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Wan L, Su S, Liu J, Zou B, Jiang Y, Jiao B, Tang S, Zhang Y, Deng C, Xiao W. The Spatio-Temporal Expression Profiles of Silkworm Pseudogenes Provide Valuable Insights into Their Biological Roles. Evol Bioinform Online 2024; 20:11769343241261814. [PMID: 38883803 PMCID: PMC11179516 DOI: 10.1177/11769343241261814] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Accepted: 05/28/2024] [Indexed: 06/18/2024] Open
Abstract
Background Pseudogenes are sequences that have lost the ability to transcribe RNA molecules or encode truncated but possibly functional proteins. While they were once considered to be meaningless remnants of evolution, recent researches have shown that pseudogenes play important roles in various biological processes. However, the studies of pseudogenes in the silkworm, an important model organism, are limited and have focused on single or only a few specific genes. Objective To fill these gaps, we present a systematic genome-wide studies of pseudogenes in the silkworm. Methods We identified the pseudogenes in the silkworm using the silkworm genome assemblies, transcriptome, protein sequences from silkworm and its related species. Then we used transcriptome datasets from 832 RNA-seq analyses to construct spatio-temporal expression profiles for these pseudogenes. Additionally, we identified tissue-specifically expressed and differentially expressed pseudogenes to further understand their characteristics. Finally, the functional roles of pseudogenes as lncRNAs were systematically analyzed. Results We identified a total of 4410 pseudogenes, which were grouped into 4 groups, including duplications (DUPs), unitary pseudogenes (Unitary), processed pseudogenes (retropseudogenes, RETs), and fragments (FRAGs). The most of pseudogenes in the domestic silkworm were generated before the divergence of wild and domestic silkworm, however, the domestication may also involve in the accumulation of pseudogenes. These pseudogenes were clearly divided into 2 cluster, a highly expressed and a lowly expressed, and the posterior silk gland was the tissue with the most tissue-specific pseudogenes (199), implying these pseudogenes may be involved in the development and function of silkgland. We identified 3299 lncRNAs in these pseudogenes, and the target genes of these lncRNAs in silkworm pseudogenes were enriched in the egg formation and olfactory function. Conclusions This study replenishes the genome annotations for silkworm, provide valuable insights into the biological roles of pseudogenes. It will also contribute to our understanding of the complex gene regulatory networks in the silkworm and will potentially have implications for other organisms as well.
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Affiliation(s)
- Linrong Wan
- Sericultural Research Institute, Sichuan Academy of Agricultural Sciences, Nanchong, Sichuan, China
- State Key Laboratory of Resource Insects, Southwest University, Chongqing, China
| | - Siyuan Su
- Sericultural Research Institute, Sichuan Academy of Agricultural Sciences, Nanchong, Sichuan, China
| | - Jinyun Liu
- Research and Development Center, LyuKang, Chengdu, China
- Department of Bioinformatics, DNA Stories Bioinformatics Center, Chengdu, China
| | - Bangxing Zou
- Sericultural Research Institute, Sichuan Academy of Agricultural Sciences, Nanchong, Sichuan, China
| | - Yaming Jiang
- Sericultural Research Institute, Sichuan Academy of Agricultural Sciences, Nanchong, Sichuan, China
| | - Beibei Jiao
- Research and Development Center, LyuKang, Chengdu, China
- Department of Bioinformatics, DNA Stories Bioinformatics Center, Chengdu, China
| | - Shaokuan Tang
- Research and Development Center, LyuKang, Chengdu, China
- Department of Bioinformatics, DNA Stories Bioinformatics Center, Chengdu, China
| | - Youhong Zhang
- Sericultural Research Institute, Sichuan Academy of Agricultural Sciences, Nanchong, Sichuan, China
| | - Cao Deng
- Research and Development Center, LyuKang, Chengdu, China
- Department of Bioinformatics, DNA Stories Bioinformatics Center, Chengdu, China
| | - Wenfu Xiao
- Sericultural Research Institute, Sichuan Academy of Agricultural Sciences, Nanchong, Sichuan, China
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Chen C, Luo D, Wang Z, Miao Y, Liu Q, Zhao T, Liu D. Complete chloroplast genomes of eight Artemisia species: Comparative analysis, molecular identification, and phylogenetic analysis. PLANT BIOLOGY (STUTTGART, GERMANY) 2024; 26:257-269. [PMID: 38169134 DOI: 10.1111/plb.13608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 11/13/2023] [Indexed: 01/05/2024]
Abstract
