99901
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Genetic polymorphism investigation of 16 X-STR loci in the Bai ethnic minority in Yunnan Province, Southwest China. Int J Legal Med 2020; 136:543-545. [PMID: 33180199 DOI: 10.1007/s00414-020-02454-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Accepted: 10/30/2020] [Indexed: 10/23/2022]
Abstract
To investigate the genetic variation and forensic efficiency of 16 X-chromosomal short tandem repeat (X-STR) loci (DX6795, DXS9902, DXS8378, HPRTB, GATA165B12, DXS7132, DXS7424, DXS6807, DXS6803, GATA172D05, DXS6800, DXS10134, GATA31E08, DXS10159, DXS6789, and DXS6810) in the Bai minority, we calculated allele frequencies, forensic parameters, and haplotype frequencies in 424 (202 males and 222 females) unrelated, healthy Bai individuals from Dali Bai Autonomous Prefecture in Yunnan Province, China. We observed a total of 132 alleles; 5-19 alleles were detected in each locus, and the corresponding allele frequencies ranged from 0.0016 to 0.7589. All of the loci detected were highly polymorphic in the Bai population in Yunnan Province, except DXS6800. The values for the combined power of discrimination in females (PDf) and males (PDm) were 0.999999999999996 and 0.999999997487061, respectively. According to a phylogenetic tree, neighboring populations and different nationalities in the same area appeared to have relatively close evolutionary relationships. This study provides and complements X-chromosome genetic polymorphism data for the Bai people in Yunnan Province, Southwest China, and enriches the available reference materials for this Chinese minority population.
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99902
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He X, Liu J, Liu B, Shi J. The use of DNA methylation clock in aging research. Exp Biol Med (Maywood) 2020; 246:436-446. [PMID: 33175612 DOI: 10.1177/1535370220968802] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
One of the key characteristics of aging is a progressive loss of physiological integrity, which weakens bodily functions and increases the risk of death. A robust biomarker is important for the assessment of biological age, the rate of aging, and a person's health status. DNA methylation clocks, novel biomarkers of aging, are composed of a group of cytosine-phosphate-guanine dinucleotides, the DNA methylation status of which can be used to accurately measure subjective age. These clocks are considered accurate biomarkers of chronological age for humans and other vertebrates. Numerous studies have demonstrated these clocks to quantify the rate of biological aging and the effects of longevity and anti-aging interventions. In this review, we describe the purpose and use of DNA methylation clocks in aging research.
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Affiliation(s)
- Xi He
- Key Laboratory of Basic Pharmacology of Ministry of Education and Joint International Research Laboratory of Ethnomedicine of Ministry of Education, 66367Zunyi Medical University, Zunyi 563003, China
| | - Jiaojiao Liu
- Key Laboratory of Basic Pharmacology of Ministry of Education and Joint International Research Laboratory of Ethnomedicine of Ministry of Education, 66367Zunyi Medical University, Zunyi 563003, China
| | - Bo Liu
- Key Laboratory of Basic Pharmacology of Ministry of Education and Joint International Research Laboratory of Ethnomedicine of Ministry of Education, 66367Zunyi Medical University, Zunyi 563003, China
| | - Jingshan Shi
- Key Laboratory of Basic Pharmacology of Ministry of Education and Joint International Research Laboratory of Ethnomedicine of Ministry of Education, 66367Zunyi Medical University, Zunyi 563003, China
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99903
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DNA barcoding reveals cryptic diversity in the underestimated genus Triplophysa (Cypriniformes: Cobitidae, Nemacheilinae) from the northeastern Qinghai-Tibet Plateau. BMC Evol Biol 2020; 20:151. [PMID: 33183225 PMCID: PMC7663858 DOI: 10.1186/s12862-020-01718-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 11/04/2020] [Indexed: 01/12/2023] Open
Abstract
Background The northeastern part of the Qinghai-Tibet Plateau (QTP) presents a high number of plateau loach species. As one of the three major groups of fishes distributed on the QTP, plateau loach has high ecological value. However, the taxonomy and systematics of these fish are still controversial, and a large number of new species have been reported. The reason for this phenomenon is that the degree of morphological variation is low, the phylogenetic information provided by morphological and anatomical features used for species identification is relatively poor, and many cryptic species are observed. Based on the high-density sampling points from the biodiversity hotspots surveyed, this study aims to evaluate the biodiversity of plateau loach in the northeastern part of the QTP and reveal the hidden diversity by comparing morphological species with molecular operational taxonomic units (MOTUs). Results After careful identification and comparison of the morphology and DNA barcoding of 1630 specimens, 22 species were identified, with 20 considered valid local species and two identified as new species that had not been previously described. Based on the combination of morphological and molecular methods, a total of 24 native species were found, two of which were cryptic species: Triplophysa robusta sp1 and Triplophysa minxianensis sp1. Fourteen of the 24 species form clusters of barcodes that allow them to be reliably identified. The remaining cases involved 10 closely related species, including rapidly differentiated species and species that seemed to have experienced incomplete lineage sorting or showed introgressions. Conclusions The results highlight the need to combine traditional taxonomies with molecular methods to correctly identify species, especially closely related species, such as the plateau loach. This study provides a basis for protecting the biodiversity of plateau loach.
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99904
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Mubarik MS, Khan SH, Ahmad A, Raza A, Khan Z, Sajjad M, Sammour RHA, Mustafa AEZM, Al-Ghamdi AA, Alajmi AH, Alshamasi FKI, Elshikh MS. Controlling Geminiviruses before Transmission: Prospects. PLANTS (BASEL, SWITZERLAND) 2020; 9:E1556. [PMID: 33198339 PMCID: PMC7697176 DOI: 10.3390/plants9111556] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 11/08/2020] [Accepted: 11/10/2020] [Indexed: 12/04/2022]
Abstract
Whitefly (Bemisia tabaci)-transmitted Geminiviruses cause serious diseases of crop plants in tropical and sub-tropical regions. Plants, animals, and their microbial symbionts have evolved complex ways to interact with each other that impact their life cycles. Blocking virus transmission by altering the biology of vector species, such as the whitefly, can be a potential approach to manage these devastating diseases. Virus transmission by insect vectors to plant hosts often involves bacterial endosymbionts. Molecular chaperonins of bacterial endosymbionts bind with virus particles and have a key role in the transmission of Geminiviruses. Hence, devising new approaches to obstruct virus transmission by manipulating bacterial endosymbionts before infection opens new avenues for viral disease control. The exploitation of bacterial endosymbiont within the insect vector would disrupt interactions among viruses, insects, and their bacterial endosymbionts. The study of this cooperating web could potentially decrease virus transmission and possibly represent an effective solution to control viral diseases in crop plants.
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Affiliation(s)
- Muhammad Salman Mubarik
- Centre for Agricultural Biochemistry and Biotechnology (CABB), University of Agriculture, Faisalabad 38040, Pakistan;
| | - Sultan Habibullah Khan
- Centre for Agricultural Biochemistry and Biotechnology (CABB), University of Agriculture, Faisalabad 38040, Pakistan;
- Center of Advanced Studies in Agriculture and Food Security (CAS-AFS), University of Agriculture, Faisalabad 38040, Pakistan;
| | - Aftab Ahmad
- Center of Advanced Studies in Agriculture and Food Security (CAS-AFS), University of Agriculture, Faisalabad 38040, Pakistan;
- Department of Biochemistry, University of Agriculture, Faisalabad 38040, Pakistan
| | - Ali Raza
- Key Lab of Biology and Genetic Improvement of Oil Crops, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Wuhan 430062, China;
| | - Zulqurnain Khan
- Institute of Plant Breeding and Biotechnology (IPBB), MNS University of Agriculture, Multan 66000, Pakistan;
| | - Muhammad Sajjad
- Department of Biosciences, COMSATS University Islamabad (CUI), Park Road, Islamabad 45550, Pakistan;
| | - Reda Helmy Ahmed Sammour
- Department of Botany and Microbiology, College of Sciences, King Saud University, P.O. Box 22452, Riyadh 11495, Saudi Arabia; (R.H.A.S.); (A.A.A.-G.); (A.H.A.); (F.K.I.A.); (M.S.E.)
| | - Abd El-Zaher M.A. Mustafa
- Department of Botany and Microbiology, College of Sciences, King Saud University, P.O. Box 22452, Riyadh 11495, Saudi Arabia; (R.H.A.S.); (A.A.A.-G.); (A.H.A.); (F.K.I.A.); (M.S.E.)
- Botany Department, Faculty of Science, Tanta University, Tanta 31511, Egypt
| | - Abdullah Ahmed Al-Ghamdi
- Department of Botany and Microbiology, College of Sciences, King Saud University, P.O. Box 22452, Riyadh 11495, Saudi Arabia; (R.H.A.S.); (A.A.A.-G.); (A.H.A.); (F.K.I.A.); (M.S.E.)
| | - Amal H. Alajmi
- Department of Botany and Microbiology, College of Sciences, King Saud University, P.O. Box 22452, Riyadh 11495, Saudi Arabia; (R.H.A.S.); (A.A.A.-G.); (A.H.A.); (F.K.I.A.); (M.S.E.)
| | - Fatin K. I. Alshamasi
- Department of Botany and Microbiology, College of Sciences, King Saud University, P.O. Box 22452, Riyadh 11495, Saudi Arabia; (R.H.A.S.); (A.A.A.-G.); (A.H.A.); (F.K.I.A.); (M.S.E.)
| | - Mohamed Soliman Elshikh
- Department of Botany and Microbiology, College of Sciences, King Saud University, P.O. Box 22452, Riyadh 11495, Saudi Arabia; (R.H.A.S.); (A.A.A.-G.); (A.H.A.); (F.K.I.A.); (M.S.E.)
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99905
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Nagahama Y, Chakraborty T, Paul-Prasanth B, Ohta K, Nakamura M. Sex determination, gonadal sex differentiation, and plasticity in vertebrate species. Physiol Rev 2020; 101:1237-1308. [PMID: 33180655 DOI: 10.1152/physrev.00044.2019] [Citation(s) in RCA: 93] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
A diverse array of sex determination (SD) mechanisms, encompassing environmental to genetic, have been found to exist among vertebrates, covering a spectrum from fixed SD mechanisms (mammals) to functional sex change in fishes (sequential hermaphroditic fishes). A major landmark in vertebrate SD was the discovery of the SRY gene in 1990. Since that time, many attempts to clone an SRY ortholog from nonmammalian vertebrates remained unsuccessful, until 2002, when DMY/dmrt1by was discovered as the SD gene of a small fish, medaka. Surprisingly, however, DMY/dmrt1by was found in only 2 species among more than 20 species of medaka, suggesting a large diversity of SD genes among vertebrates. Considerable progress has been made over the last 3 decades, such that it is now possible to formulate reasonable paradigms of how SD and gonadal sex differentiation may work in some model vertebrate species. This review outlines our current understanding of vertebrate SD and gonadal sex differentiation, with a focus on the molecular and cellular mechanisms involved. An impressive number of genes and factors have been discovered that play important roles in testicular and ovarian differentiation. An antagonism between the male and female pathway genes exists in gonads during both sex differentiation and, surprisingly, even as adults, suggesting that, in addition to sex-changing fishes, gonochoristic vertebrates including mice maintain some degree of gonadal sexual plasticity into adulthood. Importantly, a review of various SD mechanisms among vertebrates suggests that this is the ideal biological event that can make us understand the evolutionary conundrums underlying speciation and species diversity.
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Affiliation(s)
- Yoshitaka Nagahama
- Laboratory of Reproductive Biology, National Institute for Basic Biology, Okazaki, Japan.,South Ehime Fisheries Research Center, Ehime University, Ainan, Japan.,Faculty of Biological Science and Technology, Kanazawa University, Ishikawa, Japan
| | - Tapas Chakraborty
- Laboratory of Reproductive Biology, National Institute for Basic Biology, Okazaki, Japan.,South Ehime Fisheries Research Center, Ehime University, Ainan, Japan.,Laboratory of Marine Biology, Faculty of Agriculture, Kyushu University, Fukouka, Japan.,Karatsu Satellite of Aqua-Bioresource Innovation Center, Kyushu University, Karatsu, Japan
| | - Bindhu Paul-Prasanth
- Laboratory of Reproductive Biology, National Institute for Basic Biology, Okazaki, Japan.,Centre for Nanosciences and Molecular Medicine, Amrita Vishwa Vidapeetham, Kochi, Kerala, India
| | - Kohei Ohta
- Laboratory of Marine Biology, Faculty of Agriculture, Kyushu University, Fukouka, Japan
| | - Masaru Nakamura
- Sesoko Station, Tropical Biosphere Research Center, University of the Ryukyus, Okinawa, Japan.,Research Center, Okinawa Churashima Foundation, Okinawa, Japan
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99906
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Riyanti, Balansa W, Liu Y, Sharma A, Mihajlovic S, Hartwig C, Leis B, Rieuwpassa FJ, Ijong FG, Wägele H, König GM, Schäberle TF. Selection of sponge-associated bacteria with high potential for the production of antibacterial compounds. Sci Rep 2020; 10:19614. [PMID: 33184304 PMCID: PMC7665026 DOI: 10.1038/s41598-020-76256-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Accepted: 10/18/2020] [Indexed: 01/18/2023] Open
Abstract
The potential of sponge-associated bacteria for the biosynthesis of natural products with antibacterial activity was evaluated. In a preliminary screening 108 of 835 axenic isolates showed antibacterial activity. Active isolates were identified by 16S rRNA gene sequencing and selection of the most promising strains was done in a championship like approach, which can be done in every lab and field station without expensive equipment. In a competition assay, strains that inhibited most of the other strains were selected. In a second round, the strongest competitors from each host sponge competed against each other. To rule out that the best competitors selected in that way represent similar strains with the same metabolic profile, BOX PCR experiments were performed, and extracts of these strains were analysed using metabolic fingerprinting. This proved that the strains are different and have various metabolic profiles, even though belonging to the same genus, i.e. Bacillus. Furthermore, it was shown that co-culture experiments triggered the production of compounds with antibiotic activity, i.e. surfactins and macrolactin A. Since many members of the genus Bacillus possess the genetic equipment for the biosynthesis of these compounds, a potential synergism was analysed, showing synergistic effects between C14-surfactin and macrolactin A against methicillin-resistant Staphylococcus aureus (MRSA).
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Affiliation(s)
- Riyanti
- Institute for Insect Biotechnology, Justus-Liebig-University of Giessen, 35392, Giessen, Germany
- Faculty of Fisheries and Marine Science, Jenderal Soedirman University, 53122, Purwokerto, Indonesia
| | - Walter Balansa
- Department of Fisheries and Marine Science, Politeknik Negeri Nusa Utara, 95821, North Sulawesi, Indonesia
| | - Yang Liu
- Institute for Insect Biotechnology, Justus-Liebig-University of Giessen, 35392, Giessen, Germany
| | - Abha Sharma
- Institute for Insect Biotechnology, Justus-Liebig-University of Giessen, 35392, Giessen, Germany
| | - Sanja Mihajlovic
- Fraunhofer Institute for Molecular Biology and Applied Ecology (IME), Branch for Bioresources, 35392, Giessen, Germany
| | - Christoph Hartwig
- Fraunhofer Institute for Molecular Biology and Applied Ecology (IME), Branch for Bioresources, 35392, Giessen, Germany
| | - Benedikt Leis
- Fraunhofer Institute for Molecular Biology and Applied Ecology (IME), Branch for Bioresources, 35392, Giessen, Germany
| | - Frets Jonas Rieuwpassa
- Department of Fisheries and Marine Science, Politeknik Negeri Nusa Utara, 95821, North Sulawesi, Indonesia
| | - Frans Gruber Ijong
- Department of Fisheries and Marine Science, Politeknik Negeri Nusa Utara, 95821, North Sulawesi, Indonesia
| | - Heike Wägele
- Centre of Molecular Biodiversity, Zoological Research Museum Alexander Koenig, 53113, Bonn, Germany
| | - Gabriele M König
- Institute for Pharmaceutical Biology, University of Bonn, 53115, Bonn, Germany
| | - Till F Schäberle
- Institute for Insect Biotechnology, Justus-Liebig-University of Giessen, 35392, Giessen, Germany.
