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Castaño MI, Ye X, Uy FMK. First genome assembly of the order Strepsiptera using PacBio HiFi reads reveals a miniature genome. Sci Data 2024; 11:934. [PMID: 39198488 PMCID: PMC11358474 DOI: 10.1038/s41597-024-03808-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Accepted: 08/20/2024] [Indexed: 09/01/2024] Open
Abstract
Twisted-wing insects (Strepsiptera) are an enigmatic order of parasites with unusual life histories and striking sexual dimorphism. Males emerge from hosts as free-living winged adults, while females from most species remain as endoparasites that retain larval traits. Due to scarce genomic data and phylogenetic controversies, Strepsiptera was only recently placed as the closest living relative to beetles (Coleoptera). Here, we report the first PacBio HiFi genome assembly of the strepsipteran Xenos peckii (Xenidae). This de novo assembly size is 72.1 Mb, with a BUSCO score of 87.4%, N50 of 7.3 Mb, 23.4% GC content, and 38.41% repeat content. We identified 8 contigs that contain >75% of the assembly and reflect the haploid chromosome number reported from karyotypic data, and 3 contigs that exhibit sex chromosome coverage patterns. Additionally, the mitochondrial genome is 16,111 bp long and has 37 genes. This long-read assembly for Strepsiptera reveals a miniature genome and provides a unique tool to understand complex genome evolution associated with a parasitic lifestyle and extreme sexual dimorphism.
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Affiliation(s)
| | - Xinhai Ye
- College of Advanced Agriculture Science, Zhejiang A&F University, Hangzhou, Zhejiang, China
| | - Floria M K Uy
- University of Rochester, Department of Biology, Rochester, NY, USA.
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Chowdhury LM, Mohindra V, Kumar R, Jena J. Genome sequencing and assembly of Indian major carp, Cirrhinus mrigala (Hamilton, 1822). Sci Data 2024; 11:898. [PMID: 39154040 PMCID: PMC11330464 DOI: 10.1038/s41597-024-03747-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Accepted: 08/05/2024] [Indexed: 08/19/2024] Open
Abstract
The freshwater aquaculture species, Cirrhinus mrigala, commonly known as mrigal, holds significance in the carp-dominated aquaculture system, globally. Despite constituting 1.08% of the total freshwater aquaculture production, mrigal is the third most important Indian major carp. However, its genome and associated information is not available. This study aims to address this gap by generation high quality genome assembly using PacBio long reads, Illumina short reads and Hi-C scaffolding. The characterization of assembled highly contiguous genome, 1.057 Gb in size, revealed 39,091 genes with functional annotations. The orthology analysis based on direct orthologs and single copy ortholgs places C. mrigala in a distinct position within the Otophysi clade. Additionally, the study delves into Hox gene clusters, identifying 38 Hox genes distributed in seven clusters. The present genomic information offers potential applications for sustainable aquaculture management, including selection programs for economic traits.
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Affiliation(s)
- Labrechai Mog Chowdhury
- ICAR-National Bureau of Fish Genetic Resources, Canal Ring Road, Dilkusha, Lucknow, 226002, India
| | - Vindhya Mohindra
- ICAR-National Bureau of Fish Genetic Resources, Canal Ring Road, Dilkusha, Lucknow, 226002, India.
| | - Rajesh Kumar
- ICAR-National Bureau of Fish Genetic Resources, Canal Ring Road, Dilkusha, Lucknow, 226002, India
| | - Joykrushna Jena
- Indian Council of Agricultural Research (ICAR), Krishi Anusandhan Bhawan-II, New Delhi, 110012, India
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Wen J, Wu BC, Li HM, Zhou W, Song CF. Plastome structure and phylogenetic relationships of genus Hydrocotyle (apiales): provide insights into the plastome evolution of Hydrocotyle. BMC PLANT BIOLOGY 2024; 24:778. [PMID: 39148054 PMCID: PMC11325595 DOI: 10.1186/s12870-024-05483-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 08/05/2024] [Indexed: 08/17/2024]
Abstract
BACKGROUND The genus Hydrocotyle Tourn. ex L. is a key group for further study on the evolution of Apiales, comprising around 170 species globally. Previous studies mainly focused on separate sections and provided much information about this genus, but its infrageneric relationships are still confusing. In addition, the genetic basis of its adaptive evolution remains poorly understood. To investigate the phylogeny and evolution of the genus, we selected ten representative species covering two of three diversity distribution centers and exhibiting rich morphology diversity. Comparative plastome analysis was conducted to clarify the structural character of Hydrocotyle plastomes. Positive selection analyses were implemented to assess the evolution of the genus. Phylogenetic inferences with protein-coding sequences (CDS) of Hydrocotyle and 17 related species were also performed. RESULTS Plastomes within Hydrocotyle were generally conservative in structure, gene order, and size. A total of 14 regions (rps16-trnK, trnQ-rps16, atpI-atpH, trnC-petN-psbM, ycf3-trnS, accD-psaI-ycf4, petA-psbJ, rps12-rpl20, rpl16 intron, rps3-rpl16 intron, rps9-rpl22, ndhF-rpl32, ndhA intron, and ycf1a) were recognized as hotspot regions within the genus, which suggested to be promising DNA barcodes for global phylogenetic analysis of Hydrocotyle. The ycf15 gene was suggested to be a protein-coding gene for Hydrocotyle species, and it could be used as a DNA barcode to identify Hydrocotyle. In phylogenetic analysis, three monophyletic clades (Clade I, II, III) were identified with evidence of rapid radiation speciation within Clade I. The selective pressure analysis detected that six CDS genes (ycf1b, matK, atpF, accD, rps14, and psbB) of Hydrocotyle species were under positive selection. Within the genus, the last four genes were conservative, suggesting a relation to the unique evolution of the genus in Apiales. Seven genes (atpE, matK, psbH, ycf1a, ycf1b, rpoA, and ycf2) were detected to be under some degree of positive selection in different taxa within the genus Hydrocotyle, indicating their role in the adaptive evolution of species. CONCLUSIONS Our study offers new insights into the phylogeny and adaptive evolution of Hydrocotyle. The plastome sequences could significantly enhance phylogenetic resolution and provide genomic resources and potential DNA markers useful for future studies of the genus.
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Affiliation(s)
- Jun Wen
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), Nanjing, China
| | - Bao-Cheng Wu
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), Nanjing, China
| | - Hui-Min Li
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), Nanjing, China
| | - Wei Zhou
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), Nanjing, China
| | - Chun-Feng Song
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), Nanjing, China.
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4
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Sun PF, Lu MR, Liu YC, Shaw BJP, Lin CP, Chen HW, Lin YF, Hoh DZ, Ke HM, Wang IF, Lu MYJ, Young EB, Millett J, Kirschner R, Lin YCJ, Chen YL, Tsai IJ. An acidophilic fungus promotes prey digestion in a carnivorous plant. Nat Microbiol 2024:10.1038/s41564-024-01766-y. [PMID: 39090391 DOI: 10.1038/s41564-024-01766-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Accepted: 06/19/2024] [Indexed: 08/04/2024]
Abstract
Leaves of the carnivorous sundew plants (Drosera spp.) secrete mucilage that hosts microorganisms, but whether this microbiota contributes to prey digestion is unclear. We identified the acidophilic fungus Acrodontium crateriforme as the dominant species in the mucilage microbial communities, thriving in multiple sundew species across the global range. The fungus grows and sporulates on sundew glands as its preferred acidic environment, and its presence in traps increased the prey digestion process. A. crateriforme has a reduced genome similar to other symbiotic fungi. During A. crateriforme-Drosera spatulata coexistence and digestion of prey insects, transcriptomes revealed significant gene co-option in both partners. Holobiont expression patterns during prey digestion further revealed synergistic effects in several gene families including fungal aspartic and sedolisin peptidases, facilitating prey digestion in leaves, as well as nutrient assimilation and jasmonate signalling pathway expression. This study establishes that botanical carnivory is defined by adaptations involving microbial partners and interspecies interactions.
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Affiliation(s)
- Pei-Feng Sun
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
- Biodiversity Program, Taiwan International Graduate Program, Academia Sinica and National Taiwan Normal University, Taipei, Taiwan
- Department of Life Science, National Taiwan Normal University, Taipei, Taiwan
| | - Min R Lu
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Yu-Ching Liu
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Brandon J P Shaw
- Geography and Environment, Loughborough University, Loughborough, UK
- NERC Environmental Omics Facility (NEOF), NEOF Visitor Facility, School of Biosciences, University of Sheffield, Sheffield, UK
| | - Chieh-Ping Lin
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Hung-Wei Chen
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Yu-Fei Lin
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Daphne Z Hoh
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Huei-Mien Ke
- Department of Microbiology, Soochow University, Taipei, Taiwan
| | - I-Fan Wang
- Department of Biotechnology and Bioindustry Sciences, College of Bioscience and Biotechnology, National Cheng Kung University, Tainan, Taiwan
- University Center of Bioscience and Biotechnology, National Cheng Kung University, Tainan, Taiwan
| | - Mei-Yeh Jade Lu
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Erica B Young
- Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, WI, USA
| | - Jonathan Millett
- Geography and Environment, Loughborough University, Loughborough, UK
| | - Roland Kirschner
- School of Forestry and Resource Conservation, National Taiwan University, Taipei, Taiwan
| | - Ying-Chung Jimmy Lin
- Department of Life Science, College of Life Science, National Taiwan University, Taipei, Taiwan
- Institute of Plant Biology, College of Life Science, National Taiwan University, Taipei, Taiwan
| | - Ying-Lan Chen
- Department of Biotechnology and Bioindustry Sciences, College of Bioscience and Biotechnology, National Cheng Kung University, Tainan, Taiwan
- University Center of Bioscience and Biotechnology, National Cheng Kung University, Tainan, Taiwan
| | - Isheng Jason Tsai
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan.
- Biodiversity Program, Taiwan International Graduate Program, Academia Sinica and National Taiwan Normal University, Taipei, Taiwan.
- Department of Life Science, National Taiwan Normal University, Taipei, Taiwan.
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5
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Karabanov DP, Pereboev DD, Efeykin BD, Kodukhova YV, Kotov AA. Complete Mitochondrial Genome of Clupeonella abrau (Maliatsky, 1930) (Clupeiformes), an Endemic Freshwater Fish from the Lake Abrau (Russia). DOKLADY BIOLOGICAL SCIENCES : PROCEEDINGS OF THE ACADEMY OF SCIENCES OF THE USSR, BIOLOGICAL SCIENCES SECTIONS 2024; 517:63-68. [PMID: 38955884 DOI: 10.1134/s0012496624700996] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Revised: 03/15/2024] [Accepted: 03/19/2024] [Indexed: 07/04/2024]
Abstract
The Abrau sprat (tyulka or sardelka) Clupeonella abrau (Maliatsky, 1930) is an endemic fish of the Lake Abrau (Krasnodar Krai, Russia). The full C. abrau mitochondrial genome (16 650 bp) showed a gene arrangement conserved in Clupeidae and 98.8% similarity with the mitochondrial genome of the related species Black and Caspian Sea sprat C. cultriventris from the Black Sea. The COX1 gene sequence was additionally studied in a museum specimen collected in the Lake Abrau in 1938. Variability in modern Abrau sprat COX1 gene locus was estimated at approximately 0.15%, the difference between C. abrau and C. cultriventris was 1.2%, and the difference between the museum and modern C. abrau specimens from the Lake Abrau was 0.92%. The study confirmed that the Abrau sprat is present in the fish community and is capable of reproducing in the lake. Various scenarios were proposed to explain colonization of the Lake Abrau by C. abrau.
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Affiliation(s)
- D P Karabanov
- Papanin Institute for Biology of Inland Waters, Russian Academy of Sciences, Borok, Russia.
| | - D D Pereboev
- Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, Moscow, Russia
| | - B D Efeykin
- Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, Moscow, Russia
| | - Yu V Kodukhova
- Papanin Institute for Biology of Inland Waters, Russian Academy of Sciences, Borok, Russia
| | - A A Kotov
- Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, Moscow, Russia
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Li H, Liang X, Peng Y, Liu Z, Zhang L, Wang P, Jin M, Wilson K, Garvin MR, Wu K, Xiao Y. Novel Mito-Nuclear Combinations Facilitate the Global Invasion of a Major Agricultural Crop Pest. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024:e2305353. [PMID: 38965806 DOI: 10.1002/advs.202305353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 04/24/2024] [Indexed: 07/06/2024]
Abstract
A fundamental understanding of the underlying mechanisms involved in biological invasions is crucial to developing effective risk assessment and control measures against invasive species. The fall armyworm (FAW), Spodoptera frugiperda, is a highly invasive pest that has rapidly spread from its native Americas into much of the Eastern Hemisphere, with a highly homogeneous nuclear genetic background. However, the exact mechanism behind its rapid introduction and propagation remains unclear. Here, a systematic investigation is conducted into the population dynamics of FAW in China from 2019 to 2021 and found that FAW individuals carrying "rice" mitochondria (FAW-mR) are more prevalent (>98%) than that with "corn" mitochondria (FAW-mC) at the initial stage of the invasion and in newly-occupied non-overwintering areas. Further fitness experiments show that the two hybrid-strains of FAW exhibit different adaptions in the new environment in China, and this may have been facilitated by amino acid changes in mitochondrial-encoded proteins. FAW-mR used increases energy metabolism, faster wing-beat frequencies, and lower wing loadings to drive greater flight performance and subsequent rapid colonization of new habitats. In contrast, FAW-mC individuals adapt with more relaxed mitochondria and shuttle energetics into maternal investment, observed as faster development rate and higher fecundity. The presence of two different mitochondria types within FAW has the potential to significantly expand the range of damage and enhance competitive advantage. Overall, the study describes a novel invasion mechanism displayed by the FAW population that facilitates its expansion and establishment in new environments.
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Affiliation(s)
- Hongran Li
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Gene Editing Technologies (Hainan), Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518000, China
| | - Xinyue Liang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Gene Editing Technologies (Hainan), Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518000, China
| | - Yan Peng
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Gene Editing Technologies (Hainan), Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518000, China
| | - Zhenxing Liu
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Gene Editing Technologies (Hainan), Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518000, China
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Lei Zhang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Gene Editing Technologies (Hainan), Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518000, China
| | - Ping Wang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Gene Editing Technologies (Hainan), Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518000, China
- School of Life Sciences, Henan University, Kaifeng, 475004, China
| | - Minghui Jin
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Gene Editing Technologies (Hainan), Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518000, China
| | - Kenneth Wilson
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Gene Editing Technologies (Hainan), Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518000, China
- Lancaster Environment Centre, Lancaster University, Lancaster, LA1 4YQ, UK
| | - Michael R Garvin
- Oak Ridge National Laboratory, Biosciences Division, Oak Ridge, TN, 37830, USA
| | - Kongming Wu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Yutao Xiao
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Gene Editing Technologies (Hainan), Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518000, China
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7
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Lee SR, Oh A, Son DC. Characterization, comparison, and phylogenetic analyses of chloroplast genomes of Euphorbia species. Sci Rep 2024; 14:15352. [PMID: 38961172 PMCID: PMC11222452 DOI: 10.1038/s41598-024-66102-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Accepted: 06/27/2024] [Indexed: 07/05/2024] Open
Abstract
The genus Euphorbia (Euphorbiaceae) has near-cosmopolitan distribution and serves as a significant resource for both ornamental and medicinal purposes. Despite its economic importance, Euphorbia's taxonomy has long been challenged by the intricate nature of morphological traits exhibiting high levels of convergence. While molecular markers are essential for phylogenetic studies, their availability for Euphorbia has been limited. To address this gap, we conducted comparative analyses focusing on the chloroplast (CP) genomes of nine Euphorbia species, incorporating three newly sequenced and annotated accessions. In addition, phylogenetic informativeness and nucleotide diversity were computed to identify candidate markers for phylogenetic analyses among closely related taxa in the genus. Our investigation revealed relatively conserved sizes and structures of CP genomes across the studied species, with notable interspecific variations observed primarily in non-coding regions and IR/SC borders. By leveraging phylogenetic informativeness and nucleotide diversity, we identified rpoB gene as the optimal candidate for species delimitation and shallow-level phylogenetic inference within the genus. Through this comprehensive analysis of CP genomes across multiple taxa, our study sheds light on the evolutionary dynamics and taxonomic intricacies of Euphorbia, offering valuable insights into its CP genome evolution and taxonomy.
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Affiliation(s)
- Soo-Rang Lee
- Department of Biology Education, College of Education, Chosun University, Gwangju, 61452, Republic of Korea.
| | - Ami Oh
- Department of Biology Education, College of Education, Chosun University, Gwangju, 61452, Republic of Korea
| | - Dong Chan Son
- Division of Forest Biodiversity and Herbarium, Korea National Arboretum, Pocheon, 11186, Republic of Korea.
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8
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Burzyński A, Śmietanka B, Fernández-Pérez J, Lubośny M. The absence of canonical respiratory complex I subunits in male-type mitogenomes of three Donax species. Sci Rep 2024; 14:14465. [PMID: 38914611 PMCID: PMC11196677 DOI: 10.1038/s41598-024-63764-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 05/31/2024] [Indexed: 06/26/2024] Open
Abstract
Bivalves are an extraordinary class of animals in which species with a doubly uniparental inheritance (DUI) of mitochondrial DNA have been described. DUI is characterized as a mitochondrial homoplasmy of females and heteroplasmy of male individuals where F-type mitogenomes are passed to the progeny with mother egg cells and divergent M-type mitogenomes are inherited with fathers sperm cells. However, in most cases only male individuals retain divergent mitogenome inherited with spermatozoa. Additionally, in many of bivalves, unique mitochondrial features, like additional genes, gene duplication, gene extensions, mitochondrial introns, and recombination, were observed. In this study, we sequenced and assembled male-type mitogenomes of three Donax species. Comparative analysis of mitochondrial sequences revealed a lack of all seven NADH dehydrogenase subunits as well as the presence of three long additional open reading frames lacking identifiable homology to any of the existing genes.
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Affiliation(s)
- Artur Burzyński
- Department of Genetics and Marine Biotechnology, Institute of Oceanology Polish Academy of Sciences, Sopot, Poland
| | - Beata Śmietanka
- Department of Genetics and Marine Biotechnology, Institute of Oceanology Polish Academy of Sciences, Sopot, Poland
| | - Jenyfer Fernández-Pérez
- Departamento de Bioloxía, Facultade de Ciencias and CICA (Centro de Investigacións Científicas Avanzadas), Universidade da Coruña, Campus de A Zapateira, A Coruña, Spain
| | - Marek Lubośny
- Department of Genetics and Marine Biotechnology, Institute of Oceanology Polish Academy of Sciences, Sopot, Poland.
