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Yang M, Min T, Manda T, Yang L, Hwarari D. Genomic Survey of LRR-RLK Genes in Eriobotrya japonica and Their Expression Patterns Responding to Environmental Stresses. PLANTS (BASEL, SWITZERLAND) 2024; 13:2387. [PMID: 39273872 PMCID: PMC11397332 DOI: 10.3390/plants13172387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2024] [Revised: 08/20/2024] [Accepted: 08/23/2024] [Indexed: 09/15/2024]
Abstract
The impact of global warming is increasing and thus exacerbating environmental stresses that affect plant yield and distribution, including the Eriobotrya japonica Lindl (Loquat tree). Eriobotrya japonica, a member of the Rosaceae family, is valued not only for its nutritious fruit but also for its medicinal purposes, landscape uses, and other pharmacological benefits. Nonetheless, the productivity of Eriobotrya japonica has raised a lot of concern in the wake of adverse environmental conditions. Understanding the characteristics of the LRR-RLK gene family in loquat is crucial, as these genes play vital roles in plant stress responses. In this study, 283 LRR-RLK genes were identified in the genome of E. japonica that were randomly positioned on 17 chromosomes and 24 contigs. The 283 EjLRR-RLK proteins clustered into 21 classes and subclasses in the phylogenetic analysis based on domain and protein arrangements. Further explorations in the promoter regions of the EjLRR-RLK genes showed an abundance of cis-regulatory elements that functioned in growth and development, phytohormone, and biotic and abiotic responses. Most cis-elements were present in the biotic and abiotic responses suggesting that the EjLRR-RLK genes are invested in regulating both biotic and abiotic stresses. Additional investigations into the responses of EjLRR-RLK genes to abiotic stress using the RT-qPCR revealed that EjLRR-RLK genes respond to abiotic stress, especially heat and salt stresses. Particularly, EjapXI-1.6 and EjapI-2.5 exhibited constant upregulation in all stresses analyzed, indicating that these may take an active role in regulating abiotic stresses. Our findings suggest the pivotal functions of EjLRR-RLK genes although additional research is still required. This research aims to provide useful information relating to the characterization of EjLRR-RLK genes and their responses to environmental stresses, establishing a concrete base for the following research.
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Affiliation(s)
- Mengqi Yang
- State Key Laboratory of Tree Genetics and Breeding, College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China
| | - Tian Min
- State Key Laboratory of Tree Genetics and Breeding, College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China
| | - Teja Manda
- State Key Laboratory of Tree Genetics and Breeding, College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China
| | - Liming Yang
- State Key Laboratory of Tree Genetics and Breeding, College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China
| | - Delight Hwarari
- State Key Laboratory of Tree Genetics and Breeding, College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China
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Teterina AA, Willis JH, Baer CF, Phillips PC. Pervasive conservation of intron number and other genetic elements revealed by a chromosome-level genomic assembly of the hyper-polymorphic nematode Caenorhabditis brenneri. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.25.600681. [PMID: 38979286 PMCID: PMC11230420 DOI: 10.1101/2024.06.25.600681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
With within-species genetic diversity estimates that span the gambit of that seen across the entirety of animals, the Caenorhabditis genus of nematodes holds unique potential to provide insights into how population size and reproductive strategies influence gene and genome organization and evolution. Our study focuses on Caenorhabditis brenneri, currently known as one of the most genetically diverse nematodes within its genus and metazoan phyla. Here, we present a high-quality gapless genome assembly and annotation for C. brenneri, revealing a common nematode chromosome arrangement characterized by gene-dense central regions and repeat rich peripheral parts. Comparison of C. brenneri with other nematodes from the 'Elegans' group revealed conserved macrosynteny but a lack of microsynteny, characterized by frequent rearrangements and low correlation iof orthogroup sizes, indicative of high rates of gene turnover. We also assessed genome organization within corresponding syntenic blocks in selfing and outcrossing species, affirming that selfing species predominantly experience loss of both genes and intergenic DNA. Comparison of gene structures revealed strikingly small number of shared introns across species, yet consistent distributions of intron number and length, regardless of population size or reproductive mode, suggesting that their evolutionary dynamics are primarily reflective of functional constraints. Our study provides valuable insights into genome evolution and expands the nematode genome resources with the highly genetically diverse C. brenneri, facilitating research into various aspects of nematode biology and evolutionary processes.
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Affiliation(s)
- Anastasia A Teterina
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR, USA
- Center of Parasitology, Severtsov Institute of Ecology and Evolution RAS, Moscow, Russia
| | - John H Willis
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR, USA
| | - Charles F Baer
- Department of Biology, University of Florida, Gainesville, USA
| | - Patrick C Phillips
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR, USA
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3
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Cissé OH, Ma L, Kovacs JA. Retracing the evolution of Pneumocystis species, with a focus on the human pathogen Pneumocystis jirovecii. Microbiol Mol Biol Rev 2024; 88:e0020222. [PMID: 38587383 PMCID: PMC11332345 DOI: 10.1128/mmbr.00202-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/09/2024] Open
Abstract
SUMMARYEvery human being is presumed to be infected by the fungus Pneumocystis jirovecii at least once in his or her lifetime. This fungus belongs to a large group of species that appear to exclusively infect mammals, with P. jirovecii being the only one known to cause disease in humans. The mystery of P. jirovecii origin and speciation is just beginning to unravel. Here, we provide a review of the major steps of P. jirovecii evolution. The Pneumocystis genus likely originated from soil or plant-associated organisms during the period of Cretaceous ~165 million years ago and successfully shifted to mammals. The transition coincided with a substantial loss of genes, many of which are related to the synthesis of nutrients that can be scavenged from hosts or cell wall components that could be targeted by the mammalian immune system. Following the transition, the Pneumocystis genus cospeciated with mammals. Each species specialized at infecting its own host. Host specialization is presumably built at least partially upon surface glycoproteins, whose protogene was acquired prior to the genus formation. P. jirovecii appeared at ~65 million years ago, overlapping with the emergence of the first primates. P. jirovecii and its sister species P. macacae, which infects macaques nowadays, may have had overlapping host ranges in the distant past. Clues from molecular clocks suggest that P. jirovecii did not cospeciate with humans. Molecular evidence suggests that Pneumocystis speciation involved chromosomal rearrangements and the mounting of genetic barriers that inhibit gene flow among species.
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Affiliation(s)
- Ousmane H. Cissé
- Critical Care Medicine Department, Clinical Center, National Institutes of Health, Bethesda, Maryland, USA
| | - Liang Ma
- Critical Care Medicine Department, Clinical Center, National Institutes of Health, Bethesda, Maryland, USA
| | - Joseph A. Kovacs
- Critical Care Medicine Department, Clinical Center, National Institutes of Health, Bethesda, Maryland, USA
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Yin L, Wu R, An R, Feng Y, Qiu Y, Zhang M. Genome-wide identification, molecular evolution and expression analysis of the B-box gene family in mung bean (Vigna radiata L.). BMC PLANT BIOLOGY 2024; 24:532. [PMID: 38862892 PMCID: PMC11167828 DOI: 10.1186/s12870-024-05236-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 06/03/2024] [Indexed: 06/13/2024]
Abstract
BACKGROUND Mung bean (Vigna radiata L.) is an important warm-season grain legume. Adaptation to extreme environmental conditions, supported by evolution, makes mung bean a rich gene pool for stress tolerance traits. The exploration of resistance genes will provide important genetic resources and a theoretical basis for strengthening mung bean breeding. B-box (BBX) proteins play a major role in developmental processes and stress responses. However, the identification and analysis of the mung bean BBX gene family are still lacking. RESULTS In this study, 23 VrBBX genes were identified through comprehensive bioinformatics analysis and named based on their physical locations on chromosomes. All the VrBBXs were divided into five groups based on their phylogenetic relationships, the number of B-box they contained and whether there was an additional CONSTANS, CO-like and TOC1 (CCT) domain. Homology and collinearity analysis indicated that the BBX genes in mung bean and other species had undergone a relatively conservative evolution. Gene duplication analysis showed that only chromosomal segmental duplication contributed to the expansion of VrBBX genes and that most of the duplicated gene pairs experienced purifying selection pressure during evolution. Gene structure and motif analysis revealed that VrBBX genes clustered in the same group shared similar structural characteristics. An analysis of cis-acting elements indicated that elements related to stress and hormone responses were prevalent in the promoters of most VrBBXs. The RNA-seq data analysis and qRT-PCR of nine VrBBX genes demonstrated that VrBBX genes may play a role in response to environmental stress. Moreover, VrBBX5, VrBBX10 and VrBBX12 are important candidate genes for plant stress response. CONCLUSIONS In this study, we systematically analyzed the genomic characteristics and expression patterns of the BBX gene family under ABA, PEG and NaCl treatments. The results will help us better understand the complexity of the BBX gene family and provide valuable information for future functional characteristics of specific genes in this family.
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Affiliation(s)
- Lili Yin
- College of Agronomy and Life Sciences, Shanxi Datong University, Datong, 037009, People's Republic of China
| | - Ruigang Wu
- School of Landscape and Ecological Engineering, Hebei University of Engineering, Handan, 056038, People's Republic of China
| | - Ruilan An
- College of Agronomy and Life Sciences, Shanxi Datong University, Datong, 037009, People's Republic of China
| | - Yaxin Feng
- College of Agronomy and Life Sciences, Shanxi Datong University, Datong, 037009, People's Republic of China
| | - Yaqi Qiu
- College of Agronomy and Life Sciences, Shanxi Datong University, Datong, 037009, People's Republic of China
| | - Meiling Zhang
- Institute of Forestry and Pomology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100093, People's Republic of China.
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Tantrawatpan C, Maleewong W, Thanchomnang T, Pilap W, Agatsuma T, Andrews RH, Sithithaworn P, Saijuntha W. Intron Regions as Genetic Markers for Population Genetic Investigations of Opisthorchis viverrini sensu lato and Clonorchis sinensis. Animals (Basel) 2023; 13:3200. [PMID: 37893924 PMCID: PMC10603628 DOI: 10.3390/ani13203200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Revised: 09/27/2023] [Accepted: 10/10/2023] [Indexed: 10/29/2023] Open
Abstract
Opisthorchiasis and clonorchiasis are prevalent in Southeast and Far-East Asia, which are caused by the group 1 carcinogenic liver flukes Opisthorchis viverrini sensu lato and Clonorchis sinensis infection. There have been comprehensive investigations of systematics and genetic variation of these liver flukes. Previous studies have shown that O. viverrini is a species complex, called "O. viverrini sensu lato". More comprehensive investigations of molecular systematics and population genetics of each of the species that make up the species complex are required. Thus, other polymorphic genetic markers need to be developed. Therefore, this study aimed to characterize the intron regions of taurocyamine kinase gene (TK) to examine the genetic variation and population genetics of O. viverrini and C. sinensis collected from different geographical isolates and from a range of animal hosts. We screened seven intron regions embedded in TK. Of these, we selected an intron 5 of domain 1 (TkD1Int5) region to investigate the genetic variation and population genetics of theses liver flukes. The high nucleotide and haplotype diversity of TkD1Int5 was detected in O. viverrine. Heterozygosity with several insertion/deletion (indel) regions were detected in TkD1Int5 of the O. viverrine samples, whereas only an indel nucleotide was detected in one C. sinensis sample. Several O. viverrine samples contained three different haplotypes within a particular heterozygous sample. There were no genetic differences between C. sinensis isolated from various animal host. Heterozygous patterns specifically detected in humans was observed in C. sinensis. Thus, TkD1Int5 is a high polymorphic genetic marker, which could be an alternative marker for further population genetic investigations of these carcinogenic liver flukes and other related species from a wide geographical distribution and variety of animal hosts.
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Affiliation(s)
- Chairat Tantrawatpan
- Division of Cell Biology, Department of Preclinical Sciences, Faculty of Medicine, and Center of Excellence in Stem Cell Research, Thammasat University, Rangsit Campus, Khlong Nueng 12120, Thailand;
| | - Wanchai Maleewong
- Department of Parasitology, Faculty of Medicine, Khon Kaen University, Khon Kaen 40002, Thailand; (W.M.); (P.S.)
- Mekong Health Science Research Institute, Khon Kaen University, Khon Kaen 40002, Thailand
| | | | - Warayutt Pilap
- Walai Rukhavej Botanical Research Institute, Mahasarakham University, Kham Riang 44150, Thailand;
- Center of Excellence in Biodiversity Research, Mahasarakham University, Kham Riang 44150, Thailand
| | - Takeshi Agatsuma
- Department of Environmental Medicine, Kochi Medical School, Kochi University, Oko, Nankoku 783-8505, Kochi, Japan;
| | - Ross H. Andrews
- Department of Surgery & Cancer, Faculty of Medicine, Imperial College, South Kensington Campus, London SW7 2AZ, UK;
- Cholangiocarcinoma Research Institute, Faculty of Medicine, Khon Kaen University, Khon Kaen 40002, Thailand
| | - Paiboon Sithithaworn
- Department of Parasitology, Faculty of Medicine, Khon Kaen University, Khon Kaen 40002, Thailand; (W.M.); (P.S.)
- Cholangiocarcinoma Research Institute, Faculty of Medicine, Khon Kaen University, Khon Kaen 40002, Thailand
| | - Weerachai Saijuntha
- Faculty of Medicine, Mahasarakham University, Kham Riang 44000, Thailand;
- Center of Excellence in Biodiversity Research, Mahasarakham University, Kham Riang 44150, Thailand
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Mohri M, Moghadam A, Burketova L, Ryšánek P. Genome-wide identification of the opsin protein in Leptosphaeria maculans and comparison with other fungi (pathogens of Brassica napus). Front Microbiol 2023; 14:1193892. [PMID: 37692395 PMCID: PMC10485269 DOI: 10.3389/fmicb.2023.1193892] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2023] [Accepted: 06/28/2023] [Indexed: 09/12/2023] Open
Abstract
The largest family of transmembrane receptors are G-protein-coupled receptors (GPCRs). These receptors respond to perceived environmental signals and infect their host plants. Family A of the GPCR includes opsin. However, there is little known about the roles of GPCRs in phytopathogenic fungi. We studied opsin in Leptosphaeria maculans, an important pathogen of oilseed rape (Brassica napus) that causes blackleg disease, and compared it with six other fungal pathogens of oilseed rape. A phylogenetic tree analysis of 31 isoforms of the opsin protein showed six major groups and six subgroups. All three opsin isoforms of L. maculans are grouped in the same clade in the phylogenetic tree. Physicochemical analysis revealed that all studied opsin proteins are stable and hydrophobic. Subcellular localization revealed that most isoforms were localized in the endoplasmic reticulum membrane except for several isoforms in Verticillium species, which were localized in the mitochondrial membrane. Most isoforms comprise two conserved domains. One conserved motif was observed across all isoforms, consisting of the BACTERIAL_OPSIN_1 domain, which has been hypothesized to have an identical sensory function. Most studied isoforms showed seven transmembrane helices, except for one isoform of V. longisporum and four isoforms of Fusarium oxysporum. Tertiary structure prediction displayed a conformational change in four isoforms of F. oxysporum that presumed differences in binding to other proteins and sensing signals, thereby resulting in various pathogenicity strategies. Protein-protein interactions and binding site analyses demonstrated a variety of numbers of ligands and pockets across all isoforms, ranging between 0 and 13 ligands and 4 and 10 pockets. According to the phylogenetic analysis in this study and considerable physiochemically and structurally differences of opsin proteins among all studied fungi hypothesized that this protein acts in the pathogenicity, growth, sporulation, and mating of these fungi differently.
