrial genome of G. nipponensis is characterized by a high concentration of A and T nucleotides (67.1%). Notably, the mitogenome contains long TATTTTA repeats in the control region 2 at 686 bp long. This newly available genome information will be useful for studying the evolutionary relationships within the genus Gammarus and for understanding diversification among G. nipponensis populations.
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Affiliation(s)
- Joana Joy de la Cruz-Huervana
- Fishery Research Laboratory, Kyushu University, Japan
- Aquaculture Department, Southeast Asian Fisheries Development Center, Philippines
| | - Norio Miyamoto
- X-STAR, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Yuichi Kano
- Kyushu University, Fukuoka, Japan
- Kyushu Open University, Fukuoka, Japan
| | - Norio Onikura
- Fishery Research Laboratory, Kyushu University, Japan
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211
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Liang QR, Shi L. The first complete mitochondrial DNA of Tenuidactylus dadunensis (Squamata: Gekkonidae) and its phylogeny. Mitochondrial DNA B Resour 2024; 9:442-446. [PMID: 38586508 PMCID: PMC10993739 DOI: 10.1080/23802359.2024.2333566] [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: 10/30/2023] [Accepted: 03/15/2024] [Indexed: 04/09/2024] Open
Abstract
The complete mitochondrial DNA (mtDNA) of Tenuidactylus dadunensis (Squamata: Gekkonidae) was described by using next-generation sequencing. The total length of mtDNA was 16,893 bp, which contained 13 PCGs (COX1-3, ND1-6, ND4L, ATP6, ATP8, and CYTB), 22 transfer RNA(tRNA) genes, 2 ribosomal RNA (rRNA) genes, and a control region (D-loop). The Bayesian inference tree showed that T. dadunensis was included in Gekkonidae and was a sister taxon to Cyrtopodion scabrum. The complete mtDNA of T. dadunensis will be an important genetic resource to the studies of conservation and research of geckonids.
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Affiliation(s)
- Qian-Ru Liang
- Xinjiang Key Laboratory for Ecological Adaptation and Evolution of Extreme Environment Biology, College of Life Sciences, Xinjiang Agricultural University, Urumqi, China
| | - Lei Shi
- Xinjiang Key Laboratory for Ecological Adaptation and Evolution of Extreme Environment Biology, College of Life Sciences, Xinjiang Agricultural University, Urumqi, China
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212
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Ma YH, Liu Y, Li T, Xu ZQ, Chai JJ, Liu A, Ma QH, Gao LJ, Li MC. An experimental study on the visual identification of Fritillaria ussuriensis based on LAMP and nucleic acid colloidal gold technique. Anal Biochem 2024; 687:115430. [PMID: 38147947 DOI: 10.1016/j.ab.2023.115430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2023] [Revised: 12/11/2023] [Accepted: 12/13/2023] [Indexed: 12/28/2023]
Abstract
Fritillaria ussuriensis Maxim is one of the traditional Chinese valuable herbs, which is the dried bulb of Fritillaria, a plant of the lily family. The identification of authenticity about F. ussuriensis is still technically challenging. In this study, visual identification was performed by ring-mediated isothermal amplification and nucleic acid colloidal gold techniques. Firstly, multiple sequence comparative analysis was performed by DNAMAN to find the differential sites of F. ussuriensis and its mixed pseudo-products, and the specific identification primers of F. ussuriensis were designed. Genomic DNA was extracted by the modified CTAB method, and the reaction system and reaction conditions were optimized to construct LAMP for the visual detection of F. ussuriensis, meanwhile, the genuine product was cloned and the extracted plasmid was sequenced. The specificity and sensitivity were detected, and also verified by nucleic acid colloidal gold method, and 20 commercially available samples were tested. The extracted DNA met the requirements of the experiment, and the genuine F. ussuriensis PCR product titrated on a test strip showed two bands on the T and C lines, while the counterfeit and negative control showed only one band on the C line, which matched the LAMP results. The specificity was 100 %, and the sensitivity of LAMP assay was up to 0.01 ng μL-1, while that of colloidal gold assay was 0.1 ng μL-1, thus the LAMP assay had high sensitivity. 14 out of 20 commercially available samples of F. ussuriensis were qualified, and 6 were unqualified, and the results of the two methods of identification were consistent. In this study, the combined detection method of LAMP and colloidal gold for nucleic acid was established to be specific, rapid, precise and visualized, which can provide a new technical idea for the detection of F. ussuriensis.
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Affiliation(s)
- Yu-He Ma
- School of Medical Technology, Beihua University, Jilin, 132013, China
| | - Yue Liu
- School of Medical Technology, Beihua University, Jilin, 132013, China
| | - Tao Li
- School of Medical Technology, Beihua University, Jilin, 132013, China
| | - Zi-Qiang Xu
- School of Medical Technology, Beihua University, Jilin, 132013, China
| | - Jin-Jun Chai
- School of Medical Technology, Beihua University, Jilin, 132013, China
| | - Ang Liu
- School of Medical Technology, Beihua University, Jilin, 132013, China
| | - Qiu-He Ma
- School of Medical Technology, Beihua University, Jilin, 132013, China
| | - Li-Jun Gao
- School of Medical Technology, Beihua University, Jilin, 132013, China.
| | - Ming-Cheng Li
- School of Medical Technology, Beihua University, Jilin, 132013, China; Innovation Center for Detection on DNA Fingerprint of Traditional Chinese Medicine, Jilin, 132013, China
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213
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Wang HL, Lei T, Wang XW, Cameron S, Navas-Castillo J, Liu YQ, Maruthi MN, Omongo CA, Delatte H, Lee KY, Krause-Sakate R, Ng J, Seal S, Fiallo-Olivé E, Bushley K, Colvin J, Liu SS. A comprehensive framework for the delimitation of species within the Bemisia tabaci cryptic complex, a global pest-species group. INSECT SCIENCE 2024. [PMID: 38562016 DOI: 10.1111/1744-7917.13361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2023] [Revised: 01/11/2024] [Accepted: 02/27/2024] [Indexed: 04/04/2024]
Abstract
Identifying cryptic species poses a substantial challenge to both biologists and naturalists due to morphological similarities. Bemisia tabaci is a cryptic species complex containing more than 44 putative species; several of which are currently among the world's most destructive crop pests. Interpreting and delimiting the evolution of this species complex has proved problematic. To develop a comprehensive framework for species delimitation and identification, we evaluated the performance of distinct data sources both individually and in combination among numerous samples of the B. tabaci species complex acquired worldwide. Distinct datasets include full mitogenomes, single-copy nuclear genes, restriction site-associated DNA sequencing, geographic range, host speciation, and reproductive compatibility datasets. Phylogenetically, our well-supported topologies generated from three dense molecular markers highlighted the evolutionary divergence of species of the B. tabaci complex and suggested that the nuclear markers serve as a more accurate representation of B. tabaci species diversity. Reproductive compatibility datasets facilitated the identification of at least 17 different cryptic species within our samples. Native geographic range information provides a complementary assessment of species recognition, while the host range datasets provide low rate of delimiting resolution. We further summarized different data performances in species classification when compared with reproductive compatibility, indicating that combination of mtCOI divergence, nuclear markers, geographic range provide a complementary assessment of species recognition. Finally, we represent a model for understanding and untangling the cryptic species complexes based on the evidence from this study and previously published articles.
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Affiliation(s)
- Hua-Ling Wang
- College of Forestry, Hebei Agricultural University, Baoding, Hebei Province, China
- The Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
- Natural Resources Institute, University of Greenwich, Kent, UK
| | - Teng Lei
- College of Life Sciences, Taizhou University, Taizhou, Zhejiang Province, China
| | - Xiao-Wei Wang
- The Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Stephen Cameron
- Department of Entomology, Purdue University, West Lafayette, IN, USA
| | - Jesús Navas-Castillo
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora" (IHSM-UMA-CSIC), Consejo Superior de Investigaciones Científicas, Malaga, Spain
| | - Yin-Quan Liu
- The Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - M N Maruthi
- Natural Resources Institute, University of Greenwich, Kent, UK
| | | | - Hélène Delatte
- CIRAD, UMR PVBMT CIRAD, Pôle de Protection des Plantes, Saint-Pierre, France
| | - Kyeong-Yeoll Lee
- School of Applied Biosciences, Kyungpook National University, Daegu, Republic of Korea
| | | | - James Ng
- Department of Microbiology and Plant Pathology, University of California, Riverside, CA
| | - Susan Seal
- Natural Resources Institute, University of Greenwich, Kent, UK
| | - Elvira Fiallo-Olivé
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora" (IHSM-UMA-CSIC), Consejo Superior de Investigaciones Científicas, Malaga, Spain
| | - Kathryn Bushley
- USDA Agricultural Research Service, 17123, Emerging Pests and Pathogens Research Unit, Ithaca, NY, USA
| | - John Colvin
- Natural Resources Institute, University of Greenwich, Kent, UK
| | - Shu-Sheng Liu
- The Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
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214
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Yi W, Hu M, Shi L, Li T, Sun H, Qin L, Yan S. Analysis of genetic variants in protein-coding genes of Aoluguya reindeer based on the whole-genome data. Anim Genet 2024; 55:296-298. [PMID: 38319118 DOI: 10.1111/age.13402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Revised: 01/19/2024] [Accepted: 01/19/2024] [Indexed: 02/07/2024]
Affiliation(s)
- Wenfeng Yi
- College of Animal Science, Jilin University, Changchun, China
| | - Mingyue Hu
- College of Animal Science, Jilin University, Changchun, China
| | - Lulu Shi
- College of Animal Science, Jilin University, Changchun, China
| | - Ting Li
- College of Animal Science, Jilin University, Changchun, China
| | - Hao Sun
- College of Animal Science, Jilin University, Changchun, China
| | - Lihong Qin
- Institute of Animal Husbandry and Veterinary, Jilin Academy of Agricultural Sciences, Gongzhuling, China
| | - Shouqing Yan
- College of Animal Science, Jilin University, Changchun, China
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215
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Londoño-Burbano A, Britto MR. Taxonomic revision of Sturisoma Swainson, 1838 (Loricariidae: Loricariinae), with descriptions of four new species. JOURNAL OF FISH BIOLOGY 2024; 104:989-1041. [PMID: 38018606 DOI: 10.1111/jfb.15627] [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: 07/28/2023] [Revised: 10/12/2023] [Accepted: 11/20/2023] [Indexed: 11/30/2023]
Abstract
A taxonomic revision of Sturisoma is presented. Individuals including both type and non-type specimens of all valid species were examined. Sturisoma was found to comprise 10 valid species: Sturisoma barbatum, Sturisoma brevirostre, Sturisoma graffini, Sturisoma guentheri, Sturisoma lyra, Sturisoma monopelte, Sturisoma nigrirostrum, Sturisoma reisi, Sturisoma rostratum, and Sturisoma tenuirostre. Furthermore, four new species are described: Sturisoma ghazziae, new species, from the Araguaia River, belonging to the Tocantins-Araguaia basin, Central Brazil; Sturisoma careirensia, new species, from the middle Amazon basin, Brazil; Sturisoma rapppydanielae, new species, from the Purus River, Amazon basin, Brazil; and Sturisoma defranciscoi, new species, from the Putumayo and Solimões rivers, upper Amazon basin, Colombia, and Brazil. Sturisoma robustum is confirmed as synonym of S. barbatum, species registered along the Paraguay/Parana/La Plata River basin in Argentina, Brazil, and Paraguay. New records were found for S. nigrirostrum as present in the upper Amazon basin, in the Yavari River, Brazil, in addition to its already known locality, the Ucayali River, Peru. The distribution of the type species of the genus S. rostratum is limited to the lower portion of the Amazon basin in the Araguaia, Maranhão, Mearim, Tapajós, and Tocantins rivers and its affluents, Brazil, in contrast to the assumed widespread distribution across the main basins of South America, as previously proposed for the species; the Mearim River is a new record for the species. Updated diagnoses and descriptions are offered for species of Sturisoma, in addition to distribution maps and an identification key for the species.
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Affiliation(s)
- Alejandro Londoño-Burbano
- Departamento de Vertebrados-Setor de Ictiologia, Universidade Federal do Rio de Janeiro, Museu Nacional, Rio de Janeiro, Brazil
| | - Marcelo R Britto
- Departamento de Vertebrados-Setor de Ictiologia, Universidade Federal do Rio de Janeiro, Museu Nacional, Rio de Janeiro, Brazil
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216
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Lyu B, Liu Q, Wu Y, Nguyen TQ, Che J, Nguyen SN, Myers EA, Burbrink FT, Guo P, Wang J. Genomic analysis reveals deep population divergence in the water snake Trimerodytes percarinatus (Serpentes, Natricidae). Ecol Evol 2024; 14:e11278. [PMID: 38628918 PMCID: PMC11019134 DOI: 10.1002/ece3.11278] [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: 09/30/2023] [Revised: 02/26/2024] [Accepted: 04/02/2024] [Indexed: 04/19/2024] Open
Abstract
Although several phylogeographic studies of Asian snakes have been conducted, most have focused on pitvipers, with non-venomous snakes, such as colubrids or natricids, remaining poorly studied. The Chinese keelback water snake (Trimerodytes percarinatus Boulenger) is a widespread, semiaquatic, non-venomous species occurring in China and southeastern Asia. Based on mitochondrial DNA (mtDNA) and single nucleotide polymorphism (SNP) data, we explored the population genetic structure, genetic diversity, and evolutionary history of this species. MtDNA-based phylogenetic analysis showed that T. percarinatus was composed of five highly supported and geographically structured lineages. SNP-based phylogenetic analysis, principal component analysis, and population structure analysis consistently revealed four distinct, geographically non-overlapping lineages, which was different from the mtDNA-based analysis in topology. Estimation of divergence dates and ancestral area of origin suggest that T. percarinatus originated ~12.68 million years ago (95% highest posterior density: 10.36-15.96 Mya) in a region covering southwestern China and Vietnam. Intraspecific divergence may have been triggered by the Qinghai-Xizang Plateau uplift. Population demographics and ecological niche modeling indicated that the effective population size fluctuated during 0.5 Mya and 0.002 Mya. Based on the data collected here, we also comment on the intraspecific taxonomy of T. percarinatus and question the validity of the subspecies T. p. suriki.