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Lu C, Zou T, Liu Q, Huang X. Twenty-nine newly sequenced genomes and a comprehensive genome dataset for the insect endosymbiont Buchnera. Sci Data 2024; 11:673. [PMID: 38909040 PMCID: PMC11193766 DOI: 10.1038/s41597-024-03537-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2023] [Accepted: 06/17/2024] [Indexed: 06/24/2024] Open
Abstract
Most phloem-feeding insects face nutritional deficiency and rely on their intracellular symbionts to provide nutrients, and most of endosymbiont genomes have undergone reduction. However, the study of genome reduction processes of endosymbionts has been constrained by the limited availability of genome data from different insect lineages. The obligate relationship between aphids and Buchnera aphidicola (hereafter Buchnera) makes them a classic model for studying insect-endosymbiont interaction. Here, we report 29 newly sequenced Buchnera genomes from 11 aphid subfamilies, and a comprehensive dataset based on 90 Buchnera genomes from 14 aphid subfamilies. The dataset shows a significant genomic difference of Buchnera among different aphid lineages. The dataset exhibits a more balanced distribution of Buchnera (from 14 aphid subfamilies) genome sizes, ranging from 400 kb to 600 kb, which can illustrate the genome reduction process of Buchnera. The new genome data provide valuable insights into the microevolutionary processes leading to genomic reduction of insect endosymbionts.
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Affiliation(s)
- Congcong Lu
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Tianmin Zou
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Qian Liu
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Xiaolei Huang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
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10
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Storz JF, Quiroga-Carmona M, Liphardt S, Herrera ND, Bautista NM, Opazo JC, Rico-Cernohorska A, Salazar-Bravo J, Good JM, D'Elía G. Extreme High-Elevation Mammal Surveys Reveal Unexpectedly High Upper Range Limits of Andean Mice. Am Nat 2024; 203:726-735. [PMID: 38781524 DOI: 10.1086/729513] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/25/2024]
Abstract
AbstractIn the world's highest mountain ranges, uncertainty about the upper elevational range limits of alpine animals represents a critical knowledge gap regarding the environmental limits of life and presents a problem for detecting range shifts in response to climate change. Here we report results of mountaineering mammal surveys in the Central Andes, which led to the discovery of multiple species of mice living at extreme elevations that far surpass previously assumed range limits for mammals. We livetrapped small mammals from ecologically diverse sites spanning >6,700 m of vertical relief, from the desert coast of northern Chile to the summits of the highest volcanoes in the Andes. We used molecular sequence data and whole-genome sequence data to confirm the identities of species that represent new elevational records and to test hypotheses regarding species limits. These discoveries contribute to a new appreciation of the environmental limits of vertebrate life.
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11
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Mohd Talkah NS, Aziz NAKA, Rahim MFA, Hanafi NFF, Ahmad Mokhtar MA, Othman AS. The chloroplast genome inheritance pattern of the Deli-Nigerian prospection material (NPM) × Yangambi population of Elaeis guineensis Jacq. PeerJ 2024; 12:e17335. [PMID: 38818457 PMCID: PMC11138521 DOI: 10.7717/peerj.17335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2023] [Accepted: 04/15/2024] [Indexed: 06/01/2024] Open
Abstract
Background The chloroplast genome has the potential to be genetically engineered to enhance the agronomic value of major crops. As a crop plant with major economic value, it is important to understand every aspect of the genetic inheritance pattern among Elaeis guineensis individuals to ensure the traceability of agronomic traits. Methods Two parental E. guineensis individuals and 23 of their F1 progenies were collected and sequenced using the next-generation sequencing (NGS) technique on the Illumina platform. Chloroplast genomes were assembled de novo from the cleaned raw reads and aligned to check for variations. The sequences were compared and analyzed with programming language scripting and relevant bioinformatic softwares. Simple sequence repeat (SSR) loci were determined from the chloroplast genome. Results The chloroplast genome assembly resulted in 156,983 bp, 156,988 bp, 156,982 bp, and 156,984 bp. The gene content and arrangements were consistent with the reference genome published in the GenBank database. Seventy-eight SSRs were detected in the chloroplast genome, with most located in the intergenic spacer region.The chloroplast genomes of 17 F1 progenies were exact copies of the maternal parent, while six individuals showed a single variation in the sequence. Despite the significant variation displayed by the male parent, all the nucleotide variations were synonymous. This study show highly conserve gene content and sequence in Elaeis guineensis chloroplast genomes. Maternal inheritance of chloroplast genome among F1 progenies are robust with a low possibility of mutations over generations. The findings in this study can enlighten inheritance pattern of Elaeis guineensis chloroplast genome especially among crops' scientists who consider using chloroplast genome for agronomic trait modifications.
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Affiliation(s)
| | | | | | | | | | - Ahmad Sofiman Othman
- School of Biological Sciences, Universiti Sains Malaysia, Minden, Pulau Pinang, Malaysia
- Centre of Chemical Biology, Universiti Sains Malaysia, Bayan Baru, Pulau Pinang, Malaysia
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12
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Wan JN, Wang SW, Leitch AR, Leitch IJ, Jian JB, Wu ZY, Xin HP, Rakotoarinivo M, Onjalalaina GE, Gituru RW, Dai C, Mwachala G, Bai MZ, Zhao CX, Wang HQ, Du SL, Wei N, Hu GW, Chen SC, Chen XY, Wan T, Wang QF. The rise of baobab trees in Madagascar. Nature 2024; 629:1091-1099. [PMID: 38750363 PMCID: PMC11136661 DOI: 10.1038/s41586-024-07447-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2023] [Accepted: 04/19/2024] [Indexed: 05/30/2024]
Abstract
The baobab trees (genus Adansonia) have attracted tremendous attention because of their striking shape and distinctive relationships with fauna1. These spectacular trees have also influenced human culture, inspiring innumerable arts, folklore and traditions. Here we sequenced genomes of all eight extant baobab species and argue that Madagascar should be considered the centre of origin for the extant lineages, a key issue in their evolutionary history2,3. Integrated genomic and ecological analyses revealed the reticulate evolution of baobabs, which eventually led to the species diversity seen today. Past population dynamics of Malagasy baobabs may have been influenced by both interspecific competition and the geological history of the island, especially changes in local sea levels. We propose that further attention should be paid to the conservation status of Malagasy baobabs, especially of Adansonia suarezensis and Adansonia grandidieri, and that intensive monitoring of populations of Adansonia za is required, given its propensity for negatively impacting the critically endangered Adansonia perrieri.
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Affiliation(s)
- Jun-Nan Wan
- State Key Laboratory of Plant Diversity and Specialty Crops, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- Sino-Africa Joint Research Centre, Chinese Academy of Sciences, Wuhan, China
| | - Sheng-Wei Wang
- State Key Laboratory of Plant Diversity and Specialty Crops, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- Sino-Africa Joint Research Centre, Chinese Academy of Sciences, Wuhan, China
| | - Andrew R Leitch
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
| | | | - Jian-Bo Jian
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | | | - Hai-Ping Xin
- State Key Laboratory of Plant Diversity and Specialty Crops, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
| | | | | | - Robert Wahiti Gituru
- Sino-Africa Joint Research Centre, Chinese Academy of Sciences, Wuhan, China
- Department of Botany, Jomo Kenyatta University of Agriculture and Technology, Nairobi, Kenya
| | - Can Dai
- School of Resources and Environmental Science, Hubei University, Wuhan, China
| | | | - Ming-Zhou Bai
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | | | | | - Sheng-Lan Du
- State Key Laboratory of Plant Diversity and Specialty Crops, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
| | - Neng Wei
- State Key Laboratory of Plant Diversity and Specialty Crops, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- Sino-Africa Joint Research Centre, Chinese Academy of Sciences, Wuhan, China
| | - Guang-Wan Hu
- State Key Laboratory of Plant Diversity and Specialty Crops, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- Sino-Africa Joint Research Centre, Chinese Academy of Sciences, Wuhan, China
| | - Si-Chong Chen
- State Key Laboratory of Plant Diversity and Specialty Crops, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- Sino-Africa Joint Research Centre, Chinese Academy of Sciences, Wuhan, China
| | - Xiao-Ya Chen
- Sino-Africa Joint Research Centre, Chinese Academy of Sciences, Wuhan, China
- Shanghai Chenshan Botanical Garden, Shanghai, China
| | - Tao Wan
- State Key Laboratory of Plant Diversity and Specialty Crops, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China.
- Sino-Africa Joint Research Centre, Chinese Academy of Sciences, Wuhan, China.
| | - Qing-Feng Wang
- State Key Laboratory of Plant Diversity and Specialty Crops, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China.
- Sino-Africa Joint Research Centre, Chinese Academy of Sciences, Wuhan, China.
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13
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Feng X, Zheng J, Irisarri I, Yu H, Zheng B, Ali Z, de Vries S, Keller J, Fürst-Jansen JMR, Dadras A, Zegers JMS, Rieseberg TP, Dhabalia Ashok A, Darienko T, Bierenbroodspot MJ, Gramzow L, Petroll R, Haas FB, Fernandez-Pozo N, Nousias O, Li T, Fitzek E, Grayburn WS, Rittmeier N, Permann C, Rümpler F, Archibald JM, Theißen G, Mower JP, Lorenz M, Buschmann H, von Schwartzenberg K, Boston L, Hayes RD, Daum C, Barry K, Grigoriev IV, Wang X, Li FW, Rensing SA, Ben Ari J, Keren N, Mosquna A, Holzinger A, Delaux PM, Zhang C, Huang J, Mutwil M, de Vries J, Yin Y. Genomes of multicellular algal sisters to land plants illuminate signaling network evolution. Nat Genet 2024; 56:1018-1031. [PMID: 38693345 PMCID: PMC11096116 DOI: 10.1038/s41588-024-01737-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Accepted: 03/25/2024] [Indexed: 05/03/2024]
Abstract
Zygnematophyceae are the algal sisters of land plants. Here we sequenced four genomes of filamentous Zygnematophyceae, including chromosome-scale assemblies for three strains of Zygnema circumcarinatum. We inferred traits in the ancestor of Zygnematophyceae and land plants that might have ushered in the conquest of land by plants: expanded genes for signaling cascades, environmental response, and multicellular growth. Zygnematophyceae and land plants share all the major enzymes for cell wall synthesis and remodifications, and gene gains shaped this toolkit. Co-expression network analyses uncover gene cohorts that unite environmental signaling with multicellular developmental programs. Our data shed light on a molecular chassis that balances environmental response and growth modulation across more than 600 million years of streptophyte evolution.
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Affiliation(s)
- Xuehuan Feng
- Nebraska Food for Health Center, Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Jinfang Zheng
- Nebraska Food for Health Center, Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, NE, USA
- Zhejiang Lab, Hangzhou, China
| | - Iker Irisarri
- Institute of Microbiology and Genetics, Department of Applied Bioinformatics, University of Goettingen, Goettingen, Germany
- Campus Institute Data Science, University of Goettingen, Goettingen, Germany
- Section Phylogenomics, Centre for Molecular biodiversity Research, Leibniz Institute for the Analysis of Biodiversity Change, Zoological Museum Hamburg, Hamburg, Germany
| | - Huihui Yu
- University of Nebraska-Lincoln, Center for Plant Science Innovation, Lincoln, NE, USA
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Science, Yunnan, China
| | - Bo Zheng
- Nebraska Food for Health Center, Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Zahin Ali
- Nanyang Technological University, School of Biological Sciences, Singapore, Singapore
| | - Sophie de Vries
- Institute of Microbiology and Genetics, Department of Applied Bioinformatics, University of Goettingen, Goettingen, Germany
| | - Jean Keller
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, CNRS, UPS, INP Toulouse, Castanet-Tolosan, France
| | - Janine M R Fürst-Jansen
- Institute of Microbiology and Genetics, Department of Applied Bioinformatics, University of Goettingen, Goettingen, Germany
| | - Armin Dadras
- Institute of Microbiology and Genetics, Department of Applied Bioinformatics, University of Goettingen, Goettingen, Germany
| | - Jaccoline M S Zegers
- Institute of Microbiology and Genetics, Department of Applied Bioinformatics, University of Goettingen, Goettingen, Germany
| | - Tim P Rieseberg
- Institute of Microbiology and Genetics, Department of Applied Bioinformatics, University of Goettingen, Goettingen, Germany
| | - Amra Dhabalia Ashok
- Institute of Microbiology and Genetics, Department of Applied Bioinformatics, University of Goettingen, Goettingen, Germany
| | - Tatyana Darienko
- Institute of Microbiology and Genetics, Department of Applied Bioinformatics, University of Goettingen, Goettingen, Germany
| | - Maaike J Bierenbroodspot
- Institute of Microbiology and Genetics, Department of Applied Bioinformatics, University of Goettingen, Goettingen, Germany
| | - Lydia Gramzow
- University of Jena, Matthias Schleiden Institute/Genetics, Jena, Germany
| | - Romy Petroll
- Plant Cell Biology, Department of Biology, University of Marburg, Marburg, Germany
- Department of Algal Development and Evolution, Max Planck Institute for Biology Tübingen, Tübingen, Germany
| | - Fabian B Haas
- Plant Cell Biology, Department of Biology, University of Marburg, Marburg, Germany
- Department of Algal Development and Evolution, Max Planck Institute for Biology Tübingen, Tübingen, Germany
| | - Noe Fernandez-Pozo
- Plant Cell Biology, Department of Biology, University of Marburg, Marburg, Germany
- Institute for Mediterranean and Subtropical Horticulture 'La Mayora', Málaga, Spain
| | - Orestis Nousias
- Nebraska Food for Health Center, Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Tang Li
- Nebraska Food for Health Center, Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Elisabeth Fitzek
- Computational Biology, Department of Biology, Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - W Scott Grayburn
- Northern Illinois University, Molecular Core Lab, Department of Biological Sciences, DeKalb, IL, USA
| | - Nina Rittmeier
- University of Innsbruck, Department of Botany, Research Group Plant Cell Biology, Innsbruck, Austria
| | - Charlotte Permann
- University of Innsbruck, Department of Botany, Research Group Plant Cell Biology, Innsbruck, Austria
| | - Florian Rümpler
- University of Jena, Matthias Schleiden Institute/Genetics, Jena, Germany
| | - John M Archibald
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Günter Theißen
- University of Jena, Matthias Schleiden Institute/Genetics, Jena, Germany
| | - Jeffrey P Mower
- University of Nebraska-Lincoln, Center for Plant Science Innovation, Lincoln, NE, USA
| | - Maike Lorenz
- University of Goettingen, Albrecht-von-Haller-Institute for Plant Sciences, Experimental Phycology and Culture Collection of Algae at Goettingen University, Goettingen, Germany
| | - Henrik Buschmann
- University of Applied Sciences Mittweida, Faculty of Applied Computer Sciences and Biosciences, Section Biotechnology and Chemistry, Molecular Biotechnology, Mittweida, Germany
| | - Klaus von Schwartzenberg
- Universität Hamburg, Institute of Plant Science and Microbiology, Microalgae and Zygnematophyceae Collection Hamburg and Aquatic Ecophysiology and Phycology, Hamburg, Germany
| | - Lori Boston
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Richard D Hayes
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Chris Daum
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Kerrie Barry
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Igor V Grigoriev
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, USA
| | - Xiyin Wang
- North China University of Science and Technology, Tangshan, China
| | - Fay-Wei Li
- Boyce Thompson Institute, Ithaca, NY, USA
- Plant Biology Section, Cornell University, Ithaca, NY, USA
| | - Stefan A Rensing
- Plant Cell Biology, Department of Biology, University of Marburg, Marburg, Germany
- University of Freiburg, Centre for Biological Signalling Studies (BIOSS), Freiburg, Germany
| | - Julius Ben Ari
- The Hebrew University of Jerusalem, The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, Rehovot, Israel
| | - Noa Keren
- The Hebrew University of Jerusalem, The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, Rehovot, Israel
| | - Assaf Mosquna
- The Hebrew University of Jerusalem, The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, Rehovot, Israel
| | - Andreas Holzinger
- University of Innsbruck, Department of Botany, Research Group Plant Cell Biology, Innsbruck, Austria
| | - Pierre-Marc Delaux
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, CNRS, UPS, INP Toulouse, Castanet-Tolosan, France
| | - Chi Zhang
- University of Nebraska-Lincoln, Center for Plant Science Innovation, Lincoln, NE, USA
- University of Nebraska-Lincoln, School of Biological Sciences, Lincoln, NE, USA
| | - Jinling Huang
- Department of Biology, East Carolina University, Greenville, NC, USA
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, China
| | - Marek Mutwil
- Nanyang Technological University, School of Biological Sciences, Singapore, Singapore
| | - Jan de Vries
- Institute of Microbiology and Genetics, Department of Applied Bioinformatics, University of Goettingen, Goettingen, Germany.
- Campus Institute Data Science, University of Goettingen, Goettingen, Germany.
- University of Goettingen, Goettingen Center for Molecular Biosciences, Goettingen, Germany.
| | - Yanbin Yin
- Nebraska Food for Health Center, Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, NE, USA.
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14
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Zhang Q, Wang J, Li Y, Tung J, Deng Y, Baker B, Dinesh-Kumar SP, Li F. Conserved transcription factors NRZ1 and NRM1 regulate NLR receptor-mediated immunity. PLANT PHYSIOLOGY 2024; 195:832-849. [PMID: 38306630 DOI: 10.1093/plphys/kiae054] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 12/04/2023] [Accepted: 12/06/2023] [Indexed: 02/04/2024]
Abstract
Plant innate immunity mediated by the nucleotide-binding leucine-rich repeat (NLR) class of immune receptors plays an important role in defense against various pathogens. Although key biochemical events involving NLR activation and signaling have been recently uncovered, we know very little about the transcriptional regulation of NLRs and their downstream signaling components. Here, we show that the Toll-Interleukin 1 receptor homology domain containing NLR (TNL) gene N (Necrosis), which confers resistance to Tobacco mosaic virus, is transcriptionally induced upon immune activation. We identified two conserved transcription factors, N required C3H zinc finger 1 (NRZ1) and N required MYB-like transcription factor 1 (NRM1), that activate N in an immune responsive manner. Genetic analyses indicated that NRZ1 and NRM1 positively regulate coiled-coil domain-containing NLR- and TNL-mediated immunity and function independently of the signaling component Enhanced Disease Susceptibility 1. Furthermore, NRZ1 functions upstream of NRM1 in cell death signaling, and their gene overexpression induces ectopic cell death and expression of NLR signaling components. Our findings uncovered a conserved transcriptional regulatory network that is central to NLR-mediated cell death and immune signaling in plants.