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Affiliation(s)
- Marzieh Mohri
- Department of Plant Protection, Faculty of Agrobiology, Food, and Natural Resources, Czech University of Life Sciences, Prague, Czechia
| | - Ali Moghadam
- Institute of Biotechnology, Shiraz University, Shiraz, Iran
| | - Lenka Burketova
- Institute of Experimental Botany, Czech Academy of Sciences, Prague, Czechia
| | - Pavel Ryšánek
- Department of Plant Protection, Faculty of Agrobiology, Food, and Natural Resources, Czech University of Life Sciences, Prague, Czechia
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Zhang MZ, Xu JP, Callac P, Chen MY, Wu Q, Wach M, Mata G, Zhao RL. Insight into the evolutionary and domesticated history of the most widely cultivated mushroom Agaricus bisporus via mitogenome sequences of 361 global strains. BMC Genomics 2023; 24:182. [PMID: 37020265 PMCID: PMC10077685 DOI: 10.1186/s12864-023-09257-w] [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: 11/15/2022] [Accepted: 03/20/2023] [Indexed: 04/07/2023] Open
Abstract
Agaricus bisporus is the most widely cultivated edible mushroom in the world with a only around three hundred years known history of cultivation. Therefore, it represents an ideal organism not only to investigate the natural evolutionary history but also the understanding on the evolution going back to the early era of domestication. In this study, we generated the mitochondrial genome sequences of 352 A. bisporus strains and 9 strains from 4 closely related species around the world. The population mitogenomic study revealed all A. bisporus strains can be divided into seven clades, and all domesticated cultivars present only in two of those clades. The molecular dating analysis showed this species origin in Europe on 4.6 Ma and we proposed the main dispersal routes. The detailed mitogenome structure studies showed that the insertion of the plasmid-derived dpo gene caused a long fragment (MIR) inversion, and the distributions of the fragments of dpo gene were strictly in correspondence with these seven clades. Our studies also showed A. bisporus population contains 30 intron distribution patterns (IDPs), while all cultivars contain only two IDPs, which clearly exhibit intron loss compared to the others. Either the loss occurred before or after domestication, that could suggest that the change facilitates their adaptation to the cultivated environment.
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Affiliation(s)
- Ming-Zhe Zhang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, No3 1St Beichen West Road, Beijing, 100101, Chaoyang District, China
- College of Life Sciences, University of Chinese Academy of Sciences, Huairou District, Beijing, 101408, China
| | - Jian-Ping Xu
- Department of Biology, McMaster University, Hamilton, ON, Canada
| | | | - Mei-Yuan Chen
- Edible Fungi Institute of Fujian Academy of Agricultural Sciences, Fuzhou, 350014, China
| | - Qi Wu
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, No3 1St Beichen West Road, Beijing, 100101, Chaoyang District, China
- College of Life Sciences, University of Chinese Academy of Sciences, Huairou District, Beijing, 101408, China
| | - Mark Wach
- Sylvan BioSciences, Kittanning, PA, 16201, USA
| | - Gerardo Mata
- Instituto de Ecología A.C. Carretera Antigua a Coatepec, 351, El Haya, 91073, Veracruz, CPXalapa, Mexico
| | - Rui-Lin Zhao
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, No3 1St Beichen West Road, Beijing, 100101, Chaoyang District, China.
- College of Life Sciences, University of Chinese Academy of Sciences, Huairou District, Beijing, 101408, China.
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Yang Y, Zhao L, Wang J, Lu N, Ma W, Ma J, Zhang Y, Fu P, Yao C, Hu J, Wang N. Genome-wide identification of DnaJ gene family in Catalpa bungei and functional analysis of CbuDnaJ49 in leaf color formation. FRONTIERS IN PLANT SCIENCE 2023; 14:1116063. [PMID: 36968394 PMCID: PMC10038198 DOI: 10.3389/fpls.2023.1116063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Accepted: 02/06/2023] [Indexed: 06/18/2023]
Abstract
DnaJs are the common molecular chaperone proteins with strong structural and functional diversity. In recent years, only several DnaJ family members have been found to be able to regulate leaf color, and it remains to be explored whether there are other potential members that also regulate this character. Here, we identified 88 putative DnaJ proteins from Catalpa bungei, and classified them into four types according to their domain. Gene-structure analysis revealed that each member of CbuDnaJ family had same or similar exon-intron structure. Chromosome mapping and collinearity analysis showed that tandem and fragment duplication occurred in the process of evolution. Promoter analyses suggested that CbuDnaJs might be involved in a variety of biological processes. The expression levels of DnaJ family members in different color leaves of Maiyuanjinqiu were respectively extracted from the differential transcriptome. Among these, CbuDnaJ49 was the largest differentially expressed gene between the green and yellow sectors. Ectopic overexpression of CbuDnaJ49 in tobacco showed that the positive transgenic seedlings exhibited albino leaves, and the contents of chlorophyll and carotenoid were significantly reduced compared with those of wild type. The results suggested that CbuDnaJ49 played an important role in regulating leaf color. This study not only identified a novel gene of DnaJ family members regulating leaf color, but also provided new germplasm for landscaping.
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Affiliation(s)
- Yingying Yang
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Key Laboratory of Tree Breeding and Cultivation of National Forestry and Grassland Administration, National Innovation Alliance of Catalpa bungei, Beijing, China
- Biotechnology Research Center of China Three Gorges University, Yichang, China
| | - Linjiao Zhao
- Hekou Yao Autonomous County Forestry and Grassland Bureau, Hekou, China
| | - Junhui Wang
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Key Laboratory of Tree Breeding and Cultivation of National Forestry and Grassland Administration, National Innovation Alliance of Catalpa bungei, Beijing, China
| | - Nan Lu
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Key Laboratory of Tree Breeding and Cultivation of National Forestry and Grassland Administration, National Innovation Alliance of Catalpa bungei, Beijing, China
| | - Wenjun Ma
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Key Laboratory of Tree Breeding and Cultivation of National Forestry and Grassland Administration, National Innovation Alliance of Catalpa bungei, Beijing, China
| | - Jiang Ma
- Biotechnology Research Center of China Three Gorges University, Yichang, China
| | - Yu Zhang
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Key Laboratory of Tree Breeding and Cultivation of National Forestry and Grassland Administration, National Innovation Alliance of Catalpa bungei, Beijing, China
| | - Pengyue Fu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Chengcheng Yao
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Key Laboratory of Tree Breeding and Cultivation of National Forestry and Grassland Administration, National Innovation Alliance of Catalpa bungei, Beijing, China
| | - Jiwen Hu
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Key Laboratory of Tree Breeding and Cultivation of National Forestry and Grassland Administration, National Innovation Alliance of Catalpa bungei, Beijing, China
| | - Nan Wang
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Key Laboratory of Tree Breeding and Cultivation of National Forestry and Grassland Administration, National Innovation Alliance of Catalpa bungei, Beijing, China
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Yu Y, Song T, Wang Y, Zhang M, Li N, Yu M, Zhang S, Zhou H, Guo S, Bu Y, Wang T, Xiang J, Zhang X. The wheat WRKY transcription factor TaWRKY1-2D confers drought resistance in transgenic Arabidopsis and wheat (Triticum aestivum L.). Int J Biol Macromol 2023; 226:1203-1217. [PMID: 36442571 DOI: 10.1016/j.ijbiomac.2022.11.234] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 11/16/2022] [Accepted: 11/20/2022] [Indexed: 11/26/2022]
Abstract
The WRKY transcription factor family has been associated with a variety of plant biological processes, such as biotic and abiotic stress responses. In this study, 13 wheat TaWRKY DEGs in transcriptome data before and after drought stress, namely TaWRKY1 to TaWRKY8, including various copies, were identified and classified as Group I, II, or III. TaWRKY1-2D overexpression enhanced drought tolerance in transgenic Arabidopsis. Moreover, the AtRD29A, AtP5CS1, AtPOD1, AtCAT1, and AtSOD (Cu/Zn) genes, which are related to the stress response and antioxidant system, were significantly upregulated in TaWRKY1-2D transgenic Arabidopsis under drought stress. TaWRKY1-2 silencing in wheat increases the MDA content, reduces the contents of proline and chlorophyll and the activities of antioxidant enzymes, and inhibits the expression levels of antioxidant (TaPOD, TaCAT, and TaSOD (Fe))- and stress-related genes (TaP5CS) under drought stress. Yeast two-hybrid screening revealed TaDHN3 as an interaction partner of TaWRKY1-2D; their interaction was further confirmed using yeast two-hybrid and bimolecular fluorescence complementation. Furthermore, TaWRKY1-2D may play essential roles in wheat drought tolerance through posttranslational regulation of TaDHN3. Overall, these findings contribute to our knowledge of the WRKY family in wheat and identify TaWRKY1-2D as a promising candidate gene for improving wheat breeding to generate drought-tolerant wheat.
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Affiliation(s)
- Yang Yu
- College of Agronomy, Northwest A&F University, Yangling, Xianyang 712100, China
| | - Tianqi Song
- College of Agronomy, Northwest A&F University, Yangling, Xianyang 712100, China
| | - Yukun Wang
- College of Agronomy, Northwest A&F University, Yangling, Xianyang 712100, China
| | - Mingfei Zhang
- Academy of Agricultural Sciences, Key Laboratory of Agro-Ecological Protection & Exploitation and Utilization of Animal and Plant Resources in Eastern Inner Mongolia, Chifeng University, Chifeng 024000, China
| | - Nan Li
- Academy of Agricultural Sciences, Key Laboratory of Agro-Ecological Protection & Exploitation and Utilization of Animal and Plant Resources in Eastern Inner Mongolia, Chifeng University, Chifeng 024000, China
| | - Ming Yu
- College of Agronomy, Northwest A&F University, Yangling, Xianyang 712100, China
| | - Shuangxing Zhang
- College of Agronomy, Northwest A&F University, Yangling, Xianyang 712100, China
| | - Hongwei Zhou
- College of Agronomy, Northwest A&F University, Yangling, Xianyang 712100, China
| | - Sihai Guo
- College of Agronomy, Northwest A&F University, Yangling, Xianyang 712100, China
| | - Yaning Bu
- College of Agronomy, Northwest A&F University, Yangling, Xianyang 712100, China
| | - Tingting Wang
- College of Agronomy, Northwest A&F University, Yangling, Xianyang 712100, China
| | - Jishan Xiang
- Academy of Agricultural Sciences, Key Laboratory of Agro-Ecological Protection & Exploitation and Utilization of Animal and Plant Resources in Eastern Inner Mongolia, Chifeng University, Chifeng 024000, China.
| | - Xiaoke Zhang
- College of Agronomy, Northwest A&F University, Yangling, Xianyang 712100, China.
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Roy SW, Gozashti L, Bowser BA, Weinstein BN, Larue GE, Corbett-Detig R. Intron-rich dinoflagellate genomes driven by Introner transposable elements of unprecedented diversity. Curr Biol 2023; 33:189-196.e4. [PMID: 36543167 DOI: 10.1016/j.cub.2022.11.046] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 06/18/2022] [Accepted: 11/18/2022] [Indexed: 12/24/2022]
Abstract
Spliceosomal introns, which interrupt nuclear genes, are ubiquitous features of eukaryotic nuclear genes.1 Spliceosomal intron evolution is complex, with different lineages ranging from virtually zero to thousands of newly created introns.2,3,4,5 This punctate phylogenetic distribution could be explained if intron creation is driven by specialized transposable elements ("Introners"), with Introner-containing lineages undergoing frequent intron gain.6,7,8,9,10 Fragmentation of nuclear genes by spliceosomal introns reaches its apex in dinoflagellates, which have some twenty introns per gene11,12; however, little is known about dinoflagellate intron evolution. We reconstructed intron evolution in five dinoflagellate genomes, revealing a dynamic history of intron gain. We find evidence for historical creation of introns in all five species and identify recently active Introners in 4/5 studied species. In one species, Polarella glacialis, we find an unprecedented diversity of Introners, with recent Introner insertion leading to creation of some 12,253 introns, and with 15 separate families of Introners accounting for at least 100 introns each. These Introner families show diverse mechanisms of moblization and intron creation. Comparison within and between Introner families provides evidence that biases in the so-called intron phase, intron position relative to codon periodicity, could be driven by Introner insertion site requirements.9,13,14 Finally, we report additional transformations of the spliceosomal system in dinoflagellates, including widespread loss of ancestral introns, and novelties of tolerated and favored donor sequence motifs. These results reveal unappreciated diversity of intron-creating elements and spliceosomal evolutionary capacity and highlight the complex evolutionary dependencies shaping genome structures.
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Affiliation(s)
- Scott William Roy
- Department of Biology, San Francisco State University, 1600 Holloway Avenue, San Francisco, CA 94132, USA; Department of Molecular and Cell Biology, University of California, Merced, 5200 North Lake Road, Merced, CA 95343, USA.
| | - Landen Gozashti
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA 95064, USA; Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Bradley A Bowser
- Department of Molecular and Cell Biology, University of California, Merced, 5200 North Lake Road, Merced, CA 95343, USA
| | - Brooke N Weinstein
- Department of Molecular and Cell Biology, University of California, Merced, 5200 North Lake Road, Merced, CA 95343, USA
| | - Graham E Larue
- Department of Molecular and Cell Biology, University of California, Merced, 5200 North Lake Road, Merced, CA 95343, USA
| | - Russell Corbett-Detig
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA 95064, USA; Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
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11
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Pant S, Huang Y. Genome-wide studies of PAL genes in sorghum and their responses to aphid infestation. Sci Rep 2022; 12:22537. [PMID: 36581623 PMCID: PMC9800386 DOI: 10.1038/s41598-022-25214-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 11/28/2022] [Indexed: 12/30/2022] Open
Abstract
Phenylalanine ammonia-lyase (PAL, EC 4.3.1.25) plays a crucial role in plant adaptation to biotic and abiotic stresses. However, the current knowledge about PAL proteins in sorghum is essentially lacking. Thus, in this study we aimed to analyze the PAL family genes in sorghum using a genome-wide approach and to explore the role of PAL genes in host plant resistance to aphids via SA-mediated defense signaling. Here, we report gene structural features of 8 PAL (SbPAL) genes in sorghum (Sorghum bicolor), their phylogeny, protein motifs and promoter analysis. Furthermore, we demonstrated that the SbPAL genes were induced by sugarcane aphid (SCA) infestation and SbPAL exhibited differential gene expression in susceptible and resistant genotypes. PAL activity assays further validated upregulated expression of the SbPAL genes in a resistant genotype. In addition, exogenous application of SA reduced plant damage and suppressed aphid population growth and fecundity in susceptible genotype, suggesting that those SbPAL genes act as positive regulator of the SA-mediated defense signaling pathway to combat aphid pests in sorghum. This study provides insights for further examination of the defense role of PAL in sorghum against other pests and pathogens.
