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Lin MD, Chuang CH, Kao CH, Chen SH, Wang SC, Hsieh PH, Chen GY, Mao CC, Li JY, Jade Lu MY, Lin CY. Decoding the genome of bloodsucking midge Forcipomyia taiwana (Diptera: Ceratopogonidae): Insights into odorant receptor expansion. Insect Biochem Mol Biol 2024; 168:104115. [PMID: 38570118 DOI: 10.1016/j.ibmb.2024.104115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2023] [Revised: 03/10/2024] [Accepted: 03/29/2024] [Indexed: 04/05/2024]
Abstract
Biting midges, notably those within the Ceratopogonidae family, have long been recognized for their epidemiological significance, both as nuisances and vectors for disease transmission in vertebrates. Despite their impact, genomic insights into these insects, particularly beyond the Culicoides genus, remain limited. In this study, we assembled the Forcipomyia taiwana (Shiraki) genome, comprising 113 scaffolds covering 130.4 Mbps-with the longest scaffold reaching 7.6 Mbps and an N50 value of 2.6 Mbps-marking a pivotal advancement in understanding the genetic architecture of ceratopogonid biting midges. Phylogenomic analyses reveal a shared ancestry between F. taiwana and Culicoides sonorensis Wirth & Jones, dating back approximately 124 million years, and highlight a dynamic history of gene family expansions and contractions within the Ceratopogonidae family. Notably, a substantial expansion of the odorant receptor (OR) gene family was observed, which is crucial for the chemosensory capabilities that govern biting midges' interactions with their environment, including host seeking and oviposition behaviors. The distribution of OR genes across the F. taiwana genome displays notable clusters on scaffolds, indicating localized tandem gene duplication events. Additionally, several collinear regions were identified, hinting at segmental duplications, inversions, and translocations, contributing to the olfactory system's evolutionary complexity. Among the 156 ORs identified in F. taiwana, 134 are biting midge-specific ORs, distributed across three distinct clades, each exhibiting unique motif features that distinguish them from the others. Through weighted gene co-expression network analysis, we correlated distinct gene modules with sex and reproductive status, laying the groundwork for future investigations into the interplay between gene expression and adaptive behaviors in F. taiwana. In conclusion, our study not only highlights the unique olfactory repertoire of ceratopogonid biting midges but also sets the stage for future studies into the genetic underpinnings of their unique biological traits and ecological strategies.
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Affiliation(s)
- Ming-Der Lin
- Department of Molecular Biology and Human Genetics, Tzu Chi University, 701 Zhongyang Rd., Sec. 3, Hualien, 97004, Taiwan; Institute of Medical Sciences, Tzu Chi University, 701 Zhongyang Rd., Sec. 3, Hualien, 97004, Taiwan.
| | - Chia-Hsien Chuang
- Department of Otolaryngology-Head and Neck Surgery, Lausanne University Hospital and University of Lausanne, Rue du Bugnon 46, 1011, Lausanne, Switzerland; Agora Cancer Research Centre, Rue du Bugnon 25A, 1011, Lausanne, Switzerland.
| | - Chih-Hsin Kao
- Institute of Information Science, Academia Sinica, 128 Academia Road, Sec. 2, Nankang, Taipei, 11529, Taiwan; Institute of Fisheries Science, National Taiwan University, No. 1, Sec. 4, Roosevelt Rd., Taipei, 10617, Taiwan.
| | - Shu-Hwa Chen
- TMU Research Center of Cancer Translational Medicine, Taipei Medical University, 250 Wu-Xing Street, Taipei, 11031, Taiwan.
| | - Szu-Chieh Wang
- Department of Molecular Biology and Human Genetics, Tzu Chi University, 701 Zhongyang Rd., Sec. 3, Hualien, 97004, Taiwan; Institute of Information Science, Academia Sinica, 128 Academia Road, Sec. 2, Nankang, Taipei, 11529, Taiwan.
| | - Ping-Heng Hsieh
- Institute of Information Science, Academia Sinica, 128 Academia Road, Sec. 2, Nankang, Taipei, 11529, Taiwan.
| | - Guan-Yu Chen
- Department of Molecular Biology and Human Genetics, Tzu Chi University, 701 Zhongyang Rd., Sec. 3, Hualien, 97004, Taiwan.
| | - Chun-Chia Mao
- Institute of Information Science, Academia Sinica, 128 Academia Road, Sec. 2, Nankang, Taipei, 11529, Taiwan; Institute of Fisheries Science, National Taiwan University, No. 1, Sec. 4, Roosevelt Rd., Taipei, 10617, Taiwan.