- Fraunhofer Institute for Molecular Biology and Applied Ecology (IME), Branch for Bioresources, 35392, Giessen, Germany.
- German Center for Infection Research (DZIF), Partner Site Giessen-Marburg-Langen, Giessen, Germany.
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99907
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Parapar J, Capa M, Nygren A, Moreira J. To name but a few: descriptions of five new species of Terebellides (Annelida, Trichobranchidae) from the North East Atlantic. Zookeys 2020; 992:1-58. [PMID: 33223905 PMCID: PMC7677295 DOI: 10.3897/zookeys.992.55977] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 10/06/2020] [Indexed: 11/18/2022] Open
Abstract
The number of described species of the genus Terebellides Sars, 1835 (Annelida, Trichobranchidae) has greatly increased in the last years, particularly in the North East Atlantic. In this context, this paper deals with several putative species recently delineated by molecular means within a well delimited clade of Terebellides. Species are characterised here by a combination of morphological characters, and a complementary nucleotide diagnostic approach. Three species were identified as the nominal species T.stroemii Sars, 1835, T.bigeniculatus Parapar, Moreira & Helgason, 2011 and T.europaeaLavesque et al., 2019. Five species are described as new: T.bakkenisp. nov., T.kongsrudisp. nov., T.norvegicasp. nov., T.ronningaesp. nov. and T.scoticasp. nov. The distinctive morphological characters refer to the branchial shape, absence or presence of papillae on lamellae of anterior margin of branchial dorsal lobes, absence or presence of ciliated papillae dorsal to thoracic notopodia, geniculate chaetae in one or two chaetigers, and the morphology of thoracic and abdominal uncini teeth. Furthermore, the description of T.bigeniculatus is revised and complemented after examination of type specimens. An updated identification key to all species of the genus in NE Atlantic and a proposal of a classification of different types of abdominal uncini to be used in taxonomy are also included.
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Affiliation(s)
- Julio Parapar
- Departamento de Bioloxía, Universidade da Coruña, Spain Universidade da Coruña Coruña Spain
| | - María Capa
- Departament de Biologia, Universitat de les Illes Balears, Spain Universitat de les Illes Balears Mallorca Spain
| | - Arne Nygren
- Sjöfartmuseet Akvariet, Göteborg, Sweden and Institutionen för marina vetenskaper, Göteborgs Universitet, Sweden Göteborgs Universitet Göteborg Sweden
| | - Juan Moreira
- Departamento de Biología (Zoología) & Centro de Investigación en Biodiversidad y Cambio Global (CIBC-UAM), Facultad de Ciencias, Universidad Autónoma de Madrid, Spain Universidad Autónoma de Madrid Madrid Spain
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99908
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Choi JY, Purugganan M, Stacy EA. Divergent Selection and Primary Gene Flow Shape Incipient Speciation of a Riparian Tree on Hawaii Island. Mol Biol Evol 2020; 37:695-710. [PMID: 31693149 PMCID: PMC7038655 DOI: 10.1093/molbev/msz259] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
A long-standing goal of evolutionary biology is to understand the mechanisms underlying the formation of species. Of particular interest is whether or not speciation can occur in the presence of gene flow and without a period of physical isolation. Here, we investigated this process within Hawaiian Metrosideros, a hypervariable and highly dispersible woody species complex that dominates the Hawaiian Islands in continuous stands. Specifically, we investigated the origin of Metrosideros polymorpha var. newellii (newellii), a riparian ecotype endemic to Hawaii Island that is purportedly derived from the archipelago-wide M. polymorpha var. glaberrima (glaberrima). Disruptive selection across a sharp forest-riparian ecotone contributes to the isolation of these varieties and is a likely driver of newellii's origin. We examined genome-wide variation of 42 trees from Hawaii Island and older islands. Results revealed a split between glaberrima and newellii within the past 0.3-1.2 My. Admixture was extensive between lineages within Hawaii Island and between islands, but introgression from populations on older islands (i.e., secondary gene flow) did not appear to contribute to the emergence of newellii. In contrast, recurrent gene flow (i.e., primary gene flow) between glaberrima and newellii contributed to the formation of genomic islands of elevated absolute and relative divergence. These regions were enriched for genes with regulatory functions as well as for signals of positive selection, especially in newellii, consistent with divergent selection underlying their formation. In sum, our results support riparian newellii as a rare case of incipient ecological speciation with primary gene flow in trees.
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Affiliation(s)
- Jae Young Choi
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY
| | - Michael Purugganan
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY.,Center for Genomics and Systems Biology, NYU Abu Dhabi Research Institute, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Elizabeth A Stacy
- School of Life Sciences, University of Nevada, Las Vegas, Las Vegas, NV
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99909
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Selmoni O, Lecellier G, Vigliola L, Berteaux-Lecellier V, Joost S. Coral cover surveys corroborate predictions on reef adaptive potential to thermal stress. Sci Rep 2020; 10:19680. [PMID: 33184366 PMCID: PMC7661510 DOI: 10.1038/s41598-020-76604-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 10/21/2020] [Indexed: 11/22/2022] Open
Abstract
As anomalous heat waves are causing the widespread decline of coral reefs worldwide, there is an urgent need to identify coral populations tolerant to thermal stress. Heat stress adaptive potential is the degree of tolerance expected from evolutionary processes and, for a given reef, depends on the arrival of propagules from reefs exposed to recurrent thermal stress. For this reason, assessing spatial patterns of thermal adaptation and reef connectivity is of paramount importance to inform conservation strategies. In this work, we applied a seascape genomics framework to characterize the spatial patterns of thermal adaptation and connectivity for coral reefs of New Caledonia (Southern Pacific). In this approach, remote sensing of seascape conditions was combined with genomic data from three coral species. For every reef of the region, we computed a probability of heat stress adaptation, and two indices forecasting inbound and outbound connectivity. We then compared our indicators to field survey data, and observed that decrease of coral cover after heat stress was lower at reefs predicted with high probability of adaptation and inbound connectivity. Last, we discussed how these indicators can be used to inform local conservation strategies and preserve the adaptive potential of New Caledonian reefs.
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Affiliation(s)
- Oliver Selmoni
- Laboratory of Geographic Information Systems, Ecole Polytechnique Federale de Lausanne, Lausanne, Switzerland
- UMR250/9220 ENTROPIE IRD-CNRS-Ifremer-UNC-UR, Labex CORAIL, Nouméa, New Caledonia, France
| | - Gaël Lecellier
- UMR250/9220 ENTROPIE IRD-CNRS-Ifremer-UNC-UR, Labex CORAIL, Nouméa, New Caledonia, France
- UVSQ, Université de Paris-Saclay, Versailles, France
| | - Laurent Vigliola
- UMR250/9220 ENTROPIE IRD-CNRS-Ifremer-UNC-UR, Labex CORAIL, Nouméa, New Caledonia, France
| | | | - Stéphane Joost
- Laboratory of Geographic Information Systems, Ecole Polytechnique Federale de Lausanne, Lausanne, Switzerland.
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99910
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Guo Q, Wang B, Zhou Z, Ke X, Zhang L, Chen M, Lin M, Wang W, Zhang W, Li X. Ornithinimicrobium pratense sp. nov., isolated from meadow soil. Int J Syst Evol Microbiol 2020; 70:6450-6457. [PMID: 33174834 DOI: 10.1099/ijsem.0.004557] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel Gram-stain-positive, yellow, short-rod-shaped or coccoid bacterial strain, W204T, was isolated from a soil sample collected from Jiadengyu national forest park in China and characterized using a polyphasic approach. The cell-wall peptidoglycan contained ornithine as the diagnostic diamino acid. 16S rRNA gene sequence analysis indicated that strain W204T was closely related to Ornithinimicrobium flavum CPCC 203535T (97.4 %, similarity), Serinicoccus profundi CGMCC 4.5582T (96.9 %), Serinicoccus sediminis GP-T3-3T (96.8 %), Serinicoccus hydrothermalis JLT9T (96.7 %), Ornithinimicrobium cerasi CPCC 203383T (96.6 %) and Ornithinimicrobium kibberense K22-20T (96.6 %). However, the digital DNA-DNA genome hybridization value between strain W204T and the closest related strain O. flavum CPCC 203535T was 21.90 %. Complete genome analyses revealed that the size of the genome was 3.54 Mb and the genomic DNA G+C content was 70.79 mol%. The polar lipid profile consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, an unidentified glycolipid, an unidentified phospholipid and an unidentified lipid. The major menaquinone was MK-8(H4). The predominant cellular fatty acids were iso-C15 : 0, anteiso-C15 : 0 and C16 : 0. The phenotypic, chemotaxonomic and phylogenetic data suggested that strain W204T should be classified as representative of a novel species of the genus Ornithinimicrobium, for which the name Ornithinimicrobium pratense sp. nov. is proposed. The type strain is W204T (=GDMCC 1.1391T=KCTC 49237T).
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Affiliation(s)
- Qiannan Guo
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, Sichuan, PR China.,Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - Bo Wang
- Xinjiang Laboratory of Special Environmental Microbiology, Urumqi 830091, Xinjiang, PR China.,Institute of Applied Microbiology, Xinjiang Academy of Agricultural Sciences, Xinjiang, Urumqi 830091, PR China
| | - Zhengfu Zhou
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - Xiubin Ke
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - Lijuan Zhang
- Xinjiang Laboratory of Special Environmental Microbiology, Urumqi 830091, Xinjiang, PR China.,Institute of Applied Microbiology, Xinjiang Academy of Agricultural Sciences, Xinjiang, Urumqi 830091, PR China
| | - Ming Chen
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - Min Lin
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - Wei Wang
- Institute of Applied Microbiology, Xinjiang Academy of Agricultural Sciences, Xinjiang, Urumqi 830091, PR China.,Xinjiang Laboratory of Special Environmental Microbiology, Urumqi 830091, Xinjiang, PR China
| | - Wei Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - Xufeng Li
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, Sichuan, PR China
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99911
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Mokrani S, Nabti EH. Heavy metal resistance and bioremediation capacity of rhizospheric strain BioRPaz-3 Pseudomonas azotoformans endowed with antifungal activities and multi-abiotic stress tolerance in in vitro trials. SN APPLIED SCIENCES 2020. [DOI: 10.1007/s42452-020-03828-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
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99912
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Hernando C, Andújar C. Mitogenomic phylogenetics of
Diochus occultus
n. sp., a palaeoendemic endogean species within the tribe Diochini (Coleoptera: Staphylinidae: Staphylininae). J ZOOL SYST EVOL RES 2020. [DOI: 10.1111/jzs.12425] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
| | - Carmelo Andújar
- Island Ecology and Evolution Research Group Instituto de Productos Naturales y Agrobiología (IPNA‐CSIC) La Laguna Spain
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99913
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Bianconi ME, Dunning LT, Curran EV, Hidalgo O, Powell RF, Mian S, Leitch IJ, Lundgren MR, Manzi S, Vorontsova MS, Besnard G, Osborne CP, Olofsson JK, Christin PA. Contrasted histories of organelle and nuclear genomes underlying physiological diversification in a grass species. Proc Biol Sci 2020; 287:20201960. [PMID: 33171085 PMCID: PMC7735283 DOI: 10.1098/rspb.2020.1960] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
C4 photosynthesis evolved multiple times independently in angiosperms, but most origins are relatively old so that the early events linked to photosynthetic diversification are blurred. The grass Alloteropsis semialata is an exception, as this species encompasses C4 and non-C4 populations. Using phylogenomics and population genomics, we infer the history of dispersal and secondary gene flow before, during and after photosynthetic divergence in A. semialata. We further analyse the genome composition of individuals with varied ploidy levels to establish the origins of polyploids in this species. Detailed organelle phylogenies indicate limited seed dispersal within the mountainous region of origin and the emergence of a C4 lineage after dispersal to warmer areas of lower elevation. Nuclear genome analyses highlight repeated secondary gene flow. In particular, the nuclear genome associated with the C4 phenotype was swept into a distantly related maternal lineage probably via unidirectional pollen flow. Multiple intraspecific allopolyploidy events mediated additional secondary genetic exchanges between photosynthetic types. Overall, our results show that limited dispersal and isolation allowed lineage divergence, with photosynthetic innovation happening after migration to new environments, and pollen-mediated gene flow led to the rapid spread of the derived C4 physiology away from its region of origin.
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Affiliation(s)
- Matheus E Bianconi
- Department of Animal and Plant Sciences, University of Sheffield, Western Bank, Sheffield S10 2TN, UK
| | - Luke T Dunning
- Department of Animal and Plant Sciences, University of Sheffield, Western Bank, Sheffield S10 2TN, UK
| | - Emma V Curran
- Department of Animal and Plant Sciences, University of Sheffield, Western Bank, Sheffield S10 2TN, UK
| | - Oriane Hidalgo
- Comparative Plant and Fungal Biology, Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AB, UK
| | - Robyn F Powell
- Comparative Plant and Fungal Biology, Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AB, UK
| | - Sahr Mian
- Comparative Plant and Fungal Biology, Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AB, UK
| | - Ilia J Leitch
- Comparative Plant and Fungal Biology, Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AB, UK
| | - Marjorie R Lundgren
- Department of Animal and Plant Sciences, University of Sheffield, Western Bank, Sheffield S10 2TN, UK
| | - Sophie Manzi
- Laboratoire Evolution and Diversité Biologique (EDB UMR5174), Université de Toulouse III - Paul Sabatier, CNRS, IRD, 118 route de Narbonne, 31062 Toulouse, France
| | - Maria S Vorontsova
- Comparative Plant and Fungal Biology, Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AB, UK
| | - Guillaume Besnard
- Laboratoire Evolution and Diversité Biologique (EDB UMR5174), Université de Toulouse III - Paul Sabatier, CNRS, IRD, 118 route de Narbonne, 31062 Toulouse, France
| | - Colin P Osborne
- Department of Animal and Plant Sciences, University of Sheffield, Western Bank, Sheffield S10 2TN, UK
| | - Jill K Olofsson
- Department of Animal and Plant Sciences, University of Sheffield, Western Bank, Sheffield S10 2TN, UK
| | - Pascal-Antoine Christin
- Department of Animal and Plant Sciences, University of Sheffield, Western Bank, Sheffield S10 2TN, UK
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99914
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Yan H, Liu Q, Wen F, Bai B, Wen Y, Chen W, Lu W, Lin Y, Xia Q, Wang G. Characterization and potential application of an α-amylase (BmAmy1) selected during silkworm domestication. Int J Biol Macromol 2020; 167:1102-1112. [PMID: 33188814 DOI: 10.1016/j.ijbiomac.2020.11.064] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2020] [Revised: 11/07/2020] [Accepted: 11/09/2020] [Indexed: 01/06/2023]
Abstract
Efficient resource utilization plays a central role in the high productivity of domesticated plants and animals. Whether artificial selection acts on digestive enzymes in the domesticated silkworm (Bombyx mori), which is larger than its wild ancestor, Bombyx mandarina (B. mandarina), remains unknown. In this study, we present the characteristics of a novel alpha-amylase, BmAmy1, in B. mori. The activity of recombinant BmAmy1 was maximal at 35 °C and pH 9.0, and could be suppressed by amylase inhibitors from mulberry, the exclusive food source of silkworms. Three different transposable element fragments, which were independently inserted in the 5'-upstream regulatory region, might be responsible for the enhanced expression of BmAmy1 in different domesticated silkworm strains as revealed by dual-luciferase reporter assay. The BmAmy1 overexpression increased the weight of female and male B. mori by 11.9% and 6.8%, respectively, compared with non-transgenic controls. Our results emphasize that, by exploring the genetic mechanisms of human-selected traits, the domestication process could be further accelerated through genetic engineering and targeted breeding.