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Affiliation(s)
- Bing Lyu
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, Key Laboratory of Tropical Animal and Plant Ecology of Hainan Province, College of Life SciencesHainan Normal UniversityHaikouChina
- Faculty of Agriculture, Forestry and Food EngineeringYibin UniversityYibinChina
| | - Qin Liu
- Faculty of Agriculture, Forestry and Food EngineeringYibin UniversityYibinChina
| | - Yayong Wu
- Faculty of Agriculture, Forestry and Food EngineeringYibin UniversityYibinChina
| | - Truong Q. Nguyen
- Institute of Ecology and Biological ResourcesVietnam Academy of Science and TechnologyHanoiVietnam
- Vietnam Academy of Science and TechnologyGraduate University of Science and TechnologyHanoiVietnam
| | - Jing Che
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Key Laboratory of Biodiversity and Ecological Conservation of Gaoligong Mountain, Kunming Institute of ZoologyChinese Academy of SciencesKunmingChina
| | - Sang N. Nguyen
- Institute of Tropical BiologyVietnam Academy of Science and TechnologyHo Chi Minh CityVietnam
| | - Edward A. Myers
- Department of HerpetologyCalifornia Academy of SciencesSan FranciscoCaliforniaUSA
| | - Frank T. Burbrink
- Department of HerpetologyAmerican Museum of Natural HistoryNew YorkNew YorkUSA
| | - Peng Guo
- Faculty of Agriculture, Forestry and Food EngineeringYibin UniversityYibinChina
| | - Jichao Wang
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, Key Laboratory of Tropical Animal and Plant Ecology of Hainan Province, College of Life SciencesHainan Normal UniversityHaikouChina
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217
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Honka J, Kvist L, Olli S, Laaksonen T, Aspi J. Optimised PCR assays for detecting elusive waterfowl from environmental DNA. Ecol Evol 2024; 14:e11224. [PMID: 38571801 PMCID: PMC10985361 DOI: 10.1002/ece3.11224] [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: 08/04/2023] [Revised: 03/07/2024] [Accepted: 03/15/2024] [Indexed: 04/05/2024] Open
Abstract
For many aquatic and semiaquatic mammal, amphibian and fish species, environmental DNA (eDNA) methods are employed to detect species distribution and to monitor their presence, but eDNA is much less employed for avian species. Here, we developed primers for the detection of true geese and swan species using eDNA and optimised a PCR protocol for eDNA. We selected taiga bean goose (Anser fabalis fabalis) as our focal (sub)species and sampled water from lakes, from which the presence of taiga bean goose was visually confirmed. To test, if taiga bean goose DNA could be detected among DNA of other goose species, we similarly sampled eDNA from a zoo pond housing several Anatidae species. We were able to detect taiga bean goose DNA in all but one of the tested lakes, including the zoo pond. The primers developed are not species-specific, but rather specific to the genus Anser, due to the close relatedness of Anser species, which prevented the development of species-specific primers and the use of, for example, quantitative PCR. We also developed eDNA primers for Branta species and Cygnus species and tested these primers using the same samples. Canada goose (B. canadensis) and barnacle goose (B. leucopsis) DNA were only detected in the zoo pond (in which they were present), as the sampled natural lakes fall outside the range of these species. We detected whooper swan (C. cygnus) DNA in three lakes and the zoo pond (in which the species was present). The eDNA method presented here provides a potential means to monitor elusive goose species and to study the co-occurrence of large waterfowl.
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Affiliation(s)
- Johanna Honka
- Ecology and Genetics Research UnitUniversity of OuluOuluFinland
| | - Laura Kvist
- Ecology and Genetics Research UnitUniversity of OuluOuluFinland
| | - Suvi Olli
- Ecology and Genetics Research UnitUniversity of OuluOuluFinland
| | - Toni Laaksonen
- Department of BiologyUniversity of TurkuTurkuFinland
- Natural Resources Institute Finland (Luke)HelsinkiFinland
| | - Jouni Aspi
- Ecology and Genetics Research UnitUniversity of OuluOuluFinland
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218
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Luo G, Pu T, Wang J, Ran W, Zhao Y, Dietrich CH, Li C, Song Y. Genetic differentiation and phylogeography of Erythroneurini (Hemiptera, Cicadellidae, Typhlocybinae) in the southwestern karst area of China. Ecol Evol 2024; 14:e11264. [PMID: 38606344 PMCID: PMC11007260 DOI: 10.1002/ece3.11264] [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: 08/01/2023] [Revised: 03/22/2024] [Accepted: 03/27/2024] [Indexed: 04/13/2024] Open
Abstract
Erythroneurini is the largest tribe of the microleafhopper subfamily Typhlocybinae. Most prior research on this tribe has focused on traditional classification, phylogeny, and control of agricultural pests, and the phylogeography of the group remains poorly understood. In this study, the mitochondrial genomes of 10 erythroneurine species were sequenced, and sequences of four genes were obtained for 12 geographical populations of Seriana bacilla. The new sequence data were combined with previously available mitochondrial DNA sequence data and analyzed using Bayesian and Maximum-Likelihood-based phylogenetic methods to elucidate relationships among genera and species and estimate divergence times. Seriana was shown to be derived from within Empoascanara. Phylogeographic and population genetic analysis of the endemic Chinese species Seriana bacilla suggest that the species diverged about 54.85 Mya (95% HPD: 20.76-66.23 million years) in the Paleogene period and that population divergence occurred within the last 14 million years. Ancestral area reconstruction indicates that Seriana bacilla may have originated in the central region of Guizhou, and geographical barriers are the main factors affecting gene flow among populations. Ecological niche modeling using the MaxEnt model suggests that the distribution of the species was more restricted in the past but is likely to expand in the future years 2050 and 2070.
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Affiliation(s)
- Guimei Luo
- School of Karst ScienceGuizhou Norml University/State Engineering Technology Institute for Karst Desertification ControlGuiyangGuizhouChina
- Guizhou Provincial Key Laboratory for Rare Animal and Economic Insect of the Mountainous RegionGuiyang UniversityGuiyangGuizhouChina
- Illinois Natural History Survey, Prairie Research InstituteUniversity of IllinoisChampaignIllinoisUSA
| | - Tianyi Pu
- School of Karst ScienceGuizhou Norml University/State Engineering Technology Institute for Karst Desertification ControlGuiyangGuizhouChina
- Guizhou Provincial Key Laboratory for Rare Animal and Economic Insect of the Mountainous RegionGuiyang UniversityGuiyangGuizhouChina
| | - Jinqiu Wang
- School of Karst ScienceGuizhou Norml University/State Engineering Technology Institute for Karst Desertification ControlGuiyangGuizhouChina
| | - Weiwei Ran
- School of Karst ScienceGuizhou Norml University/State Engineering Technology Institute for Karst Desertification ControlGuiyangGuizhouChina
| | - Yuanqi Zhao
- School of Karst ScienceGuizhou Norml University/State Engineering Technology Institute for Karst Desertification ControlGuiyangGuizhouChina
| | - Christopher H. Dietrich
- School of Karst ScienceGuizhou Norml University/State Engineering Technology Institute for Karst Desertification ControlGuiyangGuizhouChina
- Illinois Natural History Survey, Prairie Research InstituteUniversity of IllinoisChampaignIllinoisUSA
| | - Can Li
- Guizhou Provincial Key Laboratory for Rare Animal and Economic Insect of the Mountainous RegionGuiyang UniversityGuiyangGuizhouChina
| | - Yuehua Song
- School of Karst ScienceGuizhou Norml University/State Engineering Technology Institute for Karst Desertification ControlGuiyangGuizhouChina
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219
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Walsh DJ, Bernard DJ, Fiddler JL, Pangilinan F, Esposito M, Harold D, Field MS, Parle-McDermott A, Brody LC. Vitamin B12 status and folic acid supplementation influence mitochondrial heteroplasmy levels in mice. PNAS NEXUS 2024; 3:pgae116. [PMID: 38560530 PMCID: PMC10978065 DOI: 10.1093/pnasnexus/pgae116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Accepted: 02/29/2024] [Indexed: 04/04/2024]
Abstract
One-carbon metabolism is a complex network of metabolic reactions that are essential for cellular function including DNA synthesis. Vitamin B12 and folate are micronutrients that are utilized in this pathway and their deficiency can result in the perturbation of one-carbon metabolism and subsequent perturbations in DNA replication and repair. This effect has been well characterized in nuclear DNA but to date, mitochondrial DNA (mtDNA) has not been investigated extensively. Mitochondrial variants have been associated with several inherited and age-related disease states; therefore, the study of factors that impact heteroplasmy are important for advancing our understanding of the mitochondrial genome's impact on human health. Heteroplasmy studies require robust and efficient mitochondrial DNA enrichment to carry out in-depth mtDNA sequencing. Many of the current methods for mtDNA enrichment can introduce biases and false-positive results. Here, we use a method that overcomes these limitations and have applied it to assess mitochondrial heteroplasmy in mouse models of altered one-carbon metabolism. Vitamin B12 deficiency was found to cause increased levels of mitochondrial DNA heteroplasmy across all tissues that were investigated. Folic acid supplementation also contributed to elevated mitochondrial DNA heteroplasmy across all mouse tissues investigated. Heteroplasmy analysis of human data from the Framingham Heart Study suggested a potential sex-specific effect of folate and vitamin B12 status on mitochondrial heteroplasmy. This is a novel relationship that may have broader consequences for our understanding of one-carbon metabolism, mitochondrial-related disease and the influence of nutrients on DNA mutation rates.
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Affiliation(s)
- Darren J Walsh
- Gene and Environment Interaction Section, National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA
- School of Biotechnology, Dublin City University, Dublin 9, Ireland
| | - David J Bernard
- Gene and Environment Interaction Section, National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA
| | - Joanna L Fiddler
- Division of Nutritional Sciences, Cornell University, Ithaca, NY 14850, USA
- Department of Food, Nutrition, and Packaging Sciences, Clemson University, Clemson, SC 29634, USA
| | - Faith Pangilinan
- Gene and Environment Interaction Section, National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA
| | - Madison Esposito
- Gene and Environment Interaction Section, National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA
| | - Denise Harold
- School of Biotechnology, Dublin City University, Dublin 9, Ireland
| | - Martha S Field
- Division of Nutritional Sciences, Cornell University, Ithaca, NY 14850, USA
| | | | - Lawrence C Brody
- Gene and Environment Interaction Section, National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA
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220
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Opatova V, Bourguignon K, Bond JE. Species delimitation with limited sampling: An example from rare trapdoor spider genus Cyclocosmia (Mygalomorphae, Halonoproctidae). Mol Ecol Resour 2024; 24:e13894. [PMID: 37971187 DOI: 10.1111/1755-0998.13894] [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: 07/04/2023] [Revised: 10/24/2023] [Accepted: 10/31/2023] [Indexed: 11/19/2023]
Abstract
The outcome of species delimitation depends on many factors, including conceptual framework, study design, data availability, methodology employed and subjective decision making. Obtaining sufficient taxon sampling in endangered or rare taxa might be difficult, particularly when non-lethal tissue collection cannot be utilized. The need to avoid overexploitation of the natural populations may thus limit methodological framework available for downstream data analyses and bias the results. We test species boundaries in rare North American trapdoor spider genus Cyclocosmia Ausserer (1871) inhabiting the Southern Coastal Plain biodiversity hotspot with the use of genomic data and two multispecies coalescent model methods. We evaluate the performance of each methodology within a limited sampling framework. To mitigate the risk of species over splitting, common in taxa with highly structured populations, we subsequently implement a species validation step via genealogical diversification index (gdi), which accounts for both genetic isolation and gene flow. We delimited eight geographically restricted lineages within sampled North American Cyclocosmia, suggesting that major river drainages in the region are likely barriers to dispersal. Our results suggest that utilizing BPP in the species discovery step might be a good option for datasets comprising hundreds of loci, but fewer individuals, which may be a common scenario for rare taxa. However, we also show that such results should be validated via gdi, in order to avoid over splitting.
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Affiliation(s)
- Vera Opatova
- Department of Zoology, Faculty of Sciences, Charles University, Prague 2, Czech Republic
| | - Kellie Bourguignon
- Department of Biological Sciences, Auburn University, Auburn, Alabama, USA
| | - Jason E Bond
- Department of Entomology and Nematology, University of California, Davis, California, USA
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221
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Kalapothakis Y, Miranda K, Aragão M, Larangote D, Braga-Pereira G, Noetzold M, Molina D, Langer R, Conceição IM, Guerra-Duarte C, Chávez-Olórtegui C, Kalapothakis E, Borges A. Divergence in toxin antigenicity and venom enzymes in Tityus melici, a medically important scorpion, despite transcriptomic and phylogenetic affinities with problematic Brazilian species. Int J Biol Macromol 2024; 263:130311. [PMID: 38403220 DOI: 10.1016/j.ijbiomac.2024.130311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 01/27/2024] [Accepted: 02/18/2024] [Indexed: 02/27/2024]
Abstract
The Brazilian scorpion Tityus melici, native to Minas Gerais and Bahia, is morphologically related to Tityus serrulatus, the most medically significant species in Brazil. Despite inhabiting scorpion-envenomation endemic regions, T. melici venom remains unexplored. This work evaluates T. melici venom composition and function using transcriptomics, enzymatic activities, and in vivo and in vitro immunological analyses. Next-Generation Sequencing unveiled 86 components putatively involved in venom toxicity: 39 toxins, 28 metalloproteases, seven disulfide isomerases, six hyaluronidases, three phospholipases and three amidating enzymes. T. serrulatus showed the highest number of toxin matches with 80-100 % sequence similarity. T. melici is of medical importance as it has a venom LD50 of 0.85 mg/kg in mice. We demonstrated venom phospholipase A2 activity, and elevated hyaluronidase and metalloprotease activities compared to T. serrulatus, paralleling our transcriptomic findings. Comparison of transcriptional levels for T. serrulatus and T. melici venom metalloenzymes suggests species-specific expression patterns in Tityus. Despite close phylogenetic association with T. serrulatus inferred from COI sequences and toxin similarities, partial neutralization of T. melici venom toxicity was achieved when using the anti-T. serrulatus antivenom, implying antigenic divergence among their toxins. We suggest that the Brazilian therapeutic scorpion antivenom could be improved to effectively neutralize T. melici venom.