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Affiliation(s)
- Shankar Pant
- grid.508981.dUnited States Department of Agriculture - Agricultural Research Service (USDA-ARS), Plant Science Research Laboratory, Stillwater, OK 74075 USA
| | - Yinghua Huang
- grid.508981.dUnited States Department of Agriculture - Agricultural Research Service (USDA-ARS), Plant Science Research Laboratory, Stillwater, OK 74075 USA
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12
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Gozashti L, Roy SW, Thornlow B, Kramer A, Ares M, Corbett-Detig R. Transposable elements drive intron gain in diverse eukaryotes. Proc Natl Acad Sci U S A 2022; 119:e2209766119. [PMID: 36417430 PMCID: PMC9860276 DOI: 10.1073/pnas.2209766119] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 10/19/2022] [Indexed: 11/24/2022] Open
Abstract
There is massive variation in intron numbers across eukaryotic genomes, yet the major drivers of intron content during evolution remain elusive. Rapid intron loss and gain in some lineages contrast with long-term evolutionary stasis in others. Episodic intron gain could be explained by recently discovered specialized transposons called Introners, but so far Introners are only known from a handful of species. Here, we performed a systematic search across 3,325 eukaryotic genomes and identified 27,563 Introner-derived introns in 175 genomes (5.2%). Species with Introners span remarkable phylogenetic diversity, from animals to basal protists, representing lineages whose last common ancestor dates to over 1.7 billion years ago. Aquatic organisms were 6.5 times more likely to contain Introners than terrestrial organisms. Introners exhibit mechanistic diversity but most are consistent with DNA transposition, indicating that Introners have evolved convergently hundreds of times from nonautonomous transposable elements. Transposable elements and aquatic taxa are associated with high rates of horizontal gene transfer, suggesting that this combination of factors may explain the punctuated and biased diversity of species containing Introners. More generally, our data suggest that Introners may explain the episodic nature of intron gain across the eukaryotic tree of life. These results illuminate the major source of ongoing intron creation in eukaryotic genomes.
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Affiliation(s)
- Landen Gozashti
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA95064
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA95064
| | - Scott W. Roy
- Department of Biology, San Francisco State University, San Francisco, CA94117
| | - Bryan Thornlow
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA95064
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA95064
| | - Alexander Kramer
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA95064
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA95064
| | - Manuel Ares
- Department of Molecular, Cell, and Developmental Biology, University of California Santa Cruz, Santa Cruz, CA95064
| | - Russell Corbett-Detig
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA95064
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA95064
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13
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Li F, Fan K, Guo X, Liu J, Zhang K, Lu P. Genome-wide identification, molecular evolution and expression analysis of the non-specific lipid transfer protein (nsLTP) family in Setaria italica. BMC PLANT BIOLOGY 2022; 22:547. [PMID: 36443672 PMCID: PMC9703814 DOI: 10.1186/s12870-022-03921-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/06/2022] [Accepted: 11/01/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND Foxtail millet (Setaria italica L.) is a millet species with high tolerance to stressful environments. Plant non-specific lipid transfer proteins (nsLTPs) are a kind of small, basic proteins involved in many biological processes. So far, the genome of S. italica has been fully sequenced, and a comprehensive understanding of the evolution and expression of the nsLTP family is still lacking in foxtail millet. RESULTS Forty-five nsLTP genes were identified in S. italica and clustered into 5 subfamilies except three single genes (SinsLTP38, SinsLTP7, and SinsLTP44). The proportion of SinsLTPs was different in each subfamily, and members within the same subgroup shared conserved exon-intron structures. Besides, 5 SinsLTP duplication events were investigated. Both tandem and segmental duplication contributed to nsLTP expansion in S. italica, and the duplicated SinsLTPs had mainly undergone purifying selection pressure, which suggested that the function of the duplicated SinsLTPs might not diverge much. Moreover, we identified the nsLTP members in 5 other monocots, and 41, 13, 10, 4, and 1 orthologous gene pairs were identified between S. italica and S. viridis, S. bicolor, Z. mays, O. sativa, and B. distachyon, respectively. The functional divergence within the nsLTP orthologous genes might be limited. In addition, the tissue-specific expression patterns of the SinsLTPs were investigated, and the expression profiles of the SinsLTPs in response to abiotic stress were analyzed, all the 10 selected SinsLTPs were responsive to drought, salt, and cold stress. Among the selected SinsLTPs, 2 paired duplicated genes shared almost equivalent expression profiles, suggesting that these duplicated genes might retain some essential functions during subsequent evolution. CONCLUSIONS The present study provided the first systematic analysis for the phylogenetic classification, conserved domain and gene structure, expansion pattern, and expression profile of the nsLTP family in S. italica. These findings could pave a way for further comparative genomic and evolution analysis of nsLTP family in foxtail millet and related monocots, and lay the foundation for the functional analysis of the nsLTPs in S. italica.
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Affiliation(s)
- Feng Li
- College of Agronomy and Life Sciences, Shanxi Datong University, Datong, 037009, China.
- Research and Development Center of Agricultural Facility Technology, Shanxi Datong University, Datong, 037009, China.
| | - Kai Fan
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Xuhu Guo
- College of Agronomy and Life Sciences, Shanxi Datong University, Datong, 037009, China
- Research and Development Center of Agricultural Facility Technology, Shanxi Datong University, Datong, 037009, China
| | - Jianxia Liu
- College of Agronomy and Life Sciences, Shanxi Datong University, Datong, 037009, China
- Research and Development Center of Agricultural Facility Technology, Shanxi Datong University, Datong, 037009, China
| | - Kun Zhang
- College of Agronomy and Life Sciences, Shanxi Datong University, Datong, 037009, China
- Research and Development Center of Agricultural Facility Technology, Shanxi Datong University, Datong, 037009, China
| | - Ping Lu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China.
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14
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Wan T, Gong Y, Liu Z, Zhou Y, Dai C, Wang Q. Evolution of complex genome architecture in gymnosperms. Gigascience 2022; 11:6659718. [PMID: 35946987 PMCID: PMC9364684 DOI: 10.1093/gigascience/giac078] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 06/09/2022] [Accepted: 07/15/2022] [Indexed: 11/25/2022] Open
Abstract
Gymnosperms represent an ancient lineage that diverged from early spermatophytes during the Devonian. The long fossil records and low diversity in living species prove their complex evolutionary history, which included ancient radiations and massive extinctions. Due to their ultra-large genome size, the whole-genome assembly of gymnosperms has only generated in the past 10 years and is now being further expanded into more taxonomic representations. Here, we provide an overview of the publicly available gymnosperm genome resources and discuss their assembly quality and recent findings in large genome architectures. In particular, we describe the genomic features most related to changes affecting the whole genome. We also highlight new realizations relative to repetitive sequence dynamics, paleopolyploidy, and long introns. Based on the results of relevant genomic studies of gymnosperms, we suggest additional efforts should be made toward exploring the genomes of medium-sized (5–15 gigabases) species. Lastly, more comparative analyses among high-quality assemblies are needed to understand the genomic shifts and the early species diversification of seed plants.
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Affiliation(s)
- Tao Wan
- Core Botanical Gardens/Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China.,Sino-Africa Joint Research Centre, Chinese Academy of Sciences, Wuhan 430074, China.,Key Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Science, Shenzhen 518004, China
| | - Yanbing Gong
- Department of Ecology, Tibetan Centre for Ecology and Conservation at WHU-TU, State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China.,Research Center for Ecology, College of Science, Tibet University, Lhasa 850000, China
| | - Zhiming Liu
- Key Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Science, Shenzhen 518004, China
| | - YaDong Zhou
- School of Life Science, Nanchang University, Nanchang 330031, China
| | - Can Dai
- School of Resources and Environmental Science, Hubei University, Wuhan, China
| | - Qingfeng Wang
- Core Botanical Gardens/Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China.,Sino-Africa Joint Research Centre, Chinese Academy of Sciences, Wuhan 430074, China
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15
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Deng N, Zhang Y, Ma Z, Lin R, Cheng TH, Tang H, Snyder M, Cohen S. DSIF modulates RNA polymerase II occupancy according to template G + C content. NAR Genom Bioinform 2022; 4:lqac054. [PMID: 35910045 PMCID: PMC9326580 DOI: 10.1093/nargab/lqac054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 06/03/2022] [Accepted: 07/19/2022] [Indexed: 11/12/2022] Open
Abstract
The DSIF complex comprising the Supt4h and Supt5h transcription elongation proteins clamps RNA polymerase II (RNAPII) onto DNA templates, facilitating polymerase processivity. Lowering DSIF components can differentially decrease expression of alleles containing nucleotide repeat expansions, suggesting that RNAPII transit through repeat expansions is dependent on DSIF functions. To globally identify sequence features that affect dependence of the polymerase on DSIF in human cells, we used ultra-deep ChIP-seq analysis and RNA-seq to investigate and quantify the genome-wide effects of Supt4h loss on template occupancy and transcript production. Our results indicate that RNAPII dependence on Supt4h varies according to G + C content. Effects of DSIF knockdown were prominent during transcription of sequences high in G + C but minimal for sequences low in G + C and were particularly evident for G + C-rich segments of long genes. Reanalysis of previously published ChIP-seq data obtained from mouse cells showed similar effects of template G + C composition on Supt5h actions. Our evidence that DSIF dependency varies globally in different template regions according to template sequence composition suggests that G + C content may have a role in the selectivity of Supt4h knockdown and Supt5h knockdown during transcription of gene alleles containing expansions of G + C-rich repeats.
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Affiliation(s)
- Ning Deng
- Department of Genetics, Stanford University School of Medicine , Stanford, CA 94305, USA
| | - Yue Zhang
- Department of Genetics, Stanford University School of Medicine , Stanford, CA 94305, USA
| | - Zhihai Ma
- Department of Genetics, Stanford University School of Medicine , Stanford, CA 94305, USA
| | - Richard Lin
- Department of Genetics, Stanford University School of Medicine , Stanford, CA 94305, USA
| | - Tzu-Hao Cheng
- Institute of Biochemistry and Molecular Biology, National Yang Ming Chiao Tung University , Taipei 112, Taiwan
| | - Hua Tang
- Department of Genetics, Stanford University School of Medicine , Stanford, CA 94305, USA
| | - Michael P Snyder
- Department of Genetics, Stanford University School of Medicine , Stanford, CA 94305, USA
| | - Stanley N Cohen
- Department of Genetics, Stanford University School of Medicine , Stanford, CA 94305, USA
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16
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Zhang W, Ye S, Du Y, Zhao Q, Du J, Zhang Q. Identification and Expression Analysis of bZIP Members under Abiotic Stress in Mung Bean ( Vigna radiata). Life (Basel) 2022; 12:938. [PMID: 35888028 PMCID: PMC9316212 DOI: 10.3390/life12070938] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 06/17/2022] [Accepted: 06/20/2022] [Indexed: 06/15/2023] Open
Abstract
The main aim of this study was to identify the bZIP family members in mung bean and explore their expression patterns under several abiotic stresses, with the overarching goal of elucidating their biological functions. Results identified 75 bZIP members in mung bean, which were unevenly distributed in the chromosomes (1-11), and all had a highly conserved bZIP domain. Phylogenetic analysis divided the members into 10 subgroups, with members in the same subgroup having similar structure and motif. The cis-acting elements in the promoter region revealed that most of the bZIP members might have the connection with abscisic acid, ethylene, and stress responsive elements. The transcriptome data demonstrated that bZIP members could respond to salt stress at different degrees in leaves, but the expression patterns could vary at different time points under stress. Differentially expressed genes (DEGs), such as VrbZIP12, VrbZIP37, and VrZIP45, were annotated into the plant hormone signal transduction pathway, which might be regulated the expression of abiotic stress-related gene (ABF). Quantitative real-time polymerase chain reaction (qRT-PCR) was applied to determine the expression of bZIP members in roots and leaves under drought, alkali, and low-temperature stress. Results showed that bZIP members respond differently to diverse stresses, and their expression was tissue-specific, which suggests that they may have different regulatory mechanism in different tissues. Overall, this study will provide a reference for further research on the functions of bZIP members in mung bean.
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Affiliation(s)
- Wenhui Zhang
- Agronomy College, Heilongjiang Bayi Agricultural University, Daqing 163319, China; (W.Z.); (S.Y.); (Y.D.); (Q.Z.)
- National Coarse Cereals Engineering Research Center, Daqing 163319, China
| | - Shijia Ye
- Agronomy College, Heilongjiang Bayi Agricultural University, Daqing 163319, China; (W.Z.); (S.Y.); (Y.D.); (Q.Z.)
| | - Yanli Du
- Agronomy College, Heilongjiang Bayi Agricultural University, Daqing 163319, China; (W.Z.); (S.Y.); (Y.D.); (Q.Z.)
- National Coarse Cereals Engineering Research Center, Daqing 163319, China
| | - Qiang Zhao
- Agronomy College, Heilongjiang Bayi Agricultural University, Daqing 163319, China; (W.Z.); (S.Y.); (Y.D.); (Q.Z.)
- Research Center of Saline and Alkali Land Improvement Engineering Technology in Heilongjiang Province, Daqing 163319, China
| | - Jidao Du
- Agronomy College, Heilongjiang Bayi Agricultural University, Daqing 163319, China; (W.Z.); (S.Y.); (Y.D.); (Q.Z.)
- Research Center of Saline and Alkali Land Improvement Engineering Technology in Heilongjiang Province, Daqing 163319, China
| | - Qi Zhang
- Agronomy College, Heilongjiang Bayi Agricultural University, Daqing 163319, China; (W.Z.); (S.Y.); (Y.D.); (Q.Z.)
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17
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Abstract
BACKGROUND The evolution of spliceosomal introns has been widely studied among various eukaryotic groups. Researchers nearly reached the consensuses on the pattern and the mechanisms of intron losses and gains across eukaryotes. However, according to previous studies that analyzed a few genes or genomes, Nematoda seems to be an eccentric group. RESULTS Taking advantage of the recent accumulation of sequenced genomes, we extensively analyzed the intron losses and gains using 104 nematode genomes across all the five Clades of the phylum. Nematodes have a wide range of intron density, from less than one to more than nine per kbp coding sequence. The rates of intron losses and gains exhibit significant heterogeneity both across different nematode lineages and across different evolutionary stages of the same lineage. The frequency of intron losses far exceeds that of intron gains. Five pieces of evidence supporting the model of cDNA-mediated intron loss have been observed in ten Caenorhabditis species, the dominance of the precise intron losses, frequent loss of adjacent introns, high-level expression of the intron-lost genes, preferential losses of short introns, and the preferential losses of introns close to 3'-ends of genes. Like studies in most eukaryotic groups, we cannot find the source sequences for the limited number of intron gains detected in the Caenorhabditis genomes. CONCLUSIONS These results indicate that nematodes are a typical eukaryotic group rather than an outlier in intron evolution.
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Affiliation(s)
- Ming-Yue Ma
- Chongqing Key Laboratory of Big Data for Bio Intelligence, School of Bioinformatics, Chongqing University of Posts and Telecommunications, Chongqing, 400065, China
| | - Ji Xia
- Chongqing Key Laboratory of Big Data for Bio Intelligence, School of Bioinformatics, Chongqing University of Posts and Telecommunications, Chongqing, 400065, China
| | - Kun-Xian Shu
- Chongqing Key Laboratory of Big Data for Bio Intelligence, School of Bioinformatics, Chongqing University of Posts and Telecommunications, Chongqing, 400065, China.
| | - Deng-Ke Niu
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering and Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing, 100875, China.