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Affiliation(s)
- Qingling Zhang
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan 430070, China
- Department of Plant Biology and The Genome Center, College of Biological Sciences, University of California, Davis, CA 95616, USA
- Institute of Vegetables and Flowers, Jiangxi Academy of Agricultural Sciences, Nanchang 330200, China
| | - Jubin Wang
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan 430070, China
- The Key Laboratory of Horticultural Plant Genetic and Improvement of Jiangxi Province, Institute of Biological Resources, Jiangxi Academy of Sciences, Nanchang 330299, China
| | - Yuanyuan Li
- Department of Plant Biology and The Genome Center, College of Biological Sciences, University of California, Davis, CA 95616, USA
| | - Jeffrey Tung
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA 94710, USA
| | - Yingtian Deng
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan 430070, China
| | - Barbara Baker
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA 94710, USA
| | - Savithramma P Dinesh-Kumar
- Department of Plant Biology and The Genome Center, College of Biological Sciences, University of California, Davis, CA 95616, USA
| | - Feng Li
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
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15
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Sandberg TOM, Yahalomi D, Bracha N, Haddas-Sasson M, Pupko T, Atkinson SD, Bartholomew JL, Zhang JY, Huchon D. Evolution of myxozoan mitochondrial genomes: insights from myxobolids. BMC Genomics 2024; 25:388. [PMID: 38649808 PMCID: PMC11034133 DOI: 10.1186/s12864-024-10254-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2023] [Accepted: 03/26/2024] [Indexed: 04/25/2024] Open
Abstract
BACKGROUND Myxozoa is a class of cnidarian parasites that encompasses over 2,400 species. Phylogenetic relationships among myxozoans remain highly debated, owing to both a lack of informative morphological characters and a shortage of molecular markers. Mitochondrial (mt) genomes are a common marker in phylogeny and biogeography. However, only five complete myxozoan mt genomes have been sequenced: four belonging to two closely related genera, Enteromyxum and Kudoa, and one from the genus Myxobolus. Interestingly, while cytochrome oxidase genes could be identified in Enteromyxum and Kudoa, no such genes were found in Myxobolus squamalis, and another member of the Myxobolidae (Henneguya salminicola) was found to have lost its entire mt genome. To evaluate the utility of mt genomes to reconstruct myxozoan relationships and to understand if the loss of cytochrome oxidase genes is a characteristic of myxobolids, we sequenced the mt genome of five myxozoans (Myxobolus wulii, M. honghuensis, M. shantungensis, Thelohanellus kitauei and, Sphaeromyxa zaharoni) using Illumina and Oxford Nanopore platforms. RESULTS Unlike Enteromyxum, which possesses a partitioned mt genome, the five mt genomes were encoded on single circular chromosomes. An mt plasmid was found in M. wulii, as described previously in Kudoa iwatai. In all new myxozoan genomes, five protein-coding genes (cob, cox1, cox2, nad1, and nad5) and two rRNAs (rnl and rns) were recognized, but no tRNA. We found that Myxobolus and Thelohanellus species shared unidentified reading frames, supporting the view that these mt open reading frames are functional. Our phylogenetic reconstructions based on the five conserved mt genes agree with previously published trees based on the 18S rRNA gene. CONCLUSIONS Our results suggest that the loss of cytochrome oxidase genes is not a characteristic of all myxobolids, the ancestral myxozoan mt genome was likely encoded on a single circular chromosome, and mt plasmids exist in a few lineages. Our findings indicate that myxozoan mt sequences are poor markers for reconstructing myxozoan phylogenetic relationships because of their fast-evolutionary rates and the abundance of repeated elements, which complicates assembly.
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Affiliation(s)
| | - Dayana Yahalomi
- School of Zoology, George S. Wise Faculty of Life Sciences, Tel Aviv University, 6997801, Tel Aviv, Israel
| | - Noam Bracha
- The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, 6997801, Tel Aviv, Israel
| | - Michal Haddas-Sasson
- School of Zoology, George S. Wise Faculty of Life Sciences, Tel Aviv University, 6997801, Tel Aviv, Israel
| | - Tal Pupko
- The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, 6997801, Tel Aviv, Israel
| | - Stephen D Atkinson
- Department of Microbiology, Oregon State University, 97331, Corvallis, OR, USA
| | - Jerri L Bartholomew
- Department of Microbiology, Oregon State University, 97331, Corvallis, OR, USA
| | - Jin Yong Zhang
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, China
| | - Dorothée Huchon
- School of Zoology, George S. Wise Faculty of Life Sciences, Tel Aviv University, 6997801, Tel Aviv, Israel.
- The Steinhardt Museum of Natural History and National Research Center, Tel Aviv University, 6997801, Tel Aviv, Israel.
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16
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Tomlin CM, Rajaraman S, Sebesta JT, Scheen AC, Bendiksby M, Low YW, Salojärvi J, Michael TP, Albert VA, Lindqvist C. Allopolyploid origin and diversification of the Hawaiian endemic mints. Nat Commun 2024; 15:3109. [PMID: 38600100 PMCID: PMC11006916 DOI: 10.1038/s41467-024-47247-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 03/26/2024] [Indexed: 04/12/2024] Open
Abstract
Island systems provide important contexts for studying processes underlying lineage migration, species diversification, and organismal extinction. The Hawaiian endemic mints (Lamiaceae family) are the second largest plant radiation on the isolated Hawaiian Islands. We generated a chromosome-scale reference genome for one Hawaiian species, Stenogyne calaminthoides, and resequenced 45 relatives, representing 34 species, to uncover the continental origins of this group and their subsequent diversification. We further resequenced 109 individuals of two Stenogyne species, and their purported hybrids, found high on the Mauna Kea volcano on the island of Hawai'i. The three distinct Hawaiian genera, Haplostachys, Phyllostegia, and Stenogyne, are nested inside a fourth genus, Stachys. We uncovered four independent polyploidy events within Stachys, including one allopolyploidy event underlying the Hawaiian mints and their direct western North American ancestors. While the Hawaiian taxa may have principally diversified by parapatry and drift in small and fragmented populations, localized admixture may have played an important role early in lineage diversification. Our genomic analyses provide a view into how organisms may have radiated on isolated island chains, settings that provided one of the principal natural laboratories for Darwin's thinking about the evolutionary process.
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Affiliation(s)
- Crystal M Tomlin
- Department of Biological Sciences, University at Buffalo, New York, USA
| | - Sitaram Rajaraman
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | | | | | - Mika Bendiksby
- Natural History Museum, University of Oslo, Oslo, Norway
| | - Yee Wen Low
- Singapore Botanic Gardens, National Parks Board, Singapore, Singapore
| | - Jarkko Salojärvi
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Todd P Michael
- The Plant Molecular and Cellular Biology Laboratory, Salk Institute for Biological Studies, La Jolla, California, USA
| | - Victor A Albert
- Department of Biological Sciences, University at Buffalo, New York, USA.
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17
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Aliaga F, Zapata-Cruz M, Valverde-Zavaleta SA. Plastid genome of Chenopodium petiolare from Trujillo, Peru. BMC Res Notes 2024; 17:69. [PMID: 38468356 DOI: 10.1186/s13104-024-06705-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 01/25/2024] [Indexed: 03/13/2024] Open
Abstract
OBJECTIVES The Peruvian Andean region is an important center for plant domestication. However, to date, there have been few genetic studies on native grain, which limits our understanding of their genetic diversity and the development of new genetic studies for their breeding. Herein, we revealed the plastid genome of Chenopodium petiolare to expand our knowledge of its molecular markers, evolutionary studies, and conservation genetics. DATA DESCRIPTION Total genomic DNA was extracted from fresh leaves (voucher: USM < PER > :MHN333570). The DNA was sequenced using Illumina Novaseq 6000 (Macrogen Inc., Seoul, Republic of Korea) and reads 152,064 bp in length, with a large single-copy region of 83,520 bp and small single-copy region of 18,108 bp were obtained. These reads were separated by a pair of inverted repeat regions (IR) of 25,218 bp, and the overall guanine and cytosine (GC) was 37.24%. The plastid genome contains 130 genes (111 genes were unique and 19 genes were found duplicated in each IR region), including 86 protein-coding genes, 36 transfer RNA-coding genes, eight ribosomal RNA-coding genes, and 25 genes with introns (21 genes with one intron and four genes with two introns). The phylogenetic tree reconstructed based on single-copy orthologous genes and maximum likelihood analysis indicated that Chenopodium petiolare is most closely related to Chenopodium quinoa.
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Affiliation(s)
- Flavio Aliaga
- Grupo de Investigación en Ecología Evolutiva, Protección de Cultivos, Remediación Ambiental, y Biotecnología (EPROBIO), Universidad Privada del Norte, Trujillo, 13011, Peru.
- Dirección de Investigación, Innovación y Responsabilidad Social, Universidad Privada del Norte, Trujillo, 13009, Peru.
- Capítulo de Ingeniería Agronómica, Consejo Departamental de La Libertad (CDLL), Colegio de Ingenieros del Perú (CIP), Trujillo, 13008, Peru.
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18
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Wang J, Zhang Q, Tung J, Zhang X, Liu D, Deng Y, Tian Z, Chen H, Wang T, Yin W, Li B, Lai Z, Dinesh-Kumar SP, Baker B, Li F. High-quality assembled and annotated genomes of Nicotiana tabacum and Nicotiana benthamiana reveal chromosome evolution and changes in defense arsenals. MOLECULAR PLANT 2024; 17:423-437. [PMID: 38273657 DOI: 10.1016/j.molp.2024.01.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 01/08/2024] [Accepted: 01/21/2024] [Indexed: 01/27/2024]
Abstract
Nicotiana tabacum and Nicotiana benthamiana are widely used models in plant biology research. However, genomic studies of these species have lagged. Here we report the chromosome-level reference genome assemblies for N. benthamiana and N. tabacum with an estimated 99.5% and 99.8% completeness, respectively. Sensitive transcription start and termination site sequencing methods were developed and used for accurate gene annotation in N. tabacum. Comparative analyses revealed evidence for the parental origins and chromosome structural changes, leading to hybrid genome formation of each species. Interestingly, the antiviral silencing genes RDR1, RDR6, DCL2, DCL3, and AGO2 were lost from one or both subgenomes in N. benthamiana, while both homeologs were kept in N. tabacum. Furthermore, the N. benthamiana genome encodes fewer immune receptors and signaling components than that of N. tabacum. These findings uncover possible reasons underlying the hypersusceptible nature of N. benthamiana. We developed the user-friendly Nicomics (http://lifenglab.hzau.edu.cn/Nicomics/) web server to facilitate better use of Nicotiana genomic resources as well as gene structure and expression analyses.
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Affiliation(s)
- Jubin Wang
- National Key Laboratory for Germplasm Innovation and Utilization for Fruit and Vegetable Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, Hubei 430070, China; The Key Laboratory of Horticultural Plant Genetic and Improvement of Jiangxi Province, Institute of Biological Resources, Jiangxi Academy of Sciences, Nanchang 330299, China
| | - Qingling Zhang
- National Key Laboratory for Germplasm Innovation and Utilization for Fruit and Vegetable Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, Hubei 430070, China; Institute of Vegetables and Flowers, Jiangxi Academy of Agricultural Sciences, Nanchang 330200, China
| | - Jeffrey Tung
- Plant Gene Expression Center, Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA 94706, USA
| | - Xi Zhang
- National Key Laboratory for Germplasm Innovation and Utilization for Fruit and Vegetable Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Dan Liu
- National Key Laboratory for Germplasm Innovation and Utilization for Fruit and Vegetable Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Yingtian Deng
- National Key Laboratory for Germplasm Innovation and Utilization for Fruit and Vegetable Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Zhendong Tian
- National Key Laboratory for Germplasm Innovation and Utilization for Fruit and Vegetable Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, Hubei 430070, China; Hubei Hongshan Laboratory, Wuhan, Hubei 430070, China
| | - Huilan Chen
- National Key Laboratory for Germplasm Innovation and Utilization for Fruit and Vegetable Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Taotao Wang
- National Key Laboratory for Germplasm Innovation and Utilization for Fruit and Vegetable Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Weixiao Yin
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Bo Li
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China; Hubei Hongshan Laboratory, Wuhan, Hubei 430070, China
| | - Zhibing Lai
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China; Hubei Hongshan Laboratory, Wuhan, Hubei 430070, China
| | - Savithramma P Dinesh-Kumar
- Department of Plant Biology and The Genome Center, College of Biological Sciences, University of California, Davis, Davis, CA 95616, USA
| | - Barbara Baker
- Plant Gene Expression Center, Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA 94706, USA.
| | - Feng Li
- National Key Laboratory for Germplasm Innovation and Utilization for Fruit and Vegetable Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, Hubei 430070, China; Hubei Hongshan Laboratory, Wuhan, Hubei 430070, China.
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19
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Cadorna CAE, Pahayo DG, Rey JD. The first mitochondrial genome of Calophyllum soulattri Burm.f. Sci Rep 2024; 14:5112. [PMID: 38429360 PMCID: PMC10907642 DOI: 10.1038/s41598-024-55016-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 02/19/2024] [Indexed: 03/03/2024] Open
Abstract
Calophyllum soulattri Burm.f. is traditionally used to treat skin infections and reduce rheumatic pain, yet genetic and genomic studies are still limited. Here, we present the first complete mitochondrial genome of C. soulattri. It is 378,262 bp long with 43.97% GC content, containing 55 genes (30 protein-coding, 5 rRNA, and 20 tRNA). Repeat analysis of the mitochondrial genome revealed 194 SSRs, mostly mononucleotides, and 266 pairs of dispersed repeats ( ≥ 30 bp) that were predominantly palindromic. There were 23 homologous fragments found between the mitochondrial and plastome genomes. We also predicted 345 C-to-U RNA editing sites from 30 protein-coding genes (PCGs) of the C. soulatrii mitochondrial genome. These RNA editing events created the start codon of nad1 and the stop codon of ccmFc. Most PCGs of the C. soulattri mitochondrial genome underwent negative selection, but atp4 and ccmB experienced positive selection. Phylogenetic analyses showed C. soulattri is a sister taxon of Garcinia mangostana. This study has shed light on C. soulattri's evolution and Malpighiales' phylogeny. As the first complete mitochondrial genome in Calophyllaceae, it can be used as a reference genome for other medicinal plant species within the family for future genetic studies.
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Affiliation(s)
- Charles Anthon E Cadorna
- Plant Molecular Phylogenetics Laboratory, Institute of Biology, College of Science, University of the Philippines, Diliman, 1101, Quezon City, Philippines
| | - Dexter G Pahayo
- Plant Molecular Phylogenetics Laboratory, Institute of Biology, College of Science, University of the Philippines, Diliman, 1101, Quezon City, Philippines
| | - Jessica D Rey
- Plant Molecular Phylogenetics Laboratory, Institute of Biology, College of Science, University of the Philippines, Diliman, 1101, Quezon City, Philippines.
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20
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Go S, Koo H, Jung M, Hong S, Yi G, Kim YM. Pan-chloroplast genomes for accession-specific marker development in Hibiscus syriacus. Sci Data 2024; 11:246. [PMID: 38413611 PMCID: PMC10899175 DOI: 10.1038/s41597-024-03077-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Accepted: 02/14/2024] [Indexed: 02/29/2024] Open
Abstract
Hibiscus syriacus L. is a renowned ornamental plant. We constructed 95 chloroplast genomes of H. syriacus L. cultivars using a short-read sequencing platform (Illumina) and a long-read sequencing platform (Oxford Nanopore Technology). The following genome assembly, we delineate quadripartite structures encompassing large single-copy, small single-copy, and inverted repeat (IRa and IRb) regions, from 160,231 bp to 161,041 bp. Our comprehensive analyses confirmed the presence of 79 protein-coding genes, 30 tRNA genes, and 4 rRNA genes in the pan-chloroplast genome, consistent with prior research on the H. syriacus chloroplast genome. Subsequent pangenome analysis unveiled widespread genome sequence conservation alongside unique cultivar-specific variant patterns consisting of 193 single-nucleotide polymorphisms and 61 insertions or deletions. The region containing intra-species variant patterns, as identified in this study, has the potential to develop accession-specific molecular markers, enhancing precision in cultivar classification. These findings are anticipated to drive advancements in breeding strategies, augment biodiversity, and unlock the agricultural potential inherent in H. syriacus.
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Affiliation(s)
- Sangjin Go
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea
- Department of Bioinformatics, KRIBB School of Bioscience, Korea University of Science and Technology (UST), Daejeon, 34141, Republic of Korea
| | - Hyunjin Koo
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea
| | - Minah Jung
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea
| | - Seongmin Hong
- Department of Bio-Environmental Chemistry, College of Agriculture and Life Sciences, Chungnam National University, Daejeon, 34134, Republic of Korea
| | - Gibum Yi
- Department of Bio-Environmental Chemistry, College of Agriculture and Life Sciences, Chungnam National University, Daejeon, 34134, Republic of Korea
| | - Yong-Min Kim
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea.
- Department of Bioinformatics, KRIBB School of Bioscience, Korea University of Science and Technology (UST), Daejeon, 34141, Republic of Korea.
- Digital Biotech Innovation Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea.