| | - Jeng-Yi Li
- Biodiversity Research Center, Academia Sinica, 128 Academia Road, Sec. 2, Nankang, Taipei, 11529, Taiwan.
| | - Mei-Yeh Jade Lu
- Biodiversity Research Center, Academia Sinica, 128 Academia Road, Sec. 2, Nankang, Taipei, 11529, Taiwan.
| | - Chung-Yen Lin
- Institute of Information Science, Academia Sinica, 128 Academia Road, Sec. 2, Nankang, Taipei, 11529, Taiwan; Institute of Fisheries Science, National Taiwan University, No. 1, Sec. 4, Roosevelt Rd., Taipei, 10617, Taiwan; Genome and Systems Biology Degree Program, National Taiwan University, No. 1, Sec. 4, Roosevelt Rd., Taipei, 10617, Taiwan.
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Kao HJ, Lin TY, Hsieh FJ, Chien JY, Yeh EC, Lin WJ, Chen YH, Ding KH, Yang Y, Chi SC, Tsai PH, Hsu CC, Hwang DK, Tsai HY, Peng ML, Lee SH, Chau SF, Chen CY, Cheang WM, Chen SJ, Kwok PY, Chiou SH, Lu MYJ, Huang SP. Highly efficient capture approach for the identification of diverse inherited retinal disorders. NPJ Genom Med 2024; 9:4. [PMID: 38195571 PMCID: PMC10776681 DOI: 10.1038/s41525-023-00388-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Accepted: 12/01/2023] [Indexed: 01/11/2024] Open
Abstract
Our study presents a 319-gene panel targeting inherited retinal dystrophy (IRD) genes. Through a multi-center retrospective cohort study, we validated the assay's effectiveness and clinical utility and characterized the mutation spectrum of Taiwanese IRD patients. Between January 2018 and May 2022, 493 patients in 425 unrelated families, all initially suspected of having IRD without prior genetic diagnoses, underwent detailed ophthalmic and physical examinations (with extra-ocular features recorded) and genetic testing with our customized panel. Disease-causing variants were identified by segregation analysis and clinical interpretation, with validation via Sanger sequencing. We achieved a read depth of >200× for 94.2% of the targeted 1.2 Mb region. 68.5% (291/425) of the probands received molecular diagnoses, with 53.9% (229/425) resolved cases. Retinitis pigmentosa (RP) is the most prevalent initial clinical impression (64.2%), and 90.8% of the cohort have the five most prevalent phenotypes (RP, cone-rod syndrome, Usher's syndrome, Leber's congenital amaurosis, Bietti crystalline dystrophy). The most commonly mutated genes of probands that received molecular diagnosis are USH2A (13.7% of the cohort), EYS (11.3%), CYP4V2 (4.8%), ABCA4 (4.5%), RPGR (3.4%), and RP1 (3.1%), collectively accounted for 40.8% of diagnoses. We identify 87 unique unreported variants previously not associated with IRD and refine clinical diagnoses for 21 patients (7.22% of positive cases). We developed a customized gene panel and tested it on the largest Taiwanese cohort, showing that it provides excellent coverage for diverse IRD phenotypes.
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Affiliation(s)
- Hsiao-Jung Kao
- Institute of Biomedical Sciences, Academia Sinica, Taipei, 115201, Taiwan
| | - Ting-Yi Lin
- Institute of Biomedical Sciences, Academia Sinica, Taipei, 115201, Taiwan
- Doctoral Degree Program of Translational Medicine, National Yang Ming Chiao Tung University and Academia Sinica, Taipei, 115201, Taiwan
| | - Feng-Jen Hsieh
- Institute of Biomedical Sciences, Academia Sinica, Taipei, 115201, Taiwan
| | - Jia-Ying Chien
- Institute of Medical Sciences, Tzu Chi University, Hualien, 970374, Taiwan
| | - Erh-Chan Yeh
- Institute of Biomedical Sciences, Academia Sinica, Taipei, 115201, Taiwan
| | - Wan-Jia Lin
- Institute of Biomedical Sciences, Academia Sinica, Taipei, 115201, Taiwan
| | - Yi-Hua Chen
- Biodiversity Research Center, Academia Sinica, Taipei, 115201, Taiwan
| | - Kai-Hsuan Ding
- Biodiversity Research Center, Academia Sinica, Taipei, 115201, Taiwan
| | - Yu Yang
- Department of Medical Research, Taipei Veterans General Hospital, Taipei, 112201, Taiwan
| | - Sheng-Chu Chi
- Department of Ophthalmology, Taipei Veterans General Hospital, Taipei, 112201, Taiwan
| | - Ping-Hsing Tsai
- Department of Medical Research, Taipei Veterans General Hospital, Taipei, 112201, Taiwan
- Institute of Pharmacology, National Yang Ming Chiao Tung University, Taipei, 112304, Taiwan
| | - Chih-Chien Hsu