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18
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Lal M, Bhardwaj E, Chahar N, Yadav S, Das S. Comprehensive analysis of 1R- and 2R-MYBs reveals novel genic and protein features, complex organisation, selective expansion and insights into evolutionary tendencies. Funct Integr Genomics 2022; 22:371-405. [PMID: 35260976 DOI: 10.1007/s10142-022-00836-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 02/10/2022] [Accepted: 02/23/2022] [Indexed: 11/28/2022]
Abstract
Myeloblastosis (MYB) family, the largest plant transcription factor family, has been subcategorised based on the number and type of repeats in the MYB domain. In spite of several reports, evolution of MYB genes and repeats remains enigmatic. Brassicaceae members are endowed with complex genomes, including dysploidy because of its unique history with multiple rounds of polyploidisation, genomic fractionations and rearrangements. The present study is an attempt to gain insights into the complexities of MYB family diversity, understand impacts of genome evolution on gene families and develop an evolutionary framework to understand the origin of various subcategories of MYB gene family. We identified and analysed 1129 MYBs that included 1R-, 2R-, 3R- and atypical-MYBs across sixteen species representing protists, fungi, animals and plants and exclude MYB identified from Brassicaceae except Arabidopsis thaliana; in addition, a total of 1137 2R-MYB genes from six Brassicaceae species were also analysed. Comparative analysis revealed predominance of 1R-MYBs in protists, fungi, animals and lower plants. Phylogenetic reconstruction and analysis of selection pressure suggested ancestral nature of R1-type repeat containing 1R-MYBs that might have undergone intragenic duplication to form multi-repeat MYBs. Distinct differences in gene structure between 1R-MYB and 2R-MYBs were observed regarding intron number, the ratio of gene length to coding DNA sequence (CDS) length and the length of exons encoding the MYB domain. Conserved as well as novel and lineage-specific intron phases were identified. Analyses of physicochemical properties revealed drastic differences indicating functional diversification in MYBs. Phylogenetic reconstruction of 1R- and 2R-MYB genes revealed a shared structure-function relationship in clades which was supported when transcriptome data was analysed in silico. Comparative genomics to study distribution pattern and mapping of 2R-MYBs revealed congruency and greater degree of synteny and collinearity among closely related species. Micro-synteny analysis of genomic segments revealed high conservation of genes that are immediately flanking the surrounding tandemly organised 2R-MYBs along with instances of local duplication, reorganisations and genome fractionation. In summary, polyploidy, dysploidy, reshuffling and genome fractionation were found to cause loss or gain of 2R-MYB genes. The findings need to be supported with functional validation to understand gene structure-function relationship along the evolutionary lineage and adaptive strategies based on comparative functional genomics in plants.
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Affiliation(s)
- Mukund Lal
- Department of Botany, University of Delhi, Delhi, 110007, India
| | - Ekta Bhardwaj
- Department of Botany, University of Delhi, Delhi, 110007, India
| | - Nishu Chahar
- Department of Botany, University of Delhi, Delhi, 110007, India
| | - Shobha Yadav
- Department of Botany, University of Delhi, Delhi, 110007, India
| | - Sandip Das
- Department of Botany, University of Delhi, Delhi, 110007, India.
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19
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Identification, Characterization and Comparison of the Genome-Scale UTR Introns from Six Citrus Species. HORTICULTURAE 2022. [DOI: 10.3390/horticulturae8050434] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Ever since their discovery, introns within the coding sequence (CDS) of transcripts have been paid great attention. However, the introns located in the untranslated regions (UTRs) are often ignored. Here, we identified, characterized and compared the UTR introns (UIs) from six citrus species. Results showed that the average intron number of UTRs is greatly lower than that of CDSs. Among all six citrus species, the number and density of 5′UTR introns (5UIs) are higher than those of 3′UTR introns (3UIs). The UI densities varied greatly among different citrus species. There are 11 and 9 types of splice site (SS) pairs for the UIs of C. sinensis and C. medica, respectively. However, the UIs of the other four citrus species all own only three kinds of SS pairs. The ‘GT-AG’, accounting for more than 95% of both 5UIs and 3UIs SS pairs for all the six species, is the most popular type. Moreover, 81 5UIs and 26 3UIs were identified as common UIs among the six citrus species, and the transcripts containing these common UIs were mostly involved in gene expression or gene expression regulation. Our study revealed that the UIs’ length, abundance, density and SS pair types varied among different citrus species and that many UI-containing genes play important roles in gene expression regulation. Our findings have great implications for future citrus UI function research.
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20
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Lo R, Dougan KE, Chen Y, Shah S, Bhattacharya D, Chan CX. Alignment-Free Analysis of Whole-Genome Sequences From Symbiodiniaceae Reveals Different Phylogenetic Signals in Distinct Regions. FRONTIERS IN PLANT SCIENCE 2022; 13:815714. [PMID: 35557718 PMCID: PMC9087856 DOI: 10.3389/fpls.2022.815714] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 04/04/2022] [Indexed: 05/24/2023]
Abstract
Dinoflagellates of the family Symbiodiniaceae are predominantly essential symbionts of corals and other marine organisms. Recent research reveals extensive genome sequence divergence among Symbiodiniaceae taxa and high phylogenetic diversity hidden behind subtly different cell morphologies. Using an alignment-free phylogenetic approach based on sub-sequences of fixed length k (i.e. k-mers), we assessed the phylogenetic signal among whole-genome sequences from 16 Symbiodiniaceae taxa (including the genera of Symbiodinium, Breviolum, Cladocopium, Durusdinium and Fugacium) and two strains of Polarella glacialis as outgroup. Based on phylogenetic trees inferred from k-mers in distinct genomic regions (i.e. repeat-masked genome sequences, protein-coding sequences, introns and repeats) and in protein sequences, the phylogenetic signal associated with protein-coding DNA and the encoded amino acids is largely consistent with the Symbiodiniaceae phylogeny based on established markers, such as large subunit rRNA. The other genome sequences (introns and repeats) exhibit distinct phylogenetic signals, supporting the expected differential evolutionary pressure acting on these regions. Our analysis of conserved core k-mers revealed the prevalence of conserved k-mers (>95% core 23-mers among all 18 genomes) in annotated repeats and non-genic regions of the genomes. We observed 180 distinct repeat types that are significantly enriched in genomes of the symbiotic versus free-living Symbiodinium taxa, suggesting an enhanced activity of transposable elements linked to the symbiotic lifestyle. We provide evidence that representation of alignment-free phylogenies as dynamic networks enhances the ability to generate new hypotheses about genome evolution in Symbiodiniaceae. These results demonstrate the potential of alignment-free phylogenetic methods as a scalable approach for inferring comprehensive, unbiased whole-genome phylogenies of dinoflagellates and more broadly of microbial eukaryotes.
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Affiliation(s)
- Rosalyn Lo
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, QLD, Australia
| | - Katherine E. Dougan
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, QLD, Australia
| | - Yibi Chen
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, QLD, Australia
| | - Sarah Shah
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, QLD, Australia
| | - Debashish Bhattacharya
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ, United States
| | - Cheong Xin Chan
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, QLD, Australia
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21
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New Genomic Signals Underlying the Emergence of Human Proto-Genes. Genes (Basel) 2022; 13:genes13020284. [PMID: 35205330 PMCID: PMC8871994 DOI: 10.3390/genes13020284] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 01/20/2022] [Accepted: 01/24/2022] [Indexed: 12/04/2022] Open
Abstract
De novo genes are novel genes which emerge from non-coding DNA. Until now, little is known about de novo genes’ properties, correlated to their age and mechanisms of emergence. In this study, we investigate four related properties: introns, upstream regulatory motifs, 5′ Untranslated regions (UTRs) and protein domains, in 23,135 human proto-genes. We found that proto-genes contain introns, whose number and position correlates with the genomic position of proto-gene emergence. The origin of these introns is debated, as our results suggest that 41% of proto-genes might have captured existing introns, and 13.7% of them do not splice the ORF. We show that proto-genes which emerged via overprinting tend to be more enriched in core promotor motifs, while intergenic and intronic genes are more enriched in enhancers, even if the TATA motif is most commonly found upstream in these genes. Intergenic and intronic 5′ UTRs of proto-genes have a lower potential to stabilise mRNA structures than exonic proto-genes and established human genes. Finally, we confirm that proteins expressed by proto-genes gain new putative domains with age. Overall, we find that regulatory motifs inducing transcription and translation of previously non-coding sequences may facilitate proto-gene emergence. Our study demonstrates that introns, 5′ UTRs, and domains have specific properties in proto-genes. We also emphasize that the genomic positions of de novo genes strongly impacts these properties.
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22
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Genome-wide identification of nitrate transporter 2 (NRT2) gene family and functional analysis of MeNRT2.2 in cassava (Manihot esculenta Crantz). Gene 2022; 809:146038. [PMID: 34688819 DOI: 10.1016/j.gene.2021.146038] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2021] [Revised: 10/14/2021] [Accepted: 10/19/2021] [Indexed: 12/26/2022]
Abstract
Nitrate transporter 2 (NRT2) proteins play an important role in nitrate uptake and utilization in plants. The NRT2 family has been identified and functionally characterized in many plants. However, no systematic identification of NRT2 family members has been reported in cassava (Manihot esculenta Crantz). In this study, six MeNRT2 genes were identified from cassava genome and named as MeNRT2.1-2.6 according to their chromosomal locations. Phylogenetic tree showed that NRT2 proteins were divided into four main subgroups, which was further supported by their gene structure and conserved motifs. All six MeNRT2 genes are randomly distributed on 4 chromosomes (LG8, LG11, LG13, and LG17), two tandem duplicated genes (MeNRT2.3/MeNRT2.4) and a pair of segmental duplicated gene (MeNRT2.1/MeNRT2.2) was detected. Subsequently, expression profiles of MeNRT2 genes in eight different tissues and in response to nitrate deficient treatment were analyzed. The results showed that the MeNRT2 genes had differential expression patterns. All of MeNRT2 genes induced by nitrate deficiency, of them the MeNRT2.2 had the highest expression level after treatment. Arabidopis transformed with MeNRT2.2 gene showed higher fresh weight than wild type plants in response to N starvation, suggesting that MeNRT2.2 play important role in adapting to low nitrogen. Taken together, our results provide the reference for further analyses of the molecular functions of the MeNRT2 gene family, but also some candidate genes for developing nitrogen efficient crops.
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23
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Manzoor MA, Sabir IA, Shah IH, Wang H, Yu Z, Rasool F, Mazhar MZ, Younas S, Abdullah M, Cai Y. Comprehensive Comparative Analysis of the GATA Transcription Factors in Four Rosaceae Species and Phytohormonal Response in Chinese Pear ( Pyrus bretschneideri) Fruit. Int J Mol Sci 2021; 22:12492. [PMID: 34830372 PMCID: PMC8618624 DOI: 10.3390/ijms222212492] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 11/14/2021] [Accepted: 11/15/2021] [Indexed: 12/16/2022] Open
Abstract
The GATA gene family is one of the most important transcription factors (TFs). It extensively exists in plants, contributes to diverse biological processes such as the development process, and responds to environmental stress. Although the GATA gene family has been comprehensively and systematically studied in many species, less is known about GATA genes in Chinese pears (Pyrus bretschneideri). In the current study, the GATA gene family in the four Rosaceae genomes was identified, its structural characteristics identified, and a comparative analysis of its properties was carried out. Ninety-two encoded GATA proteins were authenticated in the four Rosaceae genomes (Pyrus bretschneideri, Prunus avium, Prunus mume, and Prunus persica) and categorized into four subfamilies (Ⅰ-Ⅳ) according to phylogeny. The majority of GATA genes contained one to two introns and conserved motif composition analysis revealed their functional divergence. Whole-genome duplications (WGDs) and dispersed duplication (DSD) played a key role in the expansion of the GATA gene family. The microarray indicated that, among P. bretschneideri, P. avium, P. mume and P. persica, GATA duplicated regions were more conserved between Pyrus bretschneideri and Prunus persica with 32 orthologous genes pairs. The physicochemical parameters, duplication patterns, non-synonymous (ka), and synonymous mutation rate (ks) and GO annotation ontology were performed using different bioinformatics tools. cis-elements respond to various phytohormones, abiotic/biotic stress, and light-responsive were found in the promoter regions of GATA genes which were induced via stimuli. Furthermore, subcellular localization of the PbGATA22 gene product was investigated, showing that it was present in the nucleus of tobacco (Nicotiana tabacum) epidermal cells. Finally, in silico analysis was performed on various organs (bud, leaf, stem, ovary, petal, and sepal) and different developmental stages of fruit. Subsequently, the expression profiles of PbGATA genes were extensively expressed under exogenous hormonal treatments of SA (salicylic acid), MeJA (methyl jasmonate), and ABA (abscisic acid) indicating that play important role in hormone signaling pathways. A comprehensive analysis of GATA transcription factors was performed through systematic biological approaches and comparative genomics to establish a theoretical base for further structural and functional investigations in Rosaceae species.
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Affiliation(s)
- Muhammad Aamir Manzoor
- School of Life Sciences, Anhui Agricultural University, Hefei 230036, China; (M.A.M.); (H.W.); (Z.Y.)
| | - Irfan Ali Sabir
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China; (I.A.S.); (I.H.S.)
| | - Iftikhar Hussain Shah
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China; (I.A.S.); (I.H.S.)
| | - Han Wang
- School of Life Sciences, Anhui Agricultural University, Hefei 230036, China; (M.A.M.); (H.W.); (Z.Y.)
| | - Zhao Yu
- School of Life Sciences, Anhui Agricultural University, Hefei 230036, China; (M.A.M.); (H.W.); (Z.Y.)
| | - Faiz Rasool
- Gulab Davi Education Institute, Lahore 200240, Pakistan;
| | - Muhammad Zaid Mazhar
- Department of Agriculture, University of Agriculture, Faisalabad 38000, Pakistan;
| | - Shoaib Younas
- Department of Food Science and Technology, University of Central Punjab, Lahore 200240, Pakistan;
| | - Muhammad Abdullah
- Queenland Alliance of Agriculture and Food Innovation, The University of Queensland, Brisbane 4072, Australia;
| | - Yongping Cai
- School of Life Sciences, Anhui Agricultural University, Hefei 230036, China; (M.A.M.); (H.W.); (Z.Y.)
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24
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Dong C, Simonett SP, Shin S, Stapleton DS, Schueler KL, Churchill GA, Lu L, Liu X, Jin F, Li Y, Attie AD, Keller MP, Keleş S. INFIMA leverages multi-omics model organism data to identify effector genes of human GWAS variants. Genome Biol 2021; 22:241. [PMID: 34425882 PMCID: PMC8381555 DOI: 10.1186/s13059-021-02450-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Accepted: 08/02/2021] [Indexed: 11/24/2022] Open
Abstract
Genome-wide association studies reveal many non-coding variants associated with complex traits. However, model organism studies largely remain as an untapped resource for unveiling the effector genes of non-coding variants. We develop INFIMA, Integrative Fine-Mapping, to pinpoint causal SNPs for diversity outbred (DO) mice eQTL by integrating founder mice multi-omics data including ATAC-seq, RNA-seq, footprinting, and in silico mutation analysis. We demonstrate INFIMA's superior performance compared to alternatives with human and mouse chromatin conformation capture datasets. We apply INFIMA to identify novel effector genes for GWAS variants associated with diabetes. The results of the application are available at http://www.statlab.wisc.edu/shiny/INFIMA/ .