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21
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Bai X, Bao Y, Bei S, Bu C, Cao R, Cao Y, Cen H, Chao J, Chen F, Chen H, Chen K, Chen M, Chen M, Chen M, Chen Q, Chen R, Chen S, Chen T, Chen X, Chen X, Cheng Y, Chu Y, Cui Q, Dong L, Du Z, Duan G, Fan S, Fan Z, Fang X, Fang Z, Feng Z, Fu S, Gao F, Gao G, Gao H, Gao W, Gao X, Gao X, Gao X, Gong J, Gong J, Gou Y, Gu S, Guo AY, Guo G, Guo X, Han C, Hao D, Hao L, He Q, He S, He S, Hu W, Huang K, Huang T, Huang X, Huang Y, Jia P, Jia Y, Jiang C, Jiang M, Jiang S, Jiang T, Jiang X, Jin E, Jin W, Kang H, Kang H, Kong D, Lan L, Lei W, Li CY, Li C, Li C, Li H, Li J, Li J, Li L, Li P, Li R, Li X, Li Y, Li Y, Li Z, Liao X, Lin S, Lin Y, Ling Y, Liu B, Liu CJ, Liu D, Liu GH, Liu L, Liu S, Liu W, Liu X, Liu X, Liu Y, Liu Y, Lu M, Lu T, Luo H, Luo H, Luo M, Luo S, Luo X, Ma L, Ma Y, Mai J, Meng J, Meng X, Meng Y, Meng Y, Miao W, Miao YR, Ni L, Nie Z, Niu G, Niu X, Niu Y, Pan R, Pan S, Peng D, Peng J, Qi J, Qi Y, Qian Q, Qin Y, Qu H, Ren J, Ren J, Sang Z, Shang K, Shen WK, Shen Y, Shi Y, Song S, Song T, Su T, Sun J, Sun Y, Sun Y, Sun Y, Tang B, Tang D, Tang Q, Tang Z, Tian D, Tian F, Tian W, Tian Z, Wang A, Wang G, Wang G, Wang J, Wang J, Wang P, Wang P, Wang W, Wang Y, Wang Y, Wang Y, Wang Y, Wang Z, Wei H, Wei Y, Wei Z, Wu D, Wu G, Wu S, Wu S, Wu W, Wu W, Wu Z, Xia Z, Xiao J, Xiao L, Xiao Y, Xie G, Xie GY, Xie J, Xie Y, Xiong J, Xiong Z, Xu D, Xu S, Xu T, Xu T, Xue Y, Xue Y, Yan C, Yang D, Yang F, Yang F, Yang H, Yang J, Yang K, Yang N, Yang QY, Yang S, Yang X, Yang X, Yang X, Yang YG, Ye W, Yu C, Yu F, Yu S, Yuan C, Yuan H, Zeng J, Zhai S, Zhang C, Zhang F, Zhang G, Zhang M, Zhang P, Zhang Q, Zhang R, Zhang S, Zhang W, Zhang W, Zhang W, Zhang X, Zhang X, Zhang Y, Zhang Y, Zhang Y, Zhang YE, Zhang Y, Zhang Z, Zhang Z, Zhao D, Zhao F, Zhao G, Zhao M, Zhao W, Zhao W, Zhao X, Zhao Y, Zhao Y, Zhao Z, Zheng X, Zheng Y, Zhou C, Zhou H, Zhou X, Zhou X, Zhou Y, Zhou Y, Zhu J, Zhu L, Zhu R, Zhu T, Zong W, Zou D, Zuo Z. Database Resources of the National Genomics Data Center, China National Center for Bioinformation in 2024. Nucleic Acids Res 2024; 52:D18-D32. [PMID: 38018256 PMCID: PMC10767964 DOI: 10.1093/nar/gkad1078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 10/12/2023] [Accepted: 10/27/2023] [Indexed: 11/30/2023] Open
Abstract
The National Genomics Data Center (NGDC), which is a part of the China National Center for Bioinformation (CNCB), provides a family of database resources to support the global academic and industrial communities. With the rapid accumulation of multi-omics data at an unprecedented pace, CNCB-NGDC continuously expands and updates core database resources through big data archiving, integrative analysis and value-added curation. Importantly, NGDC collaborates closely with major international databases and initiatives to ensure seamless data exchange and interoperability. Over the past year, significant efforts have been dedicated to integrating diverse omics data, synthesizing expanding knowledge, developing new resources, and upgrading major existing resources. Particularly, several database resources are newly developed for the biodiversity of protists (P10K), bacteria (NTM-DB, MPA) as well as plant (PPGR, SoyOmics, PlantPan) and disease/trait association (CROST, HervD Atlas, HALL, MACdb, BioKA, BioKA, RePoS, PGG.SV, NAFLDkb). All the resources and services are publicly accessible at https://ngdc.cncb.ac.cn.
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22
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Xie J, Miao Y, Zhang X, Zhang G, Guo B, Luo G, Huang L. Comparative complete chloroplast genome of Geum japonicum: evolution and phylogenetic analysis. JOURNAL OF PLANT RESEARCH 2024; 137:37-48. [PMID: 37917204 DOI: 10.1007/s10265-023-01502-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 10/05/2023] [Indexed: 11/04/2023]
Abstract
Geum japonicum (Rosaceae) has been widely used in China as a traditional herbal medicine due to its high economic and medicinal value. However, the appearance of Geum species is relatively similar, making identification difficult by conventional phenotypic methods, and the studies of genomics and species evolution are lacking. To better distinguish the medicinal varieties and fill this gap, we carried out relevant research on the chloroplast genome of G. japonicum. Results show a typical quadripartite structure of the chloroplast genome of G. japonicum with a length of 156,042 bp. There are totally 131 unique genes in the genome, including 87 protein-coding genes, 36 tRNA genes, and 8 rRNA genes, and there were also 87 SSRs identified and mostly mononucleotide Adenine-Thymine. We next compared the plastid genomes among four Geum species and obtained 14 hypervariable regions, including ndhF, psbE, trnG-UCC, ccsA, trnQ-UUG, rps16, psbK, trnL-UAA, ycf1, ndhD, atpA, petN, rps14, and trnK-UUU. Phylogenetic analysis revealed that G. japonicum is most closely related to Geum aleppicum, and possibly has some evolutionary relatedness with an ancient relic plant Taihangia rupestris. This research enriched the genome resources and provided fundamental insights for evolutionary studies and the phylogeny of Geum.
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Affiliation(s)
- Junbo Xie
- Key Laboratory of Chinese Medicine Resources Conservation, Institute of Medicinal Plant Development, State Administration of Traditional Chinese Medicine of China, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100193, China
- School of Pharmacy, Jiangxi University of Chinese Medicine, Nanchang, 330000, China
| | - Yujing Miao
- Key Laboratory of Chinese Medicine Resources Conservation, Institute of Medicinal Plant Development, State Administration of Traditional Chinese Medicine of China, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100193, China
| | - Xinke Zhang
- Key Laboratory of Chinese Medicine Resources Conservation, Institute of Medicinal Plant Development, State Administration of Traditional Chinese Medicine of China, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100193, China
| | - Guoshuai Zhang
- Key Laboratory of Chinese Medicine Resources Conservation, Institute of Medicinal Plant Development, State Administration of Traditional Chinese Medicine of China, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100193, China
| | - Baolin Guo
- Key Laboratory of Chinese Medicine Resources Conservation, Institute of Medicinal Plant Development, State Administration of Traditional Chinese Medicine of China, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100193, China
| | - Guangming Luo
- School of Pharmacy, Jiangxi University of Chinese Medicine, Nanchang, 330000, China.
| | - Linfang Huang
- Key Laboratory of Chinese Medicine Resources Conservation, Institute of Medicinal Plant Development, State Administration of Traditional Chinese Medicine of China, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100193, China.
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23
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Xu MRX, Liao ZY, Brock JR, Du K, Li GY, Chen ZQ, Wang YH, Gao ZN, Agarwal G, Wei KHC, Shao F, Pang S, Platts AE, van de Velde J, Lin HM, Teresi SJ, Bird K, Niederhuth CE, Xu JG, Yu GH, Yang JY, Dai SF, Nelson A, Braasch I, Zhang XG, Schartl M, Edger PP, Han MJ, Zhang HH. Maternal dominance contributes to subgenome differentiation in allopolyploid fishes. Nat Commun 2023; 14:8357. [PMID: 38102128 PMCID: PMC10724154 DOI: 10.1038/s41467-023-43740-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 11/17/2023] [Indexed: 12/17/2023] Open
Abstract
Teleost fishes, which are the largest and most diverse group of living vertebrates, have a rich history of ancient and recent polyploidy. Previous studies of allotetraploid common carp and goldfish (cyprinids) reported a dominant subgenome, which is more expressed and exhibits biased gene retention. However, the underlying mechanisms contributing to observed 'subgenome dominance' remains poorly understood. Here we report high-quality genomes of twenty-one cyprinids to investigate the origin and subsequent subgenome evolution patterns following three independent allopolyploidy events. We identify the closest extant relatives of the diploid progenitor species, investigate genetic and epigenetic differences among subgenomes, and conclude that observed subgenome dominance patterns are likely due to a combination of maternal dominance and transposable element densities in each polyploid. These findings provide an important foundation to understanding subgenome dominance patterns observed in teleost fishes, and ultimately the role of polyploidy in contributing to evolutionary innovations.
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Affiliation(s)
- Min-Rui-Xuan Xu
- College of Pharmacy and Life Science, Jiujiang University, Jiujiang, China
| | - Zhen-Yang Liao
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Jordan R Brock
- Department of Horticulture, Michigan State University, East Lansing, MI, USA
| | - Kang Du
- The Xiphophorus Genetic Stock Center, Texas State University, San Marcos, TX, USA
| | - Guo-Yin Li
- College of Life Science and Agronomy, Zhoukou Normal University, Zhoukou, Henan, China
| | | | - Ying-Hao Wang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Zhong-Nan Gao
- College of Pharmacy and Life Science, Jiujiang University, Jiujiang, China
| | - Gaurav Agarwal
- Department of Plant Biology, Michigan State University, East Lansing, MI, USA
| | - Kevin H-C Wei
- Department of Integrative Biology, University of California Berkeley, Berkeley, CA, USA
- Department of Zoology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Feng Shao
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Southwest University, School of Life Sciences, Chongqing, China
| | | | - Adrian E Platts
- Department of Horticulture, Michigan State University, East Lansing, MI, USA
| | - Jozefien van de Velde
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Hong-Min Lin
- College of Pharmacy and Life Science, Jiujiang University, Jiujiang, China
| | - Scott J Teresi
- Department of Horticulture, Michigan State University, East Lansing, MI, USA
| | - Kevin Bird
- Department of Horticulture, Michigan State University, East Lansing, MI, USA
| | - Chad E Niederhuth
- Department of Plant Biology, Michigan State University, East Lansing, MI, USA
| | - Jin-Gen Xu
- Jiujiang Academy of Agricultural Sciences, Jiujiang, China
| | - Guo-Hua Yu
- College of Pharmacy and Life Science, Jiujiang University, Jiujiang, China
| | - Jian-Yuan Yang
- College of Pharmacy and Life Science, Jiujiang University, Jiujiang, China
| | - Si-Fa Dai
- College of Pharmacy and Life Science, Jiujiang University, Jiujiang, China
| | | | - Ingo Braasch
- Department of Integrative Biology, Michigan State University, East Lansing, MI, USA
| | - Xiao-Gu Zhang
- College of Pharmacy and Life Science, Jiujiang University, Jiujiang, China.
| | - Manfred Schartl
- The Xiphophorus Genetic Stock Center, Texas State University, San Marcos, TX, USA.
- Developmental Biochemistry, Biocenter, University of Würzburg, Würzburg, Bayern, Germany.
| | - Patrick P Edger
- Department of Horticulture, Michigan State University, East Lansing, MI, USA.
| | - Min-Jin Han
- State Key Laboratory of Resource Insects, Key Laboratory for Sericulture Functional Genomics and Biotechnology of Agricultural Ministry, Southwest University, Chongqing, China.
| | - Hua-Hao Zhang
- College of Pharmacy and Life Science, Jiujiang University, Jiujiang, China.
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24
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Liu X, Sigwart JD, Sun J. Phylogenomic analyses shed light on the relationships of chiton superfamilies and shell-eye evolution. MARINE LIFE SCIENCE & TECHNOLOGY 2023; 5:525-537. [PMID: 38045544 PMCID: PMC10689665 DOI: 10.1007/s42995-023-00207-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 11/01/2023] [Indexed: 12/05/2023]
Abstract
Mollusca is the second-largest animal phylum with over 100,000 extant species representing eight classes. Across 1000 extant species in the class Polyplacophora, chitons have a relatively constrained morphology but with some notable deviations. Several genera possess "shell eyes", i.e., true eyes with a lens and retina that are embedded within the dorsal shells. The phylogeny of the major chiton clades is mostly well established, in a set of superfamily-level and higher level taxa supported by various approaches, including morphological studies, multiple gene markers, mitogenome-phylogeny, and phylotranscriptomic approaches. However, one critical lineage has remained unclear, namely Schizochiton which was controversially suggested as being the potential independent origin of chiton shell eyes. Here, with the draft genome sequencing of Schizochiton incisus (superfamily Schizochitonoidea) plus assemblies of transcriptome data from other polyplacophorans, we present phylogenetic reconstructions using both mitochondrial genomes and phylogenomic approaches with multiple methods. We found that phylogenetic trees from mitogenomic data are inconsistent, reflecting larger scale confounding factors in molluscan mitogenomes. However, a consistent and robust topology was generated with protein-coding genes using different models and methods. Our results support Schizochitonoidea as the sister group to other Chitonoidea in Chitonina, in agreement with the established classification. Combined with evidence from fossils, our phylogenetic results suggest that the earliest origin of shell eyes is in Schizochitonoidea, and that these structures were also gained secondarily in other genera in Chitonoidea. Our results have generated a holistic review of the internal relationship within Polyplacophora, and a better understanding of the evolution of Polyplacophora.
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Affiliation(s)
- Xu Liu
- Key Laboratory of Evolution & Marine Biodiversity (Ministry of Education) and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, 266003 China
- Laoshan Laboratory, Qingdao, 266237 China
| | - Julia D. Sigwart
- Department of Marine Zoology, Senckenberg Research Institute and Natural History Museum Frankfurt, 60325 Frankfurt Am Main, Germany
| | - Jin Sun
- Key Laboratory of Evolution & Marine Biodiversity (Ministry of Education) and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, 266003 China
- Laoshan Laboratory, Qingdao, 266237 China
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25
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Bao Y, Xue Y. From BIG Data Center to China National Center for Bioinformation. GENOMICS, PROTEOMICS & BIOINFORMATICS 2023; 21:900-903. [PMID: 37832784 PMCID: PMC10928365 DOI: 10.1016/j.gpb.2023.10.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 09/30/2023] [Accepted: 10/07/2023] [Indexed: 10/15/2023]
Affiliation(s)
- Yiming Bao
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Yongbiao Xue
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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26
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She H, Liu Z, Li S, Xu Z, Zhang H, Cheng F, Wu J, Wang X, Deng C, Charlesworth D, Gao W, Qian W. Evolution of the spinach sex-linked region within a rarely recombining pericentromeric region. PLANT PHYSIOLOGY 2023; 193:1263-1280. [PMID: 37403642 DOI: 10.1093/plphys/kiad389] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 06/05/2023] [Accepted: 06/06/2023] [Indexed: 07/06/2023]
Abstract
Sex chromosomes have evolved independently in many different plant lineages. Here, we describe reference genomes for spinach (Spinacia oleracea) X and Y haplotypes by sequencing homozygous XX females and YY males. The long arm of 185-Mb chromosome 4 carries a 13-Mb X-linked region (XLR) and 24.1-Mb Y-linked region (YLR), of which 10 Mb is Y specific. We describe evidence that this reflects insertions of autosomal sequences creating a "Y duplication region" or "YDR" whose presence probably directly reduces genetic recombination in the immediately flanking regions, although both the X and Y sex-linked regions are within a large pericentromeric region of chromosome 4 that recombines rarely in meiosis of both sexes. Sequence divergence estimates using synonymous sites indicate that YDR genes started diverging from their likely autosomal progenitors about 3 MYA, around the time when the flanking YLR stopped recombining with the XLR. These flanking regions have a higher density of repetitive sequences in the YY than the XX assembly and include slightly more pseudogenes compared with the XLR, and the YLR has lost about 11% of the ancestral genes, suggesting some degeneration. Insertion of a male-determining factor would have caused Y linkage across the entire pericentromeric region, creating physically small, highly recombining, terminal pseudoautosomal regions. These findings provide a broader understanding of the origin of sex chromosomes in spinach.
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Affiliation(s)
- Hongbing She
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Zhiyuan Liu
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Shufen Li
- College of Life Sciences, Henan Normal University, Xinxiang 453007, China
| | - Zhaosheng Xu
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Helong Zhang
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Feng Cheng
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Jian Wu
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xiaowu Wang
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Chuanliang Deng
- College of Life Sciences, Henan Normal University, Xinxiang 453007, China
| | - Deborah Charlesworth
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Charlotte Auerbach Road, Edinburgh EH9 3FL, UK
| | - Wujun Gao
- College of Life Sciences, Henan Normal University, Xinxiang 453007, China
| | - Wei Qian
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
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27
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Xu C, Ji J, Zhu X, Huangfu N, Xue H, Wang L, Zhang K, Li D, Niu L, Chen R, Gao X, Luo J, Cui J. Chromosome level genome assembly of oriental armyworm Mythimna separata. Sci Data 2023; 10:597. [PMID: 37684242 PMCID: PMC10491670 DOI: 10.1038/s41597-023-02506-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 08/29/2023] [Indexed: 09/10/2023] Open
Abstract
The oriental armyworm, Mythimna separata, is an extremely destructive polyphagous pest with a broad host range that seriously threatens the safety of agricultural production. Here, a high-quality chromosome-level genome was assembled using Illumina, PacBio HiFi long sequencing, and Hi-C scaffolding technologies. The genome size was 706.30 Mb with a contig N50 of 22.08 Mb, and 99.2% of the assembled sequences were anchored to 31 chromosomes. In addition, 20,375 protein-coding genes and 258.68 Mb transposable elements were identified. The chromosome-level genome assembly of M. separata provides a significant genetic resource for future studies of this insect and contributes to the development of management strategies.
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Affiliation(s)
- Chao Xu
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
- Hubei Insect Resources Utilization and Sustainable Pest Management Key Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Jichao Ji
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China.
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China.
- Western Agricultural Research Center, Chinese Academy of Agricultural Sciences, Changji, 831100, China.
| | - Xiangzhen Zhu
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China
- Western Agricultural Research Center, Chinese Academy of Agricultural Sciences, Changji, 831100, China
| | - Ningbo Huangfu
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
- Hubei Insect Resources Utilization and Sustainable Pest Management Key Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Hui Xue
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
- Hubei Insect Resources Utilization and Sustainable Pest Management Key Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Li Wang
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China
- Western Agricultural Research Center, Chinese Academy of Agricultural Sciences, Changji, 831100, China
| | - Kaixin Zhang
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China
- Western Agricultural Research Center, Chinese Academy of Agricultural Sciences, Changji, 831100, China
| | - Dongyang Li
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China
- Western Agricultural Research Center, Chinese Academy of Agricultural Sciences, Changji, 831100, China
| | - Lin Niu
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China
- Western Agricultural Research Center, Chinese Academy of Agricultural Sciences, Changji, 831100, China
| | - Ran Chen
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
- College of Agronomy, Xinjiang Agricultural University, Urumqi, 830052, China
| | - Xueke Gao
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China.