Artemisia L. is the largest genus in the Asteraceae, and well known for its high medicinal value. The morphological features of Artemisia species are similar, making taxonomic identification and evolutionary research difficult. We sequenced chloroplast genomes of eight Artemisia species, all of which are common adulterants of A. argyi. We used novel genetic data and compared these data to the published A. argyi chloroplast genome in to develop molecular markers for species identification and reconstructing phylogenetic relationships between Artemisia species. The eight chloroplast sequences were highly similar in gene order, content, and structure, encoding a total of 114 genes (82 protein-coding genes, 28 tRNAs, and four rRNAs). All species harboured similar repeat sequences and simple sequence repeats (SSRs), ranging from 47 to 49 and 38 to 40 repeats, respectively. In addition, we identified five hypervariable regions (rpl32-trnL, rps16-trnQ, petN-psbM, trnE-rpoB, and atpA-trnR) and ten variable coding genes (ycf1, psbG, rpl36, psaC, psaI, accD, psbT, ndhD, ndhE, and psbH), which can be used to develop chloroplast molecular markers. Finally, phylogenetic reconstructions based on six datasets produced similar topologies, revealing A. argyi is closely related to species often found as adulterants, as expected. Our research provides valuable new information on the evolution and phylogenetic relationships between Artemisia chloroplast genomes and identifies valuable molecular makers to distinguish it from closely related species.
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Affiliation(s)
- C Chen
- Hubei Shizhen Laboratory, Hubei University of Chinese Medicine, Wuhan, China
| | - D Luo
- Hubei Shizhen Laboratory, Hubei University of Chinese Medicine, Wuhan, China
| | - Z Wang
- Hubei Shizhen Laboratory, Hubei University of Chinese Medicine, Wuhan, China
| | - Y Miao
- Hubei Shizhen Laboratory, Hubei University of Chinese Medicine, Wuhan, China
| | - Q Liu
- Hubei Shizhen Laboratory, Hubei University of Chinese Medicine, Wuhan, China
| | - T Zhao
- Hubei Shizhen Laboratory, Hubei University of Chinese Medicine, Wuhan, China
| | - D Liu
- Hubei Shizhen Laboratory, Hubei University of Chinese Medicine, Wuhan, China
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Xie L, Jian H, Dai H, Yang Y, Liu Y, Wei L, Tan M, Li J, Liu L. Screening of microRNAs and target genes involved in Sclerotinia sclerotiorum (Lib.) infection in Brassica napus L. BMC PLANT BIOLOGY 2023; 23:479. [PMID: 37807039 PMCID: PMC10561407 DOI: 10.1186/s12870-023-04501-7] [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: 05/23/2023] [Accepted: 09/30/2023] [Indexed: 10/10/2023]
Abstract
BACKGROUND Rapeseed (Brassica napus L.) is the third largest source of vegetable oil in the world, and Sclerotinia sclerotiorum (Lib.) is a major soil-borne fungal plant pathogen that infects more than 400 plant species, including B. napus. Sclerotinia stem rot caused an annual loss of 10 - 20% in rapeseed yield. Exploring the molecular mechanisms in response to S. sclerotiorum infection in B. napus is beneficial for breeding and cultivation of resistant varieties. To gain a better understanding of the mechanisms regarding B. napus tolerance to Sclerotinia stem rot, we employed a miRNAome sequencing approach and comprehensively investigated global miRNA expression profile among five relatively resistant lines and five susceptible lines of oilseed at 0, 24, and 48 h post-inoculation. RESULTS In this study, a total of 40 known and 1105 novel miRNAs were differentially expressed after S. sclerotiorum infection, including miR156, miR6028, miR394, miR390, miR395, miR166, miR171, miR167, miR164, and miR172. Furthermore, 8,523 genes were predicted as targets for these differentially expressed miRNAs. These target genes were mainly associated with disease resistance (R) genes, signal transduction, transcription factors, and hormones. Constitutively expressing miR156b (OX156b) plants strengthened Arabidopsis resistance against S. sclerotiorum accompanied by smaller necrotic lesions, whereas blocking miR156 expression in Arabidopsis (MIM156) led to greater susceptibility to S. sclerotiorum disease, associated with extensive cell death of necrotic lesions. CONCLUSIONS This study reveals the distinct difference in miRNA profiling between the relatively resistant lines and susceptible lines of B. napus in response to S. sclerotiorum. The identified differentially expressed miRNAs related to sclerotinia stem rot resistance are involved in regulating resistance to S. sclerotiorum in rapeseed by targeting genes related to R genes, signal transduction, transcription factors, and hormones. miR156 positively modulates the resistance to S. sclerotiorum infection by restricting colonization of S. sclerotiorum mycelia. This study provides a broad view of miRNA expression changes after S. sclerotiorum infection in oilseed and is the first to elucidate the function and mechanism underlying the miR156 response to S. sclerotiorum infection in oilseed rape.