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Affiliation(s)
- Hao Yan
- State Key Laboratory of Silkworm Genome Biology, Biological Science Research Center, Southwest University, Chongqing 400716, China; Chongqing Key Laboratory of Sericultural Science, Southwest University, Chongqing 400716, China; Chongqing Engineering and Technology Research Center for Novel Silk Materials, Southwest University, Chongqing 400716, China
| | - Qingsong Liu
- State Key Laboratory of Silkworm Genome Biology, Biological Science Research Center, Southwest University, Chongqing 400716, China; Chongqing Key Laboratory of Sericultural Science, Southwest University, Chongqing 400716, China; Chongqing Engineering and Technology Research Center for Novel Silk Materials, Southwest University, Chongqing 400716, China
| | - Feng Wen
- State Key Laboratory of Silkworm Genome Biology, Biological Science Research Center, Southwest University, Chongqing 400716, China; Chongqing Key Laboratory of Sericultural Science, Southwest University, Chongqing 400716, China; Chongqing Engineering and Technology Research Center for Novel Silk Materials, Southwest University, Chongqing 400716, China
| | - Bingchuan Bai
- State Key Laboratory of Silkworm Genome Biology, Biological Science Research Center, Southwest University, Chongqing 400716, China; Chongqing Key Laboratory of Sericultural Science, Southwest University, Chongqing 400716, China; Chongqing Engineering and Technology Research Center for Novel Silk Materials, Southwest University, Chongqing 400716, China
| | - Yuchan Wen
- State Key Laboratory of Silkworm Genome Biology, Biological Science Research Center, Southwest University, Chongqing 400716, China; Chongqing Key Laboratory of Sericultural Science, Southwest University, Chongqing 400716, China; Chongqing Engineering and Technology Research Center for Novel Silk Materials, Southwest University, Chongqing 400716, China
| | - Wenwen Chen
- State Key Laboratory of Silkworm Genome Biology, Biological Science Research Center, Southwest University, Chongqing 400716, China; Chongqing Key Laboratory of Sericultural Science, Southwest University, Chongqing 400716, China; Chongqing Engineering and Technology Research Center for Novel Silk Materials, Southwest University, Chongqing 400716, China
| | - Wei Lu
- State Key Laboratory of Silkworm Genome Biology, Biological Science Research Center, Southwest University, Chongqing 400716, China; Chongqing Key Laboratory of Sericultural Science, Southwest University, Chongqing 400716, China; Chongqing Engineering and Technology Research Center for Novel Silk Materials, Southwest University, Chongqing 400716, China
| | - Ying Lin
- State Key Laboratory of Silkworm Genome Biology, Biological Science Research Center, Southwest University, Chongqing 400716, China; Chongqing Key Laboratory of Sericultural Science, Southwest University, Chongqing 400716, China; Chongqing Engineering and Technology Research Center for Novel Silk Materials, Southwest University, Chongqing 400716, China
| | - Qingyou Xia
- State Key Laboratory of Silkworm Genome Biology, Biological Science Research Center, Southwest University, Chongqing 400716, China; Chongqing Key Laboratory of Sericultural Science, Southwest University, Chongqing 400716, China; Chongqing Engineering and Technology Research Center for Novel Silk Materials, Southwest University, Chongqing 400716, China
| | - Genhong Wang
- State Key Laboratory of Silkworm Genome Biology, Biological Science Research Center, Southwest University, Chongqing 400716, China; Chongqing Key Laboratory of Sericultural Science, Southwest University, Chongqing 400716, China; Chongqing Engineering and Technology Research Center for Novel Silk Materials, Southwest University, Chongqing 400716, China.
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99915
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Chira AM, Cooney CR, Bright JA, Capp EJR, Hughes EC, Moody CJA, Nouri LO, Varley ZK, Thomas GH. The signature of competition in ecomorphological traits across the avian radiation. Proc Biol Sci 2020; 287:20201585. [PMID: 33171084 PMCID: PMC7735287 DOI: 10.1098/rspb.2020.1585] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Competition for shared resources represents a fundamental driver of biological diversity. However, the tempo and mode of phenotypic evolution in deep-time has been predominantly investigated using trait evolutionary models which assume that lineages evolve independently from each other. Consequently, the role of species interactions in driving macroevolutionary dynamics remains poorly understood. Here, we quantify the prevalence for signatures of competition between related species in the evolution of ecomorphological traits across the bird radiation. We find that mechanistic trait models accounting for the effect of species interactions on phenotypic divergence provide the best fit for the data on at least one trait axis in 27 out of 59 clades ranging between 21 and 195 species. Where it occurs, the signature of competition generally coincides with positive species diversity-dependence, driven by the accumulation of lineages with similar ecologies, and we find scarce evidence for trait-dependent or negative diversity-dependent phenotypic evolution. Overall, our results suggest that the footprint of interspecific competition is often eroded in long-term patterns of phenotypic diversification, and that other selection pressures may predominantly shape ecomorphological diversity among extant species at macroevolutionary scales.
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Affiliation(s)
- A M Chira
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, UK.,Department of Biology, Washington University in St Louis, St Louis, MO, USA
| | - C R Cooney
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, UK
| | - J A Bright
- Department of Biological and Marine Sciences, University of Hull, Hull, UK
| | - E J R Capp
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, UK
| | - E C Hughes
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, UK
| | - C J A Moody
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, UK
| | - L O Nouri
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, UK
| | - Z K Varley
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, UK
| | - G H Thomas
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, UK.,Bird Group, Department of Life Sciences, The Natural History Museum, Tring, Hertfordshire, UK
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99916
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Guerra-Castellano A, Márquez I, Pérez-Mejías G, Díaz-Quintana A, De la Rosa MA, Díaz-Moreno I. Post-Translational Modifications of Cytochrome c in Cell Life and Disease. Int J Mol Sci 2020; 21:E8483. [PMID: 33187249 PMCID: PMC7697256 DOI: 10.3390/ijms21228483] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 11/05/2020] [Accepted: 11/07/2020] [Indexed: 02/07/2023] Open
Abstract
Mitochondria are the powerhouses of the cell, whilst their malfunction is related to several human pathologies, including neurodegenerative diseases, cardiovascular diseases, and various types of cancer. In mitochondrial metabolism, cytochrome c is a small soluble heme protein that acts as an essential redox carrier in the respiratory electron transport chain. However, cytochrome c is likewise an essential protein in the cytoplasm acting as an activator of programmed cell death. Such a dual role of cytochrome c in cell life and death is indeed fine-regulated by a wide variety of protein post-translational modifications. In this work, we show how these modifications can alter cytochrome c structure and functionality, thus emerging as a control mechanism of cell metabolism but also as a key element in development and prevention of pathologies.
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Affiliation(s)
| | | | | | | | | | - Irene Díaz-Moreno
- Instituto de Investigaciones Químicas (IIQ), Centro de Investigaciones Científicas Isla de la Cartuja (cicCartuja), Universidad de Sevilla, Consejo Superior de Investigaciones Científicas (CSIC), Avda. Américo Vespucio 49, 41092 Sevilla, Spain; (A.G.-C.); (I.M.); (G.P.-M.); (A.D.-Q.); (M.A.D.l.R.)
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99917
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Vizzini A, Consiglio G, Setti L. Testing spore amyloidity in Agaricales under light microscope: the case study of Tricholoma. IMA Fungus 2020; 11:24. [PMID: 33292837 PMCID: PMC7656700 DOI: 10.1186/s43008-020-00046-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Accepted: 10/15/2020] [Indexed: 11/10/2022] Open
Abstract
Although species of the genus Tricholoma are currently considered to produce inamyloid spores, a novel standardized method to test sporal amyloidity (which involves heating the sample in Melzer's reagent) showed evidence that in the tested species of this genus, which belong in all 10 sections currently recognized from Europe, the spores are amyloid. In two species, T. josserandii and T. terreum, the spores are also partly dextrinoid. This result provides strong indication that a positive reaction of the spores in Melzer's reagent could be a character shared by all genera in Tricholomataceae s. str.
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Affiliation(s)
- Alfredo Vizzini
- Department of Life Sciences and Systems Biology, University of Torino and Institute for Sustainable Plant Protection (IPSP-SS Turin), C.N.R, Viale P.A. Mattioli, 25, I-10125, Torino, Italy.
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99918
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Gregory AC, Zablocki O, Zayed AA, Howell A, Bolduc B, Sullivan MB. The Gut Virome Database Reveals Age-Dependent Patterns of Virome Diversity in the Human Gut. Cell Host Microbe 2020; 28:724-740.e8. [PMID: 32841606 PMCID: PMC7443397 DOI: 10.1016/j.chom.2020.08.003] [Citation(s) in RCA: 301] [Impact Index Per Article: 75.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 07/14/2020] [Accepted: 08/06/2020] [Indexed: 12/12/2022]
Abstract
The gut microbiome profoundly affects human health and disease, and their infecting viruses are likely as important, but often missed because of reference database limitations. Here, we (1) built a human Gut Virome Database (GVD) from 2,697 viral particle or microbial metagenomes from 1,986 individuals representing 16 countries, (2) assess its effectiveness, and (3) report a meta-analysis that reveals age-dependent patterns across healthy Westerners. The GVD contains 33,242 unique viral populations (approximately species-level taxa) and improves average viral detection rates over viral RefSeq and IMG/VR nearly 182-fold and 2.6-fold, respectively. GVD meta-analyses show highly personalized viromes, reveal that inter-study variability from technical artifacts is larger than any "disease" effect at the population level, and document how viral diversity changes from human infancy into senescence. Together, this compact foundational resource, these standardization guidelines, and these meta-analysis findings provide a systematic toolkit to help maximize our understanding of viral roles in health and disease.
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Affiliation(s)
- Ann C Gregory
- Department of Microbiology, Ohio State University, Columbus, OH 43210, USA
| | - Olivier Zablocki
- Department of Microbiology, Ohio State University, Columbus, OH 43210, USA; Center of Microbiome Science, Ohio State University, Columbus, OH 43210, USA
| | - Ahmed A Zayed
- Department of Microbiology, Ohio State University, Columbus, OH 43210, USA; Center of Microbiome Science, Ohio State University, Columbus, OH 43210, USA
| | - Allison Howell
- Department of Microbiology, Ohio State University, Columbus, OH 43210, USA
| | - Benjamin Bolduc
- Department of Microbiology, Ohio State University, Columbus, OH 43210, USA; Center of Microbiome Science, Ohio State University, Columbus, OH 43210, USA
| | - Matthew B Sullivan
- Department of Microbiology, Ohio State University, Columbus, OH 43210, USA; Department of Civil, Environmental and Geodetic Engineering, Ohio State University, Columbus, OH 43210, USA; Center of Microbiome Science, Ohio State University, Columbus, OH 43210, USA.
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99919
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Akter S, Huq MA. Biologically rapid synthesis of silver nanoparticles by Sphingobium sp. MAH-11 T and their antibacterial activity and mechanisms investigation against drug-resistant pathogenic microbes. ARTIFICIAL CELLS NANOMEDICINE AND BIOTECHNOLOGY 2020; 48:672-682. [PMID: 32075448 DOI: 10.1080/21691401.2020.1730390] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
The present study highlights the biological synthesis of silver nanoparticles (AgNPs) using Sphingobium sp. MAH-11 and also their antibacterial mechanisms against drug-resistant pathogenic microorganisms. The nanoparticle synthesis method used in this study was reliable, facile, rapid, cost-effective and ecofriendly. The AgNPs exhibited the highest absorbance at 423 nm. The TEM image expressed spherical shape of AgNPs and the size of synthesized AgNPs was 7-22 nm. The selected area diffraction (SAED) pattern and XRD spectrum revealed the crystalline structure of AgNPs. The results of FTIR analysis disclosed the functional groups responsible for the reduction of silver ion to metal nanoparticles. The biosynthesized AgNPs showed strong anti-microbial activity against drug-resistant pathogenic microorganisms. Moreover, Escherichia coli and Staphylococcus aureus were used to explore the antibacterial mechanisms of biosynthesized AgNPs. Minimal inhibitory concentrations (MICs) of E. coli and S. aureus were 6.25 μg/mL and 50 μg/mL, respectively and minimum bactericidal concentrations (MBCs) of E. coli and S. aureus were 25 μg/mL and 100 μg/mL, respectively. Results exhibited that biosynthesized AgNPs caused morphological changes and injured the membrane integrity of strains E. coli and S. aureus. The AgNPs synthesized by Sphingobium sp. MAH-11 may serve as a potent antimicrobial agent for many therapeutic applications.
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Affiliation(s)
- Shahina Akter
- Department of Food Science and Biotechnology, College of BioNano Technology, Gachon University, Seongnam, Republic of Korea
| | - Md Amdadul Huq
- Department of Food and Nutrition, College of Biotechnology and Natural Resource, Chung-Ang University, Anseong, Republic of Korea
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99920
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Qi S, Wang J, Grismer LL, Chen HH, Lyu ZT, Wang YY. The Stoor Hobbit of Guangdong: Goniurosaurus gollum sp. nov., a cave-dwelling Leopard Gecko (Squamata, Eublepharidae) from South China. Zookeys 2020; 991:137-153. [PMID: 33223904 PMCID: PMC7674404 DOI: 10.3897/zookeys.991.54935] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Accepted: 09/10/2020] [Indexed: 11/12/2022] Open
Abstract
A new species of the genus Goniurosaurus is described based on three specimens collected from a limestone cave in Huaiji County, Guangdong Province, China. Based on molecular phylogenetic analyses, the new species is nested within the Goniurosaurus yingdeensis species group. However, morphological analyses cannot ascribe it to any known species of that group. It is distinguished from the other three species in the group by a combination of the following characters: scales around midbody 121-128; dorsal tubercle rows at midbody 16-17; presence of 10-11 precloacal pores in males, and absent in females; nuchal loop and body bands immaculate, without black spots; iris orange, gradually darker on both sides. The discovery of yet another limestone-adapted species of Goniurosaurus in Guangdong Province underscores a growing body of evidence for the high biodiversity of limestone habitats and brings into sharp focus the urgent need for their conservation.
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Affiliation(s)
- Shuo Qi
- State Key Laboratory of Biocontrol/ The Museum of Biology, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510275, China
| | - Jian Wang
- State Key Laboratory of Biocontrol/ The Museum of Biology, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510275, China
| | - L. Lee Grismer
- Herpetology Laboratory, Department of Biology, La Sierra University, Riverside, California 92515, USA
| | - Hong-Hui Chen
- State Key Laboratory of Biocontrol/ The Museum of Biology, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510275, China
| | - Zhi-Tong Lyu
- State Key Laboratory of Biocontrol/ The Museum of Biology, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510275, China
| | - Ying-Yong Wang
- State Key Laboratory of Biocontrol/ The Museum of Biology, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510275, China
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99921
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Mighell KS, Henkel TW, Koch RA, Chin ML, Brann MA, Aime MC. Amanita in the Guineo-Congolian rainforest: Epitypes and new species from the Dja Biosphere Reserve, Cameroon. Mycologia 2020; 113:168-190. [PMID: 33175671 DOI: 10.1080/00275514.2020.1816386] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Four epitypes and three new species of Amanita (Amanitaceae, Agaricales, Agaricomycetes, Basidiomycota) are described from Guineo-Congolian rainforests of Cameroon. Amanita echinulata, A. fulvopulverulenta, A. robusta, and A. bingensis are epitypified based on collections that are the first since the species were described nearly a century ago. Morphological features of the epitypes are described and enumerated. Amanita minima, Amanita luteolamellata, and A. goossensfontanae are described as new and added to the known macromycota of tropical Africa. Habit, habitat, and known distribution are provided for each species. Sequence data for the internal transcribed spacer (ITS) locus are provided for types and other collections of all taxa, and a molecular phylogenetic analysis across the genus Amanita corroborates morphology-based infrageneric placement for each.