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Affiliation(s)
- Chenyang Dong
- Department of Statistics, University of Wisconsin-Madison, Madison, WI USA
| | - Shane P. Simonett
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI USA
| | - Sunyoung Shin
- Department of Mathematical Sciences, University of Texas at Dallas, Richardson, TX USA
| | - Donnie S. Stapleton
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI USA
| | - Kathryn L. Schueler
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI USA
| | | | - Leina Lu
- Case Western University, Cleveland, OH USA
| | | | - Fulai Jin
- Case Western University, Cleveland, OH USA
| | - Yan Li
- Case Western University, Cleveland, OH USA
| | - Alan D. Attie
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI USA
| | - Mark P. Keller
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI USA
| | - Sündüz Keleş
- Department of Statistics, University of Wisconsin-Madison, Madison, WI USA
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI USA
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25
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Ramanathan N, Ramamurthy J, Natarajan G. Numerical Characterization of DNA Sequences for Alignment-free Sequence Comparison - A Review. Comb Chem High Throughput Screen 2021; 25:365-380. [PMID: 34382516 DOI: 10.2174/1386207324666210811101437] [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: 12/30/2020] [Revised: 06/16/2021] [Accepted: 06/24/2021] [Indexed: 11/22/2022]
Abstract
BACKGROUND Biological macromolecules namely, DNA, RNA, and protein have their building blocks organized in a particular sequence and the sequential arrangement encodes evolutionary history of the organism (species). Hence, biological sequences have been used for studying evolutionary relationships among the species. This is usually carried out by multiple sequence algorithms (MSA). Due to certain limitations of MSA, alignment-free sequence comparison methods were developed. The present review is on alignment-free sequence comparison methods carried out using numerical characterization of DNA sequences. <P> Discussion: The graphical representation of DNA sequences by chaos game representation and other 2-dimesnional and 3-dimensional methods are discussed. The evolution of numerical characterization from the various graphical representations and the application of the DNA invariants thus computed in phylogenetic analysis is presented. The extension of computing molecular descriptors in chemometrics to the calculation of new set of DNA invariants and their use in alignment-free sequence comparison in a N-dimensional space and construction of phylogenetic tress is also reviewed. <P> Conclusion: The phylogenetic tress constructed by the alignment-free sequence comparison methods using DNA invariants were found to be better than those constructed using alignment-based tools such as PHLYIP and ClustalW. One of the graphical representation methods is now extended to study viral sequences of infectious diseases for the identification of conserved regions to design peptide-based vaccine by combining numerical characterization and graphical representation.
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Affiliation(s)
- Natarajan Ramanathan
- Department of Chemistry, Sri Sarada Niketan College for Women, Karur-639005, Tamil Nadu. India
| | - Jayalakshmi Ramamurthy
- Department of Computer Science, Sri Sarada Niketan College for Women, Karur-639005, Tamil Nadu. India
| | - Ganapathy Natarajan
- Department of Mechanical Engineering and Industrial Engineering, University of Wisconsin, Platteville, WI 53818. United States
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26
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Sellis D, Guérin F, Arnaiz O, Pett W, Lerat E, Boggetto N, Krenek S, Berendonk T, Couloux A, Aury JM, Labadie K, Malinsky S, Bhullar S, Meyer E, Sperling L, Duret L, Duharcourt S. Massive colonization of protein-coding exons by selfish genetic elements in Paramecium germline genomes. PLoS Biol 2021; 19:e3001309. [PMID: 34324490 PMCID: PMC8354472 DOI: 10.1371/journal.pbio.3001309] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 08/10/2021] [Accepted: 06/04/2021] [Indexed: 11/18/2022] Open
Abstract
Ciliates are unicellular eukaryotes with both a germline genome and a somatic genome in the same cytoplasm. The somatic macronucleus (MAC), responsible for gene expression, is not sexually transmitted but develops from a copy of the germline micronucleus (MIC) at each sexual generation. In the MIC genome of Paramecium tetraurelia, genes are interrupted by tens of thousands of unique intervening sequences called internal eliminated sequences (IESs), which have to be precisely excised during the development of the new MAC to restore functional genes. To understand the evolutionary origin of this peculiar genomic architecture, we sequenced the MIC genomes of 9 Paramecium species (from approximately 100 Mb in Paramecium aurelia species to >1.5 Gb in Paramecium caudatum). We detected several waves of IES gains, both in ancestral and in more recent lineages. While the vast majority of IESs are single copy in present-day genomes, we identified several families of mobile IESs, including nonautonomous elements acquired via horizontal transfer, which generated tens to thousands of new copies. These observations provide the first direct evidence that transposable elements can account for the massive proliferation of IESs in Paramecium. The comparison of IESs of different evolutionary ages indicates that, over time, IESs shorten and diverge rapidly in sequence while they acquire features that allow them to be more efficiently excised. We nevertheless identified rare cases of IESs that are under strong purifying selection across the aurelia clade. The cases examined contain or overlap cellular genes that are inactivated by excision during development, suggesting conserved regulatory mechanisms. Similar to the evolution of introns in eukaryotes, the evolution of Paramecium IESs highlights the major role played by selfish genetic elements in shaping the complexity of genome architecture and gene expression. A comparative genomics study of nine Paramecium species reveals successful invasion of genes by transposable elements in their germline genomes, showing that the internal eliminated sequences (IESs) followed an evolutionary trajectory remarkably similar to that of spliceosomal introns.
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Affiliation(s)
- Diamantis Sellis
- Université de Lyon, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR 5558, Villeurbanne, France
| | - Frédéric Guérin
- Université de Paris, CNRS, Institut Jacques Monod, Paris, France
| | - Olivier Arnaiz
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Walker Pett
- Université de Lyon, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR 5558, Villeurbanne, France
| | - Emmanuelle Lerat
- Université de Lyon, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR 5558, Villeurbanne, France
| | - Nicole Boggetto
- Université de Paris, CNRS, Institut Jacques Monod, Paris, France
| | - Sascha Krenek
- TU Dresden, Institute of Hydrobiology, Dresden, Germany
| | | | - Arnaud Couloux
- Génomique Métabolique, Genoscope, Institut de biologie François Jacob, CEA, CNRS, Université d’Évry, Université Paris-Saclay, Evry, France
| | - Jean-Marc Aury
- Génomique Métabolique, Genoscope, Institut de biologie François Jacob, CEA, CNRS, Université d’Évry, Université Paris-Saclay, Evry, France
| | - Karine Labadie
- Genoscope, Institut de biologie François-Jacob, Commissariat à l’Energie Atomique (CEA), Université Paris-Saclay, Evry, France
| | - Sophie Malinsky
- Institut de Biologie de l’Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France
- Université de Paris, Paris, France
| | - Simran Bhullar
- Institut de Biologie de l’Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Eric Meyer
- Institut de Biologie de l’Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Linda Sperling
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Laurent Duret
- Université de Lyon, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR 5558, Villeurbanne, France
- * E-mail: (LD); (SD)
| | - Sandra Duharcourt
- Université de Paris, CNRS, Institut Jacques Monod, Paris, France
- * E-mail: (LD); (SD)
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27
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Fang Y, Tambo E, Xue JB, Zhang Y, Zhou XN, Khater EIM. Molecular Analysis of Targeted Insecticide Resistance Gene Mutations in Field-Caught Mosquitos of Medical Importance From Saudi Arabia. JOURNAL OF MEDICAL ENTOMOLOGY 2021; 58:1839-1848. [PMID: 33864372 PMCID: PMC8285008 DOI: 10.1093/jme/tjab048] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2020] [Indexed: 05/11/2023]
Abstract
Gene mutations on target sites can be a valuable indicator of the status of insecticide resistance. Jeddah, a global commercial and major port-of-entry city, is bearing the brunt of dengue disease burden in Saudi Arabia. In the current study, six genotypes of three codon combinations (989, 1016, and 1534) were observed on voltage-gated sodium channel (VGSC) gene in Jeddah's Aedes aegypti population, with PGF/PGC as the dominant one. Two types of introns between exon 20 and 21 on VGSC have been identified for the first time in Ae. aegypti in Saudi Arabia. Statistical and phylogenetic analyses showed that the intron type was significantly associated with the 1016 allele and may reflect the history of insecticide treatment in different continents. In addition, fixation of the L1014F allele on VGSC and G119S on acetylcholinesterase 1 gene was detected in local Culex quinquefasciatus populations, with frequencies of 95.24 and 100%, respectively. To the best of our knowledge, this is the first report of resistant-associated mutations in field-caught Cx. quinquefasciatus in Saudi Arabia. The high prevalence of insecticide resistance gene mutations in local primary mosquito vector species highlights the urgent need to carry out comprehensive insecticide resistance surveillance in Saudi Arabia.
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Affiliation(s)
- Yuan Fang
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, Shanghai 200025, China
- Chinese Center for Tropical Diseases Research, Shanghai 200025, China
- WHO Collaborating Centre for Tropical Diseases, Shanghai 200025, China
- National Center for International Research on Tropical Diseases, Ministry of Science and Technology, Shanghai 200025, China
- Key Laboratory of Parasite and Vector Biology, Ministry of Health, Shanghai 200025, China
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention–Shenzhen Center for Disease Control and Prevention Joint Laboratory for Imported Tropical Disease Control, Shanghai 200025, China
- School of Global Health, Chinese Center for Tropical Diseases Research, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Ernest Tambo
- Public Health Pests Laboratory, Municipality of Jeddah Governorate, Jeddah 21577, Saudi Arabia
| | - Jing-Bo Xue
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, Shanghai 200025, China
- Chinese Center for Tropical Diseases Research, Shanghai 200025, China
- WHO Collaborating Centre for Tropical Diseases, Shanghai 200025, China
- National Center for International Research on Tropical Diseases, Ministry of Science and Technology, Shanghai 200025, China
- Key Laboratory of Parasite and Vector Biology, Ministry of Health, Shanghai 200025, China
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention–Shenzhen Center for Disease Control and Prevention Joint Laboratory for Imported Tropical Disease Control, Shanghai 200025, China
- School of Global Health, Chinese Center for Tropical Diseases Research, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Yi Zhang
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, Shanghai 200025, China
- Chinese Center for Tropical Diseases Research, Shanghai 200025, China
- WHO Collaborating Centre for Tropical Diseases, Shanghai 200025, China
- National Center for International Research on Tropical Diseases, Ministry of Science and Technology, Shanghai 200025, China
- Key Laboratory of Parasite and Vector Biology, Ministry of Health, Shanghai 200025, China
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention–Shenzhen Center for Disease Control and Prevention Joint Laboratory for Imported Tropical Disease Control, Shanghai 200025, China
- School of Global Health, Chinese Center for Tropical Diseases Research, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Xiao-Nong Zhou
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, Shanghai 200025, China
- Chinese Center for Tropical Diseases Research, Shanghai 200025, China
- WHO Collaborating Centre for Tropical Diseases, Shanghai 200025, China
- National Center for International Research on Tropical Diseases, Ministry of Science and Technology, Shanghai 200025, China
- Key Laboratory of Parasite and Vector Biology, Ministry of Health, Shanghai 200025, China
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention–Shenzhen Center for Disease Control and Prevention Joint Laboratory for Imported Tropical Disease Control, Shanghai 200025, China
- School of Global Health, Chinese Center for Tropical Diseases Research, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Emad I M Khater
- Public Health Pests Laboratory, Municipality of Jeddah Governorate, Jeddah 21577, Saudi Arabia
- Department of Entomology, Faculty of Science, Ain Shams University, Cairo 12413, Egypt
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28
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Lim CS, Weinstein BN, Roy SW, Brown CM. Analysis of fungal genomes reveals commonalities of intron gain or loss and functions in intron-poor species. Mol Biol Evol 2021; 38:4166-4186. [PMID: 33772558 PMCID: PMC8476143 DOI: 10.1093/molbev/msab094] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Previous evolutionary reconstructions have concluded that early eukaryotic ancestors including both the last common ancestor of eukaryotes and of all fungi had intron-rich genomes. By contrast, some extant eukaryotes have few introns, underscoring the complex histories of intron–exon structures, and raising the question as to why these few introns are retained. Here, we have used recently available fungal genomes to address a variety of questions related to intron evolution. Evolutionary reconstruction of intron presence and absence using 263 diverse fungal species supports the idea that massive intron reduction through intron loss has occurred in multiple clades. The intron densities estimated in various fungal ancestors differ from zero to 7.6 introns per 1 kb of protein-coding sequence. Massive intron loss has occurred not only in microsporidian parasites and saccharomycetous yeasts, but also in diverse smuts and allies. To investigate the roles of the remaining introns in highly-reduced species, we have searched for their special characteristics in eight intron-poor fungi. Notably, the introns of ribosome-associated genes RPL7 and NOG2 have conserved positions; both intron-containing genes encoding snoRNAs. Furthermore, both the proteins and snoRNAs are involved in ribosome biogenesis, suggesting that the expression of the protein-coding genes and noncoding snoRNAs may be functionally coordinated. Indeed, these introns are also conserved in three-quarters of fungi species. Our study shows that fungal introns have a complex evolutionary history and underappreciated roles in gene expression.
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Affiliation(s)
- Chun Shen Lim
- Department of Biochemistry, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
| | - Brooke N Weinstein
- Quantitative & Systems Biology, School of Natural Sciences, University of California-Merced, Merced, CA, USA.,Department of Biology, San Francisco State University, San Francisco, CA, USA
| | - Scott W Roy
- Quantitative & Systems Biology, School of Natural Sciences, University of California-Merced, Merced, CA, USA.,Department of Biology, San Francisco State University, San Francisco, CA, USA
| | - Chris M Brown
- Department of Biochemistry, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
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29
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Wang LX, Niu CD, Wu SF, Gao CF. Molecular characterizations and expression profiles of transient receptor potential channels in the brown planthopper, Nilaparvata lugens. PESTICIDE BIOCHEMISTRY AND PHYSIOLOGY 2021; 173:104780. [PMID: 33771259 DOI: 10.1016/j.pestbp.2021.104780] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2020] [Revised: 01/07/2021] [Accepted: 01/11/2021] [Indexed: 06/12/2023]
Abstract
Transient receptor potential (TRP) is a superfamily of important cation channels located on the cell membrane. It can regulate almost all sensory modality and control a series of behaviors, including hearing, locomotion, gentle touch, temperature sensation, dry air and food texture detection. The expression profiles of TRP channels have been well documented in the model insect Drosophila melanogaster. However, little is known about the TRP channels of agricultural pests. In this study, we cloned 9 TRP ion channel genes from brown planthopper. Their amino acid sequences are highly conserved with homologues of other insects and have typical TRP channel characteristics: six transmembrane domains (TM1 - TM6) and a pore region between TM5 and TM6. These TRP channels of N. lugens were expressed in all developmental stages and various body parts. The expression levels of almost all TRP channels were relatively higher in adults than nymph stages, and lowest in the eggs. Antenna and abdomen were the main body parts with high expression of these genes. Furthermore, the mRNA levels of these TRP genes were significantly decreased in the third-instar nymphs injected with double-stranded RNA (dsRNA). The survival rate of different TRP dsRNA injected nymphs all exceeded 81%, which was no significant difference compared with the control group. These results suggested that these 9 TRP channels are expressed throughout the body and all ages of the brown planthopper, and are involved in regulating multiple physiological and behavioral processes. The identification of TRP channel genes in this study not only provides a foundation for further exploring the potential roles of TRP channels, but also serves as targets to develop new insecticides for the control of agricultural pests.