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Affiliation(s)
- Ling Xie
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400715, China
| | - Hongju Jian
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400715, China
| | - Haoxi Dai
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400715, China
| | - Youhong Yang
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400715, China
| | - Yiling Liu
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400715, China
| | - Lijuan Wei
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400715, China
| | - Min Tan
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400715, China
| | - Jiana Li
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400715, China
| | - Liezhao Liu
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400715, China.
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Yadav S, Kalwan G, Meena S, Gill SS, Yadava YK, Gaikwad K, Jain PK. Unravelling the due importance of pseudogenes and their resurrection in plants. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 203:108062. [PMID: 37778114 DOI: 10.1016/j.plaphy.2023.108062] [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: 07/20/2023] [Revised: 09/22/2023] [Accepted: 09/26/2023] [Indexed: 10/03/2023]
Abstract
The complexities of a genome are underpinned to the vast expanses of the intergenic region, which constitutes ∼97-98% of the genome. This region is essentially composed of what is colloquially referred to as the "junk DNA" and is composed of various elements like transposons, repeats, pseudogenes, etc. The latter have long been considered as dead elements merely contributing to transcriptional noise in the genome. Many studies now describe the previously unknown regulatory functions of these genes. Recent advances in the Next-generation sequencing (NGS) technologies have allowed unprecedented access to these regions. With the availability of whole genome sequences of more than 788 different plant species in past 20 years, genome annotation has become feasible like never before. Different bioinformatic pipelines are available for the identification of pseudogenes. However, still little is known about their biological functions. The functional validation of these genes remains challenging and research in this area is still in infancy, particularly in plants. CRISPR/Cas-based genome editing could provide solutions to understand the biological roles of these genes by allowing creation of precise edits within these genes. The possibility of pseudogene reactivation or resurrection as has been demonstrated in a few studies might open new avenues of genetic manipulation to yield a desirable phenotype. This review aims at comprehensively summarizing the progress made with regards to the identification of pseudogenes and understanding their biological functions in plants.
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Affiliation(s)
- Sheel Yadav
- ICAR-National Institute for Plant Biotechnology, New Delhi, 110012, India; PG School, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India; Division of Genomic Resources, ICAR-National Bureau of Plant Genetic Resources, New Delhi, 110012, India
| | - Gopal Kalwan
- ICAR-National Institute for Plant Biotechnology, New Delhi, 110012, India; PG School, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Shashi Meena
- PG School, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India; Division of Plant Physiology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Sarvajeet Singh Gill
- Stress Physiology & Molecular Biology Lab, Centre for Biotechnology, Maharshi Dayanand University, Rohtak, 124 001, Haryana, India
| | - Yashwant K Yadava
- ICAR-National Institute for Plant Biotechnology, New Delhi, 110012, India
| | - Kishor Gaikwad
- ICAR-National Institute for Plant Biotechnology, New Delhi, 110012, India
| | - P K Jain
- ICAR-National Institute for Plant Biotechnology, New Delhi, 110012, India.