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Affiliation(s)
- Kennan S Mighell
- Department of Biological Sciences, Humboldt State University , Arcata, California 95521
| | - Terry W Henkel
- Department of Biological Sciences, Humboldt State University , Arcata, California 95521
| | - Rachel A Koch
- Department of Botany and Plant Pathology, Purdue University , West Lafayette, Indiana 47907
| | - Mei Lin Chin
- Department of Biological Sciences, Humboldt State University , Arcata, California 95521
| | - Mia A Brann
- Department of Botany and Plant Pathology, Purdue University , West Lafayette, Indiana 47907
| | - M Catherine Aime
- Department of Botany and Plant Pathology, Purdue University , West Lafayette, Indiana 47907
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99922
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Conradie W, Keates C, Lobón-Rovira J, Pinto PV, Verburgt L, Baptista NL, Harvey J, Júlio T. New insights into the taxonomic status, distribution and natural history of De Witte’s Clicking Frog (Kassinula wittei Laurent, 1940). AFRICAN ZOOLOGY 2020. [DOI: 10.1080/15627020.2020.1821771] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- Werner Conradie
- Port Elizabeth Museum, Humewood, South Africa
- School of Natural Resource Management, George Campus, Nelson Mandela University, George, South Africa
- National Geographic Okavango Wilderness Project, Wild Bird Trust, South Africa
| | - Chad Keates
- National Geographic Okavango Wilderness Project, Wild Bird Trust, South Africa
- Department of Zoology and Entomology, Rhodes University, Makhanda, South Africa
| | - Javier Lobón-Rovira
- CIBIO/InBio Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vairão, Portugal
- Faculdade de Ciências, Universidade do Porto, Porto, Portugal
| | - Pedro Vaz Pinto
- CIBIO/InBio Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vairão, Portugal
- Fundação Kissama, Luanda, Angola
- Instituto Superior de Ciências da Educação da Huíla, Lubango, Angola
| | - Luke Verburgt
- National Geographic Okavango Wilderness Project, Wild Bird Trust, South Africa
- Department of Zoology and Entomology, University of Pretoria, Pretoria, South Africa
| | - Ninda L Baptista
- National Geographic Okavango Wilderness Project, Wild Bird Trust, South Africa
- CIBIO/InBio Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vairão, Portugal
- Faculdade de Ciências, Universidade do Porto, Porto, Portugal
- Instituto Superior de Ciências da Educação da Huíla, Lubango, Angola
| | | | - Timóteo Júlio
- National Geographic Okavango Wilderness Project, Wild Bird Trust, South Africa
- Fundação Kissama, Luanda, Angola
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99923
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Cohen ZP, Brevik K, Chen YH, Hawthorne DJ, Weibel BD, Schoville SD. Elevated rates of positive selection drive the evolution of pestiferousness in the Colorado potato beetle (Leptinotarsa decemlineata, Say). Mol Ecol 2020; 30:237-254. [PMID: 33095936 DOI: 10.1111/mec.15703] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 09/28/2020] [Accepted: 10/15/2020] [Indexed: 12/16/2022]
Abstract
Contextualizing evolutionary history and identifying genomic features of an insect that might contribute to its pest status is important in developing early detection and control tactics. In order to understand the evolution of pestiferousness, which we define as the accumulation of traits that contribute to an insect population's success in an agroecosystem, we tested the importance of known genomic properties associated with rapid adaptation in the Colorado potato beetle (CPB), Leptinotarsa decemlineata Say. Within the leaf beetle genus Leptinotarsa, only CPB, and a few populations therein, has risen to pest status on cultivated nightshades, Solanum. Using whole genomes from ten closely related Leptinotarsa species native to the United States, we reconstructed a high-quality species tree and used this phylogenetic framework to assess evolutionary patterns in four genomic features of rapid adaptation: standing genetic variation, gene family expansion and contraction, transposable element abundance and location, and positive selection at protein-coding genes. Throughout approximately 20 million years of history, Leptinotarsa species show little evidence of gene family turnover and transposable element variation. However, there is a clear pattern of CPB experiencing higher rates of positive selection on protein-coding genes. We determine that these rates are associated with greater standing genetic variation due to larger effective population size, which supports the theory that the demographic history contributes to rates of protein evolution. Furthermore, we identify a suite of coding genes under positive selection that are putatively associated with pestiferousness in the Colorado potato beetle lineage. They are involved in the biological processes of xenobiotic detoxification, chemosensation and hormone function.
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Affiliation(s)
- Zachary P Cohen
- Department of Entomology, University of Wisconsin-Madison, Madison, WI, USA
| | - Kristian Brevik
- Department of Plant and Soil Sciences, University of Vermont, Burlington, VT, USA
| | - Yolanda H Chen
- Department of Plant and Soil Sciences, University of Vermont, Burlington, VT, USA
| | - David J Hawthorne
- Department of Entomology, University of Maryland, College Park, MD, USA
| | - Benjamin D Weibel
- Department of Entomology, University of Wisconsin-Madison, Madison, WI, USA
| | - Sean D Schoville
- Department of Entomology, University of Wisconsin-Madison, Madison, WI, USA
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99924
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Tan Y, Schneider T, Shukla PK, Chandrasekharan MB, Aravind L, Zhang D. Unification of the M/ORF3-related proteins points to a diversified role for ion conductance in pathogenesis of coronaviruses and other nidoviruses. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2020:2020.11.10.377366. [PMID: 33200132 PMCID: PMC7668736 DOI: 10.1101/2020.11.10.377366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The new coronavirus, SARS-CoV-2, responsible for the COVID-19 pandemic has emphasized the need for a better understanding of the evolution of virus-host conflicts. ORF3a in both SARS-CoV-1 and SARS-CoV-2 are ion channels (viroporins) and involved in virion assembly and membrane budding. Using sensitive profile-based homology detection methods, we unify the SARS-CoV ORF3a family with several families of viral proteins, including ORF5 from MERS-CoVs, proteins from beta-CoVs (ORF3c), alpha-CoVs (ORF3b), most importantly, the Matrix (M) proteins from CoVs, and more distant homologs from other nidoviruses. By sequence analysis and structural modeling, we show that these viral families utilize specific conserved polar residues to constitute an ion-conducting pore in the membrane. We reconstruct the evolutionary history of these families, objectively establish the common origin of the M proteins of CoVs and Toroviruses. We show that the divergent ORF3a/ORF3b/ORF5 families represent a duplication stemming from the M protein in alpha- and beta-CoVs. By phyletic profiling of major structural components of primary nidoviruses, we present a model for their role in virion assembly of CoVs, ToroVs and Arteriviruses. The unification of diverse M/ORF3 ion channel families in a wide range of nidoviruses, especially the typical M protein in CoVs, reveal a conserved, previously under-appreciated role of ion channels in virion assembly, membrane fusion and budding. We show that the M and ORF3 are under differential evolutionary pressures; in contrast to the slow evolution of M as core structural component, the CoV-ORF3 clade is under selection for diversification, which indicates it is likely at the interface with host molecules and/or immune attack. IMPORTANCE Coronaviruses (CoVs) have become a major threat to human welfare as the causative agents of several severe infectious diseases, namely Severe Acute Respiratory Syndrome (SARS), Middle Eastern Respiratory Syndrome (MERS), and the recently emerging human coronavirus disease 2019 (COVID-19). The rapid spread, severity of these diseases, as well as the potential re-emergence of other CoV-associated diseases have imposed a strong need for a thorough understanding of function and evolution of these CoVs. By utilizing robust domain-centric computational strategies, we have established homologous relationships between many divergent families of CoV proteins, including SARS-CoV/SARS-CoV-2 ORF3a, MERS-CoV ORF5, proteins from both beta-CoVs (ORF3c) and alpha-CoVs (ORF3b), the typical CoV Matrix proteins, and many distant homologs from other nidoviruses. We present evidence that they are active ion channel proteins, and the Cov-specific ORF3 clade proteins are under selection for rapid diversification, suggesting they might have been involved in interfering host molecules and/or immune attack.
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99925
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Abstract
Gene expression programs define shared and species-specific phenotypes, but their evolution remains largely uncharacterized beyond the transcriptome layer1. Here we report an analysis of the co-evolution of translatomes and transcriptomes using ribosome-profling and matched RNA-sequencing data for three organs (brain, liver and testis) in fve mammals (human, macaque, mouse, opossum and platypus) and a bird (chicken). Our within-species analyses reveal that translational regulation is widespread in the diferent organs, in particular across the spermatogenic cell types of the testis. The between-species divergence in gene expression is around 20% lower at the translatome layer than at the transcriptome layer owing to extensive buffering between the expression layers, which especially preserved old, essential and housekeeping genes. Translational upregulation specifcally counterbalanced global dosage reductions during the evolution of sex chromosomes and the efects of meiotic sex-chromosome inactivation during spermatogenesis. Despite the overall prevalence of bufering, some genes evolved faster at the translatome layer—potentially indicating adaptive changes in expression; testis tissue shows the highest fraction of such genes. Further analyses incorporating mass spectrometry proteomics data establish that the co-evolution of transcriptomes and translatomes is refected at the proteome layer. Together, our work uncovers co-evolutionary patterns and associated selective forces across the expression layers, and provides a resource for understanding their interplay in mammalian organs.
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99926
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Barylyuk K, Koreny L, Ke H, Butterworth S, Crook OM, Lassadi I, Gupta V, Tromer E, Mourier T, Stevens TJ, Breckels LM, Pain A, Lilley KS, Waller RF. A Comprehensive Subcellular Atlas of the Toxoplasma Proteome via hyperLOPIT Provides Spatial Context for Protein Functions. Cell Host Microbe 2020; 28:752-766.e9. [PMID: 33053376 PMCID: PMC7670262 DOI: 10.1016/j.chom.2020.09.011] [Citation(s) in RCA: 161] [Impact Index Per Article: 40.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 07/30/2020] [Accepted: 09/15/2020] [Indexed: 12/15/2022]
Abstract
Apicomplexan parasites cause major human disease and food insecurity. They owe their considerable success to highly specialized cell compartments and structures. These adaptations drive their recognition, nondestructive penetration, and elaborate reengineering of the host's cells to promote their growth, dissemination, and the countering of host defenses. The evolution of unique apicomplexan cellular compartments is concomitant with vast proteomic novelty. Consequently, half of apicomplexan proteins are unique and uncharacterized. Here, we determine the steady-state subcellular location of thousands of proteins simultaneously within the globally prevalent apicomplexan parasite Toxoplasma gondii. This provides unprecedented comprehensive molecular definition of these unicellular eukaryotes and their specialized compartments, and these data reveal the spatial organizations of protein expression and function, adaptation to hosts, and the underlying evolutionary trajectories of these pathogens.
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Affiliation(s)
| | - Ludek Koreny
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, UK
| | - Huiling Ke
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, UK
| | - Simon Butterworth
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, UK
| | - Oliver M Crook
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, UK; Milner Therapeutics Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB20 0AW, UK; MRC Biostatistics Unit, Cambridge Institute for Public Health, Cambridge CB2 0SR, UK
| | - Imen Lassadi
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, UK
| | - Vipul Gupta
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, UK
| | - Eelco Tromer
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, UK
| | - Tobias Mourier
- Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal 23955, Saudi Arabia
| | - Tim J Stevens
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| | - Lisa M Breckels
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, UK; Milner Therapeutics Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB20 0AW, UK
| | - Arnab Pain
- Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal 23955, Saudi Arabia; Global Station for Zoonosis Control, Gi-CoRE, Hokkaido University, Sapporo 060-0808, Japan; Nuffield Division of Clinical Laboratory Sciences (NDCLS), University of Oxford, Oxford OX3 9DU, UK
| | - Kathryn S Lilley
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, UK; Milner Therapeutics Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB20 0AW, UK
| | - Ross F Waller
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, UK.
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99927
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Shivambu TC, Shivambu N, Lyle R, Jacobs A, Kumschick S, Foord SH, Robertson MP. Tarantulas (Araneae: Theraphosidae) in the pet trade in South Africa. AFRICAN ZOOLOGY 2020. [DOI: 10.1080/15627020.2020.1823879] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Tinyiko C Shivambu
- Centre for Invasion Biology, School of Life Sciences, University of KwaZulu-Natal, Pietermaritzburg, South Africa
- Centre for Invasion Biology, Zoology and Entomology, University of Pretoria, Pretoria, South Africa
| | - Ndivhuwo Shivambu
- Centre for Invasion Biology, School of Life Sciences, University of KwaZulu-Natal, Pietermaritzburg, South Africa
- Centre for Invasion Biology, Zoology and Entomology, University of Pretoria, Pretoria, South Africa
| | - Robin Lyle
- Biosystematics Division, Agriculture Research Council-Plant Protection Health and Protection, Pretoria, South Africa
| | - Adriaana Jacobs
- Biosystematics Division, Agriculture Research Council-Plant Protection Health and Protection, Pretoria, South Africa
| | - Sabrina Kumschick
- Centre for Invasion Biology, Department of Botany and Zoology, Stellenbosch University, Stellenbosch, South Africa
- South African National Biodiversity Institute, Kirstenbosch Research Centre, Cape Town, South Africa
| | - Stefan H Foord
- Department of Zoology and Centre for Invasion Biology, University of Venda, Thohoyandou, South Africa
| | - Mark P Robertson
- Centre for Invasion Biology, Zoology and Entomology, University of Pretoria, Pretoria, South Africa
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99928
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Toussaint EFA, Ellis EA, Gott RJ, Warren AD, Dexter KM, Storer C, Lohman DJ, Kawahara AY. Historical biogeography of Heteropterinae skippers via Beringian and post‐Tethyan corridors. ZOOL SCR 2020. [DOI: 10.1111/zsc.12457] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Emmanuel F. A. Toussaint
- Natural History Museum of Geneva Geneva Switzerland
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History University of Florida Gainesville FL USA
| | - Emily A. Ellis
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History University of Florida Gainesville FL USA
| | - Riley J. Gott
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History University of Florida Gainesville FL USA
| | - Andrew D. Warren
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History University of Florida Gainesville FL USA
| | - Kelly M. Dexter
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History University of Florida Gainesville FL USA
| | - Caroline Storer
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History University of Florida Gainesville FL USA
| | - David J. Lohman
- Biology Department City College of New YorkCity University of New York New York NY USA
- Ph.D. Program in Biology, Graduate Center City University of New York New York NY USA
- Entomology Section National Museum of Natural History Manila Philippines
| | - Akito Y. Kawahara
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History University of Florida Gainesville FL USA
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99929
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Muliyar RK, Chowdappa P, Behera SK, Kasaragod S, Gangaraj KP, Kotimoole CN, Nekrakalaya B, Mohanty V, Sampgod RB, Banerjee G, Das AJ, Niral V, Karun A, Mahato AK, Gaikwad K, Singh NK, Prasad TSK. Assembly and Annotation of the Nuclear and Organellar Genomes of a Dwarf Coconut (Chowghat Green Dwarf) Possessing Enhanced Disease Resistance. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2020; 24:726-742. [PMID: 33170083 DOI: 10.1089/omi.2020.0147] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Coconut (Cocos nucifera L.), an important source of vegetable oil, nutraceuticals, functional foods, and housing materials, provides raw materials for a repertoire of industries engaged in the manufacture of cosmetics, soaps, detergents, paints, varnishes, and emulsifiers, among other products. The palm plays a vital role in maintaining and promoting the sustainability of farming systems of the fragile ecosystems of islands and coastal regions of the tropics. In this study, we present the genome of a dwarf coconut variety "Chowghat Green Dwarf" (CGD) from India, possessing enhanced resistance to root (wilt) disease. Utilizing short reads from the Illumina HiSeq 4000 platform and long reads from the Pacific Biosciences RSII platform, we have assembled the draft genome assembly of 1.93 Gb. The genome is distributed over 26,855 scaffolds, with ∼81.56% of the assembled genome present in scaffolds of lengths longer than 50 kb. About 77.29% of the genome was composed of transposable elements and repeats. Gene prediction yielded 51,953 genes, which upon stringent filtering, based on Annotation Edit Distance, resulted in 13,707 genes, which coded for 11,181 proteins. Among these, we gathered transcript level evidence for a total of 6828 predicted genes based on the RNA-Seq data from different coconut tissues, since they presented assembled transcripts within the genome annotation coordinates. A total of 112 nucleotide-binding and leucine-rich repeat loci, belonging to six classes, were detected. We have also undertaken the assembly and annotation of the CGD chloroplast and mitochondrial genomes. The availability of the dwarf coconut genome shall prove invaluable for deducing the origin of dwarf coconut cultivars, dissection of genes controlling plant habit and fruit color, and accelerated breeding for improved agronomic traits.