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Affiliation(s)
- Li-Xiang Wang
- College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China; State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Jiangsu, China
| | - Chun-Dong Niu
- College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China; State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Jiangsu, China
| | - Shun-Fan Wu
- College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China; State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Jiangsu, China
| | - Cong-Fen Gao
- College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China; State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Jiangsu, China.
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30
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Cai L, Arnold BJ, Xi Z, Khost DE, Patel N, Hartmann CB, Manickam S, Sasirat S, Nikolov LA, Mathews S, Sackton TB, Davis CC. Deeply Altered Genome Architecture in the Endoparasitic Flowering Plant Sapria himalayana Griff. (Rafflesiaceae). Curr Biol 2021; 31:1002-1011.e9. [DOI: 10.1016/j.cub.2020.12.045] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 12/11/2020] [Accepted: 12/23/2020] [Indexed: 12/18/2022]
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Poverennaya IV, Roytberg MA. Spliceosomal Introns: Features, Functions, and Evolution. BIOCHEMISTRY (MOSCOW) 2021; 85:725-734. [PMID: 33040717 DOI: 10.1134/s0006297920070019] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Spliceosomal introns, which have been found in most eukaryotic genes, are non-coding sequences excised from pre-mRNAs by a special complex called spliceosome during mRNA splicing. Introns occur in both protein- and RNA-coding genes and can be found in coding and untranslated gene regions. Because intron sequences vary greatly due to a high rate of polymorphism, the functions of intron had been for a long time associated only with alternative splicing, while intron evolution had been viewed not as an evolution of an individual genomic element, but rather considered within a framework of the evolution of the gene intron-exon structure. Here, we review the theories of intron origin, evolutionary events in the exon-intron structure, such as intron gain, loss, and sliding, intron functions known to date, and mechanisms by which changes in the intron features (length and phase) can affect the regulation of gene-mediated processes.
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Affiliation(s)
- I V Poverennaya
- Vavilov Institute of General Genetics, Russian Academy of Sciences, 119991, Moscow, Russia. .,Institute of Mathematical Problems in Biology, Keldysh Branch of Institute of Applied Mathematics, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia
| | - M A Roytberg
- Institute of Mathematical Problems in Biology, Keldysh Branch of Institute of Applied Mathematics, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia.,Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia.,Higher School of Economics, Moscow, 101000, Russia
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Mahmood Aamir K, Bilal M, Ramzan M, Attique Khan M, Nam Y, Kadry S. Classification of Retroviruses Based on Genomic Data Using RVGC. COMPUTERS, MATERIALS & CONTINUA 2021; 69:3829-3844. [DOI: 10.32604/cmc.2021.017835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2021] [Accepted: 04/17/2021] [Indexed: 08/25/2024]
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33
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Liu B, Iwata-Otsubo A, Yang D, Baker RL, Liang C, Jackson SA, Liu S, Ma J, Zhao M. Analysis of CACTA transposase genes unveils the mechanism of intron loss and distinct small RNA silencing pathways underlying divergent evolution of Brassica genomes. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 105:34-48. [PMID: 33098166 DOI: 10.1111/tpj.15037] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 10/19/2020] [Accepted: 10/13/2020] [Indexed: 06/11/2023]
Abstract
In comparison with retrotransposons, DNA transposons make up a smaller proportion of most plant genomes. However, these elements are often proximal to genes to affect gene expression depending on the activity of the transposons, which is largely reflected by the activity of the transposase genes. Here, we show that three AT-rich introns were retained in the TNP2-like transposase genes of the Bot1 (Brassica oleracea transposon 1) CACTA transposable elements in Brassica oleracea, but were lost in the majority of the Bot1 elements in Brassica rapa. A recent burst of transposition of Bot1 was observed in B. oleracea, but not in B. rapa. This burst of transposition is likely related to the activity of the TNP2-like transposase genes as the expression values of the transposase genes were higher in B. oleracea than in B. rapa. In addition, distinct populations of small RNAs (21, 22 and 24 nt) were detected from the Bot1 elements in B. oleracea, but the vast majority of the small RNAs from the Bot1 elements in B. rapa are 24 nt in length. We hypothesize that the different activity of the TNP2-like transposase genes is likely associated with the three introns, and intron loss is likely reverse transcriptase mediated. Furthermore, we propose that the Bot1 family is currently undergoing silencing in B. oleracea, but has already been silenced in B. rapa. Taken together, our data provide new insights into the differentiation of transposons and their role in the asymmetric evolution of these two closely related Brassica species.
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Affiliation(s)
- Beibei Liu
- Department of Biology, Miami University, Oxford, OH, 45056, USA
| | - Aiko Iwata-Otsubo
- Center for Applied Genetic Technologies, University of Georgia, 111 Riverbend Road, Athens, GA, 30602,, USA
| | - Diya Yang
- Department of Biology, Miami University, Oxford, OH, 45056, USA
| | - Robert L Baker
- Department of Biology, Miami University, Oxford, OH, 45056, USA
| | - Chun Liang
- Department of Biology, Miami University, Oxford, OH, 45056, USA
| | - Scott A Jackson
- Center for Applied Genetic Technologies, University of Georgia, 111 Riverbend Road, Athens, GA, 30602,, USA
| | - Shengyi Liu
- Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, 430062, China
| | - Jianxin Ma
- Department of Agronomy, Purdue University, West Lafayette, IN, 47907, USA
| | - Meixia Zhao
- Department of Biology, Miami University, Oxford, OH, 45056, USA
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Li F, Liu J, Guo X, Yin L, Zhang H, Wen R. Genome-wide survey, characterization, and expression analysis of bZIP transcription factors in Chenopodium quinoa. BMC PLANT BIOLOGY 2020; 20:405. [PMID: 32873228 PMCID: PMC7466520 DOI: 10.1186/s12870-020-02620-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2019] [Accepted: 08/25/2020] [Indexed: 05/06/2023]
Abstract
BACKGROUND Chenopodium quinoa Willd. (quinoa) is a pseudocereal crop of the Amaranthaceae family and represents a promising species with the nutritional content and high tolerance to stressful environments, such as soils affected by high salinity. The basic leucine zipper (bZIP) transcription factor represents exclusively in eukaryotes and can be related to many biological processes. So far, the genomes of quinoa and 3 other Amaranthaceae crops (Spinacia oleracea, Beta vulgaris, and Amaranthus hypochondriacus) have been fully sequenced. However, information about the bZIPs in these Amaranthaceae species is limited, and genome-wide analysis of the bZIP family is lacking in quinoa. RESULTS We identified 94 bZIPs in quinoa (named as CqbZIP1-CqbZIP94). All the CqbZIPs were phylogenetically splitted into 12 distinct subfamilies. The proportion of CqbZIPs was different in each subfamily, and members within the same subgroup shared conserved exon-intron structures and protein motifs. Besides, 32 duplicated CqbZIP gene pairs were investigated, and the duplicated CqbZIPs had mainly undergone purifying selection pressure, which suggested that the functions of the duplicated CqbZIPs might not diverge much. Moreover, we identified the bZIP members in 3 other Amaranthaceae species, and 41, 32, and 16 orthologous gene pairs were identified between quinoa and S. oleracea, B. vulgaris, and A. hypochondriacus, respectively. Among them, most were a single copy being present in S. oleracea, B. vulgaris, and A. hypochondriacus, and two copies being present in allotetraploid quinoa. The function divergence within the bZIP orthologous genes might be limited. Additionally, 11 selected CqbZIPs had specific spatial expression patterns, and 6 of 11 CqbZIPs were up-regulated in response to salt stress. Among the selected CqbZIPs, 3 of 4 duplicated gene pairs shared similar expression patterns, suggesting that these duplicated genes might retain some essential functions during subsequent evolution. CONCLUSIONS The present study provided the first systematic analysis for the phylogenetic classification, motif and gene structure, expansion pattern, and expression profile of the bZIP family in quinoa. Our results would lay an important foundation for functional and evolutionary analysis of CqbZIPs, and provide promising candidate genes for further investigation in tissue specificity and their functional involvement in quinoa's resistance to salt stress.
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Affiliation(s)
- Feng Li
- College of Life Science, Shanxi Datong University, Datong, 037009, People's Republic of China
- Research and Development Center of Agricultural Facility Technology, Shanxi Datong University, Datong, 037009, People's Republic of China
| | - Jianxia Liu
- College of Life Science, Shanxi Datong University, Datong, 037009, People's Republic of China
| | - Xuhu Guo
- College of Life Science, Shanxi Datong University, Datong, 037009, People's Republic of China
| | - Lili Yin
- College of Life Science, Shanxi Datong University, Datong, 037009, People's Republic of China
- Research and Development Center of Agricultural Facility Technology, Shanxi Datong University, Datong, 037009, People's Republic of China
| | - Hongli Zhang
- College of Life Science, Shanxi Datong University, Datong, 037009, People's Republic of China
- Research and Development Center of Agricultural Facility Technology, Shanxi Datong University, Datong, 037009, People's Republic of China
| | - Riyu Wen
- Maize Research Institute, Shanxi Academy of Agricultural Sciences, Xinzhou, 034000, People's Republic of China.
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Li G, Liu X, Liang Y, Zhang Y, Cheng X, Cai Y. Genome-wide characterization of the cellulose synthase gene superfamily in Pyrus bretschneideri and reveal its potential role in stone cell formation. Funct Integr Genomics 2020; 20:723-738. [PMID: 32770303 DOI: 10.1007/s10142-020-00747-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 06/20/2020] [Accepted: 07/27/2020] [Indexed: 12/29/2022]
Abstract
Members of the cellulose synthase (CesA) and cellulose synthase-like (Csl) families from the cellulose synthase gene superfamily participate in cellulose and hemicellulose synthesis in the plasma membrane. The members of this superfamily are vital for cell wall construction during plant growth and development. However, little is known about their function in pear fruit, a model for Rosaceae species and for fleshy fruit development. In our research, a total of 36 CesA/Csl family members were identified from the pear and were grouped into six subfamilies (CesA, CslB, CslC, CslD, CslE, and CslG) according to phylogenetic relationships. We performed a protein sequence physicochemical analysis, phylogenetic tree construction, a gene structure, a conserved domain, and chromosomal localization analysis. The results indicated that most of the CesA/Csl genes from pear are closely related to genes in Arabidopsis, but these families have unique characteristics in terms of their gene structure, chromosomal localization, phylogeny, and deduced protein sequences, suggesting that they have evolved through different processes. Tissue expression analysis results showed that most of the CesA/Csl genes were constitutively expressed at different levels in different organs. Furthermore, the expression levels of four genes (Pbr032894.2, Pbr016107.1, Pbr00518.1, and Pbr034218.1) tended to first increase and then decrease during fruit development, implying that these four genes may be involved in the development of stone cells of pear fruit. Our results may help elucidate the evolutionary history and functional differences of the CesA/Csl genes in pear and lay a foundation for further investigation of the CesA/Csl genes in pear and other Rosaceae species.
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Affiliation(s)
- Guohui Li
- School of Life Science, Anhui Agricultural University, No. 130, Changjiang West, Road, Hefei, 230036, China
| | - Xin Liu
- School of Life Science, Anhui Agricultural University, No. 130, Changjiang West, Road, Hefei, 230036, China
| | - Yuxuan Liang
- Faculty of Forestry, The University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Yang Zhang
- School of Life Science, Anhui Agricultural University, No. 130, Changjiang West, Road, Hefei, 230036, China
| | - Xi Cheng
- School of Life Science, Anhui Agricultural University, No. 130, Changjiang West, Road, Hefei, 230036, China.
| | - Yongping Cai
- School of Life Science, Anhui Agricultural University, No. 130, Changjiang West, Road, Hefei, 230036, China.
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36
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Bateman A. Division of labour in a matrix, rather than phagocytosis or endosymbiosis, as a route for the origin of eukaryotic cells. Biol Direct 2020; 15:8. [PMID: 32345370 PMCID: PMC7187495 DOI: 10.1186/s13062-020-00260-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Accepted: 02/25/2020] [Indexed: 12/13/2022] Open
Abstract
Abstract Two apparently irreconcilable models dominate research into the origin of eukaryotes. In one model, amitochondrial proto-eukaryotes emerged autogenously from the last universal common ancestor of all cells. Proto-eukaryotes subsequently acquired mitochondrial progenitors by the phagocytic capture of bacteria. In the second model, two prokaryotes, probably an archaeon and a bacterial cell, engaged in prokaryotic endosymbiosis, with the species resident within the host becoming the mitochondrial progenitor. Both models have limitations. A search was therefore undertaken for alternative routes towards the origin of eukaryotic cells. The question was addressed by considering classes of potential pathways from prokaryotic to eukaryotic cells based on considerations of cellular topology. Among the solutions identified, one, called here the “third-space model”, has not been widely explored. A version is presented in which an extracellular space (the third-space), serves as a proxy cytoplasm for mixed populations of archaea and bacteria to “merge” as a transitionary complex without obligatory endosymbiosis or phagocytosis and to form a precursor cell. Incipient nuclei and mitochondria diverge by division of labour. The third-space model can accommodate the reorganization of prokaryote-like genomes to a more eukaryote-like genome structure. Nuclei with multiple chromosomes and mitosis emerge as a natural feature of the model. The model is compatible with the loss of archaeal lipid biochemistry while retaining archaeal genes and provides a route for the development of membranous organelles such as the Golgi apparatus and endoplasmic reticulum. Advantages, limitations and variations of the “third-space” models are discussed. Reviewers This article was reviewed by Damien Devos, Buzz Baum and Michael Gray.
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Affiliation(s)
- Andrew Bateman
- Division of Experimental Medicine, Department of Medicine, McGill University, Glen Site Pavilion E, 1001 Boulevard Decarie, Montreal, Quebec, H4A 3J1, Canada. .,Centre for Translational Biology, Research Institute of McGill University Health Centre, Glen Site Pavilion E, 1001 Boulevard Decarie, Montreal, Quebec, H4A 3J1, Canada.
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37
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Villano C, Esposito S, D'Amelia V, Garramone R, Alioto D, Zoina A, Aversano R, Carputo D. WRKY genes family study reveals tissue-specific and stress-responsive TFs in wild potato species. Sci Rep 2020; 10:7196. [PMID: 32346026 PMCID: PMC7188836 DOI: 10.1038/s41598-020-63823-w] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Accepted: 04/06/2020] [Indexed: 01/30/2023] Open
Abstract
Wild potatoes, as dynamic resource adapted to various environmental conditions, represent a powerful and informative reservoir of genes useful for breeding efforts. WRKY transcription factors (TFs) are encoded by one of the largest families in plants and are involved in several biological processes such as growth and development, signal transduction, and plant defence against stress. In this study, 79 and 84 genes encoding putative WRKY TFs have been identified in two wild potato relatives, Solanum commersonii and S. chacoense. Phylogenetic analysis of WRKY proteins divided ScWRKYs and SchWRKYs into three Groups and seven subGroups. Structural and phylogenetic comparative analyses suggested an interspecific variability of WRKYs. Analysis of gene expression profiles in different tissues and under various stresses allowed to select ScWRKY045 as a good candidate in wounding-response, ScWRKY055 as a bacterial infection triggered WRKY and ScWRKY023 as a multiple stress-responsive WRKY gene. Those WRKYs were further studied through interactome analysis allowing the identification of potential co-expression relationships between ScWRKYs/SchWRKYs and genes of various pathways. Overall, this study enabled the discrimination of WRKY genes that could be considered as potential candidates in both breeding programs and functional studies.