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Affiliation(s)
- Yan Kalapothakis
- Departamento de Genética, Ecologia e Evolução, ICB, Universidade Federal de Minas Gerais, Av. Antônio Carlos 6627, CEP: 31270-901 Belo Horizonte, Minas Gerais, Brazil
| | - Kelton Miranda
- Departamento de Genética, Ecologia e Evolução, ICB, Universidade Federal de Minas Gerais, Av. Antônio Carlos 6627, CEP: 31270-901 Belo Horizonte, Minas Gerais, Brazil
| | - Matheus Aragão
- Departamento de Bioquímica e Imunologia, ICB, Universidade Federal de Minas Gerais, Av. Antônio Carlos 6627, CEP: 31270-901 Belo Horizonte, Minas Gerais, Brazil
| | - Débora Larangote
- Departamento de Genética, Ecologia e Evolução, ICB, Universidade Federal de Minas Gerais, Av. Antônio Carlos 6627, CEP: 31270-901 Belo Horizonte, Minas Gerais, Brazil
| | - Gracielle Braga-Pereira
- Departamento de Zoologia, ICB, Universidade Federal de Minas Gerais, Av. Antônio Carlos, 6627, CEP 31270-901 Belo Horizonte, Minas Gerais, Brazil
| | - Marina Noetzold
- Departamento de Bioquímica e Imunologia, ICB, Universidade Federal de Minas Gerais, Av. Antônio Carlos 6627, CEP: 31270-901 Belo Horizonte, Minas Gerais, Brazil
| | - Denis Molina
- Departamento de Bioquímica e Imunologia, ICB, Universidade Federal de Minas Gerais, Av. Antônio Carlos 6627, CEP: 31270-901 Belo Horizonte, Minas Gerais, Brazil
| | - Rafael Langer
- Departamento de Bioquímica e Imunologia, ICB, Universidade Federal de Minas Gerais, Av. Antônio Carlos 6627, CEP: 31270-901 Belo Horizonte, Minas Gerais, Brazil
| | - Izabela Mamede Conceição
- Departamento de Bioquímica e Imunologia, ICB, Universidade Federal de Minas Gerais, Av. Antônio Carlos 6627, CEP: 31270-901 Belo Horizonte, Minas Gerais, Brazil
| | - Clara Guerra-Duarte
- Serviço de Toxinologia Molecular, Diretoria de Pesquisa e Desenvolvimento, Fundação Ezequiel Dias, Belo Horizonte, Minas Gerais, Brazil
| | - Carlos Chávez-Olórtegui
- Departamento de Bioquímica e Imunologia, ICB, Universidade Federal de Minas Gerais, Av. Antônio Carlos 6627, CEP: 31270-901 Belo Horizonte, Minas Gerais, Brazil
| | - Evanguedes Kalapothakis
- Departamento de Genética, Ecologia e Evolução, ICB, Universidade Federal de Minas Gerais, Av. Antônio Carlos 6627, CEP: 31270-901 Belo Horizonte, Minas Gerais, Brazil
| | - Adolfo Borges
- Instituto de Medicina Experimental, Universidad Central de Venezuela, Caracas, Venezuela; Centro para el Desarrollo de la Investigación Científica, CEDIC, Asunción 1255, Paraguay.
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Chen L, Dong X, Huang H, Xu H, Rono PC, Cai X, Hu G. Assembly and comparative analysis of the initial complete mitochondrial genome of Primulina hunanensis (Gesneriaceae): a cave-dwelling endangered plant. BMC Genomics 2024; 25:322. [PMID: 38561677 PMCID: PMC10983754 DOI: 10.1186/s12864-024-10247-9] [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: 12/30/2023] [Accepted: 03/22/2024] [Indexed: 04/04/2024] Open
Abstract
BACKGROUND Primulina hunanensis, a troglobitic plant within the Primulina genus of Gesneriaceae family, exhibits robust resilience to arid conditions and holds great horticultural potential as an ornamental plant. The work of chloroplast genome (cpDNA) has been recently accomplished, however, the mitochondrial genome (mtDNA) that is crucial for plant evolution has not been reported. RESULTS In this study, we sequenced and assembled the P. hunanensis complete mtDNA, and elucidated its evolutionary and phylogenetic relationships. The assembled mtDNA spans 575,242 bp with 43.54% GC content, encompassing 60 genes, including 37 protein-coding genes (PCGs), 20 tRNA genes, and 3 rRNA genes. Notably, high number of repetitive sequences in the mtDNA and substantial sequence translocation from chloroplasts to mitochondria were observed. To determine the evolutionary and taxonomic positioning of P. hunanensis, a phylogenetic tree was constructed using mitochondrial PCGs from P. hunanensis and 32 other taxa. Furthermore, an exploration of PCGs relative synonymous codon usage, identification of RNA editing events, and an investigation of collinearity with closely related species were conducted. CONCLUSIONS This study reports the initial assembly and annotation of P. hunanensis mtDNA, contributing to the limited mtDNA repository for Gesneriaceae plants and advancing our understanding of their evolution for improved utilization and conservation.
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Affiliation(s)
- Lingling Chen
- Department of Botany, College of Life Sciences, Hunan Normal University, Changsha, 410081, China
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, 430074, China
| | - Xiang Dong
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, 430074, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Hang Huang
- Department of Botany, College of Life Sciences, Hunan Normal University, Changsha, 410081, China
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, 430074, China
| | - Haixia Xu
- Department of Botany, College of Life Sciences, Hunan Normal University, Changsha, 410081, China
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, 430074, China
| | - Peninah Cheptoo Rono
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, 430074, China
| | - Xiuzhen Cai
- Department of Botany, College of Life Sciences, Hunan Normal University, Changsha, 410081, China.
| | - Guangwan Hu
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China.
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, 430074, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- Hubei Jiangxia Laboratory, Wuhan, 430200, China.
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Lan X, Wang J, Zhang M, Zhou Q, Xiang H, Jiang W. Molecular Identification of Acrossocheilus jishouensis (Teleostei: Cyprinidae) and Its Complete Mitochondrial Genome. Biochem Genet 2024; 62:1396-1412. [PMID: 37620638 DOI: 10.1007/s10528-023-10501-x] [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: 01/11/2023] [Accepted: 08/09/2023] [Indexed: 08/26/2023]
Abstract
Molecular identification, such as DNA barcoding, is a useful tool that is widely applied in distinguishing species. To identify the cyprinid Acrossocheilus jishouensis, which was previously known to be restricted to only its type locality, we conducted molecular identification of this species based on 23 samples in five localities. Molecular identification based on the mitochondrial COI gene sequence showed that the morphologically similar samples from the five populations were all A. jishouensis, as the mean genetic distances between populations were very small (0.1-1.6%); thus, the distribution of this species was substantially expanded. The whole mitochondrial genome of one sample was also assembled, which was 16,594 bp in length and consisted of 13 protein-coding genes (PCGs), two rRNA genes, 22 tRNA genes, and one control region. All PCGs began with ATG except the COI gene, which started with GTG; seven PCGs used the complete stop codon TAA, while four terminated in T(AA) and two ended with TAG. The overall base composition reflected a higher proportion of A+T than G+C and a positive AT-skew and negative GC-skew pattern except for the opposite in ND6. Phylogenetic relationships inferred using BI and ML methods revealed that both Acrossocheilus and Onychostoma were nonmonophyletic, which indicated that the traditional diagnoses between these two genera need to be assessed further. The results of this study not only expanded the known distribution ranges of A. jishouensis, but also provided a valuable data resource for future molecular and evolutionary studies of Acrossocheilus and other cyprinids in Barbinae.
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Affiliation(s)
- Xiangying Lan
- Hunan Engineering Laboratory for Chinese Giant Salamander's Resource Protection and Comprehensive Utilization, and Key Laboratory of Hunan Forest Products and Chemical Industry Engineering, National and Local United Engineering Laboratory of Integrative Utilization Technology of Eucommia Ulmoides, Jishou University, Zhangjiajie, China
- College of Biology and Environmental Sciences, Jishou University, Jishou, China
| | - Jinxiu Wang
- Hunan Engineering Laboratory for Chinese Giant Salamander's Resource Protection and Comprehensive Utilization, and Key Laboratory of Hunan Forest Products and Chemical Industry Engineering, National and Local United Engineering Laboratory of Integrative Utilization Technology of Eucommia Ulmoides, Jishou University, Zhangjiajie, China
- College of Biology and Environmental Sciences, Jishou University, Jishou, China
| | - Mingyao Zhang
- Hunan Engineering Laboratory for Chinese Giant Salamander's Resource Protection and Comprehensive Utilization, and Key Laboratory of Hunan Forest Products and Chemical Industry Engineering, National and Local United Engineering Laboratory of Integrative Utilization Technology of Eucommia Ulmoides, Jishou University, Zhangjiajie, China
- College of Biology and Environmental Sciences, Jishou University, Jishou, China
| | - Qiang Zhou
- Hunan Engineering Laboratory for Chinese Giant Salamander's Resource Protection and Comprehensive Utilization, and Key Laboratory of Hunan Forest Products and Chemical Industry Engineering, National and Local United Engineering Laboratory of Integrative Utilization Technology of Eucommia Ulmoides, Jishou University, Zhangjiajie, China
- College of Biology and Environmental Sciences, Jishou University, Jishou, China
| | - Hongmei Xiang
- Hunan Engineering Laboratory for Chinese Giant Salamander's Resource Protection and Comprehensive Utilization, and Key Laboratory of Hunan Forest Products and Chemical Industry Engineering, National and Local United Engineering Laboratory of Integrative Utilization Technology of Eucommia Ulmoides, Jishou University, Zhangjiajie, China
| | - Wansheng Jiang
- Hunan Engineering Laboratory for Chinese Giant Salamander's Resource Protection and Comprehensive Utilization, and Key Laboratory of Hunan Forest Products and Chemical Industry Engineering, National and Local United Engineering Laboratory of Integrative Utilization Technology of Eucommia Ulmoides, Jishou University, Zhangjiajie, China.
- College of Biology and Environmental Sciences, Jishou University, Jishou, China.
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Liu Q, Jiang X, Tu W, Liu L, Huang Y, Xia Y, Xia X, Shi Y. Comparative efficiency of differential diagnostic methods for the identification of BRAF V600E gene mutation in papillary thyroid cancer (Review). Exp Ther Med 2024; 27:149. [PMID: 38476918 PMCID: PMC10928970 DOI: 10.3892/etm.2024.12437] [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: 07/13/2023] [Accepted: 02/02/2024] [Indexed: 03/14/2024] Open
Abstract
V-Raf murine sarcoma viral oncogene homolog B1 (BRAF) encodes a serine-threonine kinase. The V600E point mutation in the BRAF gene is the most common mutation, predominantly occurring in melanoma, and colorectal, thyroid and non-small cell lung cancer. Particularly in the context of thyroid cancer research, it is routinely employed as a molecular biomarker to assist in diagnosing and predicting the prognosis of papillary thyroid cancer (PTC), and to formulate targeted therapeutic strategies. Currently, several methods are utilized in clinical settings to detect BRAF V600E mutations in patients with PTC. However, the sensitivity and specificity of various detection techniques vary significantly, resulting in diverse detection outcomes. The present review highlights the advantages and disadvantages of the methods currently employed in medical practice, with the aim of guiding clinicians and researchers in selecting the most suitable detection approach for its high sensitivity, reproducibility and potential to develop targeted therapeutic regimens for patients with BRAF gene mutation-associated PTC.