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Affiliation(s)
| | - Pallem Chowdappa
- ICAR-Central Plantation Crops Research Institute (CPCRI), Kasaragod, India
| | - Santosh Kumar Behera
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, India
| | - Sandeep Kasaragod
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, India
| | | | - Chinmaya Narayana Kotimoole
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, India
| | - Bhagya Nekrakalaya
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, India
| | - Varshasnata Mohanty
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, India
| | | | | | | | - Vittal Niral
- ICAR-Central Plantation Crops Research Institute (CPCRI), Kasaragod, India
| | - Anitha Karun
- ICAR-Central Plantation Crops Research Institute (CPCRI), Kasaragod, India
| | - Ajay Kumar Mahato
- ICAR-National Research Center on Plant Biotechnology, Pusa Campus, New Delhi, India
| | - Kishor Gaikwad
- ICAR-National Research Center on Plant Biotechnology, Pusa Campus, New Delhi, India
| | - Nagendra Kumar Singh
- ICAR-National Research Center on Plant Biotechnology, Pusa Campus, New Delhi, India
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99930
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Chen X, Song Q, Huang M. Characterization of the Complete Mitochondrial Genomes from Two Nitidulid Pests with Phylogenetic Implications. INSECTS 2020; 11:insects11110779. [PMID: 33187054 PMCID: PMC7697951 DOI: 10.3390/insects11110779] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/26/2020] [Revised: 11/06/2020] [Accepted: 11/07/2020] [Indexed: 06/11/2023]
Abstract
The complete mitochondrial genomes of Xenostrongylusvariegatus and Epuraea sp. were sequenced and analyzed. The total genome lengths are 17,657 and 16,641 bp, with an A+T content of 77.2% and 76.4%, respectively. Each mitochondrial genome consists of 37 coding genes and a non-coding (AT-rich) region. All protein-coding genes (PCGs) start with the standard start codon, ATN, and end with complete stop codons, TAA and TAG, or an incomplete stop codon, T. All tRNAs can be folded into the typical clover-leaf secondary structure, with the exception of trnS1 in both species with a reduced dihydrouridine (DHU) arm. The AT-rich region has tandem repeats differing in both number and length. Genetic distance and Ka/Ks analyses show that nad6 has a higher variability and more rapid evolutionary rate than other PCGs. Both maximum likelihood and Bayesian inference phylogenetic analyses based on 13 PCGs and 2 ribosome DNAs (rDNAs) agree with the previous phylogenies in supporting the Nitidulidae monophyly and the sister-group relationship of Kateretidae + (Monotomidae + Nitidulidae).
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Affiliation(s)
| | | | - Min Huang
- Correspondence: ; Tel.: +86-029-87092705
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99931
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Adawaren EO, Du Plessis M, Suleman E, Kindler D, Oosthuizen AO, Mukandiwa L, Naidoo V. The complete mitochondrial genome of Gyps coprotheres (Aves, Accipitridae, Accipitriformes): phylogenetic analysis of mitogenome among raptors. PeerJ 2020; 8:e10034. [PMID: 33240589 PMCID: PMC7666543 DOI: 10.7717/peerj.10034] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Accepted: 09/03/2020] [Indexed: 11/20/2022] Open
Abstract
Three species of Old World vultures on the Asian peninsula are slowly recovering from the lethal consequences of diclofenac. At present the reason for species sensitivity to diclofenac is unknown. Furthermore, it has since been demonstrated that other Old World vultures like the Cape (Gyps coprotheres; CGV) and griffon (G. fulvus) vultures are also susceptible to diclofenac toxicity. Oddly, the New World Turkey vulture (Cathartes aura) and pied crow (Corvus albus) are not susceptible to diclofenac toxicity. As a result of the latter, we postulate an evolutionary link to toxicity. As a first step in understanding the susceptibility to diclofenac toxicity, we use the CGV as a model species for phylogenetic evaluations, by comparing the relatedness of various raptor species known to be susceptible, non-susceptible and suspected by their relationship to the Cape vulture mitogenome. This was achieved by next generation sequencing and assembly. The Cape vulture mitogenome had a genome size of 16,908 bp. The mitogenome phylogenetic analysis indicated a close evolutionary relationship between Old World vultures and other members of the Accipitridae as indicated by bootstrap value of 100% on the phylogenetic trees. Based on this, we postulate that the other species could also be sensitive to the toxic effects of diclofenac. This warrants further investigations.
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Affiliation(s)
- Emmanuel Oluwasegun Adawaren
- Department of Paraclinical Science/Faculty of Veterinary Science, University of Pretoria, Pretoria, Gauteng, South Africa
| | - Morne Du Plessis
- Bioinformatics and Comparative Genomics, South African National Biodiversity Institute, Pretoria, Gauteng, South Africa
| | - Essa Suleman
- Molecular Diagnostics, Council for Scientific and Industrial Research, Pretoria, Gauteng, South Africa.,Current affiliation: Bioinformatics and Comparative Genomics, South African National Biodiversity Institute, Pretoria, Gauteng, South Africa
| | - Duodane Kindler
- Molecular Diagnostics, Council for Scientific and Industrial Research, Pretoria, Gauteng, South Africa
| | - Almero O Oosthuizen
- Bioinformatics and Comparative Genomics, South African National Biodiversity Institute, Pretoria, Gauteng, South Africa
| | - Lillian Mukandiwa
- Department of Paraclinical Science/Faculty of Veterinary Science, University of Pretoria, South Africa
| | - Vinny Naidoo
- Paraclinical Science/Faculty of Veterinary Science, University of Pretoria, Pretoria, Gauteng, South Africa
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99932
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Leal-Gutiérrez JD, Elzo MA, Carr C, Mateescu RG. RNA-seq analysis identifies cytoskeletal structural genes and pathways for meat quality in beef. PLoS One 2020; 15:e0240895. [PMID: 33175867 PMCID: PMC7657496 DOI: 10.1371/journal.pone.0240895] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Accepted: 10/05/2020] [Indexed: 01/03/2023] Open
Abstract
RNA sequencing (RNA-seq) has allowed for transcriptional profiling of biological systems through the identification of differentially expressed (DE) genes and pathways. A total of 80 steers with extreme phenotypes were selected from the University of Florida multibreed Angus-Brahman herd. The average slaughter age was 12.91±8.69 months. Tenderness, juiciness and connective tissue assessed by sensory panel, along with marbling, Warner-Bratzler Shear Force (WBSF) and cooking loss, were measured in longissimus dorsi muscle. Total RNA was extracted from muscle and one RNA-seq library per sample was constructed, multiplexed, and sequenced based on protocols by Illumina HiSeq-3000 platform to generate 2×101 bp paired-end reads. The overall read mapping rate using the Btau_4.6.1 reference genome was 63%. A total of 8,799 genes were analyzed using two different methodologies, an expression association and a DE analysis. A gene and exon expression association analysis was carried out using a meat quality index on all 80 samples as a continuous response variable. The expression of 208 genes and 3,280 exons from 1,565 genes was associated with the meat quality index (p-value ≤ 0.05). A gene and isoform DE evaluation was performed analyzing two groups with extreme WBSF, tenderness and marbling. A total of 676 (adjusted p-value≤0.05), 70 (adjusted p-value≤0.1) and 198 (adjusted p-value≤0.1) genes were DE for WBSF, tenderness and marbling, respectively. A total of 106 isoforms from 98 genes for WBSF, 13 isoforms from 13 genes for tenderness and 43 isoforms from 42 genes for marbling (FDR≤0.1) were DE. Cytoskeletal and transmembrane anchoring genes and pathways were identified in the expression association, DE and the gene enrichment analyses; these proteins can have a direct effect on meat quality. Cytoskeletal proteins and transmembrane anchoring molecules can influence meat quality by allowing cytoskeletal interaction with myocyte and organelle membranes, contributing to cytoskeletal structure and architecture maintenance postmortem.
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Affiliation(s)
- Joel D. Leal-Gutiérrez
- Department of Animal Sciences, University of Florida, Gainesville, Florida, United States of America
| | - Mauricio A. Elzo
- Department of Animal Sciences, University of Florida, Gainesville, Florida, United States of America
| | - Chad Carr
- Department of Animal Sciences, University of Florida, Gainesville, Florida, United States of America
| | - Raluca G. Mateescu
- Department of Animal Sciences, University of Florida, Gainesville, Florida, United States of America
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99933
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Zhu C, Zhang S, Zhou C, Chen L, Zaripov T, Zhan D, Weng J, Lin Y, Lai Z, Guo Y. Integrated Transcriptome, microRNA, and Phytochemical Analyses Reveal Roles of Phytohormone Signal Transduction and ABC Transporters in Flavor Formation of Oolong Tea ( Camellia sinensis) during Solar Withering. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:12749-12767. [PMID: 33112139 DOI: 10.1021/acs.jafc.0c05750] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
The unique aroma and flavor of oolong tea develop during the withering stage of postharvest processing. We explored the roles of miRNA-related regulatory networks during tea withering and their effects on oolong tea quality. We conducted transcriptome and miRNA analyses to identify differentially expressed (DE) miRNAs and target genes among fresh leaves, indoor-withered leaves, and solar-withered leaves. We identified 32 DE-miRNAs and 41 target genes involved in phytohormone signal transduction and ABC transporters. Further analyses indicated that these two pathways regulated the accumulation of flavor-related metabolites during tea withering. Flavonoid accumulation was correlated with the miR167d_1-ARF-GH3, miR845-ABCC1-3/ABCC2, miR166d-5p_1-ABCC1-2, and miR319c_3-PIF-ARF modules. Terpenoid content was correlated with the miR171b-3p_2-DELLA-MYC2 and miR166d-5p_1-ABCG2-MYC2 modules. These modules inhibited flavonoid biosynthesis and enhanced terpenoid biosynthesis in solar-withered leaves. Low auxin and gibberellic acid contents and circRNA-related regulatory networks also regulated the accumulation of flavor compounds in solar-withered leaves. Our analyses reveal how solar withering produces high-quality oolong tea.
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Affiliation(s)
- Chen Zhu
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Key Laboratory of Tea Science in Universities of Fujian Province, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Shuting Zhang
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Chengzhe Zhou
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Key Laboratory of Tea Science in Universities of Fujian Province, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Lan Chen
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Key Laboratory of Tea Science in Universities of Fujian Province, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Timur Zaripov
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Key Laboratory of Tea Science in Universities of Fujian Province, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Dongmei Zhan
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Key Laboratory of Tea Science in Universities of Fujian Province, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Jingjing Weng
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Key Laboratory of Tea Science in Universities of Fujian Province, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yuling Lin
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Zhongxiong Lai
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yuqiong Guo
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Key Laboratory of Tea Science in Universities of Fujian Province, Fujian Agriculture and Forestry University, Fuzhou 350002, China
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99934
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Triplex Real-Time PCR Approach for the Detection of Crucial Fungal Berry Pathogens- Botrytis spp., Colletotrichum spp. and Verticillium spp. Int J Mol Sci 2020; 21:ijms21228469. [PMID: 33187143 PMCID: PMC7697166 DOI: 10.3390/ijms21228469] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 11/04/2020] [Accepted: 11/08/2020] [Indexed: 12/30/2022] Open
Abstract
Phytopathogens cause undeniably serious damage in agriculture by harming fruit cultivations and lowering harvest yields, which as a consequence substantially reduces food production efficiency. Fungi of the Botrytis, Colletotrichum and Verticillium genera are a main concern in berry production. However, no rapid detection method for detecting all of these pathogens simultaneously has been developed to date. Therefore, in this study, a multiplex real-time PCR assay for this purpose was established. Universal fungal primers for the D2 region of the large subunit ribosomal DNA and three multiplexable fluorogenic probes specific for the chosen fungi were designed and deployed. The triplex approach for the molecular detection of these fungi, which was developed in this study, allows for the rapid and effective detection of crucial berry pathogens, which contributes to a more rapid implementation of protective measures in plantations and a significant reduction in losses caused by fungal diseases.
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99935
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Yoon HJ, Park JS, Jeong SY, Lee KY, Kim I. Mitochondrial genome of the mason bee, Osmia pedicornis (Hymenopetra: Megachilidae). MITOCHONDRIAL DNA PART B-RESOURCES 2020; 5:3764-3766. [PMID: 33367092 PMCID: PMC7671597 DOI: 10.1080/23802359.2020.1833775] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The mason bee, Osmia pedicornis Cockerell, 1919, which is importantly used as the pollinator, particularly for apples in Korea. We sequenced the mitochondrial genome (mitogenome) of O. pedicornis as an initial study for species identification and subsequent population genetic study. The size of the incomplete genome was 14,505 bp, excluding the trnA, trnC, and the A + T-rich region that were unable to sequence, but including partially sequenced trnM and srRNA. The genome included typical sets of protein-coding genes (PCGs), rRNA genes, and one non-coding region, tRNAs, excluding two unidentified tRNAs. Although positions of the two tRNAs that were not sequenced are unknown the gene arrangement of O. pedicornis mitogenome has the tRNA arrangement, trnM-trnQ-trnI, at the A + T-rich region and ND2 junction that differed from that of previously published O. excavate, which has trnA-trnQ-trnI arrangement at the junction. Phylogenetic analyses were performed using concatenated sequences of the 13 PCGs genes and the maximum likelihood method with the inclusion of a total of 12 mitogenome sequences belonging to three families in the superfamily Apoidea. Current O. pedicornis was placed as the sister to the O. bicornis, with the highest nodal support. The Apidae and Megachilidae were placed as the sister group, with the placement of Colletidae as the basal lineage for the group with the highest nodal support.
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Affiliation(s)
- Hyung Joo Yoon
- Department of Agricultural Biology, National Academy of Agricultural Science, Rural Development Administration, Jeollabuk-do, Republic of Korea
| | - Jeong Sun Park
- Department of Applied Biology, College of Agriculture & Life Sciences, Chonnam National University, Gwangju, Republic of Korea
| | - Su Yeon Jeong
- Department of Applied Biology, College of Agriculture & Life Sciences, Chonnam National University, Gwangju, Republic of Korea
| | - Kyeong Yong Lee
- Department of Agricultural Biology, National Academy of Agricultural Science, Rural Development Administration, Jeollabuk-do, Republic of Korea
| | - Iksoo Kim
- Department of Applied Biology, College of Agriculture & Life Sciences, Chonnam National University, Gwangju, Republic of Korea
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99936
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Watanabe J, Field DJ, Matsuoka H. Wing Musculature Reconstruction in Extinct Flightless Auks ( Pinguinus and Mancalla) Reveals Incomplete Convergence with Penguins (Spheniscidae) Due to Differing Ancestral States. Integr Org Biol 2020; 3:obaa040. [PMID: 34258512 PMCID: PMC8271220 DOI: 10.1093/iob/obaa040] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Despite longstanding interest in convergent evolution, factors that result in deviations from fully convergent phenotypes remain poorly understood. In birds, the evolution of flightless wing-propelled diving has emerged as a classic example of convergence, having arisen in disparate lineages including penguins (Sphenisciformes) and auks (Pan-Alcidae, Charadriiformes). Nevertheless, little is known about the functional anatomy of the wings of flightless auks because all such taxa are extinct, and their morphology is almost exclusively represented by skeletal remains. Here, in order to re-evaluate the extent of evolutionary convergence among flightless wing-propelled divers, wing muscles and ligaments were reconstructed in two extinct flightless auks, representing independent transitions to flightlessness: Pinguinus impennis (a crown-group alcid), and Mancalla (a stem-group alcid). Extensive anatomical data were gathered from dissections of 12 species of extant charadriiforms and 4 aequornithine waterbirds including a penguin. The results suggest that the wings of both flightless auk taxa were characterized by an increased mechanical advantage of wing elevator/retractor muscles, and decreased mobility of distal wing joints, both of which are likely advantageous for wing-propelled diving and parallel similar functional specializations in penguins. However, the conformations of individual muscles and ligaments underlying these specializations differ markedly between penguins and flightless auks, instead resembling those in each respective group's close relatives. Thus, the wings of these flightless wing-propelled divers can be described as convergent as overall functional units, but are incompletely convergent at lower levels of anatomical organization-a result of retaining differing conditions from each group's respective volant ancestors. Detailed investigations such as this one may indicate that, even in the face of similar functional demands, courses of phenotypic evolution are dictated to an important degree by ancestral starting points.