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Affiliation(s)
- Clizia Villano
- Department of Agricultural Sciences, University of Naples Federico II, via Università 100, 80055, Portici, Italy
| | - Salvatore Esposito
- Department of Agricultural Sciences, University of Naples Federico II, via Università 100, 80055, Portici, Italy.,CREA Via Cavalleggeri 25, 84098, Pontecagnano-Faiano, Italy
| | - Vincenzo D'Amelia
- Department of Agricultural Sciences, University of Naples Federico II, via Università 100, 80055, Portici, Italy.,National Research Council of Italy, Institute of Biosciences and Bioresources (CNR-IBBR), Via Università 133, Portici, NA, Italy
| | - Raffaele Garramone
- Department of Agricultural Sciences, University of Naples Federico II, via Università 100, 80055, Portici, Italy
| | - Daniela Alioto
- Department of Agricultural Sciences, University of Naples Federico II, via Università 100, 80055, Portici, Italy
| | | | - Riccardo Aversano
- Department of Agricultural Sciences, University of Naples Federico II, via Università 100, 80055, Portici, Italy.
| | - Domenico Carputo
- Department of Agricultural Sciences, University of Naples Federico II, via Università 100, 80055, Portici, Italy.
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Cui Y, Su Y, Wang J, Jia B, Wu M, Pei W, Zhang J, Yu J. Genome-Wide Characterization and Analysis of CIPK Gene Family in Two Cultivated Allopolyploid Cotton Species: Sequence Variation, Association with Seed Oil Content, and the Role of GhCIPK6. Int J Mol Sci 2020; 21:E863. [PMID: 32013234 PMCID: PMC7037685 DOI: 10.3390/ijms21030863] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 01/24/2020] [Accepted: 01/27/2020] [Indexed: 01/16/2023] Open
Abstract
Calcineurin B-like protein-interacting protein kinases (CIPKs), as key regulators, play an important role in plant growth and development and the response to various stresses. In the present study, we identified 80 and 78 CIPK genes in the Gossypium hirsutum and G. barbadense, respectively. The phylogenetic and gene structure analysis divided the cotton CIPK genes into five groups which were classified into an exon-rich clade and an exon-poor clade. A synteny analysis showed that segmental duplication contributed to the expansion of Gossypium CIPK gene family, and purifying selection played a major role in the evolution of the gene family in cotton. Analyses of expression profiles showed that GhCIPK genes had temporal and spatial specificity and could be induced by various abiotic stresses. Fourteen GhCIPK genes were found to contain 17 non-synonymous single nucleotide polymorphisms (SNPs) and co-localized with oil or protein content quantitative trait loci (QTLs). Additionally, five SNPs from four GhCIPKs were found to be significantly associated with oil content in one of the three field tests. Although most GhCIPK genes were not associated with natural variations in cotton oil content, the overexpression of the GhCIPK6 gene reduced the oil content and increased C18:1 and C18:1+C18:1d6 in transgenic cotton as compared to wild-type plants. In addition, we predicted the potential molecular regulatory mechanisms of the GhCIPK genes. In brief, these results enhance our understanding of the roles of CIPK genes in oil synthesis and stress responses.
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Affiliation(s)
- Yupeng Cui
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Key Laboratory of Cotton Genetic Improvement, Ministry of Agriculture, Anyang 455000, China; (Y.C.); (J.W.); (B.J.); (M.W.); (W.P.)
| | - Ying Su
- Laboratory of Cotton Genetics, Genomics and Breeding, College of Agronomy and Biotechnology/Key Laboratory of Crop Heterosis and Utilization of Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China;
| | - Junjuan Wang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Key Laboratory of Cotton Genetic Improvement, Ministry of Agriculture, Anyang 455000, China; (Y.C.); (J.W.); (B.J.); (M.W.); (W.P.)
| | - Bing Jia
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Key Laboratory of Cotton Genetic Improvement, Ministry of Agriculture, Anyang 455000, China; (Y.C.); (J.W.); (B.J.); (M.W.); (W.P.)
| | - Man Wu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Key Laboratory of Cotton Genetic Improvement, Ministry of Agriculture, Anyang 455000, China; (Y.C.); (J.W.); (B.J.); (M.W.); (W.P.)
| | - Wenfeng Pei
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Key Laboratory of Cotton Genetic Improvement, Ministry of Agriculture, Anyang 455000, China; (Y.C.); (J.W.); (B.J.); (M.W.); (W.P.)
| | - Jinfa Zhang
- Department of Plant and Environmental Sciences, New Mexico State University, Las Cruces, NM 88003, USA;
| | - Jiwen Yu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Key Laboratory of Cotton Genetic Improvement, Ministry of Agriculture, Anyang 455000, China; (Y.C.); (J.W.); (B.J.); (M.W.); (W.P.)
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Baumgartner M, Drake K, Kanadia RN. An Integrated Model of Minor Intron Emergence and Conservation. Front Genet 2019; 10:1113. [PMID: 31798628 PMCID: PMC6865273 DOI: 10.3389/fgene.2019.01113] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2019] [Accepted: 10/16/2019] [Indexed: 12/12/2022] Open
Abstract
Minor introns constitute <0.5% of the introns in the human genome and have remained an enigma since their discovery. These introns are removed by a distinct splicing complex, the minor spliceosome. Both are ancient, tracing back to the last eukaryotic common ancestor (LECA), which is reflected by minor intron enrichment in specific gene families, such as the mitogen activated-protein kinase kinases, voltage-gated sodium and calcium ion channels, and E2F transcription factors. Most minor introns occur as single introns in genes with predominantly major introns. Due to this organization, minor intron-containing gene (MIG) expression requires the coordinated action of two spliceosomes, which increases the probability of missplicing. Thus, one would expect loss of minor introns via purifying selection. This has resulted in complete minor intron loss in at least nine eukaryotic lineages. However, minor introns are highly conserved in land plants and metazoans, where their importance is underscored by embryonic lethality when the minor spliceosome is inactivated. Conditional inactivation of the minor spliceosome has shown that rapidly dividing progenitor cells are highly sensitive to minor spliceosome loss. Indeed, we found that MIGs were significantly enriched in a screen for genes essential for survival in 341 cycling cell lines. Here, we propose that minor introns inserted randomly into genes in LECA or earlier and were subsequently conserved in genes crucial for cycling cell survival. We hypothesize that the essentiality of MIGs allowed minor introns to endure through the unicellularity of early eukaryotic evolution. Moreover, we identified 59 MIGs that emerged after LECA, and that many of these are essential for cycling cell survival, reinforcing our essentiality model for MIG conservation. This suggests that minor intron emergence is dynamic across eukaryotic evolution, and that minor introns should not be viewed as molecular fossils. We also posit that minor intron splicing was co-opted in multicellular evolution as a regulatory switch for en masse control of MIG expression and the biological processes they regulate. Specifically, this mode of regulation could control cell proliferation and thus body size, an idea supported by domestication syndrome, wherein MIGs are enriched in common candidate animal domestication genes.
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Affiliation(s)
- Marybeth Baumgartner
- Department of Physiology and Neurobiology, University of Connecticut, Mansfield, CT, United States.,Institute of Brain and Cognitive Sciences, University of Connecticut, Mansfield, CT, United States
| | - Kyle Drake
- Department of Physiology and Neurobiology, University of Connecticut, Mansfield, CT, United States
| | - Rahul N Kanadia
- Department of Physiology and Neurobiology, University of Connecticut, Mansfield, CT, United States.,Institute of Systems Genomics, University of Connecticut, Mansfield, CT, United States
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40
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Parenteau J, Abou Elela S. Introns: Good Day Junk Is Bad Day Treasure. Trends Genet 2019; 35:923-934. [PMID: 31668856 DOI: 10.1016/j.tig.2019.09.010] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 08/28/2019] [Accepted: 09/19/2019] [Indexed: 02/01/2023]
Abstract
Introns are ubiquitous in eukaryotic transcripts. They are often viewed as junk RNA but the huge energetic burden of transcribing, removing, and degrading them suggests a significant evolutionary advantage. Ostensibly, an intron functions within the host pre-mRNA to regulate its splicing, transport, and degradation. However, recent studies have revealed an entirely new class of trans-acting functions where the presence of intronic RNA in the cell impacts the expression of other genes in trans. Here, we review possible new mechanisms of intron functions, with a focus on the role of yeast introns in regulating the cell growth response to starvation.
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Affiliation(s)
- Julie Parenteau
- Département de microbiologie et d'infectiologie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, QC J1E 4K8, Canada
| | - Sherif Abou Elela
- Département de microbiologie et d'infectiologie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, QC J1E 4K8, Canada.
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41
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Sinha S, Manoj N. Molecular evolution of proteins mediating mitochondrial fission-fusion dynamics. FEBS Lett 2019; 593:703-718. [PMID: 30861107 DOI: 10.1002/1873-3468.13356] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Revised: 03/02/2019] [Accepted: 03/07/2019] [Indexed: 01/24/2023]
Abstract
Eukaryotes employ a subset of dynamins to mediate mitochondrial fusion and fission dynamics. Here we report the molecular evolution and diversification of the dynamin-related mitochondrial proteins that drive the fission (Drp1) and the fusion processes (mitofusin and OPA1). We demonstrate that the three paralogs emerged concurrently in an early mitochondriate eukaryotic ancestor. Furthermore, multiple independent duplication events from an ancestral bifunctional fission protein gave rise to specialized fission proteins. The evolutionary history of these proteins is marked by transformations that include independent gain and loss events occurring at the levels of entire genes, specific functional domains, and intronic regions. The domain level variations primarily comprise loss-gain of lineage specific domains that are present in the terminal regions of the sequences.
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Affiliation(s)
- Sansrity Sinha
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, India
| | - Narayanan Manoj
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, India
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42
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Bhattachan P, Dong B. Multivariate analysis of genomic variables, effective population size, and mutation rate. BMC Res Notes 2019; 12:60. [PMID: 30683153 PMCID: PMC6347809 DOI: 10.1186/s13104-019-4097-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Accepted: 01/19/2019] [Indexed: 11/26/2022] Open
Abstract
Objective The relationship between genomic variables (genome size, gene number, intron size, and intron number) and evolutionary forces has two implications. First, they help to unravel the mechanism underlying genome evolution. Second, they provide a solution to the debate over discrepancy between genome size variation and organismal complexity. Previously, a clear correlation between genomic variables and effective population size and mutation rate (Neu) led to an important hypothesis to consider random genetic drift as a major evolutionary force during evolution of genome size and complexity. But recent reports also support natural selection as the leading evolutionary force. As such, the debate remains unresolved. Results Here, we used a multivariate method to explore the relationship between genomic variables and Neu in order to understand the evolution of genome. Previously reported patterns between genomic variables and Neu were not observed in our multivariate study. We found only one association between intron number and Neu, but no relationships were observed between genome size, intron size, gene number, and Neu, suggesting that Neu of the organisms solely does not influence genome evolution. We, therefore, concluded that Neu influences intron evolution, while it may not be the only force that provides mechanistic insights into genome evolution and complexity. Electronic supplementary material The online version of this article (10.1186/s13104-019-4097-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Punit Bhattachan
- Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, No. 5 Yushan Road, Qingdao, 266003, China
| | - Bo Dong
- Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, No. 5 Yushan Road, Qingdao, 266003, China. .,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China. .,Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, 266003, China.
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Li W, Sun K, Ren Z, Song C, Pei X, Liu Y, Wang Z, He K, Zhang F, Zhou X, Ma X, Yang D. Molecular Evolution and Stress and Phytohormone Responsiveness of SUT Genes in Gossypium hirsutum. Front Genet 2018; 9:494. [PMID: 30405700 PMCID: PMC6205988 DOI: 10.3389/fgene.2018.00494] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2018] [Accepted: 10/04/2018] [Indexed: 11/13/2022] Open
Abstract
Sucrose transporters (SUTs) play key roles in allocating the translocation of assimilates from source to sink tissues. Although the characteristics and biological roles of SUTs have been intensively investigated in higher plants, this gene family has not been functionally characterized in cotton. In this study, we performed a comprehensive analysis of SUT genes in the tetraploid cotton Gossypium hirsutum. A total of 18 G. hirsutum SUT genes were identified and classified into three groups based on their evolutionary relationships. Up to eight SUT genes in G. hirsutum were placed in the dicot-specific SUT1 group, while four and six SUT genes were, respectively, clustered into SUT4 and SUT2 groups together with members from both dicot and monocot species. The G. hirsutum SUT genes within the same group displayed similar exon/intron characteristics, and homologous genes in G. hirsutum At and Dt subgenomes, G. arboreum, and G. raimondii exhibited one-to-one relationships. Additionally, the duplicated genes in the diploid and polyploid cotton species have evolved through purifying selection, suggesting the strong conservation of SUT loci in these species. Expression analysis in different tissues indicated that SUT genes might play significant roles in cotton fiber elongation. Moreover, analyses of cis-acting regulatory elements in promoter regions and expression profiling under different abiotic stress and exogenous phytohormone treatments implied that SUT genes, especially GhSUT6A/D, might participate in plant responses to diverse abiotic stresses and phytohormones. Our findings provide valuable information for future studies on the evolution and function of SUT genes in cotton.
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Affiliation(s)
- Wei Li
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, China
| | - Kuan Sun
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, China
| | - Zhongying Ren
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, China
| | | | - Xiaoyu Pei
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, China
| | - Yangai Liu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, China
| | - Zhenyu Wang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, China
| | - Kunlun He
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, China
| | - Fei Zhang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, China
| | - Xiaojian Zhou
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, China
| | - Xiongfeng Ma
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, China
| | - Daigang Yang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, China
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Beta-defensin genes of the Colubridae snakes Phalotris mertensi , Thamnodynastes hypoconia , and T. strigatus. Toxicon 2018; 146:124-128. [DOI: 10.1016/j.toxicon.2018.02.048] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2017] [Revised: 02/22/2018] [Accepted: 02/26/2018] [Indexed: 01/16/2023]
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Mittal S, Mallikarjuna MG, Rao AR, Jain PA, Dash PK, Thirunavukkarasu N. Comparative Analysis of CDPK Family in Maize, Arabidopsis, Rice, and Sorghum Revealed Potential Targets for Drought Tolerance Improvement. Front Chem 2017; 5:115. [PMID: 29312925 PMCID: PMC5742180 DOI: 10.3389/fchem.2017.00115] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Accepted: 11/28/2017] [Indexed: 12/19/2022] Open
Abstract
Calcium dependent protein kinases (CDPKs) play significant role in regulation of plant growth and development in response to various stresses including drought. A set of 32 CDPK genes identified in maize were further used for searching of orthologs in the model plant Arabidopsis (72) and major food crops such as rice (78) and sorghum (91). We comprehensively studied the phylogenetic relationship, annotations, gene duplications, gene structure, divergence time, 3-D protein structures and tissue-specific drought induced expression of CDPK genes in all four species. Variation in intron frequency in the studied species was one of the reasons for the functional diversity of CDPK genes to various stress responses. Protein kinase and protein kinase C phosphorylation site domains were the most conserved motifs identified in all species. Four groups were identified from the sequence-based phylogenetic analysis, in which maize CDPKs were clustered in group III. Expression data showed that the CDPK genes were highly expressed in leaf of maize, rice, and sorghum whereas in Arabidopsis the maximum expression was observed in root. The expression assay showed 5, 6, 11, and 9 were the commonly and differentially expressed drought-related orthologous genes in maize, Arabidopsis, rice, and sorghum, respectively. 3-D protein structure were predicted for the nine genes (Arabidopsis: 2, maize: 2, rice: 3, and sorghum: 2) showing differential expression in at least three species. The predicted 3-D structures were further evaluated and validated by Ramachandran plot, ANOLEA, ProSA, and Verify-3D. The superimposed 3-D structure of drought-related orthologous proteins retained similar folding pattern owing to their conserved nature. Functional annotation revealed the involvement of CDPK genes in various pathways such as osmotic homeostasis, cell protection, and root growth. The interactions of CDPK genes in various pathways play crucial role in imparting drought tolerance through different ABA and MAPK signaling cascades. These selected candidate genes could be targeted in development of drought tolerant genotypes in maize, rice, and sorghum through appropriate breeding approaches. Our comparative experiments of CDPK genes could also be extended in the drought stress breeding programmes of the related species.