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Affiliation(s)
- Qian Liu
- Department of Nuclear Medicine, The Second Affiliated Hospital of Chengdu Medical College, China National Nuclear Corporation 416 Hospital, Chengdu, Sichuan 610000, P.R. China
| | - Xue Jiang
- Department of Nuclear Medicine, The Second Affiliated Hospital of Chengdu Medical College, China National Nuclear Corporation 416 Hospital, Chengdu, Sichuan 610000, P.R. China
| | - Wenling Tu
- Department of Nuclear Medicine, The Second Affiliated Hospital of Chengdu Medical College, China National Nuclear Corporation 416 Hospital, Chengdu, Sichuan 610000, P.R. China
| | - Lina Liu
- Department of Nuclear Medicine, The Second Affiliated Hospital of Chengdu Medical College, China National Nuclear Corporation 416 Hospital, Chengdu, Sichuan 610000, P.R. China
| | - Ying Huang
- Department of Nuclear Medicine, The Second Affiliated Hospital of Chengdu Medical College, China National Nuclear Corporation 416 Hospital, Chengdu, Sichuan 610000, P.R. China
| | - Yuxiao Xia
- Department of Nuclear Medicine, The Second Affiliated Hospital of Chengdu Medical College, China National Nuclear Corporation 416 Hospital, Chengdu, Sichuan 610000, P.R. China
| | - Xuliang Xia
- Department of General Surgery, The Second Affiliated Hospital of Chengdu Medical College, China National Nuclear Corporation 416 Hospital, Chengdu, Sichuan 610000, P.R. China
| | - Yuhong Shi
- Department of Nuclear Medicine, The Second Affiliated Hospital of Chengdu Medical College, China National Nuclear Corporation 416 Hospital, Chengdu, Sichuan 610000, P.R. China
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Teixeira MAL, Fourreau CJL, Sempere-Valverde J, Carvalho S. Two new records and description of a new Perinereis (Annelida, Nereididae) species for the Saudi Arabian Red Sea region. Zookeys 2024; 1196:331-354. [PMID: 38726099 PMCID: PMC11079592 DOI: 10.3897/zookeys.1196.115260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2023] [Accepted: 01/26/2024] [Indexed: 05/12/2024] Open
Abstract
Annelid biodiversity studies in the Red Sea are limited and integrative taxonomy is needed to accurately improve reference libraries in the region. As part of the bioblitz effort in Saudi Arabia to assess the invertebrate biodiversity in the northern Red Sea and Gulf of Aqaba, Perinereis specimens from intertidal marine and lagoon-like rocky environments were selected for an independent assessment, given the known taxonomic ambiguities in this genus. This study used an integrative approach, combining molecular with morphological and geographic data. Our results demonstrate that specimens found mainly in the Gulf of Aqaba are not only morphologically different from other five similar Perinereis Group I species reported in the region, but phylogenetic analysis using available COI sequences from GenBank revealed different molecular operational taxonomic units, suggesting an undescribed species, P.kaustianasp. nov. The new species is genetically close and shares a similar paragnath pattern to the Indo-Pacific distributed P.helleri, in particular in Area III and Areas VII-VIII. Therefore, we suggest it may belong to the same species complex. However, P.kaustianasp. nov. differs from the latter mainly in the shorter length of the postero-dorsal tentacular cirri, median parapodia with much longer dorsal Tentacular cirri, posteriormost parapodia with much wider and greatly expanded dorsal ligules. Additionally, two new records are reported for the Saudi Neom area belonging to P.damietta and P.suezensis, previously described only for the Egyptian coast (Suez Canal) and are distributed sympatrically with the new species, but apparently not sympatric with each other.
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Affiliation(s)
- Marcos A. L. Teixeira
- Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Chloé Julie Loïs Fourreau
- Molecular Invertebrate Systematics and Ecology (MISE) Lab, Graduate School of Engineering and Science, University of the Ryukyus, Nishihara, Okinawa, Japan
| | - Juan Sempere-Valverde
- Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
- Laboratorio de Biología Marina/Estación de Biología Marina del Estrecho (Ceuta), Departamento de Zoología, Facultad de Biología, Universidad de Sevilla, Avda. Reina Mercedes s/n, 41012, Sevilla, Spain
| | - Susana Carvalho
- Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
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226
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Durango-Manrique YS, López-Rubio A, Gutiérrez LA, Isaza JP, Gómez GF. Mitochondrial genome comparison and phylogenetic position of Fannia pusio among the Calyptratae flies. Heliyon 2024; 10:e27697. [PMID: 38524611 PMCID: PMC10958369 DOI: 10.1016/j.heliyon.2024.e27697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 02/07/2024] [Accepted: 03/05/2024] [Indexed: 03/26/2024] Open
Abstract
Fannia pusio, the chicken dung fly species, remains unexplored despite its forensic, sanitary, and veterinary importance in the Nearctic and Neotropical regions. In this study, we obtained the complete mitochondrial genome of Fannia pusio for the first time using next-generation sequencing. We compared it with previously published mitogenomes of the genus from the Palearctic region, and its phylogenetic position was studied based on the concatenated protein-coding genes (PCGs) dataset of Calyptratae flies. The circular mitochondrial genome of F. pusio is 16,176 bp in length, with a high A + T content (78.3%), whose gene synteny, codon usage analysis, and amino acid frequency are similar to previously reported Fannia mitogenomes. All PCGs underwent purifying selection except the nad2 gene. Interspecific K2P distances of PCGs of Fannia yielded an average of 12.4% (8.1%-21.1%). The Fannia genus is monophyletic and closely related to Muscidae based on molecular data. Further taxonomic sampling is required to deep into the phylogenetic relationships of the originally proposed species-groups and subgroups within the genus. These results provide a valuable dataset for studying the mitochondrial genome evolution and a resource for the taxonomy and systematics of Fannia.
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Affiliation(s)
- Yesica S Durango-Manrique
- Grupo de investigación Bioforense, Facultad de Derecho y Ciencias Forenses, Tecnológico de Antioquia, Institución Universitaria, Medellín, Colombia
| | - Andrés López-Rubio
- Grupo de investigación Bioforense, Facultad de Derecho y Ciencias Forenses, Tecnológico de Antioquia, Institución Universitaria, Medellín, Colombia
| | - Lina A Gutiérrez
- Grupo Biología de Sistemas, Escuela de Ciencias de La Salud, Facultad de Medicina, Universidad Pontificia Bolivariana, Medellín, Colombia
| | - Juan P Isaza
- Grupo Biología de Sistemas, Escuela de Ciencias de La Salud, Facultad de Medicina, Universidad Pontificia Bolivariana, Medellín, Colombia
| | - Giovan F Gómez
- Universidad Nacional de Colombia - Sede de La Paz - Dirección Académica, Escuela de Pregrados - Km 9 vía Valledupar - La Paz, La Paz, Colombia
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227
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Wang Z, Xu X, Zheng Y, Xu Z, Li Y, Chen H. Analysis of the Overlength Main Noncoding Region in Metacarcinus magister (Decapoda: Brachyura) and a Phylogenetic Study of the Cancroidea Species. Genes (Basel) 2024; 15:437. [PMID: 38674372 PMCID: PMC11049931 DOI: 10.3390/genes15040437] [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: 01/26/2024] [Revised: 03/19/2024] [Accepted: 03/26/2024] [Indexed: 04/28/2024] Open
Abstract
Complete mitochondrial genomes (mitogenomes) can provide important information regarding the molecular evolution and phylogenetic relationships of marine invertebrates, especially in Brachyura. Only one Cancroidea species of mitogenomes has been sequenced before; in this research, the mitogenomic characteristics of Metacarcinus magister (Cancridae: Cancroidea) are newly studied. The length of the M. magister mitogenome was 48,820 bp, and it contained the typical 13 protein-coding genes, 2 ribosomal RNA genes, and 22 transfer RNA genes. We performed a series of analyses on the characteristics of the mNCR of M. magister. The phylogenetics, life circumstances, and selective pressures were all analyzed to explain the formation of this length, which revealed the length of the M. magister mitogenome to be approximately three times greater than the normal length of Brachyuran mitogenomes. Phylogenetic analyses based on a dataset of 215 Decapodan mitogenomes indicated that all Eriphioidea crabs were clustered together as a group. Moreover, the rearrangement mechanism of the Cancroidea species was predicted to provide stronger evidence for the phylogenetic analysis. In general, the results obtained in this study will contribute to a better understanding of the cause of the unusual length of the M. magister mitogenome and provide new insights into the phylogeny of Brachyura.
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228
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Pereira Dos Santos M, Zotta Mota AP, Coiti Togawa R, Florencio Martins N, Fabricio de Melo Bellard do Nascimento E, Lucena VS, Castellani MA, Saliba Albuquerque EV, Hilliou F. The complete mitochondrial genome of Leucoptera coffeella (Lepidoptera: Lyonetiidae) and phylogenetic relationships within the Yponomeutoidea superfamily. Sci Rep 2024; 14:7119. [PMID: 38531918 DOI: 10.1038/s41598-024-57869-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Accepted: 03/22/2024] [Indexed: 03/28/2024] Open
Abstract
The coffee leaf miner (Leucoptera coffeella) is one of the major pests of coffee crops in the neotropical regions, and causes major economic losses. Few molecular data are available to identify this pest and advances in the knowledge of the genome of L. coffeella will contribute to improving pest identification and also clarify taxonomy of this microlepidoptera. L. coffeella DNA was extracted and sequenced using PacBio HiFi technology. Here we report the complete L. coffeella circular mitochondrial genome (16,407 bp) assembled using Aladin software. We found a total of 37 genes, including 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), 2 ribosomal RNA genes (rRNAs) and an A + T rich-region and a D-loop. The L. coffeella mitochondrial gene organization is highly conserved with similarities to lepidopteran mitochondrial gene rearrangements (trnM-trnI-trnQ). We concatenated the 13 PCG to construct a phylogenetic tree and inferred the relationship between L. coffeella and other lepidopteran species. L. coffeella is found in the Lyonetiidae clade together with L. malifoliella and Lyonetia clerkella, both leaf miners. Interestingly, this clade is assigned in the Yponomeutoidea superfamily together with Gracillariidae, and both superfamilies displayed species with leaf-mining feeding habits.
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Affiliation(s)
- Mateus Pereira Dos Santos
- Department of Crop Science and Animal Science, State University of Southwestern Bahia, Vitória da Conquista, 45083-300, Brazil
- INRAE, Institut Sophia Agrobiotech, Université Côte D'Azur, CNRS, Sophia Antipolis, France
| | - Ana Paula Zotta Mota
- INRAE, Institut Sophia Agrobiotech, Université Côte D'Azur, CNRS, Sophia Antipolis, France
| | | | | | | | | | - Maria Aparecida Castellani
- Department of Crop Science and Animal Science, State University of Southwestern Bahia, Vitória da Conquista, 45083-300, Brazil
| | | | - Frédérique Hilliou
- INRAE, Institut Sophia Agrobiotech, Université Côte D'Azur, CNRS, Sophia Antipolis, France.
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229
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Zhiyuan H, Lin C, Yihan W, Meng D, Yanzi L, Zhenggang X. Reexamination of Aspergillus cristatus phylogeny in dark tea: Characteristics of the mitochondrial genome. Open Life Sci 2024; 19:20220838. [PMID: 38585639 PMCID: PMC10997147 DOI: 10.1515/biol-2022-0838] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 01/18/2024] [Accepted: 02/12/2024] [Indexed: 04/09/2024] Open
Abstract
To enhance our understanding of Aspergillus cristatus, an important functional microorganism, the characteristics of its mitochondrial genome were analyzed and compared with related species. The mitochondrial genome of A. cristatus was determined to be 77,649 bp in length, with 15 protein-coding regions. Notably, its length surpassed that of the other species, primarily attributable to the intron length. Gene order exhibited significant variations, with greater conservation observed in the genus Penicillium compared to Aspergillus. Phylogenetic tree analyses indicated that the genera Aspergillus and Penicillium are closely related but monophyletic. Furthermore, the phylogenetic tree constructed based on protein-coding genes effectively distinguished all strains with high branching confidence. This approach provides a robust reflection of the evolutionary relationship between A. cristatus and its related species, offering potential for the development of molecular markers suitable for Aspergillus and Penicillium.
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Affiliation(s)
- Hu Zhiyuan
- Hunan Provincial Key Lab of Dark Tea and Jin-hua, School of Materials and Chemical Engineering, Hunan City University, Yiyang413000, Hunan, China
| | - Chen Lin
- Hunan Provincial Key Lab of Dark Tea and Jin-hua, School of Materials and Chemical Engineering, Hunan City University, Yiyang413000, Hunan, China
| | - Wang Yihan
- Hunan Provincial Key Lab of Dark Tea and Jin-hua, School of Materials and Chemical Engineering, Hunan City University, Yiyang413000, Hunan, China
| | - Dong Meng
- Hunan Provincial Key Lab of Dark Tea and Jin-hua, School of Materials and Chemical Engineering, Hunan City University, Yiyang413000, Hunan, China
| | - Li Yanzi
- Hunan Provincial Key Lab of Dark Tea and Jin-hua, School of Materials and Chemical Engineering, Hunan City University, Yiyang413000, Hunan, China
| | - Xu Zhenggang
- Hunan Provincial Key Lab of Dark Tea and Jin-hua, School of Materials and Chemical Engineering, Hunan City University, Yiyang413000, Hunan, China
- College of Forestry, Northwest A & F University, Yangling712100, Shaanxi, China
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230
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Wang L, Hu Z, Wang Z, Zhu P, Wei G, Fan X, Huang J, Wang R, Wang H, Xie Y. Complete Mitogenome sequencing of the fish louse Argulus japonicus (Crustacea: Branchiura): Comparative analyses and phylogenetic implications. Front Vet Sci 2024; 11:1376898. [PMID: 38590542 PMCID: PMC10999652 DOI: 10.3389/fvets.2024.1376898] [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: 01/26/2024] [Accepted: 03/05/2024] [Indexed: 04/10/2024] Open
Abstract
The fish louse Argulus japonicus, a branchiuran crustacean of the Argulidae family, is attracting increasing attention because of its parasitic tendencies and significant health threats to global fish farming. The mitogenomes can yield a foundation for studying epidemiology, genetic diversity, and molecular ecology and therefore may be used to assist in the surveillance and control of A. japonicus. In this study, we sequenced and assembled the complete mitogenome of A. japonicus to shed light on its genetic and evolutionary blueprint. Our investigation indicated that the 15,045-bp circular genome of A. japonicus encodes 13 protein-coding genes (PCGs), 22 transfer RNAs (tRNAs), and 2 ribosomal RNAs (rRNAs) with significant AT and GC skews. Comparative genomics provided an evolutionary scenario for the genetic diversity of 13 PCGs: all were under purifying selection, with cox1 and nad6 having the lowest and highest evolutionary rates, respectively. Genome-wide phylogenetic trees established a close relationship between species of the families Argulidae (Arguloida) and Armilliferidae (Porocephalida) within Crustacea, and further, A. japonicus and Argulus americanus were determined to be more closely related to each other than to others within the family Argulidae. Single PCG-based phylogenies supported nad1 and nad6 as the best genetic markers for evolutionary and phylogenetic studies for branchiuran crustaceans due to their similar phylogenetic topologies with those of genome-based phylogenetic analyses. To sum up, these comprehensive mitogenomic data of A. japonicus and related species refine valuable marker resources and should contribute to molecular diagnostic methods, epidemiological investigations, and ecological studies of the fish ectoparasites in Crustacea.