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Affiliation(s)
- Junya Watanabe
- Department of Earth Sciences, University of Cambridge, Downing Street, Cambridge, CB2 3EQ, UK.,Department of Geology and Mineralogy, Kyoto University, Sakyoku Kitashirakawa Oiwakecho, Kyoto, 606-8502, Japan
| | - Daniel J Field
- Department of Earth Sciences, University of Cambridge, Downing Street, Cambridge, CB2 3EQ, UK
| | - Hiroshige Matsuoka
- Department of Geology and Mineralogy, Kyoto University, Sakyoku Kitashirakawa Oiwakecho, Kyoto, 606-8502, Japan
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99937
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Wang J, Fu W, Wang R, Hu D, Cheng H, Zhao J, Jiang Y, Kang Z. WGVD: an integrated web-database for wheat genome variation and selective signatures. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2020; 2020:5979748. [PMID: 33181826 PMCID: PMC7661095 DOI: 10.1093/database/baaa090] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/01/2020] [Revised: 09/10/2020] [Accepted: 09/16/2020] [Indexed: 01/08/2023]
Abstract
Bread wheat is one of the most important crops worldwide. With the release of the complete wheat reference genome and the development of next-generation sequencing technology, a mass of genomic data from bread wheat and its progenitors has been yield and has provided genomic resources for wheat genetics research. To conveniently and effectively access and use these data, we established Wheat Genome Variation Database, an integrated web-database including genomic variations from whole-genome resequencing and exome-capture data for bread wheat and its progenitors, as well as selective signatures during the process of wheat domestication and improvement. In this version, WGVD contains 7 346 814 single nucleotide polymorphisms (SNPs) and 1 044 400 indels focusing on genic regions and upstream or downstream regions. We provide allele frequency distribution patterns of these variations for 5 ploidy wheat groups or 17 worldwide bread wheat groups, the annotation of the variant types and the genotypes of all individuals for 2 versions of bread wheat reference genome (IWGSC RefSeq v1.0 and IWGSC RefSeq v2.0). Selective footprints for Aegilops tauschii, wild emmer, domesticated emmer, bread wheat landrace and bread wheat variety are evaluated with two statistical tests (FST and Pi) based on SNPs from whole-genome resequencing data. In addition, we provide the Genome Browser to visualize the genomic variations, the selective footprints, the genotype patterns and the read coverage depth, and the alignment tool Blast to search the homologous regions between sequences. All of these features of WGVD will promote wheat functional studies and wheat breeding. Database URL http://animal.nwsuaf.edu.cn/code/index.php/Wheat
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Affiliation(s)
- Jierong Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, 3 Taicheng Rd, Yangling 712100, Shaanxi, China
| | - Weiwei Fu
- College of Animal Science and Technology, Northwest A&F University, 22 Xinong Rd, Yangling, 712100, Shaanxi, China
| | - Rui Wang
- College of Animal Science and Technology, Northwest A&F University, 22 Xinong Rd, Yangling, 712100, Shaanxi, China
| | - Dexiang Hu
- College of Animal Science and Technology, Northwest A&F University, 22 Xinong Rd, Yangling, 712100, Shaanxi, China
| | - Hong Cheng
- College of Animal Science and Technology, Northwest A&F University, 22 Xinong Rd, Yangling, 712100, Shaanxi, China
| | - Jing Zhao
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, 3 Taicheng Rd, Yangling 712100, Shaanxi, China
| | - Yu Jiang
- College of Animal Science and Technology, Northwest A&F University, 22 Xinong Rd, Yangling, 712100, Shaanxi, China
| | - Zhensheng Kang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, 3 Taicheng Rd, Yangling 712100, Shaanxi, China
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99938
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Wu H, Qu X, Dong Z, Luo L, Shao C, Forner J, Lohmann JU, Su M, Xu M, Liu X, Zhu L, Zeng J, Liu S, Tian Z, Zhao Z. WUSCHEL triggers innate antiviral immunity in plant stem cells. Science 2020; 370:227-231. [PMID: 33033220 DOI: 10.1126/science.abb7360] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2020] [Revised: 07/28/2020] [Accepted: 08/21/2020] [Indexed: 02/05/2023]
Abstract
Stem cells in plants constantly supply daughter cells to form new organs and are expected to safeguard the integrity of the cells from biological invasion. Here, we show how stem cells of the Arabidopsis shoot apical meristem and their nascent daughter cells suppress infection by cucumber mosaic virus (CMV). The stem cell regulator WUSCHEL responds to CMV infection and represses virus accumulation in the meristem central and peripheral zones. WUSCHEL inhibits viral protein synthesis by repressing the expression of plant S-adenosyl-l-methionine-dependent methyltransferases, which are involved in ribosomal RNA processing and ribosome stability. Our results reveal a conserved strategy in plants to protect stem cells against viral intrusion and provide a molecular basis for WUSCHEL-mediated broad-spectrum innate antiviral immunity in plants.
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Affiliation(s)
- Haijun Wu
- Hefei National Laboratory for Physical Sciences at the Microscale, CAS Center for Excellence in Molecular Plant Sciences, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China
| | - Xiaoya Qu
- Hefei National Laboratory for Physical Sciences at the Microscale, CAS Center for Excellence in Molecular Plant Sciences, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China
| | - Zhicheng Dong
- School of Life Sciences, Guangzhou University, Guangzhou Higher Education Mega Center, Guangzhou 510006, China
| | - Linjie Luo
- Hefei National Laboratory for Physical Sciences at the Microscale, CAS Center for Excellence in Molecular Plant Sciences, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China
| | - Chen Shao
- Hefei National Laboratory for Physical Sciences at the Microscale, CAS Center for Excellence in Molecular Plant Sciences, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China
| | - Joachim Forner
- Department of Stem Cell Biology, Centre for Organismal Studies, Heidelberg University, Heidelberg D-69120, Germany
| | - Jan U Lohmann
- Department of Stem Cell Biology, Centre for Organismal Studies, Heidelberg University, Heidelberg D-69120, Germany
| | - Meng Su
- Hefei National Laboratory for Physical Sciences at the Microscale, CAS Center for Excellence in Molecular Plant Sciences, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China
| | - Mengchu Xu
- Hefei National Laboratory for Physical Sciences at the Microscale, CAS Center for Excellence in Molecular Plant Sciences, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China
| | - Xiaobin Liu
- School of Life Sciences, Guangzhou University, Guangzhou Higher Education Mega Center, Guangzhou 510006, China
| | - Lei Zhu
- State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Jian Zeng
- Hefei National Laboratory for Physical Sciences at the Microscale, CAS Center for Excellence in Molecular Plant Sciences, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China
| | - Sumei Liu
- Hefei National Laboratory for Physical Sciences at the Microscale, CAS Center for Excellence in Molecular Plant Sciences, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China
| | - Zhaoxia Tian
- Hefei National Laboratory for Physical Sciences at the Microscale, CAS Center for Excellence in Molecular Plant Sciences, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China.
| | - Zhong Zhao
- Hefei National Laboratory for Physical Sciences at the Microscale, CAS Center for Excellence in Molecular Plant Sciences, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China.
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99939
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Quiles A, Wattier RA, Bacela-Spychalska K, Grabowski M, Rigaud T. Dictyocoela microsporidia diversity and co-diversification with their host, a gammarid species complex (Crustacea, Amphipoda) with an old history of divergence and high endemic diversity. BMC Evol Biol 2020; 20:149. [PMID: 33176694 PMCID: PMC7659068 DOI: 10.1186/s12862-020-01719-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 11/04/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Although the processes of co-evolution between parasites and their hosts are well known, evidence of co-speciation remains scarce. Microsporidian intracellular parasites, due to intimate relationships with their hosts and mixed mode of transmission (horizontal but also vertical, from mother to offspring), may represent an interesting biological model for investigating co-speciation. Amphipod crustaceans, especially gammarids, are regular hosts of microsporidian parasites, in particular the Dictyocoela spp., which have so far been found limited to these amphipods and are known to use a vertical mode of transmission. The amphipod genus Gammarus has a diversification history spanning the last 50-60 Mya and an extensive cryptic diversity in most of the nominal species. Here, we investigated the degree of co-diversification between Dictyocoela and Gammarus balcanicus, an amphipod with high degrees of ancient cryptic diversification and lineage endemism, by examining the genetic diversity of these parasites over the entire geographic range of the host. We hypothesised that the strong host diversification and vertical transmission of Dictyocoela would promote co-diversification. RESULTS Using the parasite SSU rDNA as a molecular marker, analyzing 2225 host specimens from 88 sites covering whole host range, we found 31 haplogroups of Dictyocoela, 30 of which were novel, belonging to four Dictyocoela species already known to infect other Gammarus spp. The relationships between Dictyocoela and gammarids is therefore ancient, with the speciation in parasites preceding those of the hosts. Each novel haplogroup was nevertheless specific to G. balcanicus, leaving the possibility for subsequent co-diversification process during host diversification. A Procrustean Approach to Co-phylogeny (PACo) analysis revealed that diversification of Dictyocoela was not random with respect to that of the host. We found high degrees of congruence between the diversification of G. balcanicus and that of Dictyocoela roeselum and D. muelleri. However, we also found some incongruences between host and Dictyocoela phylogenies, e.g. in D. duebenum, probably due to host shifts between different G. balcanicus cryptic lineages. CONCLUSION The evolutionary history of Dictyocoela and Gammarus balcanicus represents an example of an overall host-parasite co-diversification, including cases of host shifts.
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Affiliation(s)
- Adrien Quiles
- Université Bourgogne Franche-Comté, Laboratoire Biogéosciences, UMR CNRS 6282, 6 boulevard Gabriel, 21000, Dijon, France
- Department of Invertebrate Zoology and Hydrobiology, Faculty of Biology and Environmental Protection, University of Łódź, Banacha 12/16, 90-237, Łódź, Poland
| | - Rémi A Wattier
- Université Bourgogne Franche-Comté, Laboratoire Biogéosciences, UMR CNRS 6282, 6 boulevard Gabriel, 21000, Dijon, France
| | - Karolina Bacela-Spychalska
- Department of Invertebrate Zoology and Hydrobiology, Faculty of Biology and Environmental Protection, University of Łódź, Banacha 12/16, 90-237, Łódź, Poland
| | - Michal Grabowski
- Department of Invertebrate Zoology and Hydrobiology, Faculty of Biology and Environmental Protection, University of Łódź, Banacha 12/16, 90-237, Łódź, Poland
| | - Thierry Rigaud
- Université Bourgogne Franche-Comté, Laboratoire Biogéosciences, UMR CNRS 6282, 6 boulevard Gabriel, 21000, Dijon, France.
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99940
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Guo DL, Wang ZG, Pei MS, Guo LL, Yu YH. Transcriptome analysis reveals mechanism of early ripening in Kyoho grape with hydrogen peroxide treatment. BMC Genomics 2020; 21:784. [PMID: 33176674 PMCID: PMC7657363 DOI: 10.1186/s12864-020-07180-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Accepted: 10/22/2020] [Indexed: 02/06/2023] Open
Abstract
Background In a previous study, the early ripening of Kyoho grape following H2O2 treatment was explored at the physiological level, but the mechanism by which H2O2 promotes ripening at the molecular level is unclear. To reveal the molecular mechanism, RNA-sequencing analysis was conducted on the different developmental stages of Kyoho berry treated with H2O2. Results In the comparison of treatment and control groups, 406 genes were up-regulated and 683 were down-regulated. Time course sequencing (TCseq) analysis showed that the expression patterns of most of the genes were similar between the treatment and control, except for some genes related to chlorophyll binding and photosynthesis. Differential expression analysis and the weighted gene co-expression network were used to screen significantly differentially expressed genes and hub genes associated with oxidative stress (heat shock protein, HSP), cell wall deacetylation (GDSL esterase/lipase, GDSL), cell wall degradation (xyloglucan endotransglucosylase/ hydrolase, XTH), and photosynthesis (chlorophyll a-b binding protein, CAB1). Gene expression was verified with RT-qPCR, and the results were largely consistent with those of RNA sequencing. Conclusions The RNA-sequencing analysis indicated that H2O2 treatment promoted the early ripening of Kyoho berry by affecting the expression levels of HSP, GDSL, XTH, and CAB1 and- photosynthesis- pathways. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-020-07180-y.
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Affiliation(s)
- Da-Long Guo
- College of Forestry, Henan University of Science and Technology, Luoyang, 471023, Henan Province, China. .,Henan Engineering Technology Research Center of Quality Regulation and Controlling of Horticultural Plants, Luoyang, 471023, Henan Province, China.
| | - Zhen-Guang Wang
- College of Forestry, Henan University of Science and Technology, Luoyang, 471023, Henan Province, China.,Henan Engineering Technology Research Center of Quality Regulation and Controlling of Horticultural Plants, Luoyang, 471023, Henan Province, China
| | - Mao-Song Pei
- College of Forestry, Henan University of Science and Technology, Luoyang, 471023, Henan Province, China.,Henan Engineering Technology Research Center of Quality Regulation and Controlling of Horticultural Plants, Luoyang, 471023, Henan Province, China
| | - Li-Li Guo
- Henan Engineering Technology Research Center of Quality Regulation and Controlling of Horticultural Plants, Luoyang, 471023, Henan Province, China
| | - Yi-He Yu
- College of Forestry, Henan University of Science and Technology, Luoyang, 471023, Henan Province, China.,Henan Engineering Technology Research Center of Quality Regulation and Controlling of Horticultural Plants, Luoyang, 471023, Henan Province, China
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99941
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Moseley M, Naidoo K, Bastos A, Retief L, Frean J, Telfer S, Rossouw J. Multi-locus sequence analyses reveal a clonal L. borgpetersenii genotype in a heterogeneous invasive Rattus spp. community across the City of Johannesburg, South Africa. Parasit Vectors 2020; 13:570. [PMID: 33176846 PMCID: PMC7659165 DOI: 10.1186/s13071-020-04444-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Accepted: 10/30/2020] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Rattus spp. are frequently implicated as key reservoir hosts for leptospirosis, one of the most common, but neglected, bacterial zoonoses in the world. Although leptospirosis is predicted to be a significant public health threat in Africa, studies from the continent are limited. METHODS Rattus spp. (n = 171) were sampled (January-May 2016) across the City of Johannesburg, South Africa's largest inland metropole. Rattus spp. genetic diversity was evaluated by full length (1140 bp) cyt b sequencing of 42 samples. For comparison, a further 12 Rattus norvegicus samples collected in Cape Town, South Africa's largest coastal metropole, were also genotyped. Leptospira infections were identified and genotyped using real-time PCR and multi-locus (lfb1, secY and lipL41) DNA sequencing. RESULTS Five R. norvegicus haplotypes were identified across Johannesburg, four of which have not previously been detected in South Africa, and one in Cape Town. Across Johannesburg we identified a Leptospira spp. infection prevalence of 44% (75/171) and noted significant differences in the prevalence between administrative regions within the metropole. Multi-locus sequence analyses identified a clonal genotype consistent with L. borgpetersenii serogroup Javanica (serovar Ceylonica). DISCUSSION The prevalence of infection identified in this study is amongst the highest detected in Rattus spp. in similar contexts across Africa. Despite the complex invasion history suggested by the heterogeneity in R. norvegicus haplotypes identified in Johannesburg, a single L. borgpetersenii genotype was identified in all infected rodents. The lack of L. interrogans in a rodent community dominated by R. norvegicus is notable, given the widely recognised host-pathogen association between these species and evidence for L. interrogans infection in R. norvegicus in Cape Town. It is likely that environmental conditions (cold, dry winters) in Johannesburg may limit the transmission of L. interrogans. Spatial heterogeneity in prevalence suggest that local factors, such as land use, influence disease risk in the metropole. CONCLUSIONS In South Africa, as in other African countries, leptospirosis is likely underdiagnosed. The high prevalence of infection in urban rodents in Johannesburg suggest that further work is urgently needed to understand the potential public health risk posed by this neglected zoonotic pathogen.