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China.
- Western Agricultural Research Center, Chinese Academy of Agricultural Sciences, Changji, 831100, China.
| | - Junyu Luo
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China.
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China.
- Western Agricultural Research Center, Chinese Academy of Agricultural Sciences, Changji, 831100, China.
| | - Jinjie Cui
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China.
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China.
- Western Agricultural Research Center, Chinese Academy of Agricultural Sciences, Changji, 831100, China.
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Cruz Plancarte D, Solórzano S. Structural and gene composition variation of the complete mitochondrial genome of Mammillaria huitzilopochtli (Cactaceae, Caryophyllales), revealed by de novo assembly. BMC Genomics 2023; 24:509. [PMID: 37653379 PMCID: PMC10468871 DOI: 10.1186/s12864-023-09607-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 08/20/2023] [Indexed: 09/02/2023] Open
Abstract
BACKGROUND Structural descriptions of complete genomes have elucidated evolutionary processes in angiosperms. In Cactaceae (Caryophyllales), a high structural diversity of the chloroplast genome has been identified within and among genera. In this study, we assembled the first mitochondrial genome (mtDNA) for the short-globose cactus Mammillaria huitzilopochtli. For comparative purposes, we used the published genomes of 19 different angiosperms and the gymnosperm Cycas taitungensis as an external group for phylogenetic issues. RESULTS The mtDNA of M. huitzilopochtli was assembled into one linear chromosome of 2,052,004 bp, in which 65 genes were annotated. These genes account for 57,606 bp including 34 protein-coding genes (PCGs), 27 tRNAs, and three rRNAs. In the non-coding sequences, repeats were abundant, with a total of 4,550 (179,215 bp). In addition, five complete genes (psaC and four tRNAs) of chloroplast origin were documented. Negative selection was estimated for most (23) of the PCGs. The phylogenetic tree showed a topology consistent with previous analyses based on the chloroplast genome. CONCLUSIONS The number and type of genes contained in the mtDNA of M. huitzilopochtli were similar to those reported in 19 other angiosperm species, regardless of their phylogenetic relationships. Although other Caryophyllids exhibit strong differences in structural arrangement and total size of mtDNA, these differences do not result in an increase in the typical number and types of genes found in M. huitzilopochtli. We concluded that the total size of mtDNA in angiosperms increases by the lengthening of the non-coding sequences rather than a significant gain of coding genes.
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Affiliation(s)
- David Cruz Plancarte
- Laboratorio de Ecología Molecular y Evolución, Universidad Nacional Autónoma de México, FES Iztacala, Avenida de los Barrios 1, Los Reyes Iztacala, Tlalnepantla de Baz, 54090, Mexico
- Posgrado en Ciencias Biológicas, UNAM, Circuito de Posgrados, Ciudad Universitaria, Coyoacán, Ciudad de México, 04510, Mexico
| | - Sofía Solórzano
- Laboratorio de Ecología Molecular y Evolución, Universidad Nacional Autónoma de México, FES Iztacala, Avenida de los Barrios 1, Los Reyes Iztacala, Tlalnepantla de Baz, 54090, Mexico.
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29
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Kapoor S, Young ND, Yang YT, Batterham P, Gasser RB, Bowles VM, Anstead CA, Perry T. Mitochondrial genomic investigation reveals a clear association between species and genotypes of Lucilia and geographic origin in Australia. Parasit Vectors 2023; 16:279. [PMID: 37573420 PMCID: PMC10423422 DOI: 10.1186/s13071-023-05902-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Accepted: 07/27/2023] [Indexed: 08/14/2023] Open
Abstract
BACKGROUND Lucilia cuprina and L. sericata (family Calliphoridae) are globally significant ectoparasites of sheep. Current literature suggests that only one of these blowfly subspecies, L. cuprina dorsalis, is a primary parasite causing myiasis (flystrike) in sheep in Australia. These species and subspecies are difficult to distinguish using morphological features. Hence, being able to accurately identify blowflies is critical for diagnosis and for understanding their relationships with their hosts and environment. METHODS In this study, adult blowflies (5 pools of 17 flies; n = 85) were collected from five locations in different states [New South Wales (NSW), Queensland (QLD), Tasmania (TAS), Victoria (VIC) and Western Australia (WA)] of Australia and their mitochondrial (mt) genomes were assembled. RESULTS Each mt genome assembled was ~ 15 kb in size and encoded 13 protein-coding genes, 2 ribosomal RNAs, 22 transfer RNAs and a control region. The Lucilia species mt genomes were conserved in structure, and the genes retained the same order and direction. The overall nucleotide composition was heavily biased towards As and Ts-77.7% of the whole genomes. Pairwise nucleotide diversity suggested divergence between Lucilia cuprina cuprina, L. c. dorsalis and L. sericata. Comparative analyses of these mt genomes with published data demonstrated that the blowflies collected from sheep farm in TAS clustered within a clade with L. sericata. The flies collected from an urban location in QLD were more closely related to L. sericata and represented the subspecies L. c. cuprina, whereas the flies collected from sheep farms in NSW, VIC and WA represented the subspecies L. c. dorsalis. CONCLUSIONS Phylogenetic analyses of the mt genomes representing Lucilia from the five geographic locations in Australia supported the previously demonstrated paraphyly of L. cuprina with respect to L. sericata and revealed that L. c. cuprina is distinct from L. c. dorsalis and that L. c. cuprina is more closely related to L. sericata than L. c. dorsalis. The mt genomes reported here provide an important molecular resource to develop tools for species- and subspecies-level identification of Lucilia from different geographical regions across Australia.
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Affiliation(s)
- Shilpa Kapoor
- Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC 3010 Australia
- Department of Veterinary Biosciences, Faculty of Science, Melbourne Veterinary School, The University of Melbourne, Building 400, Parkville, VIC 3010 Australia
| | - Neil D. Young
- Department of Veterinary Biosciences, Faculty of Science, Melbourne Veterinary School, The University of Melbourne, Building 400, Parkville, VIC 3010 Australia
| | - Ying Ting Yang
- Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC 3010 Australia
| | - Philip Batterham
- Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC 3010 Australia
| | - Robin B. Gasser
- Department of Veterinary Biosciences, Faculty of Science, Melbourne Veterinary School, The University of Melbourne, Building 400, Parkville, VIC 3010 Australia
| | - Vernon M. Bowles
- Department of Veterinary Biosciences, Faculty of Science, Melbourne Veterinary School, The University of Melbourne, Building 400, Parkville, VIC 3010 Australia
| | - Clare A. Anstead
- Department of Veterinary Biosciences, Faculty of Science, Melbourne Veterinary School, The University of Melbourne, Building 400, Parkville, VIC 3010 Australia
| | - Trent Perry
- Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC 3010 Australia
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Jin X, Du H, Zhu C, Wan H, Liu F, Ruan J, Mower JP, Zhu A. Haplotype-resolved genomes of wild octoploid progenitors illuminate genomic diversifications from wild relatives to cultivated strawberry. NATURE PLANTS 2023; 9:1252-1266. [PMID: 37537397 DOI: 10.1038/s41477-023-01473-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2022] [Accepted: 07/03/2023] [Indexed: 08/05/2023]
Abstract
Strawberry is an emerging model for studying polyploid genome evolution and rapid domestication of fruit crops. Here we report haplotype-resolved genomes of two wild octoploids (Fragaria chiloensis and Fragaria virginiana), the progenitor species of cultivated strawberry. Substantial variation is identified between species and between haplotypes. We redefine the four subgenomes and track the genetic contributions of diploid species by additional sequencing of the diploid F. nipponica genome. We provide multiple lines of evidence that F. vesca and F. iinumae, rather than other described extant species, are the closest living relatives of these wild and cultivated octoploids. In response to coexistence with quadruplicate gene copies, the octoploid strawberries have experienced subgenome dominance, homoeologous exchanges and coordinated expression of homoeologous genes. However, some homoeologues have substantially altered expression bias after speciation and during domestication. These findings enhance our understanding of the origin, genome evolution and domestication of strawberries.
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Affiliation(s)
- Xin Jin
- Germplasm Bank of Wild Species, Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Haiyuan Du
- Germplasm Bank of Wild Species, Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Chumeng Zhu
- Germplasm Bank of Wild Species, Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Hong Wan
- Horticultural Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, China
| | - Fang Liu
- Germplasm Bank of Wild Species, Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Jiwei Ruan
- Flower Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, China.
| | - Jeffrey P Mower
- Center for Plant Science Innovation, University of Nebraska, Lincoln, NE, USA.
- Department of Agronomy and Horticulture, University of Nebraska, Lincoln, NE, USA.
| | - Andan Zhu
- Germplasm Bank of Wild Species, Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China.
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Yu L, Khachaturyan M, Matschiner M, Healey A, Bauer D, Cameron B, Cusson M, Emmett Duffy J, Joel Fodrie F, Gill D, Grimwood J, Hori M, Hovel K, Hughes AR, Jahnke M, Jenkins J, Keymanesh K, Kruschel C, Mamidi S, Menning DM, Moksnes PO, Nakaoka M, Pennacchio C, Reiss K, Rossi F, Ruesink JL, Schultz ST, Talbot S, Unsworth R, Ward DH, Dagan T, Schmutz J, Eisen JA, Stachowicz JJ, Van de Peer Y, Olsen JL, Reusch TBH. Ocean current patterns drive the worldwide colonization of eelgrass (Zostera marina). NATURE PLANTS 2023; 9:1207-1220. [PMID: 37474781 PMCID: PMC10435387 DOI: 10.1038/s41477-023-01464-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Accepted: 06/21/2023] [Indexed: 07/22/2023]
Abstract
Currents are unique drivers of oceanic phylogeography and thus determine the distribution of marine coastal species, along with past glaciations and sea-level changes. Here we reconstruct the worldwide colonization history of eelgrass (Zostera marina L.), the most widely distributed marine flowering plant or seagrass from its origin in the Northwest Pacific, based on nuclear and chloroplast genomes. We identified two divergent Pacific clades with evidence for admixture along the East Pacific coast. Two west-to-east (trans-Pacific) colonization events support the key role of the North Pacific Current. Time-calibrated nuclear and chloroplast phylogenies yielded concordant estimates of the arrival of Z. marina in the Atlantic through the Canadian Arctic, suggesting that eelgrass-based ecosystems, hotspots of biodiversity and carbon sequestration, have only been present there for ~243 ky (thousand years). Mediterranean populations were founded ~44 kya, while extant distributions along western and eastern Atlantic shores were founded at the end of the Last Glacial Maximum (~19 kya), with at least one major refuge being the North Carolina region. The recent colonization and five- to sevenfold lower genomic diversity of the Atlantic compared to the Pacific populations raises concern and opportunity about how Atlantic eelgrass might respond to rapidly warming coastal oceans.
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Affiliation(s)
- Lei Yu
- Marine Evolutionary Ecology, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
| | - Marina Khachaturyan
- Marine Evolutionary Ecology, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
- Institute of General Microbiology, Kiel University, Kiel, Germany
| | - Michael Matschiner
- Department of Paleontology and Museum, University of Zurich, Zurich, Switzerland
- Natural History Museum, University of Oslo, Oslo, Norway
| | - Adam Healey
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Diane Bauer
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Brenda Cameron
- Department of Evolution and Ecology, University of California, Davis, CA, USA
| | - Mathieu Cusson
- Département des sciences fondamentales, Université du Québec à Chicoutimi, Chicoutimi, Quebec, Canada
| | - J Emmett Duffy
- Tennenbaum Marine Observatories Network, Smithsonian Environmental Research Center, Edgewater, MD, USA
| | - F Joel Fodrie
- Institute of Marine Sciences (UNC-CH), Morehead City, NC, USA
| | - Diana Gill
- Marine Evolutionary Ecology, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
| | - Jane Grimwood
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Masakazu Hori
- Japan Fisheries Research and Education Agency, Yokohama, Japan
| | - Kevin Hovel
- Department of Biology, San Diego State University, San Diego, CA, USA
| | | | - Marlene Jahnke
- Tjärnö Marine Laboratory, Department of Marine Sciences, University of Gothenburg, Strömstad, Sweden
| | - Jerry Jenkins
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Keykhosrow Keymanesh
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | | | - Sujan Mamidi
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | | | - Per-Olav Moksnes
- Department of Marine Sciences, University of Gothenburg, Gothenburg, Sweden
| | | | - Christa Pennacchio
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | | | - Francesca Rossi
- Department of Integrative Marine Ecology (EMI), Stazione Zoologica Anton Dohrn-National Institute of Marine Biology, Ecology and Biotechnology, Genoa, Italy
| | | | | | - Sandra Talbot
- Far Northwestern Institute of Art and Science, Anchorage, AK, USA
| | - Richard Unsworth
- Department of Biosciences, Swansea University, Swansea, UK
- Project Seagrass, the Yard, Bridgend, UK
| | - David H Ward
- US Geological Survey, Alaska Science Center, Anchorage, AK, USA
| | - Tal Dagan
- Institute of General Microbiology, Kiel University, Kiel, Germany
| | - Jeremy Schmutz
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Jonathan A Eisen
- Department of Evolution and Ecology, University of California, Davis, CA, USA
| | - John J Stachowicz
- Department of Evolution and Ecology, University of California, Davis, CA, USA
- Center for Population Biology, University of California, Davis, CA, USA
| | - Yves Van de Peer
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Gent, Belgium
- Center for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
- College of Horticulture, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing, China
- VIB-UGent Center for Plant Systems Biology, Gent, Belgium
| | - Jeanine L Olsen
- Groningen Institute for Evolutionary Life Sciences, Groningen, The Netherlands
| | - Thorsten B H Reusch
- Marine Evolutionary Ecology, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany.
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Tanaka H, Hori T, Yamamoto S, Toyoda A, Yano K, Yamane K, Itoh T. Haplotype-resolved chromosomal-level assembly of wasabi (Eutrema japonicum) genome. Sci Data 2023; 10:441. [PMID: 37433828 DOI: 10.1038/s41597-023-02356-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Accepted: 06/30/2023] [Indexed: 07/13/2023] Open
Abstract
In Japan, wasabi (Eutrema japonicum) is an important traditional condiment, and is recognized as an endemic species. In the present study, we generated a chromosome-level and haplotype-resolved reference genome for E. japonicum using PacBio CLR (continuous long reads), Illumina, and Hi-C sequencing data. The genome consists of 28 chromosomes that contain 1,512.1 Mb of sequence data, with a scaffold N50 length of 55.67 Mb. We also reported the subgenome and haplotype assignment of the 28 chromosomes by read-mapping and phylogenic analysis. Three validation methods (Benchmarking Universal Single-Copy Orthologs, Merqury, and Inspector) indicated that our obtained genome sequences were a high-quality and high-completeness genome assembly. Comparison of genome assemblies from previously published genomes showed that our obtained genome was of higher quality. Therefore, our genome will serve as a valuable genetic resource for both chemical ecology and evolution research of the genera Eutrema and Brassicaceae, as well as for wasabi breeding.
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Affiliation(s)
- Hiroyuki Tanaka
- School of Life Science and Technology, Tokyo Institute of Technology, Meguro-ku, Tokyo, 152-8550, Japan
| | - Tatsuki Hori
- School of Life Science and Technology, Tokyo Institute of Technology, Meguro-ku, Tokyo, 152-8550, Japan
| | - Shohei Yamamoto
- Gifu University, Faculty of Applied Biological Sciences, 1-1 Yanagido, Gifu City, Gifu, 501-1193, Japan
| | - Atsushi Toyoda
- Comparative Genomics Laboratory, National Institute of Genetics, Mishima, Shizuoka, 411-8540, Japan
| | - Kentaro Yano
- Department of Biological Sciences, Tokyo Metropolitan University, Tokyo, 192-0397, Japan
| | - Kyoko Yamane
- Gifu University, Faculty of Applied Biological Sciences, 1-1 Yanagido, Gifu City, Gifu, 501-1193, Japan.
| | - Takehiko Itoh
- School of Life Science and Technology, Tokyo Institute of Technology, Meguro-ku, Tokyo, 152-8550, Japan.
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Guo X, Wang F, Fang D, Lin Q, Sahu SK, Luo L, Li J, Chen Y, Dong S, Chen S, Liu Y, Luo S, Guo Y, Liu H. The genome of Acorus deciphers insights into early monocot evolution. Nat Commun 2023; 14:3662. [PMID: 37339966 DOI: 10.1038/s41467-023-38836-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 05/17/2023] [Indexed: 06/22/2023] Open
Abstract
Acorales is the sister lineage to all the other extant monocot plants. Genomic resource enhancement of this genus can help to reveal early monocot genomic architecture and evolution. Here, we assemble the genome of Acorus gramineus and reveal that it has ~45% fewer genes than the majority of monocots, although they have similar genome size. Phylogenetic analyses based on both chloroplast and nuclear genes consistently support that A. gramineus is the sister to the remaining monocots. In addition, we assemble a 2.2 Mb mitochondrial genome and observe many genes exhibit higher mutation rates than that of most angiosperms, which could be the reason leading to the controversies of nuclear genes- and mitochondrial genes-based phylogenetic trees existing in the literature. Further, Acorales did not experience tau (τ) whole-genome duplication, unlike majority of monocot clades, and no large-scale gene expansion is observed. Moreover, we identify gene contractions and expansions likely linking to plant architecture, stress resistance, light harvesting, and essential oil metabolism. These findings shed light on the evolution of early monocots and genomic footprints of wetland plant adaptations.