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Affiliation(s)
- Lidan Wang
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Zun Hu
- Department of Food Technology and Science, College of Food Science, Shanghai Ocean University, Shanghai, China
| | - Zhao Wang
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Pengchen Zhu
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Guoshan Wei
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Xinyi Fan
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Jiali Huang
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Ruixi Wang
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Hui Wang
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Yue Xie
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
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231
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Akther KR, Hossain MA, Mian S, Chandra Roy N. Ecological Insights, and Fin Fish Diversity in Carps Spawning Grounds: Case Studies from the Surma River and Tanguar Haor, Bangladesh. SCIENTIFICA 2024; 2024:7195596. [PMID: 38566625 PMCID: PMC10985277 DOI: 10.1155/2024/7195596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 03/13/2024] [Accepted: 03/15/2024] [Indexed: 04/04/2024]
Abstract
This study aims to provide a thorough ecological understanding of fin fish diversity within carp spawning grounds in the Surma River and Tanguar haor. Over two spawning seasons, this research investigates ecological factors impacting fin fish diversity and abundance in carp spawning grounds of the Surma River and Tanguar haor, emphasizing water quality, habitat features, spawn availability, and environmental influences. Fish spawn samples were collected with eight "Savar nets" at chosen sites and reared in a fiberglass tank at the mini hatchery for species identification. The representative spawn samples were examined under a microscope for preliminary species identification before rearing. The study found that both the Surma River and Tanguar haor offer ideal conditions for carp spawning due to factors such as water quality, natural food availability, habitat suitability, and favorable climatic conditions. The study identified 39 fish species under the 10 fish groups from both locations, with a higher percentage of carp species (31.42%) in the Surma River in 2021 compared to 2022 (22.50%). In Tanguar haor, the percentage of carp species was 7.55% and 6.50% in 2021 and 2022, respectively. The Surma River's ecological indices (2021-2022) indicated decreased diversity, likely due to environmental degradation, while Tanguar haor showed lower diversity possibly attributable to multiple environmental stressors. The dominant carp species, Labeo calbasu, Labeo bata, and Labeo gonius, were identified in both the Surma River and Tanguar haor. The spawning distribution varied among different locations, with some sites showing a presence of carp species, such as Hajipur (T1) in the Surma River and Alam Duar (T2) in Tanguar haor. The findings highlight the importance of hydrological and environmental parameters in shaping carp spawning habitat distribution and abundance, contributing to aquatic biodiversity conservation and resource management.
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Affiliation(s)
- Kazi Rabeya Akther
- Laboratory of Aquatic Biodiversity and Ecophysiology, Department of Fish Biology and Genetics, Faculty of Fisheries, Sylhet Agricultural University, Sylhet 3100, Bangladesh
| | - Mohammad Amzad Hossain
- Laboratory of Aquatic Biodiversity and Ecophysiology, Department of Fish Biology and Genetics, Faculty of Fisheries, Sylhet Agricultural University, Sylhet 3100, Bangladesh
| | - Sohel Mian
- Laboratory of Aquatic Biodiversity and Ecophysiology, Department of Fish Biology and Genetics, Faculty of Fisheries, Sylhet Agricultural University, Sylhet 3100, Bangladesh
| | - Nirmal Chandra Roy
- Laboratory of Aquatic Biodiversity and Ecophysiology, Department of Fish Biology and Genetics, Faculty of Fisheries, Sylhet Agricultural University, Sylhet 3100, Bangladesh
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232
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Despabiladeras JB, Bautista MAM. Complete Mitochondrial Genome of the Eggplant Fruit and Shoot Borer, Leucinodes orbonalis Guenée (Lepidoptera: Crambidae), and Comparison with Other Pyraloid Moths. INSECTS 2024; 15:220. [PMID: 38667350 PMCID: PMC11050083 DOI: 10.3390/insects15040220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2024] [Revised: 03/17/2024] [Accepted: 03/18/2024] [Indexed: 04/28/2024]
Abstract
The eggplant fruit and shoot borer (EFSB) (Leucinodes orbonalis Guenée) is a devastating lepidopteran pest of eggplant (Solanum melongena L.) in the Philippines. Management of an insect pest like the EFSB requires an understanding of its biology, evolution, and adaptations. Genomic resources provide a starting point for understanding EFSB biology, as the resources can be used for phylogenetics and population structure studies. To date, genomic resources are scarce for EFSB; thus, this study generated its complete mitochondrial genome (mitogenome). The circular mitogenome is 15,244 bp-long. It contains 37 genes, namely 13 protein-coding, 22 tRNA, and 2 rRNA genes, and has conserved noncoding regions, motifs, and gene syntenies characteristic of lepidopteran mitogenomes. Some protein-coding genes start and end with non-canonical codons. The tRNA genes exhibit a conserved cloverleaf structure, with the exception in trnS1. Partitioned phylogenetic analysis using 72 pyraloids generated highly supported maximum likelihood and Bayesian inference trees revealing expected basal splits between Crambidae and Pyralidae, and Spilomelinae and Pyraustinae. Spilomelinae was recovered to be paraphyletic, with the EFSB robustly placed before the split of Spilomelinae and Pyraustinae. Overall, the EFSB mitogenome resource will be useful for delineations within Spilomelinae and population structure analysis.
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Affiliation(s)
| | - Ma. Anita M. Bautista
- Functional Genomics Laboratory, National Institute of Molecular Biology and Biotechnology, College of Science, University of the Philippines-Diliman, Quezon City 1101, Philippines;
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233
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Guo C, Wang Y, Li W, Cao J. The mitochondrial genome of Neoperla bimaculata (Li et al. 2021) (plecoptera: perlidae) from Tibet of southwest China and its phylogenetic analysis. Mitochondrial DNA B Resour 2024; 9:381-384. [PMID: 38529109 PMCID: PMC10962291 DOI: 10.1080/23802359.2024.2333564] [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: 12/18/2023] [Accepted: 03/15/2024] [Indexed: 03/27/2024] Open
Abstract
The complete mitochondrial genome (mitogenome) of Neoperla bimaculata was sequenced and annotated in this study. We found that the mitogenome of N. bimaculata is 15,774 bp in length with an A + T content of 64.3%. It exhibits the classic structure of a mitogenome. Most protein-coding genes (PCGs) of the mitogenome initiate with the standard start codon ATN. Ten PCGs use the standard stop codon TAA/TAG, while the COI, COII, and ND5 genes terminate with a single T nucleotide. Phylogenetic analyses suggested that N. bimaculata, along with two unpublished Neoperla species, formed a cluster within the phylogenetic tree. Our results indicated that the genus Neoperla and Neoperlops were sister groups. Meanwhile, the monophyly of Perlinae and Acroneuriinae was supported in the mitochondrial phylogeny.
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Affiliation(s)
- Caiyue Guo
- Henan International Joint Laboratory of Taxonomy and Systematic Evolution of Insecta, Henan Institute of Science and Technology, Xinxiang, China
| | - Ying Wang
- Henan International Joint Laboratory of Taxonomy and Systematic Evolution of Insecta, Henan Institute of Science and Technology, Xinxiang, China
| | - Weihai Li
- Henan International Joint Laboratory of Taxonomy and Systematic Evolution of Insecta, Henan Institute of Science and Technology, Xinxiang, China
| | - Jinjun Cao
- Henan International Joint Laboratory of Taxonomy and Systematic Evolution of Insecta, Henan Institute of Science and Technology, Xinxiang, China
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234
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Liao Y, Fang Y, Chen W, Wang J. Complete mitochondrial genome of Basilepta melanopus Lefèvre, 1893 (coleoptera: chrysomelidae: eumolpinae), a tea pest from Southern China. Mitochondrial DNA B Resour 2024; 9:394-397. [PMID: 38529112 PMCID: PMC10962304 DOI: 10.1080/23802359.2024.2333573] [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: 12/18/2023] [Accepted: 03/15/2024] [Indexed: 03/27/2024] Open
Abstract
The tea pest, Basilepta melanopus Lefèvre 1893 (Chrysomelidae), belongs to the subfamily Eumolpinae. In this study, the complete mitochondrial genome sequence of B. melanopus from southern China was sequenced using the next-generation sequencing technique, assembled, and annotated using bioinformatics tools. The complete mitochondrial genome was 15,905 bp in length. The overall GC content was 22.51%, in which the percentages for the bases A, T, C, and G were 41.23%, 36.26%, 8.92%, and 13.59%, respectively. Thirty-seven genes were predicted, including 13 protein-coding, 22 transfer RNA, and two ribosomal RNA genes. Phylogenetic analysis based on the complete mitochondrial genome sequences of 18 Chrysomelidae taxa revealed that B. melanopus was closely related to Basilepta fulvipes.
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Affiliation(s)
- Yonglin Liao
- Institute of Plant Protection, Guangdong Academy of Agricultural Science, Guangdong Provincial Key Laboratory High Technology for Plant Protection, Guangzhou, China
| | - Yurong Fang
- Tianyang Plant Protection Station, Baise, China
| | - Weiping Chen
- Institute of Plant Protection, Guangdong Academy of Agricultural Science, Guangdong Provincial Key Laboratory High Technology for Plant Protection, Guangzhou, China
| | - Jihua Wang
- Guangdong Key Laboratory for Crops Genetic Improvement, Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
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235
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Zhang Q, Lu YW, Liu XY, Li Y, Gao WN, Sun JT, Hong XY, Shao R, Xue XF. Phylogenomics resolves the higher-level phylogeny of herbivorous eriophyoid mites (Acariformes: Eriophyoidea). BMC Biol 2024; 22:70. [PMID: 38519936 PMCID: PMC10960459 DOI: 10.1186/s12915-024-01870-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2023] [Accepted: 03/14/2024] [Indexed: 03/25/2024] Open
Abstract
BACKGROUND Eriophyoid mites (Eriophyoidea) are among the largest groups in the Acariformes; they are strictly phytophagous. The higher-level phylogeny of eriophyoid mites, however, remains unresolved due to the limited number of available morphological characters-some of them are homoplastic. Nevertheless, the eriophyoid mites sequenced to date showed highly variable mitochondrial (mt) gene orders, which could potentially be useful for resolving the higher-level phylogenetic relationships. RESULTS Here, we sequenced and compared the complete mt genomes of 153 eriophyoid mite species, which showed 54 patterns of rearranged mt gene orders relative to that of the hypothetical ancestor of arthropods. The shared derived mt gene clusters support the monophyly of eriophyoid mites (Eriophyoidea) as a whole and the monophylies of six clades within Eriophyoidea. These monophyletic groups and their relationships were largely supported in the phylogenetic trees inferred from mt genome sequences as well. Our molecular dating results showed that Eriophyoidea originated in the Triassic and diversified in the Cretaceous, coinciding with the diversification of angiosperms. CONCLUSIONS This study reveals multiple molecular synapomorphies (i.e. shared derived mt gene clusters) at different levels (i.e. family, subfamily or tribe level) from the complete mt genomes of 153 eriophyoid mite species. We demonstrated the use of derived mt gene clusters in unveiling the higher-level phylogeny of eriophyoid mites, and underlines the origin of these mites and their co-diversification with angiosperms.
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Affiliation(s)
- Qi Zhang
- Department of Entomology, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Yi-Wen Lu
- Department of Entomology, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Xin-Yu Liu
- Department of Entomology, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Ye Li
- Department of Entomology, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Wei-Nan Gao
- Department of Entomology, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Jing-Tao Sun
- Department of Entomology, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Xiao-Yue Hong
- Department of Entomology, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Renfu Shao
- Centre for Bioinnovation, School of Science, Technology and Engineering, University of the Sunshine Coast, Sippy Downs, Queensland, 4556, Australia
| | - Xiao-Feng Xue
- Department of Entomology, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China.
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236
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Wu T, Ma R, Pan X, Wang F, Zhang Z, Shi Q, Shan X, Gao G. Comparison of the efficacy of Aeromonas veronii Δ hisJ vaccine in Carassius auratus via different immunization routes. Front Vet Sci 2024; 11:1378448. [PMID: 38577546 PMCID: PMC10993147 DOI: 10.3389/fvets.2024.1378448] [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: 01/29/2024] [Accepted: 03/12/2024] [Indexed: 04/06/2024] Open
Abstract
Introdction Aeromonas veronii is a significant pathogen to various aquatic life. Infections in fish can lead to high mortality rates, causing substantial economic losses in aquaculture. Vaccination is proposed as a substitute for antibiotics in aquaculture to decrease disease-related mortality and morbidity. Our study previously constructed a hisJ-deleted strain of A. veronii, which provided protective effect to Loach. Methods To further assess the vaccine's applicability, this study evaluated its genetic stability and safety, and the immune protective effects in Carassius auratus through four distinct administration routes: intraperitoneal injection, intramuscular injection, oral administration, and immersion, to determine the efficacy of these administration routes. Results The results showed that the vaccine remained genetically stable after 45 generations. Immunization via these administration routes was safe for Carassius auratus, with intraperitoneal and intramuscular injections causing stronger adverse reactions. Immersion immunization resulted in mild adverse reactions, and no significant adverse reactions were observed following oral immunization. Immunizing Carassius auratus at safe concentrations via these routes enhanced the phagocytic activity in serum, increased the levels of non-specific immune-related enzymes (ACP, AKP, C3, C4, LZM, SOD, and IgM), and improved specific serum antibody levels. It also elevated levels of cytokines related to inflammatory responses (IL-1β, IL-10, TNF-α, TGF-β) in organ tissues (liver, spleen, kidney, mid-post intestine, and gills). The survival rates of Carassius auratus were measured after challenging with the virulent strain A. veronii TH0426, resulting in the relative survival rates of 64% for Intraperitoneal vaccine group, 56% for Intramuscular vaccine group, 52% for oral vaccine group, and 48% for immersion vaccine group. Analysis of bacterial load in the liver, spleen, and kidney post-challenge showed a decreasing trend in the control group, indicating that the vaccine strain ΔhisJ could gradually restrict the rapid proliferation of bacteria in these tissues, thereby providing a certain level of immune protection against A. veronii. Discussion In brief, the vaccine strain ΔhisJ can serve as a safe live attenuated vaccine for Carassius auratus, and this study lays the foundation for the development of live attenuated vaccines against Aeromonas veronii.