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Affiliation(s)
- Mark Moseley
- School of Biological Sciences, University of Aberdeen, Aberdeen, UK
| | - Kovashnee Naidoo
- National Institute for Communicable Diseases, Division of National Health Laboratory Service, Johannesburg, South Africa
| | - Armanda Bastos
- Department of Zoology and Entomology, University of Pretoria, Pretoria, South Africa
| | - Liezl Retief
- Department of Zoology and Entomology, University of Pretoria, Pretoria, South Africa
| | - John Frean
- National Institute for Communicable Diseases, Division of National Health Laboratory Service, Johannesburg, South Africa
- Wits Research Institute for Malaria, University of the Witwatersrand, Johannesburg, South Africa
| | - Sandra Telfer
- School of Biological Sciences, University of Aberdeen, Aberdeen, UK
| | - Jennifer Rossouw
- National Institute for Communicable Diseases, Division of National Health Laboratory Service, Johannesburg, South Africa
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99942
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Tian L, Zou Y, Tan J, Wang Y, Chen J, Xia L, Xu L, Chen G, Wu Q, Huang O. Androgen receptor gene mutations in 258 Han Chinese patients with polycystic ovary syndrome. Exp Ther Med 2020; 21:31. [PMID: 33262817 PMCID: PMC7690241 DOI: 10.3892/etm.2020.9463] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Accepted: 05/15/2020] [Indexed: 01/12/2023] Open
Abstract
Polycystic ovary syndrome (PCOS) affects 8-13% of reproductive-age females worldwide and mutations or aberrant expression of androgen receptor (AR) may cause the onset of this disease. In the present study, 258 samples from Han Chinese patients with PCOS were analyzed for the presence of AR mutations via sequencing of all coding exons of the AR gene. A total of five heterozygous missense mutations, namely p.V3M, p.Q72R, p.S158L, p.S176R and p.G396R, were identified in five of the patients. Among these, p.S158L was a novel mutation that, to the best of our knowledge, has not been reported previously. Although the remaining four mutations have been reported previously, they existed at low frequencies or were absent in the control subjects and in the Exome Aggregation Consortium database. The results of evolutionary conservation and in silico analysis revealed that the p.V3M, p.S158L and p.S176R mutations were pathogenic, whereas the p.Q72R and p.G396R mutations were benign. Compared with the patients with PCOS without AR mutations or with benign AR mutations, markedly lower estrogen levels on the day of human chorionic gonadotropin injection were observed in the three patients with PCOS with potentially pathogenic mutations. In addition, patients with PCOS with pathogenic mutations had lower numbers of oocytes; however, the difference was not statistically significant. Of note, these observations should be interpreted with caution due to the relatively small sample size in the present study. Therefore, a larger number of samples should be collected to validate the results of the present study in future studies. In summary, the present study identified three potential pathogenic mutations in 258 Han Chinese patients with PCOS and these mutations may have an implication in the pathogenesis of PCOS.
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Affiliation(s)
- Lifeng Tian
- Department of Gynecology and Obstetrics, Jiangxi Medical College, Graduate School of Nanchang University, Nanchang, Jiangxi 330031, P.R. China.,Reproductive Medicine Center, Jiangxi Provincial Maternal and Child Health Hospital, Nanchang, Jiangxi 330006, P.R. China.,Key Laboratory of Women's Reproductive Health of Jiangxi Province, Jiangxi Provincial Maternal and Child Health Hospital, Nanchang, Jiangxi 330006, P.R. China
| | - Yang Zou
- Key Laboratory of Women's Reproductive Health of Jiangxi Province, Jiangxi Provincial Maternal and Child Health Hospital, Nanchang, Jiangxi 330006, P.R. China.,Central Laboratory, Jiangxi Provincial Maternal and Child Health Hospital, Nanchang, Jiangxi 330006, P.R. China
| | - Jun Tan
- Reproductive Medicine Center, Jiangxi Provincial Maternal and Child Health Hospital, Nanchang, Jiangxi 330006, P.R. China.,Key Laboratory of Women's Reproductive Health of Jiangxi Province, Jiangxi Provincial Maternal and Child Health Hospital, Nanchang, Jiangxi 330006, P.R. China
| | - Yaoqing Wang
- Department of Gynecology and Obstetrics, Jiangxi Medical College, Graduate School of Nanchang University, Nanchang, Jiangxi 330031, P.R. China
| | - Jia Chen
- Department of Gynecology and Obstetrics, Jiangxi Medical College, Graduate School of Nanchang University, Nanchang, Jiangxi 330031, P.R. China
| | - Leizhen Xia
- Reproductive Medicine Center, Jiangxi Provincial Maternal and Child Health Hospital, Nanchang, Jiangxi 330006, P.R. China
| | - Lixian Xu
- Key Laboratory of Women's Reproductive Health of Jiangxi Province, Jiangxi Provincial Maternal and Child Health Hospital, Nanchang, Jiangxi 330006, P.R. China
| | - Ge Chen
- Key Laboratory of Women's Reproductive Health of Jiangxi Province, Jiangxi Provincial Maternal and Child Health Hospital, Nanchang, Jiangxi 330006, P.R. China.,Central Laboratory, Jiangxi Provincial Maternal and Child Health Hospital, Nanchang, Jiangxi 330006, P.R. China
| | - Qiongfang Wu
- Reproductive Medicine Center, Jiangxi Provincial Maternal and Child Health Hospital, Nanchang, Jiangxi 330006, P.R. China.,Key Laboratory of Women's Reproductive Health of Jiangxi Province, Jiangxi Provincial Maternal and Child Health Hospital, Nanchang, Jiangxi 330006, P.R. China
| | - Ouping Huang
- Department of Gynecology and Obstetrics, Jiangxi Medical College, Graduate School of Nanchang University, Nanchang, Jiangxi 330031, P.R. China.,Key Laboratory of Women's Reproductive Health of Jiangxi Province, Jiangxi Provincial Maternal and Child Health Hospital, Nanchang, Jiangxi 330006, P.R. China.,Department of Gynecology, Jiangxi Provincial Maternal and Child Health Hospital, Nanchang, Jiangxi 330006, P.R. China
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99943
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Ovalle TM, Vásquez-Ordóñez AA, Jimenez J, Parsa S, Cuellar WJ, Becerra Lopez-Lavalle LA. A simple PCR-based method for the rapid and accurate identification of spider mites (Tetranychidae) on cassava. Sci Rep 2020; 10:19496. [PMID: 33177527 PMCID: PMC7658231 DOI: 10.1038/s41598-020-75743-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Accepted: 10/14/2020] [Indexed: 11/10/2022] Open
Abstract
The morphological identification of mites entails great challenges. Characteristics such as dorsal setae and aedeagus are widely used, but they show variations between populations, and the technique is time consuming and demands specialized taxonomic expertise that is difficult to access. A successful alternative has been to exploit a region of the mitochondrial cytochrome oxidase I (COI) gene to classify specimens to the species level. We analyzed the COI sequences of four mite species associated with cassava and classified them definitively by detailed morphological examinations. We then developed an identification kit based on the restriction fragment length polymorphism-polymerase chain reaction of subunit I of the COI gene focused on the three restriction enzymes AseI, MboII, and ApoI. This set of enzymes permitted the simple, accurate identification of Mononychellus caribbeanae, M. tanajoa, M. mcgregori, and Tetranychus urticae, rapidly and with few resources. This kit could be a vital tool for the surveillance and monitoring of mite pests in cassava crop protection programs in Africa, Asia, and Latin America.
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Affiliation(s)
- Tatiana M Ovalle
- Centro Internacional de Agricultura Tropical (CIAT), Km 17, Recta Cali-Palmira, 763537, Cali, Valle del Cauca, Colombia.,CGIAR Research Program for Root Tubers and Bananas, Lima, Peru
| | - Aymer Andrés Vásquez-Ordóñez
- Centro Internacional de Agricultura Tropical (CIAT), Km 17, Recta Cali-Palmira, 763537, Cali, Valle del Cauca, Colombia.,Entomology Section, Universidad del Valle, Ciudad Universitaria Melendez, Cali, Valle del Cauca, Colombia
| | - Jenyfer Jimenez
- Centro Internacional de Agricultura Tropical (CIAT), Km 17, Recta Cali-Palmira, 763537, Cali, Valle del Cauca, Colombia.,CGIAR Research Program for Root Tubers and Bananas, Lima, Peru
| | - Soroush Parsa
- Centro Internacional de Agricultura Tropical (CIAT), Km 17, Recta Cali-Palmira, 763537, Cali, Valle del Cauca, Colombia.,International Potato Center (CIP), Av. La Molina 1895, La Molina, Lima, Lima12, Perú
| | - Wilmer J Cuellar
- Centro Internacional de Agricultura Tropical (CIAT), Km 17, Recta Cali-Palmira, 763537, Cali, Valle del Cauca, Colombia.,CGIAR Research Program for Root Tubers and Bananas, Lima, Peru
| | - Luis A Becerra Lopez-Lavalle
- Centro Internacional de Agricultura Tropical (CIAT), Km 17, Recta Cali-Palmira, 763537, Cali, Valle del Cauca, Colombia. .,CGIAR Research Program for Root Tubers and Bananas, Lima, Peru.
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99944
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Landínez-García RM, Narváez JC, Márquez EJ. Population genetics of the freshwater fish Prochilodus magdalenae (Characiformes: Prochilodontidae), using species-specific microsatellite loci. PeerJ 2020; 8:e10327. [PMID: 33240645 PMCID: PMC7666565 DOI: 10.7717/peerj.10327] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Accepted: 10/19/2020] [Indexed: 11/29/2022] Open
Abstract
Prochilodus magdalenae is a freshwater fish endemic to the Colombian Magdalena-Cauca and Caribbean hydrographic basins. The genetic structure patterns of populations of different members of Prochilodus and the historic restocking of its depleted natural populations suggest that P. magdalenae exhibits genetic stocks that coexist and co-migrate throughout the rivers Magdalena, Cauca, Cesar, Sinú and Atrato. To test this hypothesis and explore the levels of genetic diversity and population demography of 725 samples of P. magdalenae from the studied rivers, we developed a set of 11 species-specific microsatellite loci using next-generation sequencing, bioinformatics, and experimental tests of the levels of diversity of the microsatellite loci. The results evidenced that P. magdalenae exhibits high genetic diversity, significant inbreeding coefficient ranging from 0.162 to 0.202, and signs of erosion of the genetic pool. Additionally, the population genetic structure constitutes a mixture of genetic stocks heterogeneously distributed along the studied rivers, and moreover, a highly divergent genetic stock was detected in Chucurí, Puerto Berrío and Palagua that may result from restocking practices. This study provides molecular tools and a wide framework regarding the genetic diversity and structure of P. magdalenae, which is crucial to complement its baseline information, diagnosis and monitoring of populations, and to support the implementation of adequate regulation, management, and conservation policies.
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Affiliation(s)
- Ricardo M Landínez-García
- Facultad de Ciencias, Escuela de Biociencias, Laboratorio de Biología Molecular y Celular, Universidad Nacional de Colombia-Sede Medellín, Medellín, Colombia
| | - Juan Carlos Narváez
- Grupo de Biodiversidad y Ecología Aplicada, Laboratorio de Genética Molecular, Universidad del Magdalena, Santa Marta, Magdalena, Colombia
| | - Edna J Márquez
- Facultad de Ciencias, Escuela de Biociencias, Laboratorio de Biología Molecular y Celular, Universidad Nacional de Colombia-Sede Medellín, Medellín, Colombia
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99945
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The Medical Triazole Voriconazole Can Select for Tandem Repeat Variations in Azole-Resistant Aspergillus Fumigatus Harboring TR 34/L98H Via Asexual Reproduction. J Fungi (Basel) 2020; 6:jof6040277. [PMID: 33187077 PMCID: PMC7711461 DOI: 10.3390/jof6040277] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 10/30/2020] [Accepted: 11/06/2020] [Indexed: 12/15/2022] Open
Abstract
Azole-resistant Aspergillus fumigatus isolates recovered at high frequency from patients, harbor mutations that are associated with variation of promoter length in the cyp51A gene. Following the discovery of the TR34/L98H genotype, new variations in tandem repeat (TR) length and number of repeats were identified, as well as additional single nucleotide polymorphisms (SNPs) in the cyp51A gene, indicating that the diversity of resistance mutations in A. fumigatus is likely to continue to increase. Investigating the development routes of TR variants is critical to be able to design preventive interventions. In this study, we tested the potential effects of azole exposure on the selection of TR variations, while allowing haploid A. fumigatus to undergo asexual reproduction. Through experimental evolution involving voriconazole (VOR) exposure, an isolate harboring TR343/L98H evolved from a clinical TR34/L98H ancestor isolate, confirmed by whole genome sequencing. TR343/L98H was associated with increased cyp51A expression and high VOR and posaconazole MICs, although additional acquired SNPs could also have contributed to the highly azole-resistant phenotype. Exposure to medical azoles was found to select for TR343, thus supporting the possibility of in-host selection of TR34 variants.
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99946
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Tayyrov A, Schnetzler M, Gillis-Germitsch N, Schnyder M. Genetic diversity of the cardiopulmonary canid nematode Angiostrongylus vasorum within and between rural and urban fox populations. INFECTION GENETICS AND EVOLUTION 2020; 87:104618. [PMID: 33188914 DOI: 10.1016/j.meegid.2020.104618] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 10/24/2020] [Accepted: 11/02/2020] [Indexed: 02/08/2023]
Abstract
Angiostrongylus vasorum is an emerging parasitic cardiopulmonary nematode of dogs, foxes, and other canids. In dogs, the infection causes respiratory and bleeding disorders along with other clinical signs collectively known as canine angiostrongylosis, while foxes represent an important wildlife reservoir. Despite the spread of A. vasorum across various countries in Europe and the Americas, little is known about the genetic diversity of A. vasorum populations at a local level in a highly endemic area. Thus, in the present study, we investigated the genetic diversity of 323 adult A. vasorum nematodes from 64 foxes living in the canton of Zurich, Switzerland. Among those, 279 worms isolated from 20 foxes were analyzed separately to investigate the genetic diversity of multiple worms within individual foxes. Part of the mitochondrial cytochrome c oxidase subunit I (mtCOI) gene was amplified and sequenced. Overall, 16 mitochondrial haplotypes were identified. The analysis of multiple worms per host revealed 12 haplotypes, with up to 5 different haplotypes in single individuals. Higher haplotype diversity (n = 10) of nematodes from foxes of urban areas than in rural areas (n = 7) was observed, with 5 shared haplotypes. Comparing our data with published GenBank sequences, five haplotypes were found to be unique within the Zurich nematode population. Interestingly, A. vasorum nematodes obtained from foxes in London and Zurich shared the same dominating haplotype. Further studies are needed to clarify if this haplotype has a different pathogenicity that may contribute to its dominance. Our findings show the importance of foxes as a reservoir for genetic parasite recombination and indicate that high fox population densities in urban areas with small and overlapping home ranges allow multiple infection events that lead to high genetic variability of A. vasorum.