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Affiliation(s)
- Xing Guo
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, Guangdong, 518083, PR China
| | - Fang Wang
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, Guangdong, 518083, PR China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, PR China
| | - Dongming Fang
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, Guangdong, 518083, PR China
| | - Qiongqiong Lin
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, Guangdong, 518083, PR China
- College of Life Science, South China Agricultural University, Guangzhou, Guangdong, 510642, PR China
| | - Sunil Kumar Sahu
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, Guangdong, 518083, PR China
| | - Liuming Luo
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, Guangdong, 518083, PR China
- College of Life Science, South China Agricultural University, Guangzhou, Guangdong, 510642, PR China
| | - Jiani Li
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, Guangdong, 518083, PR China
- College of Life Sciences, Northwest University, Xi'an, Shaanxi, 710069, PR China
| | - Yewen Chen
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, Guangdong, 518083, PR China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, PR China
| | - Shanshan Dong
- Key Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Sciences, Shenzhen, Guangdong, 518004, PR China
| | - Sisi Chen
- Key Laboratory of Plant Resource Conservation and Sustainable Utilization, The Chinese Academy of Sciences, South China Botanical Garden, Guangzhou, Guangdong, 510650, PR China
| | - Yang Liu
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, Guangdong, 518083, PR China
- Key Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Sciences, Shenzhen, Guangdong, 518004, PR China
| | - Shixiao Luo
- Key Laboratory of Plant Resource Conservation and Sustainable Utilization, The Chinese Academy of Sciences, South China Botanical Garden, Guangzhou, Guangdong, 510650, PR China
| | - Yalong Guo
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, PR China
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, PR China
| | - Huan Liu
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, Guangdong, 518083, PR China.
- BGI Life Science Joint Research Center, Northeast Forestry University, Harbin, Heilongjiang, 150040, PR China.
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Lee Y, Cho CH, Noh C, Yang JH, Park SI, Lee YM, West JA, Bhattacharya D, Jo K, Yoon HS. Origin of minicircular mitochondrial genomes in red algae. Nat Commun 2023; 14:3363. [PMID: 37291154 PMCID: PMC10250338 DOI: 10.1038/s41467-023-39084-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 05/30/2023] [Indexed: 06/10/2023] Open
Abstract
Eukaryotic organelle genomes are generally of conserved size and gene content within phylogenetic groups. However, significant variation in genome structure may occur. Here, we report that the Stylonematophyceae red algae contain multipartite circular mitochondrial genomes (i.e., minicircles) which encode one or two genes bounded by a specific cassette and a conserved constant region. These minicircles are visualized using fluorescence microscope and scanning electron microscope, proving the circularity. Mitochondrial gene sets are reduced in these highly divergent mitogenomes. Newly generated chromosome-level nuclear genome assembly of Rhodosorus marinus reveals that most mitochondrial ribosomal subunit genes are transferred to the nuclear genome. Hetero-concatemers that resulted from recombination between minicircles and unique gene inventory that is responsible for mitochondrial genome stability may explain how the transition from typical mitochondrial genome to minicircles occurs. Our results offer inspiration on minicircular organelle genome formation and highlight an extreme case of mitochondrial gene inventory reduction.
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Affiliation(s)
- Yongsung Lee
- Department of Biological Sciences, Sungkyunkwan University, Suwon, 16419, Korea
| | - Chung Hyun Cho
- Department of Biological Sciences, Sungkyunkwan University, Suwon, 16419, Korea
| | - Chanyoung Noh
- Department of Chemistry, Sogang University, Seoul, 04107, Korea
| | - Ji Hyun Yang
- Department of Biological Sciences, Sungkyunkwan University, Suwon, 16419, Korea
| | - Seung In Park
- Department of Biological Sciences, Sungkyunkwan University, Suwon, 16419, Korea
| | - Yu Min Lee
- Department of Biological Sciences, Sungkyunkwan University, Suwon, 16419, Korea
| | - John A West
- School of Biosciences 2, University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Debashish Bhattacharya
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, 08901, USA
| | - Kyubong Jo
- Department of Chemistry, Sogang University, Seoul, 04107, Korea.
| | - Hwan Su Yoon
- Department of Biological Sciences, Sungkyunkwan University, Suwon, 16419, Korea.
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Castro AA, Nunes R, Carvalho LR, Targueta CP, Dos Santos Braga-Ferreira R, de Melo-Ximenes AA, Corvalán LCJ, Bertoni BW, Pereira AMS, de Campos Telles MP. Chloroplast genome characterization of Uncaria guianensis and Uncaria tomentosa and evolutive dynamics of the Cinchonoideae subfamily. Sci Rep 2023; 13:8390. [PMID: 37225737 DOI: 10.1038/s41598-023-34334-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Accepted: 04/27/2023] [Indexed: 05/26/2023] Open
Abstract
Uncaria species are used in traditional medicine and are considered of high therapeutic value and economic importance. This work describes the assembly and annotation of the chloroplast genomes of U. guianensis and U. tomentosa, as well as a comparative analysis. The genomes were sequenced on MiSeq Illumina, assembled with NovoPlasty, and annotated using CHLOROBOX GeSeq. Addictionaly, comparative analysis were performed with six species from NCBI databases and primers were designed in Primer3 for hypervariable regions based on the consensus sequence of 16 species of the Rubiaceae family and validated on an in-silico PCR in OpenPrimeR. The genome size of U. guianensis and U. tomentosa was 155,505 bp and 156,390 bp, respectively. Both Species have 131 genes and GC content of 37.50%. The regions rpl32-ccsA, ycf1, and ndhF-ccsA showed the three highest values of nucleotide diversity within the species of the Rubiaceae family and within the Uncaria genus, these regions were trnH-psbA, psbM-trnY, and rps16-psbK. Our results indicates that the primer of the region ndhA had an amplification success for all species tested and can be promising for usage in the Rubiaceae family. The phylogenetic analysis recovered a congruent topology to APG IV. The gene content and the chloroplast genome structure of the analyzed species are conserved and most of the genes are under negative selection. We provide the cpDNA of Neotropical Uncaria species, an important genomic resource for evolutionary studies of the group.
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Affiliation(s)
- Andrezza Arantes Castro
- Laboratório de Genética and Biodiversidade (LGBio), Instituto de Ciências Biológicas - Universidade Federal de Goiás (UFG), Goiânia, GO, 74045-155, Brazil
| | - Rhewter Nunes
- Laboratório de Genética and Biodiversidade (LGBio), Instituto de Ciências Biológicas - Universidade Federal de Goiás (UFG), Goiânia, GO, 74045-155, Brazil.
- Instituto Federal de Goiás - Campus Cidade de Goiás (IFG), Goiás, GO, 74600-000, Brazil.
| | - Larissa Resende Carvalho
- Laboratório de Genética and Biodiversidade (LGBio), Instituto de Ciências Biológicas - Universidade Federal de Goiás (UFG), Goiânia, GO, 74045-155, Brazil
| | - Cíntia Pelegrineti Targueta
- Laboratório de Genética and Biodiversidade (LGBio), Instituto de Ciências Biológicas - Universidade Federal de Goiás (UFG), Goiânia, GO, 74045-155, Brazil
| | - Ramilla Dos Santos Braga-Ferreira
- Laboratório de Genética and Biodiversidade (LGBio), Instituto de Ciências Biológicas - Universidade Federal de Goiás (UFG), Goiânia, GO, 74045-155, Brazil
| | - Amanda Alves de Melo-Ximenes
- Laboratório de Genética and Biodiversidade (LGBio), Instituto de Ciências Biológicas - Universidade Federal de Goiás (UFG), Goiânia, GO, 74045-155, Brazil
| | - Leonardo Carlos Jeronimo Corvalán
- Laboratório de Genética and Biodiversidade (LGBio), Instituto de Ciências Biológicas - Universidade Federal de Goiás (UFG), Goiânia, GO, 74045-155, Brazil
| | | | | | - Mariana Pires de Campos Telles
- Laboratório de Genética and Biodiversidade (LGBio), Instituto de Ciências Biológicas - Universidade Federal de Goiás (UFG), Goiânia, GO, 74045-155, Brazil
- Escola de Ciências Médicas e da Vida, Pontifícia Universidade Católica de Goiás (PUC - GO), Goiânia, GO, 74605-050, Brazil
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36
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Kiefer JST, Bauer E, Okude G, Fukatsu T, Kaltenpoth M, Engl T. Cuticle supplementation and nitrogen recycling by a dual bacterial symbiosis in a family of xylophagous beetles. THE ISME JOURNAL 2023:10.1038/s41396-023-01415-y. [PMID: 37085551 DOI: 10.1038/s41396-023-01415-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 04/05/2023] [Accepted: 04/12/2023] [Indexed: 04/23/2023]
Abstract
Many insects engage in stable nutritional symbioses with bacteria that supplement limiting essential nutrients to their host. While several plant sap-feeding Hemipteran lineages are known to be simultaneously associated with two or more endosymbionts with complementary biosynthetic pathways to synthesize amino acids or vitamins, such co-obligate symbioses have not been functionally characterized in other insect orders. Here, we report on the characterization of a dual co-obligate, bacteriome-localized symbiosis in a family of xylophagous beetles using comparative genomics, fluorescence microscopy, and phylogenetic analyses. Across the beetle family Bostrichidae, most investigated species harbored the Bacteroidota symbiont Shikimatogenerans bostrichidophilus that encodes the shikimate pathway to produce tyrosine precursors in its severely reduced genome, likely supplementing the beetles' cuticle biosynthesis, sclerotisation, and melanisation. One clade of Bostrichid beetles additionally housed the co-obligate symbiont Bostrichicola ureolyticus that is inferred to complement the function of Shikimatogenerans by recycling urea and provisioning the essential amino acid lysine, thereby providing additional benefits on nitrogen-poor diets. Both symbionts represent ancient associations within the Bostrichidae that have subsequently experienced genome erosion and co-speciation with their hosts. While Bostrichicola was repeatedly lost, Shikimatogenerans has been retained throughout the family and exhibits a perfect pattern of co-speciation. Our results reveal that co-obligate symbioses with complementary metabolic capabilities occur beyond the well-known sap-feeding Hemiptera and highlight the importance of symbiont-mediated cuticle supplementation and nitrogen recycling for herbivorous beetles.
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Affiliation(s)
- Julian Simon Thilo Kiefer
- Department of Evolutionary Ecology, Institute of Organismic and Molecular Evolution, Johannes Gutenberg-University, Mainz, Germany
| | - Eugen Bauer
- Department of Evolutionary Ecology, Institute of Organismic and Molecular Evolution, Johannes Gutenberg-University, Mainz, Germany
| | - Genta Okude
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, 305-8566, Japan
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Tokyo, 113-0033, Japan
| | - Takema Fukatsu
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, 305-8566, Japan
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Tokyo, 113-0033, Japan
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, 305-8571, Japan
| | - Martin Kaltenpoth
- Department of Evolutionary Ecology, Institute of Organismic and Molecular Evolution, Johannes Gutenberg-University, Mainz, Germany
- Department of Insect Symbiosis, Max-Planck-Institute for Chemical Ecology, Jena, Germany
| | - Tobias Engl
- Department of Evolutionary Ecology, Institute of Organismic and Molecular Evolution, Johannes Gutenberg-University, Mainz, Germany.
- Department of Insect Symbiosis, Max-Planck-Institute for Chemical Ecology, Jena, Germany.
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37
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Saini JS, Manni M, Hassler C, Cable RN, Duhaime MB, Zdobnov EM. Genomic insights into the coupling of a Chlorella-like microeukaryote and sulfur bacteria in the chemocline of permanently stratified Lake Cadagno. THE ISME JOURNAL 2023; 17:903-915. [PMID: 37031343 DOI: 10.1038/s41396-023-01396-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 03/14/2023] [Accepted: 03/16/2023] [Indexed: 04/10/2023]
Abstract
Meromictic Lake Cadagno is a permanently stratified system with a persistent microbial bloom within the oxic-anoxic boundary called the chemocline. The association between oxygenic and anoxygenic photosynthesis within the chemocline has been known for at least two decades. Although anoxygenic purple and green sulfur bacteria have been well studied, reports on oxygenic phytoplankton have remained sparse since their discovery in the 1920s. Nearly a century later, this study presents the first near-complete genome of a photosynthetic microbial eukaryote from the chemocline of Lake Cadagno, provisionally named Chlorella-like MAG. The 18.9 Mbp nuclear genome displays a high GC content (71.5%), and the phylogenetic placement suggests that it is a novel species of the genus Chlorella of Chlorophytes. Functional annotation of the Chlorella-like metagenome-assembled genome predicted 10,732 protein-coding genes, with an approximate 0.6% proportion potentially involved in carbon, sulfur, and nitrogen (C, N, and S) metabolism. In addition to C4 photosynthesis, this study detected genes for heat shock proteins (HSPs) in the Chlorella-like algae, consistent with the other Chlorella species. Altogether, the genomic insights in this study suggest the cooperation of photosynthetic algae with phototrophic sulfur bacteria via C, N, and S metabolism, which may aid their collective persistence in the Lake Cadagno chemocline. Furthermore, this work additionally presents the chloroplast genome of Cryptomonas-like species, which was likely to be presumed as cyanobacteria in previous studies because of the presence of phycobilisomes.
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Affiliation(s)
- Jaspreet S Saini
- Department F.-A Forel for Environmental and Aquatic Sciences, Earth and Environmental Sciences, University of Geneva, Geneva, Switzerland.
- Department of Genetic Medicine and Development, University of Geneva, Geneva, Switzerland.
- Swiss Institute of Bioinformatics, Lausanne, Switzerland.
- Laboratory for Environmental Biotechnology, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.
| | - Mosè Manni
- Department of Genetic Medicine and Development, University of Geneva, Geneva, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Christel Hassler
- Department F.-A Forel for Environmental and Aquatic Sciences, Earth and Environmental Sciences, University of Geneva, Geneva, Switzerland
- Institute of Earth Sciences, University of Lausanne, Lausanne, Switzerland
| | - Rachel N Cable
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA
| | - Melissa B Duhaime
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA
| | - Evgeny M Zdobnov
- Department of Genetic Medicine and Development, University of Geneva, Geneva, Switzerland.
- Swiss Institute of Bioinformatics, Lausanne, Switzerland.
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38
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Li Q, Xiao W, Wu P, Zhang T, Xiang P, Wu Q, Zou L, Gui M. The first two mitochondrial genomes from Apiotrichum reveal mitochondrial evolution and different taxonomic assignment of Trichosporonales. IMA Fungus 2023; 14:7. [PMID: 37004131 PMCID: PMC10064765 DOI: 10.1186/s43008-023-00112-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 03/21/2023] [Indexed: 04/03/2023] Open
Abstract
Apiotrichum is a diverse anamorphic basidiomycetous yeast genus, and its mitogenome characterization has not been revealed. In this study, we assembled two Apiotrichum mitogenomes and compared them with mitogenomes from Agaricomycotina, Pucciniomycotina and Ustilaginomycotina. The mitogenomes of Apiotrichum gracile and A. gamsii comprised circular DNA molecules, with sizes of 34,648 bp and 38,096 bp, respectively. Intronic regions were found contributed the most to the size expansion of A. gamsii mitogenome. Comparative mitogenomic analysis revealed that 6.85-38.89% of nucleotides varied between tRNAs shared by the two Apiotrichum mitogenomes. The GC content of all core PCGs in A. gamsii was lower than that of A. gracile, with an average low value of 4.97%. The rps3 gene differentiated the most among Agaricomycotina, Pucciniomycotina and Ustilaginomycotina species, while nad4L gene was the most conserved in evolution. The Ka/Ks values for cob and rps3 genes were > 1, indicating the two genes may be subjected to positive selection in Agaricomycotina, Pucciniomycotina and Ustilaginomycotina. Frequent intron loss/gain events and potential intron transfer events have been detected in evolution of Agaricomycotina, Pucciniomycotina and Ustilaginomycotina. We further detected large-scale gene rearrangements between the 19 mitogenomes from Agaricomycotina, Pucciniomycotina and Ustilaginomycotina, and fifteen of the 17 mitochondrial genes shared by Apiotrichum varied in gene arrangements. Phylogenetic analyses based on maximum likelihood and Bayesian inference methods using a combined mitochondrial gene dataset revealed different taxonomic assignment of two Apiotrichum species, wherein A. gamsii had a more closely relationship with Trichosporon asahii. This study served as the first report on mitogenomes from the genus Apiotrichum, which promotes the understanding of evolution, genomics, and phylogeny of Apiotrichum.
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Affiliation(s)
- Qiang Li
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, School of Food and Biological Engineering, Chengdu University, Chengdu, Sichuan, China
| | - Wenqi Xiao
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, School of Food and Biological Engineering, Chengdu University, Chengdu, Sichuan, China
| | - Peng Wu
- Yunnan Plateau Characteristic Agricultural Industry Research Institute, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Ting Zhang
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, School of Food and Biological Engineering, Chengdu University, Chengdu, Sichuan, China
| | - Peng Xiang
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, School of Food and Biological Engineering, Chengdu University, Chengdu, Sichuan, China
| | - Qian Wu
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, School of Food and Biological Engineering, Chengdu University, Chengdu, Sichuan, China
| | - Liang Zou
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, School of Food and Biological Engineering, Chengdu University, Chengdu, Sichuan, China.
- School of Food and Biological Engineering, Chengdu University, 2025 # Chengluo Avenue, Chengdu, 610106, Sichuan, China.
| | - Mingying Gui
- Yunnan Plateau Characteristic Agricultural Industry Research Institute, Yunnan Agricultural University, Kunming, Yunnan, China.
- School of Food and Biological Engineering, Chengdu University, 2025 # Chengluo Avenue, Chengdu, 610106, Sichuan, China.
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Li Z, Qing Y, Cui G, Li M, Liu T, Zeng Y, Zhou C, Hu X, Jiang J, Wang D, Gao Y, Zhang J, Cai C, Wang T, Wan C. Shotgun metagenomics reveals abnormal short-chain fatty acid-producing bacteria and glucose and lipid metabolism of the gut microbiota in patients with schizophrenia. Schizophr Res 2023; 255:59-66. [PMID: 36965360 DOI: 10.1016/j.schres.2023.03.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 01/11/2023] [Accepted: 03/03/2023] [Indexed: 03/27/2023]
Abstract
Evidence has shown that the gut microbiota is closely related to the pathogenesis of schizophrenia, but temporal changes in the gut microbiota of patients with schizophrenia (SZ) during treatment remain unclear. Here, to evaluate temporal changes in the gut microbiota in schizophrenia, we performed whole-genome shotgun metagenomics on fecal samples from 36 healthy controls (HCs) and 19 baseline-period patients, and followed up with patients upon treatment. Compared to that in HCs, beta diversity in SZ was significantly distinct. The genera Bacteroides, Prevotella and Clostridium were the top 3 altered genera between SZ and HCs, and the Bacteroides-Prevotella ratio was significantly increased in SZ. Thirty-three percent of differentially abundant species were short-chain fatty acid (SCFA)-producing bacteria. Functional analysis showed that glucose and lipid metabolism of the gut microbiota was decreased in SZ compared with those in HCs. The abundances of two rate-limiting enzymes in glucose and lipid metabolism, phosphofructokinase (PFK) and acetyl-CoA carboxylase (ACC), were significantly decreased in SZ, and differentially abundant metabolism-related enzymes were significantly associated with SCFA-producing bacteria. Next, we found that the abundance of SCFA-producing bacteria also changed after treatment and that Clostridium was significantly negatively correlated with the total positive and negative syndrome scale (PANSS) score in patients. Functional analysis showed that glycoside hydrolase family 30 incrementally increased in abundance during treatment and were significantly associated with SCFA-producing bacteria. Our findings help to provide evidence for the role of gut microbiota in the occurrence and development of schizophrenia.