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Zhang YX, Wang XF, Niu YQ, Wang YG, Zhang WJ, Song ZP, Yang J, Li LF. Evolutionary roles of polyploidization-derived structural variations in the phenotypic diversification of Panax species. Mol Ecol 2023; 32:4999-5012. [PMID: 37525516 DOI: 10.1111/mec.17088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 07/10/2023] [Accepted: 07/19/2023] [Indexed: 08/02/2023]
Abstract
Genomic structural variations (SVs) are widespread in plant and animal genomes and play important roles in phenotypic novelty and species adaptation. Frequent whole genome duplications followed by (re)diploidizations have resulted in high diversity of genome architecture among extant species. In this study, we identified abundant genomic SVs in the Panax genus that are hypothesized to have occurred through during the repeated polyploidizations/(re)diploidizations. Our genome-wide comparisons demonstrated that although these polyploidization-derived SVs have evolved at distinct evolutionary stages, a large number of SV-intersecting genes showed enrichment in functionally important pathways related to secondary metabolites, photosynthesis and basic cellular activities. In line with these observations, our metabolic analyses of these Panax species revealed high diversity of primary and secondary metabolites both at the tissue and interspecific levels. In particular, genomic SVs identified at ginsenoside biosynthesis genes, including copy number variation and large fragment deletion, appear to have played important roles in the evolution and diversification of ginsenosides. A further herbivore deterrence experiment demonstrated that, as major triterpenoidal saponins found exclusively in Panax, ginsenosides provide protection against insect herbivores. Our study provides new insights on how polyploidization-derived SVs have contributed to phenotypic novelty and plant adaptation.
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Affiliation(s)
- Yu-Xin Zhang
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Xin-Feng Wang
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Yu-Qian Niu
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Yu-Guo Wang
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Wen-Ju Zhang
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Zhi-Ping Song
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Ji Yang
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Lin-Feng Li
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai, China
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He W, Yang J, Jing Y, Xu L, Yu K, Fang X. NGenomeSyn: an easy-to-use and flexible tool for publication-ready visualization of syntenic relationships across multiple genomes. BIOINFORMATICS (OXFORD, ENGLAND) 2023; 39:7072460. [PMID: 36883694 PMCID: PMC10027429 DOI: 10.1093/bioinformatics/btad121] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 02/19/2023] [Accepted: 02/23/2023] [Indexed: 03/09/2023]
Abstract
SUMMARY Large-scale comparative genomic studies have provided important insights into species evolution and diversity, but also lead to a great challenge to visualize. Quick catching or presenting key information hidden in the vast amount of genomic data and relationships among multiple genomes requires an efficient visualization tool. However, current tools for such visualization remain inflexible in layout and/or require advanced computation skills, especially for visualization of genome-based synteny. Here, we developed an easy-to-use and flexible layout tool, NGenomeSyn [multiple (N) Genome Synteny], for publication-ready visualization of syntenic relationships of the whole genome or local region and genomic features (e.g. repeats, structural variations, genes) across multiple genomes with a high customization. NGenomeSyn provides an easy way for its users to visualize a large amount of data with a rich layout by simply adjusting options for moving, scaling, and rotation of target genomes. Moreover, NGenomeSyn could be applied on the visualization of relationships on non-genomic data with similar input formats. AVAILABILITY AND IMPLEMENTATION NGenomeSyn is freely available at GitHub (https://github.com/hewm2008/NGenomeSyn) and Zenodo (https://doi.org/10.5281/zenodo.7645148).
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Affiliation(s)
- Weiming He
- BGI-Sanya, BGI-Shenzhen, Sanya 572025, China
- BGI-Shenzhen, Shenzhen 518103, China
| | - Jian Yang
- Key Laboratory of Neuroregeneration, Ministry of Education and Jiangsu Province, Co-Innovation Center of Neuroregeneration, Nantong University, Nantong, Jiangsu 226001, China
| | - Yi Jing
- BGI-Sanya, BGI-Shenzhen, Sanya 572025, China
| | - Lian Xu
- Key Laboratory of Neuroregeneration, Ministry of Education and Jiangsu Province, Co-Innovation Center of Neuroregeneration, Nantong University, Nantong, Jiangsu 226001, China
| | - Kang Yu
- BGI-Shenzhen, Shenzhen 518103, China
| | - Xiaodong Fang
- BGI-Sanya, BGI-Shenzhen, Sanya 572025, China
- BGI-Shenzhen, Shenzhen 518103, China
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