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Affiliation(s)
- Annageldi Tayyrov
- Institute of Parasitology, Vetsuisse-Faculty, University of Zurich, Winterthurerstrasse 266a, 8057 Zurich, Switzerland
| | - Michèle Schnetzler
- Institute of Parasitology, Vetsuisse-Faculty, University of Zurich, Winterthurerstrasse 266a, 8057 Zurich, Switzerland
| | - Nina Gillis-Germitsch
- Institute of Parasitology, Vetsuisse-Faculty, University of Zurich, Winterthurerstrasse 266a, 8057 Zurich, Switzerland; Graduate School for Cellular and Biomedical Sciences, University of Bern, Switzerland
| | - Manuela Schnyder
- Institute of Parasitology, Vetsuisse-Faculty, University of Zurich, Winterthurerstrasse 266a, 8057 Zurich, Switzerland.
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99947
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Lu Y, Boswell M, Boswell W, Salinas RY, Savage M, Reyes J, Walter S, Marks R, Gonzalez T, Medrano G, Warren WC, Schartl M, Walter RB. Global assessment of organ specific basal gene expression over a diurnal cycle with analyses of gene copies exhibiting cyclic expression patterns. BMC Genomics 2020; 21:787. [PMID: 33176680 PMCID: PMC7659085 DOI: 10.1186/s12864-020-07202-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Accepted: 10/28/2020] [Indexed: 11/25/2022] Open
Abstract
Background Studying functional divergences between paralogs that originated from genome duplication is a significant topic in investigating molecular evolution. Genes that exhibit basal level cyclic expression patterns including circadian and light responsive genes are important physiological regulators. Temporal shifts in basal gene expression patterns are important factors to be considered when studying genetic functions. However, adequate efforts have not been applied to studying basal gene expression variation on a global scale to establish transcriptional activity baselines for each organ. Furthermore, the investigation of cyclic expression pattern comparisons between genome duplication created paralogs, and potential functional divergence between them has been neglected. To address these questions, we utilized a teleost fish species, Xiphophorus maculatus, and profiled gene expression within 9 organs at 3-h intervals throughout a 24-h diurnal period. Results Our results showed 1.3–21.9% of genes in different organs exhibited cyclic expression patterns, with eye showing the highest fraction of cycling genes while gonads yielded the lowest. A majority of the duplicated gene pairs exhibited divergences in their basal level expression patterns wherein only one paralog exhibited an oscillating expression pattern, or both paralogs exhibit oscillating expression patterns, but each gene duplicate showed a different peak expression time, and/or in different organs. Conclusions These observations suggest cyclic genes experienced significant sub-, neo-, or non-functionalization following the teleost genome duplication event. In addition, we developed a customized, web-accessible, gene expression browser to facilitate data mining and data visualization for the scientific community.
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Affiliation(s)
- Yuan Lu
- The Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry, Texas State University, 419 Centennial Hall, 601 University Drive, San Marcos, TX, 78666, USA.
| | - Mikki Boswell
- The Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry, Texas State University, 419 Centennial Hall, 601 University Drive, San Marcos, TX, 78666, USA
| | - William Boswell
- The Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry, Texas State University, 419 Centennial Hall, 601 University Drive, San Marcos, TX, 78666, USA
| | - Raquel Ybanez Salinas
- The Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry, Texas State University, 419 Centennial Hall, 601 University Drive, San Marcos, TX, 78666, USA.,The University of Texas MD Anderson Cancer Center, Graduate School of Biomedical Sciences, Houston, TX, USA
| | - Markita Savage
- The Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry, Texas State University, 419 Centennial Hall, 601 University Drive, San Marcos, TX, 78666, USA
| | - Jose Reyes
- The Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry, Texas State University, 419 Centennial Hall, 601 University Drive, San Marcos, TX, 78666, USA
| | - Sean Walter
- The Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry, Texas State University, 419 Centennial Hall, 601 University Drive, San Marcos, TX, 78666, USA
| | - Rebecca Marks
- The Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry, Texas State University, 419 Centennial Hall, 601 University Drive, San Marcos, TX, 78666, USA
| | - Trevor Gonzalez
- The Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry, Texas State University, 419 Centennial Hall, 601 University Drive, San Marcos, TX, 78666, USA
| | - Geraldo Medrano
- The Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry, Texas State University, 419 Centennial Hall, 601 University Drive, San Marcos, TX, 78666, USA
| | - Wesley C Warren
- Bond Life Sciences Center, University of Missouri, Columbia, MO, USA
| | - Manfred Schartl
- The Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry, Texas State University, 419 Centennial Hall, 601 University Drive, San Marcos, TX, 78666, USA.,Developmental Biochemistry, Theodor-Boveri-Institute, Biozentrum, University of Würzburg, Würzburg, Germany
| | - Ronald B Walter
- The Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry, Texas State University, 419 Centennial Hall, 601 University Drive, San Marcos, TX, 78666, USA
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99948
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Somarelli JA, Rupprecht G, Altunel E, Flamant EM, Rao S, Sivaraj D, Lazarides AL, Hoskinson SM, Sheth MU, Cheng S, Kim SY, Ware KE, Agarwal A, Cullen MM, Selmic LE, Everitt JI, McCall SJ, Eward C, Eward WC, Hsu DS. A Comparative Oncology Drug Discovery Pipeline to Identify and Validate New Treatments for Osteosarcoma. Cancers (Basel) 2020; 12:cancers12113335. [PMID: 33187254 PMCID: PMC7696249 DOI: 10.3390/cancers12113335] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Revised: 10/31/2020] [Accepted: 11/06/2020] [Indexed: 02/07/2023] Open
Abstract
Simple Summary Osteosarcoma is a rare bone cancer that occurs primarily in children. The discovery of new treatments for osteosarcoma and other rare cancer types has been severely limited by access to patient samples to study these often-complex diseases. Here we capitalize on naturally-occurring cancers in pet dogs to study the biology of these rare cancers. Using living cells from canine and human patients to test thousands of drugs simultaneously, we identify a unique combination of drugs that disrupts protein degradation and protein trafficking in cancer cells. This drug combination represents a promising new treatment to treat both dogs and people with osteosarcoma. Abstract Background: Osteosarcoma is a rare but aggressive bone cancer that occurs primarily in children. Like other rare cancers, treatment advances for osteosarcoma have stagnated, with little improvement in survival for the past several decades. Developing new treatments has been hampered by extensive genomic heterogeneity and limited access to patient samples to study the biology of this complex disease. Methods: To overcome these barriers, we combined the power of comparative oncology with patient-derived models of cancer and high-throughput chemical screens in a cross-species drug discovery pipeline. Results: Coupling in vitro high-throughput drug screens on low-passage and established cell lines with in vivo validation in patient-derived xenografts we identify the proteasome and CRM1 nuclear export pathways as therapeutic sensitivities in osteosarcoma, with dual inhibition of these pathways inducing synergistic cytotoxicity. Conclusions: These collective efforts provide an experimental framework and set of new tools for osteosarcoma and other rare cancers to identify and study new therapeutic vulnerabilities.
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Affiliation(s)
- Jason A. Somarelli
- Department of Medicine, Duke University Medical Center, Durham, NC 27710, USA; (G.R.); (E.A.); (E.M.F.); (D.S.); (M.U.S.); (S.C.); (K.E.W.); (A.A.); (D.S.H.)
- Duke Cancer Institute, Durham, NC 27710, USA; (J.I.E.); (S.J.M.); (W.C.E.)
- Correspondence:
| | - Gabrielle Rupprecht
- Department of Medicine, Duke University Medical Center, Durham, NC 27710, USA; (G.R.); (E.A.); (E.M.F.); (D.S.); (M.U.S.); (S.C.); (K.E.W.); (A.A.); (D.S.H.)
| | - Erdem Altunel
- Department of Medicine, Duke University Medical Center, Durham, NC 27710, USA; (G.R.); (E.A.); (E.M.F.); (D.S.); (M.U.S.); (S.C.); (K.E.W.); (A.A.); (D.S.H.)
| | - Etienne M. Flamant
- Department of Medicine, Duke University Medical Center, Durham, NC 27710, USA; (G.R.); (E.A.); (E.M.F.); (D.S.); (M.U.S.); (S.C.); (K.E.W.); (A.A.); (D.S.H.)
| | - Sneha Rao
- Department of Orthopaedics, Duke University Medical Center, Durham, NC 27710, USA; (S.R.); (A.L.L.); (S.M.H.); (M.M.C.)
| | - Dharshan Sivaraj
- Department of Medicine, Duke University Medical Center, Durham, NC 27710, USA; (G.R.); (E.A.); (E.M.F.); (D.S.); (M.U.S.); (S.C.); (K.E.W.); (A.A.); (D.S.H.)
| | - Alexander L. Lazarides
- Department of Orthopaedics, Duke University Medical Center, Durham, NC 27710, USA; (S.R.); (A.L.L.); (S.M.H.); (M.M.C.)
| | - Sarah M. Hoskinson
- Department of Orthopaedics, Duke University Medical Center, Durham, NC 27710, USA; (S.R.); (A.L.L.); (S.M.H.); (M.M.C.)
| | - Maya U. Sheth
- Department of Medicine, Duke University Medical Center, Durham, NC 27710, USA; (G.R.); (E.A.); (E.M.F.); (D.S.); (M.U.S.); (S.C.); (K.E.W.); (A.A.); (D.S.H.)
| | - Serene Cheng
- Department of Medicine, Duke University Medical Center, Durham, NC 27710, USA; (G.R.); (E.A.); (E.M.F.); (D.S.); (M.U.S.); (S.C.); (K.E.W.); (A.A.); (D.S.H.)
| | - So Young Kim
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA;
| | - Kathryn E. Ware
- Department of Medicine, Duke University Medical Center, Durham, NC 27710, USA; (G.R.); (E.A.); (E.M.F.); (D.S.); (M.U.S.); (S.C.); (K.E.W.); (A.A.); (D.S.H.)
| | - Anika Agarwal
- Department of Medicine, Duke University Medical Center, Durham, NC 27710, USA; (G.R.); (E.A.); (E.M.F.); (D.S.); (M.U.S.); (S.C.); (K.E.W.); (A.A.); (D.S.H.)
| | - Mark M. Cullen
- Department of Orthopaedics, Duke University Medical Center, Durham, NC 27710, USA; (S.R.); (A.L.L.); (S.M.H.); (M.M.C.)
| | - Laura E. Selmic
- College of Veterinary Medicine, The Ohio State University, Columbus, OH 43210, USA;
| | - Jeffrey I. Everitt
- Duke Cancer Institute, Durham, NC 27710, USA; (J.I.E.); (S.J.M.); (W.C.E.)
- Department of Pathology, Duke University Medical Center, Durham, NC 27710, USA
| | - Shannon J. McCall
- Duke Cancer Institute, Durham, NC 27710, USA; (J.I.E.); (S.J.M.); (W.C.E.)
- Department of Pathology, Duke University Medical Center, Durham, NC 27710, USA
| | - Cindy Eward
- Surgery Service, Triangle Veterinary Referral Hospital, Durham, NC 27710, USA;
| | - William C. Eward
- Duke Cancer Institute, Durham, NC 27710, USA; (J.I.E.); (S.J.M.); (W.C.E.)
- Department of Orthopaedics, Duke University Medical Center, Durham, NC 27710, USA; (S.R.); (A.L.L.); (S.M.H.); (M.M.C.)
| | - David S. Hsu
- Department of Medicine, Duke University Medical Center, Durham, NC 27710, USA; (G.R.); (E.A.); (E.M.F.); (D.S.); (M.U.S.); (S.C.); (K.E.W.); (A.A.); (D.S.H.)
- Duke Cancer Institute, Durham, NC 27710, USA; (J.I.E.); (S.J.M.); (W.C.E.)
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99949
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Schinner S, Preusse M, Kesthely C, Häussler S. Analysis of the organization and expression patterns of the convergent Pseudomonas aeruginosa lasR/rsaL gene pair uncovers mutual influence. Mol Microbiol 2020; 115:643-657. [PMID: 33073409 DOI: 10.1111/mmi.14628] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 10/10/2020] [Accepted: 10/11/2020] [Indexed: 11/30/2022]
Abstract
The two adjacent genes encoding the major Pseudomonas aeruginosa quorum-sensing regulator, LasR, and its opponent, RsaL, overlap in their coding 3' ends and produce mRNA transcripts with long untranslated 3' ends that overlap with the sense transcripts of the gene on the opposing DNA strand. In this study, we evaluated whether the overlapping genes are involved in mutual regulatory events and studied interference by natural antisense transcripts. We introduced various gene expression constructs into a P. aeruginosa PA14 lasR/rsaL double deletion mutant, and found that although complementary RNA is produced, this does not interfere with the sense gene expression levels of lasR and rsaL and does not have functional consequences on down-stream gene regulation. Nevertheless, expression of lasR, but not of rsaL, was shown to be enhanced if transcription was terminated at the end of the respective gene so that no overlapping transcription was allowed. Our data indicate that the natural organization with a partial overlap at the 3' ends of the lasR/rsaL genes gives rise to a system of checks and balances to prevent dominant and unilateral control by LasR over the RsaL transcriptional regulator of opposing function.
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Affiliation(s)
- Silvia Schinner
- Department of Molecular Bacteriology, Helmholtz Centre for Infection Research, Braunschweig, Germany.,Institute of Molecular Bacteriology, TWINCORE Centre for Experimental and Clinical Infection Research, Hannover, Germany
| | - Matthias Preusse
- Department of Molecular Bacteriology, Helmholtz Centre for Infection Research, Braunschweig, Germany.,Institute of Molecular Bacteriology, TWINCORE Centre for Experimental and Clinical Infection Research, Hannover, Germany
| | - Christopher Kesthely
- Institute of Molecular Bacteriology, TWINCORE Centre for Experimental and Clinical Infection Research, Hannover, Germany
| | - Susanne Häussler
- Department of Molecular Bacteriology, Helmholtz Centre for Infection Research, Braunschweig, Germany.,Institute of Molecular Bacteriology, TWINCORE Centre for Experimental and Clinical Infection Research, Hannover, Germany.,Department of Clinical Microbiology, Copenhagen University Hospital -Rigshospitalet, Copenhagen, Denmark.,Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, Hannover, Germany
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99950
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Diaz-Lara A, Mollov D, Golino D, Al Rwahnih M. Detection and characterization of a second carlavirus in Rosa sp. Arch Virol 2020; 166:321-323. [PMID: 33175220 DOI: 10.1007/s00705-020-04864-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 09/18/2020] [Indexed: 10/23/2022]
Abstract
A new virus resembling members in the genus Carlavirus was identified in an Out of Yesteryear rose (Rosa sp.) by high-throughput sequencing. The virus was discovered during the screening of a rose virus collection belonging to Foundation Plant Services (UC-Davis). The full genome of the virus is 8825 nt long, excluding a poly(A) tail, and includes six predicted genes coding for replicase, triple gene block, coat protein (CP), and nucleic acid binding protein. The closest relative of the putative virus is rose virus A (RVA; genus Carlavirus), with 75% and 78% aa sequence identity in the replicase and CP, respectively. The relationship with RVA and other carlaviruses was supported by phylogenetic analyses using replicase and CP sequences. Based on genome organization, sequence identity, and phylogenetic analysis, the virus found in the Out of Yesteryear plant represents a new member of the genus Carlavirus and is provisionally named "rose virus B" (RVB). Further testing by reverse transcription PCR confirmed the presence of RVB in the original source and seven additional rose selections from the same collection.
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Affiliation(s)
- Alfredo Diaz-Lara
- Department of Plant Pathology, University of California-Davis, Davis, CA, 95616, USA
| | - Dimitre Mollov
- USDA-ARS, National Germplasm Resources Laboratory, Beltsville, MD, 20705, USA
| | - Deborah Golino
- Department of Plant Pathology, University of California-Davis, Davis, CA, 95616, USA
| | - Maher Al Rwahnih
- Department of Plant Pathology, University of California-Davis, Davis, CA, 95616, USA.
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