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Affiliation(s)
- Tonglei Wu
- College of Animal Science and Technology, Hebei Normal University of Science & Technology, Qinhuangdao, China
| | - Ruitao Ma
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, China
| | - Xiaoyi Pan
- Zhejiang Institute of Freshwater Fisheries, Huzhou, China
| | - Fengjie Wang
- College of Animal Science and Technology, Hebei Normal University of Science & Technology, Qinhuangdao, China
| | - Zhiqiang Zhang
- College of Animal Science and Technology, Hebei Normal University of Science & Technology, Qinhuangdao, China
| | - Qiumei Shi
- College of Animal Science and Technology, Hebei Normal University of Science & Technology, Qinhuangdao, China
| | - Xiaofeng Shan
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, China
| | - Guisheng Gao
- College of Animal Science and Technology, Hebei Normal University of Science & Technology, Qinhuangdao, China
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237
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Ibragimova M, Kussainova A, Aripova A, Bersimbaev R, Bulgakova O. The Molecular Mechanisms in Senescent Cells Induced by Natural Aging and Ionizing Radiation. Cells 2024; 13:550. [PMID: 38534394 DOI: 10.3390/cells13060550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Revised: 03/17/2024] [Accepted: 03/19/2024] [Indexed: 03/28/2024] Open
Abstract
This review discusses the relationship between cellular senescence and radiation exposure. Given the wide range of ionizing radiation sources encountered by people in professional and medical spheres, as well as the influence of natural background radiation, the question of the effect of radiation on biological processes, particularly on aging processes, remains highly relevant. The parallel relationship between natural and radiation-induced cellular senescence reveals the common aspects underlying these processes. Based on recent scientific data, the key points of the effects of ionizing radiation on cellular processes associated with aging, such as genome instability, mitochondrial dysfunction, altered expression of miRNAs, epigenetic profile, and manifestation of the senescence-associated secretory phenotype (SASP), are discussed. Unraveling the molecular mechanisms of cellular senescence can make a valuable contribution to the understanding of the molecular genetic basis of age-associated diseases in the context of environmental exposure.
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Affiliation(s)
- Milana Ibragimova
- Department of General Biology and Genomics, Institute of Cell Biology and Biotechnology, L.N. Gumilyov Eurasian National University, Astana 010008, Kazakhstan
| | - Assiya Kussainova
- Department of General Biology and Genomics, Institute of Cell Biology and Biotechnology, L.N. Gumilyov Eurasian National University, Astana 010008, Kazakhstan
- Department of Health Sciences, University of Genova, Via Pastore 1, 16132 Genoa, Italy
| | - Akmaral Aripova
- Department of General Biology and Genomics, Institute of Cell Biology and Biotechnology, L.N. Gumilyov Eurasian National University, Astana 010008, Kazakhstan
| | - Rakhmetkazhi Bersimbaev
- Department of General Biology and Genomics, Institute of Cell Biology and Biotechnology, L.N. Gumilyov Eurasian National University, Astana 010008, Kazakhstan
| | - Olga Bulgakova
- Department of General Biology and Genomics, Institute of Cell Biology and Biotechnology, L.N. Gumilyov Eurasian National University, Astana 010008, Kazakhstan
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238
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Benito JB, Porter ML, Niemiller ML. Comparative mitogenomic analysis of subterranean and surface amphipods (Crustacea, Amphipoda) with special reference to the family Crangonyctidae. BMC Genomics 2024; 25:298. [PMID: 38509489 PMCID: PMC10956265 DOI: 10.1186/s12864-024-10111-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 02/09/2024] [Indexed: 03/22/2024] Open
Abstract
Mitochondrial genomes play important roles in studying genome evolution, phylogenetic analyses, and species identification. Amphipods (Class Malacostraca, Order Amphipoda) are one of the most ecologically diverse crustacean groups occurring in a diverse array of aquatic and terrestrial environments globally, from freshwater streams and lakes to groundwater aquifers and the deep sea, but we have a limited understanding of how habitat influences the molecular evolution of mitochondrial energy metabolism. Subterranean amphipods likely experience different evolutionary pressures on energy management compared to surface-dwelling taxa that generally encounter higher levels of predation and energy resources and live in more variable environments. In this study, we compared the mitogenomes, including the 13 protein-coding genes involved in the oxidative phosphorylation (OXPHOS) pathway, of surface and subterranean amphipods to uncover potentially different molecular signals of energy metabolism between surface and subterranean environments in this diverse crustacean group. We compared base composition, codon usage, gene order rearrangement, conducted comparative mitogenomic and phylogenomic analyses, and examined evolutionary signals of 35 amphipod mitogenomes representing 13 families, with an emphasis on Crangonyctidae. Mitogenome size, AT content, GC-skew, gene order, uncommon start codons, location of putative control region (CR), length of rrnL and intergenic spacers differed between surface and subterranean amphipods. Among crangonyctid amphipods, the spring-dwelling Crangonyx forbesi exhibited a unique gene order, a long nad5 locus, longer rrnL and rrnS loci, and unconventional start codons. Evidence of directional selection was detected in several protein-encoding genes of the OXPHOS pathway in the mitogenomes of surface amphipods, while a signal of purifying selection was more prominent in subterranean species, which is consistent with the hypothesis that the mitogenome of surface-adapted species has evolved in response to a more energy demanding environment compared to subterranean amphipods. Overall, gene order, locations of non-coding regions, and base-substitution rates points to habitat as an important factor influencing the evolution of amphipod mitogenomes.
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Affiliation(s)
- Joseph B Benito
- Department of Biological Sciences, The University of Alabama in Huntsville, Huntsville, AL, 35899, USA
| | - Megan L Porter
- School of Life Sciences, University of Hawai'i at Mānoa, Honolulu, HI, 96822, USA
| | - Matthew L Niemiller
- Department of Biological Sciences, The University of Alabama in Huntsville, Huntsville, AL, 35899, USA.
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239
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Ben Romdhane W, Al-Doss A, Hassairi A. The newly assembled chloroplast genome of Aeluropus littoralis: molecular feature characterization and phylogenetic analysis with related species. Sci Rep 2024; 14:6472. [PMID: 38499663 PMCID: PMC10948853 DOI: 10.1038/s41598-024-57141-8] [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: 01/04/2024] [Accepted: 03/14/2024] [Indexed: 03/20/2024] Open
Abstract
Aeluropus littoralis, a halophyte grass, is widely distributed from the Mediterranean to the Indian subcontinent through the Mongolian Gobi. This model halophyte has garnered increasing attention owing to its use as forage and its high tolerance to environmental stressors. The chloroplast genomes of many plants have been extensively examined for molecular, phylogenetic and transplastomic applications. However, no published research on the A. littoralis chloroplast (cp) genome was discovered. Here, the entire chloroplast genome of A. littoralis was assembled implementing accurate long-read sequences. The entire chloroplast genome, with an estimated length of 135,532 bp (GC content: 38.2%), has a quadripartite architecture and includes a pair of inverted repeat (IR) regions, IRa and IRb (21,012 bp each), separated by a large and a small single-copy regions (80,823 and 12,685 bp, respectively). The features of A. littoralis consist of 133 genes that synthesize 87 peptides, 38 transfer RNAs, and 8 ribosomal RNAs. Of these genes, 86 were unique, whereas 19 were duplicated in IR regions. Additionally, a total of forty-six simple sequence repeats, categorized into 32-mono, four-di, two-tri, and eight-tetranucleotides, were discovered. Furthermore, ten sets of repeats greater than 20 bp were located primarily in the LSC region. Evolutionary analysis based on chloroplast sequence data revealed that A. littoralis with A. lagopoides and A. sinensis belong to the Aeluropodinae subtribe, which is a sister to the Eleusininae in the tribe Cynodonteae and the subfamily Chloridoideae. This subfamily belongs to the PACMAD clade, which contains the majority of the C4 photosynthetic plants in the Poaceae. The newly constructed A. littoralis cp genome offers valuable knowledge for DNA barcoding, phylogenetic, transplastomic research, and other biological studies.
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Affiliation(s)
- Walid Ben Romdhane
- College of Food and Agricultural Sciences, Plant Production Department, King Saud University, P.O. Box 2460, 11451, Riyadh, Saudi Arabia.
| | - Abdullah Al-Doss
- College of Food and Agricultural Sciences, Plant Production Department, King Saud University, P.O. Box 2460, 11451, Riyadh, Saudi Arabia
| | - Afif Hassairi
- College of Food and Agricultural Sciences, Plant Production Department, King Saud University, P.O. Box 2460, 11451, Riyadh, Saudi Arabia.
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240
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Pedersen KM, von Beeren C, Oggioni A, Blüthgen N. Mammal dung-dung beetle trophic networks: an improved method based on gut-content DNA. PeerJ 2024; 12:e16627. [PMID: 38500531 PMCID: PMC10946388 DOI: 10.7717/peerj.16627] [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: 01/07/2023] [Accepted: 11/16/2023] [Indexed: 03/20/2024] Open
Abstract
Background Dung beetles provide many important ecosystem services, including dung decomposition, pathogen control, soil aeration, and secondary seed dispersal. Yet, the biology of most dung beetles remains unknown. Natural diets are poorly studied, partly because previous research has focused on choice or attraction experiments using few, easily accessible dung types from zoo animals, farm animals, or humans. This way, many links within natural food webs have certainly been missed. In this work, we aimed to establish a protocol to analyze the natural diets of dung beetles using DNA gut barcoding. Methods First, the feasibility of gut-content DNA extraction and amplification of 12s rDNA from six different mammal dung types was tested in the laboratory. We then applied the method to beetles caught in pitfall traps in Ecuador and Germany by using 12s rDNA primers. For a subset of the dung beetles caught in the Ecuador sampling, we also used 16s rDNA primers to see if these would improve the number of species we could identify. We predicted the likelihood of amplifying DNA using gut fullness, DNA concentration, PCR primer, collection method, and beetle species as predictor variables in a dominance analysis. Based on the gut barcodes, we generated a dung beetle-mammal network for both field sites (Ecuador and Germany) and analyzed the levels of network specificity. Results We successfully amplified mammal DNA from dung beetle gut contents for 128 specimens, which included such prominent species as Panthera onca (jaguar) and Puma concolor (puma). The overall success rate of DNA amplification was 53%. The best predictors for amplification success were gut fullness and DNA concentration, suggesting the success rate can be increased by focusing on beetles with a full gut. The mammal dung-dung beetle networks differed from purely random network models and showed a moderate degree of network specialization (H2': Ecuador = 0.49; Germany = 0.41). Conclusion We here present a reliable method of extracting and amplifying gut-content DNA from dung beetles. Identifying mammal dung via DNA reference libraries, we created mammal dung-dung beetle trophic networks. This has benefits over previous methods because we inventoried the natural mammal dung resources of dung beetles instead of using artificial mammal baits. Our results revealed higher levels of specialization than expected and more rodent DNA than expected in Germany, suggesting that the presented method provides more detailed insights into mammal dung-dung beetle networks. In addition, the method could have applications for mammal monitoring in many ecosystems.
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Affiliation(s)
- Karen M. Pedersen
- Biology, Technical University of Darmstadt, Darmstadt, Hessen, Germany
| | | | - Arianna Oggioni
- Biology, Technical University of Darmstadt, Darmstadt, Hessen, Germany
| | - Nico Blüthgen
- Biology, Technical University of Darmstadt, Darmstadt, Hessen, Germany
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241
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Shi L, Jiao Y, Xue F, Yu XL, Yin X, Xu LL, Chen J, Wang B, Guo DX, Cheng XL, Ma SC, Liu HB, Lin YQ. Discovery and identification of interspecies peptide biomarkers in the seahorse species using liquid chromatography tandem mass spectrometry and chemometrics. J Pharm Biomed Anal 2024; 240:115967. [PMID: 38219441 DOI: 10.1016/j.jpba.2024.115967] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 01/04/2024] [Accepted: 01/04/2024] [Indexed: 01/16/2024]
Abstract
Seahorses have important edible and medicinal values including strengthening the body, tonifying the liver and kidneys, and reducing swelling. And there are abundant seahorse species on Earth. Many seahorses have large price differences due to the scarcity of resources, and some seahorses with similar appearances appear to be confused for use. While in market trading, Hippocampus is susceptible to loss of specialized morphology characteristics, making it difficult to distinguish between specific species. Here we report an effective method based on peptide biomarkers for the identification of seahorse species. Peptide biomarkers for each species were predicted using nano-liquid chromatography-tandem mass spectrometry (Nano-LC-MS/MS) combined with chemometrics software. One unique biomarker peptide for each species was synthesized and verified, and finally developed a liquid chromatography tandem mass spectrometry (LC-MS/MS) multiple reaction monitoring method. The results indicate that the method has great potential for species-specific identification of seahorses and their preparations, among others.