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Affiliation(s)
- Shikha Mittal
- Division of Genetics, Indian Agricultural Research Institute (ICAR), New Delhi, India
| | | | - Atmakuri R. Rao
- Centre for Agricultural Bioinformatics, Indian Agricultural Statistics Research Institute (ICAR), New Delhi, India
| | - Prashant A. Jain
- Department of Computational Biology & Bioinformatics, Sam Higginbottom University of Agriculture, Technology, and Sciences, Allahabad, India
| | - Prasanta K. Dash
- ICAR-National Research Centre on Plant Biotechnology, New Delhi, India
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De Tiège A, Van de Peer Y, Braeckman J, Tanghe KB. The sociobiology of genes: the gene's eye view as a unifying behavioural-ecological framework for biological evolution. HISTORY AND PHILOSOPHY OF THE LIFE SCIENCES 2017; 40:6. [PMID: 29168053 DOI: 10.1007/s40656-017-0174-x] [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: 12/04/2016] [Accepted: 08/10/2017] [Indexed: 06/07/2023]
Abstract
Although classical evolutionary theory, i.e., population genetics and the Modern Synthesis, was already implicitly 'gene-centred', the organism was, in practice, still generally regarded as the individual unit of which a population is composed. The gene-centred approach to evolution only reached a logical conclusion with the advent of the gene-selectionist or gene's eye view in the 1960s and 1970s. Whereas classical evolutionary theory can only work with (genotypically represented) fitness differences between individual organisms, gene-selectionism is capable of working with fitness differences among genes within the same organism and genome. Here, we explore the explanatory potential of 'intra-organismic' and 'intra-genomic' gene-selectionism, i.e., of a behavioural-ecological 'gene's eye view' on genetic, genomic and organismal evolution. First, we give a general outline of the framework and how it complements the-to some extent-still 'organism-centred' approach of classical evolutionary theory. Secondly, we give a more in-depth assessment of its explanatory potential for biological evolution, i.e., for Darwin's 'common descent with modification' or, more specifically, for 'historical continuity or homology with modular evolutionary change' as it has been studied by evolutionary developmental biology (evo-devo) during the last few decades. In contrast with classical evolutionary theory, evo-devo focuses on 'within-organism' developmental processes. Given the capacity of gene-selectionism to adopt an intra-organismal gene's eye view, we outline the relevance of the latter model for evo-devo. Overall, we aim for the conceptual integration between the gene's eye view on the one hand, and more organism-centred evolutionary models (both classical evolutionary theory and evo-devo) on the other.
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Affiliation(s)
- Alexis De Tiège
- Department of Philosophy and Moral Science, Ghent University, Blandijnberg 2, 9000, Ghent, Belgium.
| | - Yves Van de Peer
- Department of Plant Biotechnology and Bioinformatics, VIB & Ghent University, Ghent, Belgium
| | - Johan Braeckman
- Department of Philosophy and Moral Science, Ghent University, Blandijnberg 2, 9000, Ghent, Belgium
| | - Koen B Tanghe
- Department of Philosophy and Moral Science, Ghent University, Blandijnberg 2, 9000, Ghent, Belgium
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Li M, Ling C, Xu Q, Gao J. Classification of G-protein coupled receptors based on a rich generation of convolutional neural network, N-gram transformation and multiple sequence alignments. Amino Acids 2017; 50:255-266. [PMID: 29151135 DOI: 10.1007/s00726-017-2512-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2017] [Accepted: 11/14/2017] [Indexed: 10/18/2022]
Abstract
Sequence classification is crucial in predicting the function of newly discovered sequences. In recent years, the prediction of the incremental large-scale and diversity of sequences has heavily relied on the involvement of machine-learning algorithms. To improve prediction accuracy, these algorithms must confront the key challenge of extracting valuable features. In this work, we propose a feature-enhanced protein classification approach, considering the rich generation of multiple sequence alignment algorithms, N-gram probabilistic language model and the deep learning technique. The essence behind the proposed method is that if each group of sequences can be represented by one feature sequence, composed of homologous sites, there should be less loss when the sequence is rebuilt, when a more relevant sequence is added to the group. On the basis of this consideration, the prediction becomes whether a query sequence belonging to a group of sequences can be transferred to calculate the probability that the new feature sequence evolves from the original one. The proposed work focuses on the hierarchical classification of G-protein Coupled Receptors (GPCRs), which begins by extracting the feature sequences from the multiple sequence alignment results of the GPCRs sub-subfamilies. The N-gram model is then applied to construct the input vectors. Finally, these vectors are imported into a convolutional neural network to make a prediction. The experimental results elucidate that the proposed method provides significant performance improvements. The classification error rate of the proposed method is reduced by at least 4.67% (family level I) and 5.75% (family Level II), in comparison with the current state-of-the-art methods. The implementation program of the proposed work is freely available at: https://github.com/alanFchina/CNN .
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Affiliation(s)
- Man Li
- Department of Computer Science and Technology, College of Information Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Cheng Ling
- Department of Computer Science and Technology, College of Information Science and Technology, Beijing University of Chemical Technology, Beijing, China.
| | - Qi Xu
- Department of Computer Science and Technology, College of Information Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Jingyang Gao
- Department of Computer Science and Technology, College of Information Science and Technology, Beijing University of Chemical Technology, Beijing, China
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Kaur S, Dhugga KS, Beech R, Singh J. Genome-wide analysis of the cellulose synthase-like (Csl) gene family in bread wheat (Triticum aestivum L.). BMC PLANT BIOLOGY 2017; 17:193. [PMID: 29100539 PMCID: PMC5670714 DOI: 10.1186/s12870-017-1142-z] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Accepted: 10/26/2017] [Indexed: 05/24/2023]
Abstract
BACKGROUND Hemicelluloses are a diverse group of complex, non-cellulosic polysaccharides, which constitute approximately one-third of the plant cell wall and find use as dietary fibres, food additives and raw materials for biofuels. Genes involved in hemicellulose synthesis have not been extensively studied in small grain cereals. RESULTS In efforts to isolate the sequences for the cellulose synthase-like (Csl) gene family from wheat, we identified 108 genes (hereafter referred to as TaCsl). Each gene was represented by two to three homeoalleles, which are named as TaCslXY_ZA, TaCslXY_ZB, or TaCslXY_ZD, where X denotes the Csl subfamily, Y the gene number and Z the wheat chromosome where it is located. A quarter of these genes were predicted to have 2 to 3 splice variants, resulting in a total of 137 putative translated products. Approximately 45% of TaCsl genes were located on chromosomes 2 and 3. Sequences from the subfamilies C and D were interspersed between the dicots and grasses but those from subfamily A clustered within each group of plants. Proximity of the dicot-specific subfamilies B and G, to the grass-specific subfamilies H and J, respectively, points to their common origin. In silico expression analysis in different tissues revealed that most of the genes were expressed ubiquitously and some were tissue-specific. More than half of the genes had introns in phase 0, one-third in phase 2, and a few in phase 1. CONCLUSION Detailed characterization of the wheat Csl genes has enhanced the understanding of their structural, functional, and evolutionary features. This information will be helpful in designing experiments for genetic manipulation of hemicellulose synthesis with the goal of developing improved cultivars for biofuel production and increased tolerance against various stresses.
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Affiliation(s)
- Simerjeet Kaur
- Department of Plant Science, McGill University, Sainte Anne de Bellevue, QC, Canada
| | - Kanwarpal S. Dhugga
- International Maize and Wheat Improvement Center (CIMMYT), El Batán, Texcoco, Estado de México Mexico
| | - Robin Beech
- Institute of Parasitology, McGill University, Sainte Anne de Bellevue, Montreal, QC Canada
| | - Jaswinder Singh
- Department of Plant Science, McGill University, Sainte Anne de Bellevue, QC, Canada
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Fekete E, Flipphi M, Ág N, Kavalecz N, Cerqueira G, Scazzocchio C, Karaffa L. A mechanism for a single nucleotide intron shift. Nucleic Acids Res 2017; 45:9085-9092. [PMID: 28595329 PMCID: PMC5587772 DOI: 10.1093/nar/gkx520] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Accepted: 06/01/2017] [Indexed: 01/11/2023] Open
Abstract
Spliceosomal introns can occupy nearby rather than identical positions in orthologous genes (intron sliding or shifting). Stwintrons are complex intervening sequences, where an ‘internal’ intron interrupts one of the sequences essential for splicing, generating after its excision, a newly formed canonical intron defined as ‘external’. In one experimentally demonstrated configuration, two alternatively excised internal introns, overlapping by one G, disrupt respectively the donor and the acceptor sequence of an external intron, leading to mRNAs encoding identical proteins. In a gene encoding a DHA1 antiporter in Pezizomycotina, we find a variety of predicted intron configurations interrupting the DNA stretch encoding a conserved peptidic sequence. Some sport a stwintron where the internal intron interrupts the donor of the external intron (experimentally confirmed for Aspergillus nidulans). In others, we found and demonstrate (for Trichoderma reesei) alternative, overlapping internal introns. Discordant canonical introns, one nt apart, are present in yet other species, exactly as predicted by the alternative loss of either of the internal introns at the DNA level from an alternatively spliced stwintron. An evolutionary pathway of 1 nt intron shift, involving an alternatively spliced stwintron intermediate is proposed on the basis of the experimental and genomic data presented.
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Affiliation(s)
- Erzsébet Fekete
- Department of Biochemical Engineering, University of Debrecen, 4032, Hungary
| | - Michel Flipphi
- Department of Biochemical Engineering, University of Debrecen, 4032, Hungary
| | - Norbert Ág
- Department of Biochemical Engineering, University of Debrecen, 4032, Hungary
| | - Napsugár Kavalecz
- Department of Biochemical Engineering, University of Debrecen, 4032, Hungary
| | | | - Claudio Scazzocchio
- Department of Microbiology, Imperial College London, SW7 2AZ, UK.,Institut de Biologie Intégrative de la Cellule, CEA/CNRS/Université Paris-Saclay UMR 9198, 91405 Gif-sur-Yvette, France
| | - Levente Karaffa
- Department of Biochemical Engineering, University of Debrecen, 4032, Hungary
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Grau-Bové X, Torruella G, Donachie S, Suga H, Leonard G, Richards TA, Ruiz-Trillo I. Dynamics of genomic innovation in the unicellular ancestry of animals. eLife 2017; 6:26036. [PMID: 28726632 PMCID: PMC5560861 DOI: 10.7554/elife.26036] [Citation(s) in RCA: 84] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Accepted: 07/11/2017] [Indexed: 12/29/2022] Open
Abstract
Which genomic innovations underpinned the origin of multicellular animals is still an open debate. Here, we investigate this question by reconstructing the genome architecture and gene family diversity of ancestral premetazoans, aiming to date the emergence of animal-like traits. Our comparative analysis involves genomes from animals and their closest unicellular relatives (the Holozoa), including four new genomes: three Ichthyosporea and Corallochytrium limacisporum. Here, we show that the earliest animals were shaped by dynamic changes in genome architecture before the emergence of multicellularity: an early burst of gene diversity in the ancestor of Holozoa, enriched in transcription factors and cell adhesion machinery, was followed by multiple and differently-timed episodes of synteny disruption, intron gain and genome expansions. Thus, the foundations of animal genome architecture were laid before the origin of complex multicellularity – highlighting the necessity of a unicellular perspective to understand early animal evolution. DOI:http://dx.doi.org/10.7554/eLife.26036.001 Hundreds of millions of years ago, some single-celled organisms gained the ability to work together and form multicellular organisms. This transition was a major step in evolution and took place at separate times in several parts of the tree of life, including in animals, plants, fungi and algae. Animals are some of the most complex organisms on Earth. Their single-celled ancestors were also quite genetically complex themselves and their genomes (the complete set of the organism’s DNA) already contained many genes that now coordinate the activity of the cells in a multicellular organism. The genome of an animal typically has certain features: it is large, diverse and contains many segments (called introns) that are not genes. By seeing if the single-celled relatives of animals share these traits, it is possible to learn more about when specific genetic features first evolved, and whether they are linked to the origin of animals. Now, Grau-Bové et al. have studied the genomes of several of the animal kingdom’s closest single-celled relatives using a technique called whole genome sequencing. This revealed that there was a period of rapid genetic change in the single-celled ancestors of animals during which their genes became much more diverse. Another ‘explosion’ of diversity happened after animals had evolved. Furthermore, the overall amount of the genomic content inside cells and the number of introns found in the genome rapidly increased in separate, independent events in both animals and their single-celled ancestors. Future research is needed to investigate whether other multicellular life forms – such as plants, fungi and algae – originated in the same way as animal life. Understanding how the genetic material of animals evolved also helps us to understand the genetic structures that affect our health. For example, genes that coordinate the behavior of cells (and so are important for multicellular organisms) also play a role in cancer, where cells break free of this regulation to divide uncontrollably. DOI:http://dx.doi.org/10.7554/eLife.26036.002
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Affiliation(s)
- Xavier Grau-Bové
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Barcelona, Catalonia, Spain.,Departament de Genètica, Microbiologia i Estadística, Universitat de Barelona, Barcelona, Catalonia, Spain
| | - Guifré Torruella
- Unité d'Ecologie, Systématique et Evolution, Université Paris-Sud/Paris-Saclay, AgroParisTech, Orsay, France
| | - Stuart Donachie
- Department of Microbiology, University of Hawai'i at Mānoa, Honolulu, United States.,Advanced Studies in Genomics, Proteomics and Bioinformatics, University of Hawai'i at Mānoa, Honolulu, United States
| | - Hiroshi Suga
- Faculty of Life and Environmental Sciences, Prefectural University of Hiroshima, Hiroshima, Japan
| | - Guy Leonard
- Department of Biosciences, University of Exeter, Exeter, United Kingdom
| | - Thomas A Richards
- Department of Biosciences, University of Exeter, Exeter, United Kingdom
| | - Iñaki Ruiz-Trillo
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Barcelona, Catalonia, Spain.,Departament de Genètica, Microbiologia i Estadística, Universitat de Barelona, Barcelona, Catalonia, Spain.,ICREA, Passeig Lluís Companys, Barcelona, Catalonia, Spain
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