- Department of Ophthalmology, Taipei Veterans General Hospital, Taipei, 112201, Taiwan
- School of Medicine, National Yang Ming Chiao Tung University, Taipei, 112304, Taiwan
| | - De-Kuang Hwang
- Department of Ophthalmology, Taipei Veterans General Hospital, Taipei, 112201, Taiwan
- School of Medicine, National Yang Ming Chiao Tung University, Taipei, 112304, Taiwan
| | - Hsien-Yang Tsai
- Department of Ophthalmology, Taichung Tzu Chi Hospital, Taichung, 427003, Taiwan
| | - Mei-Ling Peng
- Department of Ophthalmology, Taichung Tzu Chi Hospital, Taichung, 427003, Taiwan
| | - Shi-Huang Lee
- Department of Ophthalmology, Taichung Tzu Chi Hospital, Taichung, 427003, Taiwan
| | - Siu-Fung Chau
- Department of Ophthalmology, Taichung Tzu Chi Hospital, Taichung, 427003, Taiwan
| | - Chen Yu Chen
- Department of Ophthalmology, Taichung Tzu Chi Hospital, Taichung, 427003, Taiwan
| | - Wai-Man Cheang
- Department of Ophthalmology, Taichung Tzu Chi Hospital, Taichung, 427003, Taiwan
| | - Shih-Jen Chen
- Department of Ophthalmology, Taipei Veterans General Hospital, Taipei, 112201, Taiwan
- School of Medicine, National Yang Ming Chiao Tung University, Taipei, 112304, Taiwan
| | - Pui-Yan Kwok
- Institute of Biomedical Sciences, Academia Sinica, Taipei, 115201, Taiwan.
- Institute for Human Genetics, Cardiovascular Research Institute, and Department of Dermatology, University of California, San Francisco, CA, USA.
| | - Shih-Hwa Chiou
- Department of Medical Research, Taipei Veterans General Hospital, Taipei, 112201, Taiwan.
- Institute of Pharmacology, National Yang Ming Chiao Tung University, Taipei, 112304, Taiwan.
- Genomic Research Center, Academia Sinica, Taipei, 115201, Taiwan.
| | - Mei-Yeh Jade Lu
- Biodiversity Research Center, Academia Sinica, Taipei, 115201, Taiwan.
| | - Shun-Ping Huang
- Institute of Medical Sciences, Tzu Chi University, Hualien, 970374, Taiwan.
- Department of Ophthalmology, Taichung Tzu Chi Hospital, Taichung, 427003, Taiwan.
- Department of Molecular Biology and Human Genetics, Tzu Chi University, Hualien, 970374, Taiwan.
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Lee TJ, Liu Y, Liu WA, Lin YF, Lee HH, Ke HM, Huang JP, Lu MYJ, Hsieh CL, Chung KF, Liti G, Tsai IJ. Extensive sampling of Saccharomyces cerevisiae in Taiwan reveals ecology and evolution of predomesticated lineages. Genome Res 2022; 32:864-877. [PMID: 35361625 PMCID: PMC9104698 DOI: 10.1101/gr.276286.121] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 03/25/2022] [Indexed: 11/24/2022]
Abstract
The ecology and genetic diversity of the model yeast Saccharomyces cerevisiae before human domestication remain poorly understood. Taiwan is regarded as part of this yeast's geographic birthplace, where the most divergent natural lineage was discovered. Here, we extensively sampled the broadleaf forests across this continental island to probe the ancestral species’ diversity. We found that S. cerevisiae is distributed ubiquitously at low abundance in the forests. Whole-genome sequencing of 121 isolates revealed nine distinct lineages that diverged from Asian lineages during the Pleistocene, when a transient continental shelf land bridge connected Taiwan to other major landmasses. Three lineages are endemic to Taiwan and six are widespread in Asia, making this region a focal biodiversity hotspot. Both ancient and recent admixture events were detected between the natural lineages, and a genetic ancestry component associated with isolates from fruits was detected in most admixed isolates. Collectively, Taiwanese isolates harbor genetic diversity comparable to that of the whole Asia continent, and different lineages have coexisted at a fine spatial scale even on the same tree. Patterns of variations within each lineage revealed that S. cerevisiae is highly clonal and predominantly reproduces asexually in nature. We identified different selection patterns shaping the coding sequences of natural lineages and found fewer gene family expansion and contractions that contrast with domesticated lineages. This study establishes that S. cerevisiae has rich natural diversity sheltered from human influences, making it a powerful model system in microbial ecology.