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Affiliation(s)
- Zhuyun Li
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, China
| | - Ying Qing
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, China
| | - Gaoping Cui
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, China
| | - Minghui Li
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, China
| | - Tiantian Liu
- Department of Bioinformatics and Biostatistics, Shanghai Jiao Tong University, Shanghai, China; SJTU-Yale Joint Center for Biostatistics and Data Science, Shanghai Jiao Tong University, Shanghai, China
| | - Yanyan Zeng
- Department of Bioinformatics and Biostatistics, Shanghai Jiao Tong University, Shanghai, China; SJTU-Yale Joint Center for Biostatistics and Data Science, Shanghai Jiao Tong University, Shanghai, China
| | - Chao Zhou
- Department of Bioinformatics and Biostatistics, Shanghai Jiao Tong University, Shanghai, China; SJTU-Yale Joint Center for Biostatistics and Data Science, Shanghai Jiao Tong University, Shanghai, China
| | - Xiaowen Hu
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, China
| | - Jie Jiang
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, China
| | - Dandan Wang
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, China
| | - Yan Gao
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, China
| | - Juan Zhang
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, China
| | - Changqun Cai
- The Fourth People's Hospital of Wuhu, Wuhu, China
| | - Tao Wang
- Department of Bioinformatics and Biostatistics, Shanghai Jiao Tong University, Shanghai, China; SJTU-Yale Joint Center for Biostatistics and Data Science, Shanghai Jiao Tong University, Shanghai, China.
| | - Chunling Wan
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, China.
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40
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Jin X, Guo X, Chen J, Li J, Zhang S, Zheng S, Wang Y, Peng Y, Zhang K, Liu Y, Liu B. The complete mitochondrial genome of Hemigrapsus sinensis (Brachyura, Grapsoidea, Varunidae) and its phylogenetic position within Grapsoidea. Genes Genomics 2023; 45:377-391. [PMID: 36346542 DOI: 10.1007/s13258-022-01319-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2022] [Accepted: 09/24/2022] [Indexed: 11/10/2022]
Abstract
BACKGROUND In this study, the complete mitogenome of Hemigrapsus sinensis was the first identified and analyzed. OBJECTIVE The complete mitochondrial genome of Hemigrapsus sinensis (Brachyura, Grapsoidea, Varunidae) and its phylogenetic position within Grapsoidea. METHODS The sample of Hemigrapsus sinensis was collected and DNA was extracted. After sequencing, NOVOPlasty was used for sequence assembly. Annotate sequences with MITOS WebServer, tRNAscan-SE2.0, and NCBI database. MEGA was used for sequence analysis and Phylosuite was used for phylogenetic tree construction. DnaSP was used to calculate Ka/Ks. RESULTS This mitochondrial genome shows that it was 15,900 bp and encoded 13 PCGs, 22 tRNA genes, two rRNA genes, and one control region. The genome composition tends to A + T (74.34%) and presents a negative GC-skew (- 0.22) and AT-skew (- 0.03). The PCGs initiation codon was the typical ATN and termination codon was the typical TAN, incomplete T or missing. The ML and BI trees showed that H. sinensis was most closely related to Hemigrapsus and clustered together with the Varunidae. And our phylogenetic trees provide proof that Ocypodoidea and Grapsoidea may be of common origin. Meanwhile, in the phylogenetic tree, parallel mixing of Chiromantes and Orisarma raised doubts over the traditional classification system. Besides, Incomplete Lineage sorting (ILS) was observed in Varunidae. In the subsequent analysis of evolution rate, we found that all of the PCGs (NAD4 was not calculated) had undergone negative selections, indicating the conservation of mitochondrial genes of H. sinensis during the evolution. CONCLUSION Therefore, researching the complete mitogenome of H. sinensis would be contributing to molecular taxonomy, phylogenetic relationship, and breeding optimization within the Grapsoidea superfamily.
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Affiliation(s)
- Xun Jin
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, Zhoushan, 316022, China.,National Engineering Research Center for Facilitated Marine Aquaculture, Marine Science and Technology College, Zhejiang Ocean University, No. 1, Haida South Road, Zhoushan, 316022, Zhejiang, China
| | - Xingle Guo
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, Zhoushan, 316022, China.,National Engineering Research Center for Facilitated Marine Aquaculture, Marine Science and Technology College, Zhejiang Ocean University, No. 1, Haida South Road, Zhoushan, 316022, Zhejiang, China
| | - Jian Chen
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, Zhoushan, 316022, China.,National Engineering Research Center for Facilitated Marine Aquaculture, Marine Science and Technology College, Zhejiang Ocean University, No. 1, Haida South Road, Zhoushan, 316022, Zhejiang, China
| | - Jiasheng Li
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, Zhoushan, 316022, China.,National Engineering Research Center for Facilitated Marine Aquaculture, Marine Science and Technology College, Zhejiang Ocean University, No. 1, Haida South Road, Zhoushan, 316022, Zhejiang, China
| | - Shufei Zhang
- Guangdong Provincial Key Laboratory of Fishery Ecology and Environment, South China Sea Fisheries Research Institute, Chinese Academy of Fisheries Sciences, Guangzhou, 510300, Guangdong, China
| | - Sixu Zheng
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, Zhoushan, 316022, China.,National Engineering Research Center for Facilitated Marine Aquaculture, Marine Science and Technology College, Zhejiang Ocean University, No. 1, Haida South Road, Zhoushan, 316022, Zhejiang, China
| | - Yunpeng Wang
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, Zhoushan, 316022, China.,National Engineering Research Center for Facilitated Marine Aquaculture, Marine Science and Technology College, Zhejiang Ocean University, No. 1, Haida South Road, Zhoushan, 316022, Zhejiang, China
| | - Ying Peng
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, Zhoushan, 316022, China.,National Engineering Research Center for Facilitated Marine Aquaculture, Marine Science and Technology College, Zhejiang Ocean University, No. 1, Haida South Road, Zhoushan, 316022, Zhejiang, China
| | - Kun Zhang
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, Zhoushan, 316022, China.,National Engineering Research Center for Facilitated Marine Aquaculture, Marine Science and Technology College, Zhejiang Ocean University, No. 1, Haida South Road, Zhoushan, 316022, Zhejiang, China
| | - Yifan Liu
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, Zhoushan, 316022, China.,National Engineering Research Center for Facilitated Marine Aquaculture, Marine Science and Technology College, Zhejiang Ocean University, No. 1, Haida South Road, Zhoushan, 316022, Zhejiang, China
| | - Bingjian Liu
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, Zhoushan, 316022, China. .,National Engineering Research Center for Facilitated Marine Aquaculture, Marine Science and Technology College, Zhejiang Ocean University, No. 1, Haida South Road, Zhoushan, 316022, Zhejiang, China.
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Feng C, Wang K, Xu W, Yang L, Wanghe K, Sun N, Wu B, Wu F, Yang L, Qiu Q, Gan X, Chen Y, He S. Monsoon boosted radiation of the endemic East Asian carps. SCIENCE CHINA. LIFE SCIENCES 2023; 66:563-578. [PMID: 36166180 DOI: 10.1007/s11427-022-2141-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 04/21/2022] [Indexed: 10/14/2022]
Abstract
Major historical events often trigger the rapid flourishing of a few lineages, which in turn shape established biodiversity patterns. How did this process occur and develop? This study provides a window into this issue. The endemic East Asian carps (EEAC) dominated the ichthyofauna of East Asia and exhibited a high degree of adaptation to monsoonal river-lake ecosystems. A series of evidence, including ecogeography, phylogenetics, and macroevolution, suggests that the EEAC is a lineage that arose with the East Asian monsoon and thrived intimately with subsequent monsoon activities. We further deduce the evolution of the EEAC and find that a range of historical events in the monsoon setting (e.g., marine transgression and regression and glacial-interglacial cycle) have further reshaped the distribution patterns of EEAC's members. Comparative genomics analyses reveal that introgressions during the initial period of EEAC radiation and innovations in the regulation of the brain and nervous system may have aided their adaptation to river-lake ecosystems in a monsoon setting, which boosted radiation. Overall, this study strengthens knowledge of the evolutionary patterns of freshwater fishes in East Asia and provides a model case for understanding the impact of major historical events on the evolution of biota.
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Affiliation(s)
- Chenguang Feng
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, 710072, China
| | - Kun Wang
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, 710072, China
| | - Wenjie Xu
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, 710072, China
| | - Liandong Yang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Kunyuan Wanghe
- Key Laboratory of Adaptation and Evolution of Plateau Biota of Chinese Academy of Sciences, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, 810008, China
| | - Ning Sun
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
- University of Chinese Academy of Sciences, Beijing, 100039, China
| | - Baosheng Wu
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, 710072, China
| | - Feixiang Wu
- Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing, 100044, China
| | - Lei Yang
- Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
| | - Qiang Qiu
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, 710072, China
| | - Xiaoni Gan
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Yiyu Chen
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
- National Natural Science Foundation of China, Beijing, 100085, China
| | - Shunping He
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.
- Center for Excellence in Animal Evolution and Genetics, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.
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42
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Adaptations of Pseudoxylaria towards a comb-associated lifestyle in fungus-farming termite colonies. THE ISME JOURNAL 2023; 17:733-747. [PMID: 36841903 PMCID: PMC10119272 DOI: 10.1038/s41396-023-01374-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Revised: 01/12/2023] [Accepted: 01/17/2023] [Indexed: 02/27/2023]
Abstract
Characterizing ancient clades of fungal symbionts is necessary for understanding the evolutionary process underlying symbiosis development. In this study, we investigated a distinct subgeneric taxon of Xylaria (Xylariaceae), named Pseudoxylaria, whose members have solely been isolated from the fungus garden of farming termites. Pseudoxylaria are inconspicuously present in active fungus gardens of termite colonies and only emerge in the form of vegetative stromata, when the fungus comb is no longer attended ("sit and wait" strategy). Insights into the genomic and metabolic consequences of their association, however, have remained sparse. Capitalizing on viable Pseudoxylaria cultures from different termite colonies, we obtained genomes of seven and transcriptomes of two Pseudoxylaria isolates. Using a whole-genome-based comparison with free-living members of the genus Xylaria, we document that the association has been accompanied by significant reductions in genome size, protein-coding gene content, and reduced functional capacities related to oxidative lignin degradation, oxidative stress responses and secondary metabolite production. Functional studies based on growth assays and fungus-fungus co-cultivations, coupled with isotope fractionation analysis, showed that Pseudoxylaria only moderately antagonizes growth of the termite food fungus Termitomyces, and instead extracts nutrients from the food fungus biomass for its own growth. We also uncovered that Pseudoxylaria is still capable of producing structurally unique metabolites, which was exemplified by the isolation of two novel metabolites, and that the natural product repertoire correlated with antimicrobial and insect antifeedant activity.
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43
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Leng M, Liu Q, Zhao HY, Yu XF, Yang MF. Complete mitochondrial genome of Gortyna guizhouensis Wu, Yang, and Han, 2022 (Lepidoptera, Noctuidae) from China. Mitochondrial DNA B Resour 2023; 8:260-263. [PMID: 36816061 PMCID: PMC9930848 DOI: 10.1080/23802359.2023.2176183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2023] Open
Abstract
Gortyna guizhouensis Wu, Yang, and Han, 2022 (Lepidoptera, Noctuidae) is a newly discovered moth species that feeds on tobacco piths during the larval stage. In this study, we sequenced and analyzed the complete mitochondrial genome (mitogenome) of G. guizhouensis larvae via next-generation sequencing. The mitogenome was 15,441 bp long with an overall A + T content of 79.1%, 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), two ribosomal RNA subunit genes and one control region. The phylogenetic tree, based on the nucleic acid sequences of 13 shared PCGs of 20 Noctuidae species, revealed that G. guizhouensis is in a well-supported clade with Striacosta albicosta.
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Affiliation(s)
- Meng Leng
- College of Tobacco Science, Guizhou University, Guiyang, China,Guizhou Provincial Key Laboratory of Tobacco Quality Research, Guiyang, China
| | - Qiong Liu
- Guizhou Tobacco Company, Bijie Branch Company, Bijie, China
| | - Hai-yan Zhao
- College of Tobacco Science, Guizhou University, Guiyang, China,Guizhou Provincial Key Laboratory of Tobacco Quality Research, Guiyang, China,CONTACT Hai-Yan Zhao ; Mao-fa Yang College of Tobacco Science, Guizhou University, Guiyang, China; Guizhou Provincial Key Laboratory of Tobacco Quality Research, Guiyang, China
| | - Xiao-fei Yu
- College of Tobacco Science, Guizhou University, Guiyang, China,Guizhou Provincial Key Laboratory of Tobacco Quality Research, Guiyang, China
| | - Mao-fa Yang
- College of Tobacco Science, Guizhou University, Guiyang, China,Institute of Entomology, Guizhou University, Guiyang, China
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44
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Hu Y, Sun Y, Zhu QH, Fan L, Li J. Poaceae Chloroplast Genome Sequencing: Great Leap Forward in Recent Ten Years. Curr Genomics 2023; 23:369-384. [PMID: 37920556 PMCID: PMC10173419 DOI: 10.2174/1389202924666221201140603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 10/02/2022] [Accepted: 10/19/2022] [Indexed: 12/11/2022] Open
Abstract
The first complete chloroplast genome of rice (Oryza sativa) was published in 1989, ushering in a new era of studies of chloroplast genomics in Poaceae. Progresses in Next-Generation Sequencing (NGS) and Third-Generation Sequencing (TGS) technologiesand in the development of genome assembly software, have significantly advanced chloroplast genomics research. Poaceae is one of the most targeted families in chloroplast genome research because of its agricultural, ecological, and economic importance. Over the last 30 years, 2,050 complete chloroplast genome sequences from 40 tribes and 282 genera have been generated, most (97%) of them in the recent ten years. The wealth of data provides the groundwork for studies on species evolution, phylogeny, genetic transformation, and other aspects of Poaceae chloroplast genomes. As a result, we have gained a deeper understanding of the properties of Poaceae chloroplast genomes. Here, we summarize the achievements of the studies of the Poaceae chloroplast genomes and envision the challenges for moving the area ahead.
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Affiliation(s)
- Yiyu Hu
- Department of Rehabilitation Medicine, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Institute of Crop Science & Institute of Bioinformatics, Zhejiang University, Hangzhou 310058, China
| | - Yanqing Sun
- Institute of Crop Science & Institute of Bioinformatics, Zhejiang University, Hangzhou 310058, China
| | - Qian-Hao Zhu
- CSIRO, Agriculture and Food, Canberra, ACT 2601, Australia
| | - Longjiang Fan
- Institute of Crop Science & Institute of Bioinformatics, Zhejiang University, Hangzhou 310058, China
| | - Jianhua Li
- Department of Rehabilitation Medicine, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
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45
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Healey AL, Piatkowski B, Lovell JT, Sreedasyam A, Carey SB, Mamidi S, Shu S, Plott C, Jenkins J, Lawrence T, Aguero B, Carrell AA, Nieto-Lugilde M, Talag J, Duffy A, Jawdy S, Carter KR, Boston LB, Jones T, Jaramillo-Chico J, Harkess A, Barry K, Keymanesh K, Bauer D, Grimwood J, Gunter L, Schmutz J, Weston DJ, Shaw AJ. Newly identified sex chromosomes in the Sphagnum (peat moss) genome alter carbon sequestration and ecosystem dynamics. NATURE PLANTS 2023; 9:238-254. [PMID: 36747050 PMCID: PMC9946827 DOI: 10.1038/s41477-022-01333-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 12/13/2022] [Indexed: 06/18/2023]
Abstract
Peatlands are crucial sinks for atmospheric carbon but are critically threatened due to warming climates. Sphagnum (peat moss) species are keystone members of peatland communities where they actively engineer hyperacidic conditions, which improves their competitive advantage and accelerates ecosystem-level carbon sequestration. To dissect the molecular and physiological sources of this unique biology, we generated chromosome-scale genomes of two Sphagnum species: S. divinum and S. angustifolium. Sphagnum genomes show no gene colinearity with any other reference genome to date, demonstrating that Sphagnum represents an unsampled lineage of land plant evolution. The genomes also revealed an average recombination rate an order of magnitude higher than vascular land plants and short putative U/V sex chromosomes. These newly described sex chromosomes interact with autosomal loci that significantly impact growth across diverse pH conditions. This discovery demonstrates that the ability of Sphagnum to sequester carbon in acidic peat bogs is mediated by interactions between sex, autosomes and environment.
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Affiliation(s)
- Adam L Healey
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA.
| | - Bryan Piatkowski
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - John T Lovell
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Avinash Sreedasyam
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Sarah B Carey
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
- Department of Crop, Soil, and Environmental Sciences, Auburn University, Auburn, AL, USA
| | - Sujan Mamidi
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Shengqiang Shu
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Chris Plott
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Jerry Jenkins
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Travis Lawrence
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Blanka Aguero
- Department of Biology, Duke University, Durham, NC, USA
| | - Alyssa A Carrell
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | | | - Jayson Talag
- Arizona Genomics Institute, University of Arizona, Tucson, AZ, USA
| | - Aaron Duffy
- Department of Biology, Duke University, Durham, NC, USA
| | - Sara Jawdy
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Kelsey R Carter
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
- Earth and Environmental Sciences Division, Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Lori-Beth Boston
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Teresa Jones
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | | | - Alex Harkess
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
- Department of Crop, Soil, and Environmental Sciences, Auburn University, Auburn, AL, USA
| | - Kerrie Barry
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Keykhosrow Keymanesh
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Diane Bauer
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Jane Grimwood
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Lee Gunter
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Jeremy Schmutz
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - David J Weston
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA.