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Affiliation(s)
- Li Shi
- Shandong Engineering Laboratory for Standard Innovation and Quality Evaluation of TCM, Shangdong Engineering Research Center for Generic Technologies of Traditional Chinese Medicine Formula Granules, NMPA Key Laboratory for Quality Evaluation of Gelatin Products, Shandong Institute for Food and Drug Control, Jinan 250101, China; Ocean University of China, Qingdao 266003, China
| | - Yang Jiao
- Shandong Engineering Laboratory for Standard Innovation and Quality Evaluation of TCM, Shangdong Engineering Research Center for Generic Technologies of Traditional Chinese Medicine Formula Granules, NMPA Key Laboratory for Quality Evaluation of Gelatin Products, Shandong Institute for Food and Drug Control, Jinan 250101, China
| | - Fei Xue
- Shandong Engineering Laboratory for Standard Innovation and Quality Evaluation of TCM, Shangdong Engineering Research Center for Generic Technologies of Traditional Chinese Medicine Formula Granules, NMPA Key Laboratory for Quality Evaluation of Gelatin Products, Shandong Institute for Food and Drug Control, Jinan 250101, China
| | - Xin-Lan Yu
- Xinjiang Uygur Autonomous Region Institute for drug Inspection and Reasearch Institute, Urumqi 830054, China
| | - Xue Yin
- Shandong Engineering Laboratory for Standard Innovation and Quality Evaluation of TCM, Shangdong Engineering Research Center for Generic Technologies of Traditional Chinese Medicine Formula Granules, NMPA Key Laboratory for Quality Evaluation of Gelatin Products, Shandong Institute for Food and Drug Control, Jinan 250101, China
| | - Li-Li Xu
- Shandong Engineering Laboratory for Standard Innovation and Quality Evaluation of TCM, Shangdong Engineering Research Center for Generic Technologies of Traditional Chinese Medicine Formula Granules, NMPA Key Laboratory for Quality Evaluation of Gelatin Products, Shandong Institute for Food and Drug Control, Jinan 250101, China
| | - Juan Chen
- Shandong University of Traditional Chinese Medicine, Jinan 250101, China
| | - Bing Wang
- Shandong Engineering Laboratory for Standard Innovation and Quality Evaluation of TCM, Shangdong Engineering Research Center for Generic Technologies of Traditional Chinese Medicine Formula Granules, NMPA Key Laboratory for Quality Evaluation of Gelatin Products, Shandong Institute for Food and Drug Control, Jinan 250101, China
| | - Dong-Xiao Guo
- Shandong Engineering Laboratory for Standard Innovation and Quality Evaluation of TCM, Shangdong Engineering Research Center for Generic Technologies of Traditional Chinese Medicine Formula Granules, NMPA Key Laboratory for Quality Evaluation of Gelatin Products, Shandong Institute for Food and Drug Control, Jinan 250101, China
| | - Xian-Long Cheng
- National Institutes for Food and Drug Control, Beijing 100050, China
| | - Shuang-Cheng Ma
- National Institutes for Food and Drug Control, Beijing 100050, China
| | | | - Yong-Qiang Lin
- Shandong Engineering Laboratory for Standard Innovation and Quality Evaluation of TCM, Shangdong Engineering Research Center for Generic Technologies of Traditional Chinese Medicine Formula Granules, NMPA Key Laboratory for Quality Evaluation of Gelatin Products, Shandong Institute for Food and Drug Control, Jinan 250101, China; Ocean University of China, Qingdao 266003, China.
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242
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Wang H, Zeng S, Zhang Z, Yang D. The complete mitochondrial genome of Rhynchocinetes brucei Okuno 1994 (Decapoda: Rhynchocinetidae). Mitochondrial DNA B Resour 2024; 9:347-351. [PMID: 38476839 PMCID: PMC10930117 DOI: 10.1080/23802359.2023.2261636] [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: 07/10/2023] [Accepted: 09/17/2023] [Indexed: 03/14/2024] Open
Abstract
We report the complete mitochondrial genome of Rhynchocinetes brucei Okuno 1994. The mitogenome was found to contain 16158 bp with 13 protein-coding genes (PCGs), 22 tRNA genes (tRNAs), 2 rRNA genes (rRNAs), and 1 putative control region. Phylogenetic analysis indicated that R. brucei was sister to Rhynchocinetes durbanensis (PP= 1), of the same family Rhynchocinetidae. These results are helpful for research on the phylogenetic and evolutionary studies of this group.
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Affiliation(s)
- Hangjun Wang
- Wenzhou Marine Center, Ministry of Natural Resources of the People’s Republic of China, Beijing, China
- Marine Ecosystem Observation and Research Station on the Yangtze River Estuary, Wenzhou, China
| | - Sheng Zeng
- College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Zhao Zhang
- Wenzhou Marine Center, Ministry of Natural Resources of the People’s Republic of China, Beijing, China
- Marine Ecosystem Observation and Research Station on the Yangtze River Estuary, Wenzhou, China
| | - Deyuan Yang
- College of the Environment and Ecology, Xiamen University, Xiamen, China
- National Taiwan Ocean University, Keelung, Taiwan, China
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243
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Fan F, Pei L, Jiang L, Ye Y, Liu Y, Liu B. Gene Rearrangements in the Mitochondrial Genome of Gonatopsis borealis and Onychoteuthis compacta Reveal Their Phylogenetic Implications for Oegopsida. Biochem Genet 2024:10.1007/s10528-024-10707-7. [PMID: 38466493 DOI: 10.1007/s10528-024-10707-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Accepted: 01/16/2024] [Indexed: 03/13/2024]
Abstract
The complete mitochondrial genome provides crucial information for comprehending gene rearrangement, molecular evolution, and phylogenetic analysis. Here, we have determined the complete mitogenome sequence of Gonatopsis borealis and Onychoteuthis compacta for the first time. Their genome sizes were 20,148 bp and 20,491 bp, respectively, including 18 protein-coding genes, COI-COIII, ATP6, and ATP8 are duplicated, 23 transfer RNA genes, and 2 ribosomal RNA (rRNA) genes (12S and 16S rRNA). Specifically, the overall A+T content is 70.69% and 72.67%. It shows a significant AT bias. The whole mitogenomes indicate positive AT skew (0.070 and 0.062). Furthermore, the gene order has been rearranged within Oegopsida. The tandem duplication random loss model was determined as most likely to explain the observed gene rearrangements. Phylogenetic analysis was performed, and the result tree was found to be consistent with the morphological identification classification. Estimation of divergence time for 35 species showed that the main differentiation of Oegopsida occurred in 140.70 Mya. These results will help to better understand the gene rearrangements and evolution of G. borealis and O. compacta and lay a foundation for further phylogeny genetic studies of Oegopsida.
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Affiliation(s)
- Fan Fan
- National Engineering Research Center of Marine Facilities Aquaculture, Zhejiang Ocean University, Zhoushan, 316022, China
| | - Liyi Pei
- National Engineering Research Center of Marine Facilities Aquaculture, Zhejiang Ocean University, Zhoushan, 316022, China
| | - Lihua Jiang
- National Engineering Research Center of Marine Facilities Aquaculture, Zhejiang Ocean University, Zhoushan, 316022, China.
| | - Yingying Ye
- National Engineering Research Center of Marine Facilities Aquaculture, Zhejiang Ocean University, Zhoushan, 316022, China
| | - Yifan Liu
- National Engineering Research Center of Marine Facilities Aquaculture, Zhejiang Ocean University, Zhoushan, 316022, China
| | - Bilin Liu
- College of Marine Sciences, Shanghai Ocean University, Shanghai, 201306, China
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244
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Lu H, Nie Y, Huang B. The second complete mitochondrial genome of Capillidium rhysosporum within the family Capillidiaceae, Entomophthorales. Mitochondrial DNA B Resour 2024; 9:332-337. [PMID: 38476836 PMCID: PMC10930110 DOI: 10.1080/23802359.2024.2324938] [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: 01/03/2024] [Accepted: 02/24/2024] [Indexed: 03/14/2024] Open
Abstract
The complete mitochondrial genome of the entomophthoroid fungus Capillidium rhysosporum (strain no.: ATCC 12588) was sequenced using next-generation sequencing technology. The assembled circular genome has a length of 46,756 base pairs with a GC content of 27.06%. Gene prediction identified 15 core protein-coding genes (PCGs), two rRNA genes, and 27 tRNA genes. Phylogenetic analysis confirmed that C. rhysosporum belongs to the Zoopagomycota clade and is closely related to C. heterosporum. This study presents the second complete mitochondrial genome within the family Capillidiaceae, contributing to the mitochondrial DNA database of entomophthoroid fungi.
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Affiliation(s)
- Hanwen Lu
- Anhui Provincial Key Laboratory for Microbial Pest Control, Anhui Agricultural University, Hefei, China
| | - Yong Nie
- School of Civil Engineering and Architecture, Anhui University of Technology, Ma’anshan, China
| | - Bo Huang
- Anhui Provincial Key Laboratory for Microbial Pest Control, Anhui Agricultural University, Hefei, China
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245
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Chandra S, Abhilash R, Sidharthan A, Raghavan R, Dahanukar N. Complete mitogenome of Lepidopygopsis typus, an evolutionarily-distinct, endangered cyprinid fish from the Western Ghats Biodiversity Hotspot: Phylogenetic relationships and implications for conservation. Gene 2024; 898:148098. [PMID: 38128794 DOI: 10.1016/j.gene.2023.148098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2023] [Revised: 12/08/2023] [Accepted: 12/18/2023] [Indexed: 12/23/2023]
Abstract
The mitogenome of Lepidopygopsis typus, an evolutionarily distinct, endangered, cyprinid fish from the Western Ghats Biodiversity Hotspot, was characterized. Total length of the mitogenome was 16,729 bp, and comprised of 13 protein coding, 22 tRNA and two rRNA genes. Thirteen protein coding genes contributed a total nucleotide length of 11,408 bp, which coded for a total of 3794 amino acids and accounting for 68.2 % of the mitogenome. A maximum likelihood phylogenetic tree based on mitogenomes of members of cyprinid subfamilies Torinae, Schizothoracinae and Schizopygopsinae, recovered L. typus in a well-resolved clade of Torinae with members of the Western Ghats endemic genus Hypselobarbus as sister taxa. Selection analysis suggested that the branch of L. typus and Hypselobarbus spp. was under intensified selection with reference to other members of Torinae. There were 19 codons under diversifying selection in L. typus, which could be the result of positive selection for adapting to high-altitude, upstream tributaries of Periyar River, where the species has a restricted distribution. With respect to Hypselobarbus spp., L. typus was under relaxed selection with about 68 % of codons experiencing neutral evolution. Restricted distribution, low population size and relaxation in selection can likely trigger extinction in L. typus, and therefore urgent conservation and monitoring plans are required to secure the future of this evolutionary distinct, and globally endangered species.
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Affiliation(s)
- Swetha Chandra
- Zoology Research Group, St. Stephen's College, Pathanapuram, University of Kerala, India
| | - Ravimohanan Abhilash
- Department of Zoology, Christian College, Chengannur, University of Kerala, Kerala, India
| | - Arya Sidharthan
- Faculty of Ocean Science and Technology, Kerala University of Fisheries and Ocean Studies (KUFOS), Kochi, India
| | - Rajeev Raghavan
- Department of Fisheries Resource Management, Kerala University of Fisheries and Ocean Studies (KUFOS), Kochi, India
| | - Neelesh Dahanukar
- Department of Life Sciences, School of Natural Sciences, Shiv Nadar Institution of Eminence, Delhi-NCR, India.
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246
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Escobar Camacho D, Barragán KS, Guayasamin JM, Gavilanes G, Encalada AC. New records of native and introduced fish species in a river basin of Western Ecuador, the Chocó-Darien Ecoregion, using DNA barcoding. PLoS One 2024; 19:e0298970. [PMID: 38457426 PMCID: PMC10923491 DOI: 10.1371/journal.pone.0298970] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Accepted: 02/01/2024] [Indexed: 03/10/2024] Open
Abstract
DNA barcoding, based on mitochondrial markers, is widely applied in species identification and biodiversity studies. The aim of this study was to establish a barcoding reference database of fishes inhabiting the Cube River from Western Ecuador in the Chocó-Darien Global Ecoregion (CGE), a threatened ecoregion with high diversity and endemism, and evaluate the applicability of using barcoding for the identification of fish species. Barcode sequences were obtained from seven orders, 17 families, 23 genera and 26 species, which were validated through phylogenetic analysis, morphological measurements, and literature review. Our results showed that 43% of fish species in this region are endemic, confirmed the presence of known species in the area, and included the addition of three new records of native (Hoplias microlepis, Rhamdia guatemalensis and Sicydium salvini) and an introduced species (Xiphophorus maculatus) to Ecuador. In addition, eight species were barcoded for the first time. Species identification based on barcoding and morphology showed discrepancy with species lists from previous studies in the CGE, suggesting that the current baseline of western fishes of Ecuador is still incomplete. Because this study analyzed fishes from a relatively small basin (165 km2), more molecular-based studies focusing on fish are needed to achieve a robust sequence reference library of species inhabiting Western Ecuador. The new sequences of this study will be useful for future comparisons and biodiversity monitoring, supporting the application of barcoding tools for studying fish diversity in genetically unexplored regions and to develop well-informed conservation programs.