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46
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Xue Y, Bao Y, Zhang Z, Zhao W, Xiao J, He S, Zhang G, Li Y, Zhao G, Chen R, Ma Y, Chen M, Li C, Jiang S, Zou D, Gong Z, Zhao X, Wang Y, Zhu J, Zhang Z, Zhao W, Xue Y, Bao Y, Song S, Zhang G, Ling Y, Wang Y, Yang J, Zhuang X, Duan G, Wu G, Chen X, Tian D, Li Z, Sun Y, Du Z, Hao L, Song S, Gao Y, Xiao J, Zhang Z, Bao Y, Tang B, Zhao W, Zhang Y, Zhang H, Zhang Z, Qian Q, Zhang Z, Xiao J, Kang H, Huang T, Chen X, Xia Z, Zhou X, Chao J, Tang B, Wang Z, Zhu J, Du Z, Zhang S, Xiao J, Tian W, Wang W, Zhao W, Wu S, Huang Y, Zhang M, Gong Z, Wang G, Zheng X, Zong W, Zhao W, Xing P, Li R, Liu Z, Bao Y, Lu M, Zhang Y, Yang F, Mai J, Gao Q, Xu X, Kang H, Hou L, Shang Y, Qain Q, Liu J, Jiang M, Zhang H, Bu C, Wang J, Zhang Z, Zhang Z, Zeng J, Li J, Xiao J, Pan S, Kang H, Liu X, Lin S, Yuan N, Zhang Z, Bao Y, Jia P, Zheng X, Zong W, Li Z, Sun Y, Ma Y, Xiong Z, Wu S, Yang F, Zhao W, Bu C, Du Z, Xiao J, Bao Y, Chen X, Chen T, Zhang S, Sun Y, Yu C, Tang B, Zhu J, Dong L, Zhai S, Sun Y, Chen Q, Yang X, Zhang X, Sang Z, Wang Y, Zhao Y, Chen H, Lan L, Wang Y, Zhao W, Wang A, Yu C, Wang Y, Zhang S, Ma Y, Jia Y, Zhao X, Chen M, Li C, Tian D, Tang B, Pan Y, Dong L, Liu X, Song S, Liu X, Tian D, Li C, Tang B, Wang Z, Zhang R, Pan Y, Wang Y, Zou D, Song S, Li C, Zou D, Ma L, Gong Z, Zhu J, Teng X, Li L, Li N, Cui Y, Duan G, Zhang M, Jin T, Kang H, Wang Z, Wu G, Huang T, Zhao W, Jin E, Zhang T, Zhang Z, Zhao W, Xue Y, Bao Y, Song S, Xu T, Zou D, Chen M, Niu G, Pan R, Zhu T, Chu Y, Hao L, Sang J, Pan R, Zou D, Zhang Y, Wang Z, Chen M, Zhang Y, Xu T, Yao Q, Zhu T, Niu G, Hao L, Xiong Z, Yang F, Wang G, Li R, Zong W, Zhang M, Zou D, Zhao W, Wang G, Yang F, Wu S, Zhang X, Guo X, Ma Y, Xiong Z, Li R, Li Z, Liu L, Feng C, Qin Y, Xiao J, Ma L, Jing W, Luo S, Li Z, Ma L, Jiang S, Qian Q, Zhu T, Zong W, Shang Y, Jin T, Zhang Y, Chen M, Wu Z, Chu Y, Zhang R, Luo S, Jing W, Zou D, Bao Y, Xiao J, Zhang Z, Zou D, Liu L, Qin Y, Luo S, Jing W, Li Q, Liu P, Sun Y, Ma L, Jiang S, Fan Z, Zhao W, Xiao J, Bao Y, Zhang Z, Shen WK, Guo AY, Zuo Z, Ren J, Zhang X, Xiao Y, Li X, Zhang X, Xiao Y, Li X, Liu D, Zhang C, Xue Y, Zhao Z, Jiang T, Wu W, Zhao F, Meng X, Chen M, Gou Y, Chen M, Xue Y, Peng D, Xue Y, Luo H, Gao F, Ning W, Xue Y, Liu W, Ling Y, Cao R, Zhang G, Wei Y, Xue Y, Liu CJ, Guo AY, Xie GY, Guo AY, Yuan H, Su T, Zhang YE, Zhou C, Wang P, Zhang G, Zhou Y, Chen M, Guo G, Zhang Q, Guo AY, Fu S, Tan X, Xue Y, Tang D, Xue Y, Zhang W, Xue Y, Luo M, Guo AY, Xie Y, Ren J, Miao YR, Guo AY, Zhou Y, Chen M, Guo G, Huang X, Feng Z, Xue Y, Liu CJ, Guo AY, Liao X, Gao X, Wang J, Xie G, Guo AY, Yuan C, Chen M, Yang D, Tian F, Gao G, Wu W, Chen M, Han C, Xue Y, Cui Q, Xiao C, Li CY, Luo X, Ren J, Zhang X, Xiao Y, Li X, Tang Q, Guo AY, Luo H, Gao F, Xue Y, Bao Y, Zhang Z, Zhao W, Xiao J, He S, Zhang G, Li Y, Zhao G, Chen R. Database Resources of the National Genomics Data Center, China National Center for Bioinformation in 2023. Nucleic Acids Res 2023; 51:D18-D28. [PMID: 36420893 PMCID: PMC9825504 DOI: 10.1093/nar/gkac1073] [Citation(s) in RCA: 97] [Impact Index Per Article: 97.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 10/14/2022] [Accepted: 10/27/2022] [Indexed: 11/27/2022] Open
Abstract
The National Genomics Data Center (NGDC), part of the China National Center for Bioinformation (CNCB), provides a family of database resources to support global academic and industrial communities. With the explosive accumulation of multi-omics data generated at an unprecedented rate, CNCB-NGDC constantly expands and updates core database resources by big data archive, integrative analysis and value-added curation. In the past year, efforts have been devoted to integrating multiple omics data, synthesizing the growing knowledge, developing new resources and upgrading a set of major resources. Particularly, several database resources are newly developed for infectious diseases and microbiology (MPoxVR, KGCoV, ProPan), cancer-trait association (ASCancer Atlas, TWAS Atlas, Brain Catalog, CCAS) as well as tropical plants (TCOD). Importantly, given the global health threat caused by monkeypox virus and SARS-CoV-2, CNCB-NGDC has newly constructed the monkeypox virus resource, along with frequent updates of SARS-CoV-2 genome sequences, variants as well as haplotypes. All the resources and services are publicly accessible at https://ngdc.cncb.ac.cn.
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47
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Chloroplast genome assemblies and comparative analyses of commercially important Vaccinium berry crops. Sci Rep 2022; 12:21600. [PMID: 36517490 PMCID: PMC9751094 DOI: 10.1038/s41598-022-25434-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 11/29/2022] [Indexed: 12/15/2022] Open
Abstract
Vaccinium is a large genus of shrubs that includes a handful of economically important berry crops. Given the numerous hybridizations and polyploidization events, the taxonomy of this genus has remained the subject of long debate. In addition, berries and berry-based products are liable to adulteration, either fraudulent or unintentional due to misidentification of species. The availability of more genomic information could help achieve higher phylogenetic resolution for the genus, provide molecular markers for berry crops identification, and a framework for efficient genetic engineering of chloroplasts. Therefore, in this study we assembled five Vaccinium chloroplast sequences representing the economically relevant berry types: northern highbush blueberry (V. corymbosum), southern highbush blueberry (V. corymbosum hybrids), rabbiteye blueberry (V. virgatum), lowbush blueberry (V. angustifolium), and bilberry (V. myrtillus). Comparative analyses showed that the Vaccinium chloroplast genomes exhibited an overall highly conserved synteny and sequence identity among them. Polymorphic regions included the expansion/contraction of inverted repeats, gene copy number variation, simple sequence repeats, indels, and single nucleotide polymorphisms. Based on their in silico discrimination power, we suggested variants that could be developed into molecular markers for berry crops identification. Phylogenetic analysis revealed multiple origins of highbush blueberry plastomes, likely due to the hybridization events that occurred during northern and southern highbush blueberry domestication.
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48
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Tikhonenkov DV, Mikhailov KV, Gawryluk RMR, Belyaev AO, Mathur V, Karpov SA, Zagumyonnyi DG, Borodina AS, Prokina KI, Mylnikov AP, Aleoshin VV, Keeling PJ. Microbial predators form a new supergroup of eukaryotes. Nature 2022; 612:714-719. [PMID: 36477531 DOI: 10.1038/s41586-022-05511-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 11/02/2022] [Indexed: 12/12/2022]
Abstract
Molecular phylogenetics of microbial eukaryotes has reshaped the tree of life by establishing broad taxonomic divisions, termed supergroups, that supersede the traditional kingdoms of animals, fungi and plants, and encompass a much greater breadth of eukaryotic diversity1. The vast majority of newly discovered species fall into a small number of known supergroups. Recently, however, a handful of species with no clear relationship to other supergroups have been described2-4, raising questions about the nature and degree of undiscovered diversity, and exposing the limitations of strictly molecular-based exploration. Here we report ten previously undescribed strains of microbial predators isolated through culture that collectively form a diverse new supergroup of eukaryotes, termed Provora. The Provora supergroup is genetically, morphologically and behaviourally distinct from other eukaryotes, and comprises two divergent clades of predators-Nebulidia and Nibbleridia-that are superficially similar to each other, but differ fundamentally in ultrastructure, behaviour and gene content. These predators are globally distributed in marine and freshwater environments, but are numerically rare and have consequently been overlooked by molecular-diversity surveys. In the age of high-throughput analyses, investigation of eukaryotic diversity through culture remains indispensable for the discovery of rare but ecologically and evolutionarily important eukaryotes.
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Affiliation(s)
- Denis V Tikhonenkov
- Papanin Institute for Biology of Inland Waters, Russian Academy of Sciences, Borok, Russian Federation. .,AquaBioSafe Laboratory, University of Tyumen, Tyumen, Russian Federation.
| | - Kirill V Mikhailov
- Belozersky Institute for Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russian Federation.,Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russian Federation
| | - Ryan M R Gawryluk
- Department of Biology, University of Victoria, Victoria, British Columbia, Canada
| | - Artem O Belyaev
- Papanin Institute for Biology of Inland Waters, Russian Academy of Sciences, Borok, Russian Federation.,Department of Zoology and Ecology, Penza State University, Penza, Russian Federation
| | - Varsha Mathur
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada.,Department of Zoology, University of Oxford, Oxford, UK
| | - Sergey A Karpov
- Zoological Institute, Russian Academy of Sciences, Saint Petersburg, Russian Federation.,Department of Invertebrate Zoology, Faculty of Biology, Saint Petersburg State University, Saint Petersburg, Russian Federation
| | - Dmitry G Zagumyonnyi
- Papanin Institute for Biology of Inland Waters, Russian Academy of Sciences, Borok, Russian Federation.,AquaBioSafe Laboratory, University of Tyumen, Tyumen, Russian Federation
| | - Anastasia S Borodina
- Papanin Institute for Biology of Inland Waters, Russian Academy of Sciences, Borok, Russian Federation.,Department of Zoology and Parasitology, Voronezh State University, Voronezh, Russian Federation
| | - Kristina I Prokina
- Papanin Institute for Biology of Inland Waters, Russian Academy of Sciences, Borok, Russian Federation.,Ecologie Systématique Evolution, CNRS, Université Paris-Saclay, AgroParisTech, Gif-sur-Yvette, France
| | - Alexander P Mylnikov
- Papanin Institute for Biology of Inland Waters, Russian Academy of Sciences, Borok, Russian Federation
| | - Vladimir V Aleoshin
- Belozersky Institute for Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russian Federation.,Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russian Federation
| | - Patrick J Keeling
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
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49
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Milián-García Y, Hempel CA, Janke LAA, Young RG, Furukawa-Stoffer T, Ambagala A, Steinke D, Hanner RH. Mitochondrial genome sequencing, mapping, and assembly benchmarking for Culicoides species (Diptera: Ceratopogonidae). BMC Genomics 2022; 23:584. [PMID: 35962326 PMCID: PMC9375341 DOI: 10.1186/s12864-022-08743-x] [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: 01/06/2022] [Accepted: 07/05/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Mitochondrial genomes are the most sequenced genomes after bacterial and fungal genomic DNA. However, little information on mitogenomes is available for multiple metazoan taxa, such as Culicoides, a globally distributed, megadiverse genus containing 1,347 species. AIM Generating novel mitogenomic information from single Culicoides sonorensis and C. biguttatus specimens, comparing available mitogenome mapping and de novo assembly tools, and identifying the best performing strategy and tools for Culicoides species. RESULTS We present two novel and fully annotated mitochondrial haplotypes for two Culicoides species, C. sonorensis and C. biguttatus. We also annotated or re-annotated the only available reference mitogenome for C. sonorensis and C. arakawae. All species present a high similarity in mitogenome organization. The general gene arrangement for all Culicoides species was identical to the ancestral insect mitochondrial genome. Only short spacers were found in C. sonorensis (up to 30 bp), contrary to C. biguttatus (up to 114 bp). The mitochondrial genes ATP8, NAD2, NAD6, and LSU rRNA exhibited the highest nucleotide diversity and pairwise interspecific p genetic distance, suggesting that these genes might be suitable and complementary molecular barcodes for Culicoides identification in addition to the commonly utilized COI gene. We observed performance differences between the compared mitogenome generation strategies. The mapping strategy outperformed the de novo assembly strategy, but mapping results were partially biased in the absence of species-specific reference mitogenome. Among the utilized tools, BWA performed best for C. sonorensis while SPAdes, MEGAHIT, and MitoZ were among the best for C. biguttatus. The best-performing mitogenome annotator was MITOS2. Additionally, we were able to recover exogenous mitochondrial DNA from Bos taurus (biting midges host) from a C. biguttatus blood meal sample. CONCLUSIONS Two novel annotated mitogenome haplotypes for C. sonorensis and C. biguttatus using High-Throughput Sequencing are presented. Current results are useful as the baseline for mitogenome reconstruction of the remaining Culicoides species from single specimens to HTS and genome annotation. Mapping to a species-specific reference mitogenome generated better results for Culicoides mitochondrial genome reconstruction than de novo assembly, while de novo assembly resulted better in the absence of a closely related reference mitogenome. These results have direct implications for molecular-based identification of these vectors of human and zoonotic diseases, setting the basis for using the whole mitochondrial genome as a marker in Culicoides identification.
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Affiliation(s)
- Yoamel Milián-García
- Department of Integrative Biology, University of Guelph, 50 Stone Rd E, Guelph, ON, N1G 2W1, Canada.
| | - Christopher A Hempel
- Department of Integrative Biology, University of Guelph, 50 Stone Rd E, Guelph, ON, N1G 2W1, Canada
| | - Lauren A A Janke
- Department of Integrative Biology, University of Guelph, 50 Stone Rd E, Guelph, ON, N1G 2W1, Canada.,John H. Daniels Faculty of Architecture, Landscape, and Design, University of Toronto, 33 Willcocks Street, Toronto, ON, M5S 3B3, Canada
| | - Robert G Young
- Department of Integrative Biology, University of Guelph, 50 Stone Rd E, Guelph, ON, N1G 2W1, Canada
| | - Tara Furukawa-Stoffer
- Canadian Food Inspection Agency, National Centre for Animal Disease, 225090 Township Road 9-1, Lethbridge LaboratoryLethbridge, AB, T1J 0P3, Canada
| | - Aruna Ambagala
- National Centre for Foreign Animal Disease, 1015, Arlington Street, Winnipeg, MB, R3E 3M4, Canada
| | - Dirk Steinke
- Department of Integrative Biology, University of Guelph, 50 Stone Rd E, Guelph, ON, N1G 2W1, Canada
| | - Robert H Hanner
- Department of Integrative Biology, University of Guelph, 50 Stone Rd E, Guelph, ON, N1G 2W1, Canada
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Meng YF, Wang Y, Wang M, Huang YX, Wang X. The first complete mitochondrial genome of the hawkmoth Marumba saishiuana (Lepidoptera: Sphingidae) and insights into its phylogenetic position. Mitochondrial DNA B Resour 2022; 7:1525-1527. [PMID: 36034536 PMCID: PMC9415441 DOI: 10.1080/23802359.2022.2110009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022] Open
Abstract
In this study, we sequenced and analyzed the complete mitogenome of Marumba saishiuana Okamoto, 1924. The complete mitogenome sequence of M. saishiuana is circular, 15,662 bp in size and encodes 13 protein-coding genes (PCGs), two ribosomal RNA genes (rRNAs), 22 transfer RNA genes (tRNAs), and a control region (CR). Nucleotide composition is highly biased toward A + T nucleotides (81.2%). Most of 13 PCGs initiate with the standard start codon of ATN, except cox1, which starts with CGA. Phylogenetic analyses were performed using nucleotide sequences. A total of 32 Smerinthinae species were selected. The topology based on mitogenome showed that M. saishiuana, M. gaschkewitschii, and M. sperchius formed a clade, and this indicated that M. saishiuana was a member of genus Marumba. Polyptychus trilineatus was the most closely related to genus Marumba on the phylogenetic tree reconstructed by mitogenomes.
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Affiliation(s)
- Yin-Feng Meng
- College of Biology Pharmacy and Food Engineering, Shangluo University, Shangluo, China
- Shangluo Technology & Research Institute of Chinese Medicinal Materials Integrated Pest Management, Shangluo, China
| | - Yang Wang
- College of Biology Pharmacy and Food Engineering, Shangluo University, Shangluo, China
- Shangluo Technology & Research Institute of Chinese Medicinal Materials Integrated Pest Management, Shangluo, China
| | - Mei Wang
- Wuwei Forestry and Grassland Bureau, Wuwei, China
| | - Yi-Xin Huang
- Collaborative Innovation Center of Recovery and Reconstruction of Degraded Ecosystem in Wanjiang Basin Co-founded by Anhui Province and Ministry of Education, Wuhu, China
- School of Ecology and Environment, Anhui Normal University, Wuhu, China
| | - Xu Wang
- College of Life Sciences, Anhui Provincial Key Lab. of the Conservation and Exploitation of Biological Resources, Anhui Normal University, Wuhu, China
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