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Affiliation(s)
- Daniel Escobar Camacho
- Laboratorio de Ecología Acuática, Instituto BIOSFERA, Universidad San Francisco de Quito, Quito, Ecuador
| | - Karla S. Barragán
- Laboratorio de Ecología Acuática, Instituto BIOSFERA, Universidad San Francisco de Quito, Quito, Ecuador
| | - Juan M. Guayasamin
- Laboratorio de Biología Evolutiva, Instituto BIOSFERA, Universidad San Francisco de Quito, Quito, Ecuador
| | - Gabriela Gavilanes
- Laboratorio de Biología Evolutiva, Instituto BIOSFERA, Universidad San Francisco de Quito, Quito, Ecuador
| | - Andrea C. Encalada
- Laboratorio de Ecología Acuática, Instituto BIOSFERA, Universidad San Francisco de Quito, Quito, Ecuador
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247
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Diehl N, Li H, Scheschonk L, Burgunter-Delamare B, Niedzwiedz S, Forbord S, Sæther M, Bischof K, Monteiro C. The sugar kelp Saccharina latissima I: recent advances in a changing climate. ANNALS OF BOTANY 2024; 133:183-212. [PMID: 38109285 PMCID: PMC10921839 DOI: 10.1093/aob/mcad173] [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: 07/10/2023] [Revised: 09/26/2023] [Accepted: 11/07/2023] [Indexed: 12/20/2023]
Abstract
BACKGROUND The sugar kelp Saccharina latissima is a Laminariales species widely distributed in the Northern Hemisphere. Its physiology and ecology have been studied since the 1960s, given its ecological relevance on western temperate coasts. However, research interest has been rising recently, driven mainly by reports of negative impacts of anthropogenically induced environmental change and by the increased commercial interest in cultivating the species, with several industrial applications for the resulting biomass. SCOPE We used a variety of sources published between 2009 to May 2023 (but including some earlier literature where required), to provide a comprehensive review of the ecology, physiology, biochemical and molecular biology of S. latissima. In so doing we aimed to better understand the species' response to stressors in natural communities, but also inform the sustainable cultivation of the species. CONCLUSION Due to its wide distribution, S. latissima has developed a variety of physiological and biochemical mechanisms to adjust to environmental changes, including adjustments in photosynthetic parameters, modulation of osmolytes and antioxidants, reprogramming of gene expression and epigenetic modifications, among others summarized in this review. This is particularly important because massive changes in the abundance and distribution of S. latissima have already been observed. Namely, presence and abundance of S. latissima has significantly decreased at the rear edges on both sides of the Atlantic, and increased in abundance at the polar regions. These changes were mainly caused by climate change and will therefore be increasingly evident in the future. Recent developments in genomics, transcriptomics and epigenomics have clarified the existence of genetic differentiation along its distributional range with implications in the fitness at some locations. The complex biotic and abiotic interactions unraveled here demonstrated the cascading effects the disappearance of a kelp forest can have in a marine ecosystem. We show how S. latissima is an excellent model to study acclimation and adaptation to environmental variability and how to predict future distribution and persistence under climate change.
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Affiliation(s)
- Nora Diehl
- Marine Botany, Faculty of Biology and Chemistry, University of Bremen, 28359 Bremen, Germany
| | - Huiru Li
- Key Laboratory of Mariculture (Ministry of Education), Fisheries College, Ocean University of China, Qingdao 266003, China
| | | | - Bertille Burgunter-Delamare
- Matthias Schleiden Institute of Genetics, Bioinformatics and Molecular Botany, Friedrich Schiller University Jena, 07743 Jena, Germany
| | - Sarina Niedzwiedz
- Marine Botany, Faculty of Biology and Chemistry, University of Bremen, 28359 Bremen, Germany
| | - Silje Forbord
- Department of Fisheries and New Biomarine Industry, SINTEF Ocean AS, 7465 Trondheim, Norway
| | - Maren Sæther
- Seaweed Solutions AS, Bynesveien 50C, 7018 Trondheim, Norway
| | - Kai Bischof
- Marine Botany, Faculty of Biology and Chemistry, University of Bremen, 28359 Bremen, Germany
| | - Catia Monteiro
- CIBIO, Research Centre in Biodiversity and Genetic Resources – InBIO Associate Laboratory, Campus of Vairão, University of Porto, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus of Vairão, Vairão, Portugal
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Yussif I, Kugonza DR, Masembe C. Uganda chicken genetic resources: II. genetic diversity and population demographic history inferred from mitochondrial DNA D-loop sequences. Front Genet 2024; 15:1325569. [PMID: 38516375 PMCID: PMC10955702 DOI: 10.3389/fgene.2024.1325569] [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: 10/21/2023] [Accepted: 02/12/2024] [Indexed: 03/23/2024] Open
Abstract
The genetic diversity of indigenous chickens, which comprise over 80% of the chicken resources in Uganda, is largely not well-characterized for their genetic contribution. This study assessed the genetic diversity and population structure of the indigenous chicken population in Uganda to serve as an essential component for improvement and conservation strategies. A set of 344 mitochondrial DNA (mtDNA) D-loop sequences among 12 Ugandan chicken populations was evaluated. Twenty-eight polymorphic sites, accounting for 4.26% of the total analyzed loci of 658 bp, defined 32 haplotypes. The haplotype diversity (Hd) was 0.437, with a nucleotide diversity (π) of 0.0169, while the average number of nucleotide differences (k) was 0.576, indicating a population that is moderately genetically diverse. Analysis of molecular variance found 98.39% (ρ < 0.01) of the total sequence variation among the chicken haplotypes within populations, 1.08% (ρ < 0.05) among populations, and 0.75% (ρ > 0.05) among populations within regions. This revealed subtle genetic differentiation among the populations, which appeared to be influenced by population fragmentation, probably due to neutral mutation, random genetic drift, and/or balancing selection. All the haplotypes showed affinity exclusively to the haplogroup-E mtDNA phylogeny, with haplotype UGA01 signaling an ancestral haplotype in Uganda. Neutrality tests Tajima's D (-2.320) and Fu's Fs (-51.369), augmented with mismatch distribution to measure signatures of recent historical demographic events, supported a population expansion across the chicken populations. The results show one matrilineal ancestry of Ugandan chickens from a lineage widespread throughout the world that began in the Indian subcontinent. The lack of phylogeographic signals is consistent with recent expansion events with extensive within-country genetic intermixing among haplotypes. Thus, the findings in this study hold the potential to guide conservation strategies and breeding programs in Uganda, given that higher genetic diversity comes from within the chicken population.
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Affiliation(s)
- Illyass Yussif
- College of Agricultural and Environmental Sciences, Makerere University, Kampala, Uganda
| | - Donald Rugira Kugonza
- College of Agricultural and Environmental Sciences, Makerere University, Kampala, Uganda
| | - Charles Masembe
- College of Natural Resources, Makerere University, Kampala, Uganda
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Zhang Y, Li Z, Deng Y, Liu B, Huang M, Chen Z. Characterization of the complete mitochondrial genome of Paecilomyces variotii and comparative evolutionary mitochondriomics of 36 fungi. Mol Biol Rep 2024; 51:390. [PMID: 38446255 DOI: 10.1007/s11033-024-09330-x] [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: 07/08/2023] [Accepted: 02/07/2024] [Indexed: 03/07/2024]
Abstract
BACKGROUD Paecilomyces variotii has important economic value in stimulating crop growth, biodegradation, and other aspects. Up to now, there are no research reports on its mitochondrial genome. METHODS AND RESULTS The mitochondrial genome of Paecilomyces variotii was determined with the next-generation sequencing method (Illumina, NovaSeq), and its characteristics were analyzed using various bioinformatics approaches. The length of complete mitochondrial genome sequence of P. variotii is 40,965 bp and consists of 14 protein-coding genes, 2 ribosomal RNA genes, 1 ribosomal protein S3 gene, 26 transport RNA genes. The results of phylogenetics analysis using Bayesian inference and Maximum likelihood methods showed that P. variotii belongs to the Eurotiales order in the Thermoascaceae family, and 9 genera within the Eurotiomycetes class were effectively distinguished with high support rates (bootstrap value > 92% and posterior probabilities > 99%). The analysis of synonymous substitution rates and nonsynonymous substitution rates indicated that the Ka/Ks values of the 14 PCGs in the mitochondrial genomes of the two orders in the Eurotiomycetes class ranged from 0 to 0.4333. CONCLUSIONS This study revealed the structural and sequence information characteristics of the mitochondrial genome of P. variotii, and the phylogenetic results strongly support its classification within the family Thermoascaceae, consistent with traditional morphological taxonomy studies. The 14 PCGs in the mitochondrial genomes of the two orders in the Eurotiomycetes class are subject to strong purifying (negative) selection. The results of this research provides an important molecular basis for the development of genomics, evolutionary genetics and molecular markers of P. variotii in the future.
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Affiliation(s)
- Yujie Zhang
- Key Laboratory of Green Control of Crop Pests in Hunan Higher Education, and Hunan Provincial Collaborative Innovation Center for Field Weeds Control, Hunan University of Humanities, Science and Technology, Loudi, 417000, China
- Loudi Institute of Agricultural and Sciences, Loudi, 417000, China
| | - Zhengyi Li
- Key Laboratory of Green Control of Crop Pests in Hunan Higher Education, and Hunan Provincial Collaborative Innovation Center for Field Weeds Control, Hunan University of Humanities, Science and Technology, Loudi, 417000, China
- Loudi Institute of Agricultural and Sciences, Loudi, 417000, China
| | - Yijia Deng
- Key Laboratory of Green Control of Crop Pests in Hunan Higher Education, and Hunan Provincial Collaborative Innovation Center for Field Weeds Control, Hunan University of Humanities, Science and Technology, Loudi, 417000, China
- Loudi Institute of Agricultural and Sciences, Loudi, 417000, China
| | - Bin Liu
- Key Laboratory of Green Control of Crop Pests in Hunan Higher Education, and Hunan Provincial Collaborative Innovation Center for Field Weeds Control, Hunan University of Humanities, Science and Technology, Loudi, 417000, China
- Loudi Institute of Agricultural and Sciences, Loudi, 417000, China
| | - Minyi Huang
- Key Laboratory of Green Control of Crop Pests in Hunan Higher Education, and Hunan Provincial Collaborative Innovation Center for Field Weeds Control, Hunan University of Humanities, Science and Technology, Loudi, 417000, China
- Loudi Institute of Agricultural and Sciences, Loudi, 417000, China
| | - Zhiyin Chen
- Key Laboratory of Green Control of Crop Pests in Hunan Higher Education, and Hunan Provincial Collaborative Innovation Center for Field Weeds Control, Hunan University of Humanities, Science and Technology, Loudi, 417000, China.
- Loudi Institute of Agricultural and Sciences, Loudi, 417000, China.
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250
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Zhang C, Liu H, Huang X, Yuan Z, Zhang S, Xu S, Liu J, Wang Y, Wang D, Hu J. Comparative Analysis of the Systematics and Evolution of the Pampus Genus of Fish (Perciformes: Stromateidae) Based on Osteology, Population Genetics and Complete Mitogenomes. Animals (Basel) 2024; 14:814. [PMID: 38473197 DOI: 10.3390/ani14050814] [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: 10/31/2023] [Revised: 01/20/2024] [Accepted: 02/14/2024] [Indexed: 03/14/2024] Open
Abstract
Pampus is a widespread species of fish in the western Pacific and Indian Oceans that has significant commercial worth. Its evolutionary history and phylogenetics are still poorly understood, and details on its intraspecific taxonomy are debatable, despite some morphological and molecular research. Here, we analyzed this species using skeletal structure data as well as nuclear (S7 gene) and mitochondrial genetic information (COI, D-loop and mitogenomes). We found that the genetic distance between P. argenteus and P. echinogaster was much smaller than that between other Pampus species, and both maximum likelihood and Bayesian phylogenetic trees yielded almost identical tree topologies. An additional and adjacent M repeat was found in the downstream region of the IQM gene cluster of P. argenteus and P. echinogaster, and the trnL2 gene of P. minor was translocated. The genus Pampus experienced early rapid radiation during the Palaeocene with major lineages diversifying within a relatively narrow timescale. Additionally, three different methods were conducted to distinguish the genus Pampus species, proving that P. argenteus and P. echinogaster are the same species, and P. liuorum is speculated to be a valid species. Overall, our study provides new insights not only into the evolutionary history of Pampus but its intraspecific taxonomy as well.
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Affiliation(s)
- Cheng Zhang
- School of Marine Science, Ningbo University, Ningbo 315211, China
| | - Hanjing Liu
- School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Xiang Huang
- School of Marine Science, Ningbo University, Ningbo 315211, China
| | - Zi Yuan
- School of Marine Science, Ningbo University, Ningbo 315211, China
| | - Shun Zhang
- School of Marine Science, Ningbo University, Ningbo 315211, China
| | - Shanliang Xu
- School of Marine Science, Ningbo University, Ningbo 315211, China
| | - Jing Liu
- Laboratory of Marine Organism Taxonomy and Phylogeny, Qingdao Key Laboratory of Marine Biodiversity and Conservation, and The Key Laboratory of Experimental Marine Biology, Centre for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
| | - Yajun Wang
- School of Marine Science, Ningbo University, Ningbo 315211, China
- Key Laboratory of Applied Marine Biotechnology (Ningbo University), Ministry of Education, Ningbo 315211, China
- Key Laboratory of Marine Biotechnology of Zhejiang Province, Ningbo University, Ningbo 315211, China
| | - Danli Wang
- School of Marine Science, Ningbo University, Ningbo 315211, China
| | - Jiabao Hu
- School of Marine Science, Ningbo University, Ningbo 315211, China
- Key Laboratory of Applied Marine Biotechnology (Ningbo University), Ministry of Education, Ningbo 315211, China
- Key Laboratory of Marine Biotechnology of Zhejiang Province, Ningbo University, Ningbo 315211, China
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