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Affiliation(s)
- Tracy J Lee
- Biodiversity Research Center, Academia Sinica
| | - Yuching Liu
- Biodiversity Research Center, Academia Sinica
| | - Wei-An Liu
- Biodiversity Research Center, Academia Sinica
| | - Yu-Fei Lin
- Biodiversity Research Center, Academia Sinica
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Hsieh DK, Chuang SC, Chen CY, Chao YT, Lu MYJ, Lee MH, Shih MC. Comparative Genomics of Three Colletotrichum scovillei Strains and Genetic Analysis Revealed Genes Involved in Fungal Growth and Virulence on Chili Pepper. Front Microbiol 2022; 13:818291. [PMID: 35154058 PMCID: PMC8828978 DOI: 10.3389/fmicb.2022.818291] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 01/04/2022] [Indexed: 11/13/2022] Open
Abstract
Colletotrichum scovillei causes anthracnose of chili pepper in many countries. Three strains of this pathogen, Coll-524, Coll-153, and Coll-365, show varied virulence on chili pepper. Among the three strains, Coll-365 showed significant defects in growth and virulence. To decipher the genetic variations among these strains and identify genes contributing to growth and virulence, comparative genomic analysis and gene transformation to show gene function were applied in this study. Compared to Coll-524, Coll-153, and Coll-365 had numerous gene losses including 32 candidate effector genes that are mainly exist in acutatum species complex. A cluster of 14 genes in a 34-kb genomic fragment was lost in Coll-365. Through gene transformation, three genes in the 34-kb fragment were identified to have functions in growth and/or virulence of C. scovillei. CsPLAA encoding a phospholipase A2-activating protein enhanced the growth of Coll-365. A combination of CsPLAA with one transcription factor CsBZTF and one C6 zinc finger domain-containing protein CsCZCP was found to enhance the pathogenicity of Coll-365. Introduction of CsGIP, which encodes a hypothetical protein, into Coll-365 caused a reduction in the germination rate of Coll-365. In conclusion, the highest virulent strain Coll-524 had more genes and encoded more pathogenicity related proteins and transposable elements than the other two strains, which may contribute to the high virulence of Coll-524. In addition, the absence of the 34-kb fragment plays a critical role in the defects of growth and virulence of strain Coll-365.
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Affiliation(s)
- Dai-Keng Hsieh
- Ph.D. Program in Microbial Genomics, National Chung Hsing University and Academia Sinica, Taichung, Taiwan
- Advanced Plant Biotechnology Center, National Chung Hsing University, Taichung, Taiwan
| | - Shu-Cheng Chuang
- Ph.D. Program in Microbial Genomics, National Chung Hsing University and Academia Sinica, Taichung, Taiwan
| | - Chun-Yi Chen
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
| | - Ya-Ting Chao
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
| | - Mei-Yeh Jade Lu
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Miin-Huey Lee
- Ph.D. Program in Microbial Genomics, National Chung Hsing University and Academia Sinica, Taichung, Taiwan
- Advanced Plant Biotechnology Center, National Chung Hsing University, Taichung, Taiwan
- Department of Plant Pathology, National Chung Hsing University, Taichung, Taiwan
- *Correspondence: Miin-Huey Lee,
| | - Ming-Che Shih
- Ph.D. Program in Microbial Genomics, National Chung Hsing University and Academia Sinica, Taichung, Taiwan
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
- Ming-Che Shih,
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Liu HH, Wang J, Wu PH, Lu MYJ, Li JY, Shen YM, Tzeng MN, Kuo CH, Lin YH, Chang HX. Whole-Genome Sequence Resource of Calonectria ilicicola, the Casual Pathogen of Soybean Red Crown Rot. Mol Plant Microbe Interact 2021; 34:848-851. [PMID: 33683143 DOI: 10.1094/mpmi-11-20-0315-a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Calonectria ilicicola (anamorph: Cylindrocladium parasiticum) is a soilborne plant-pathogenic fungus with a broad host range, and it can cause red crown rot of soybean and Cylindrocladium black rot of peanut, which has become an emerging threat to crop production worldwide. Limited molecular studies have focused on Calonectria ilicicola and one of the possible difficulties is the lack of genomic resources. This study presents the first high quality and near-completed genome of C. ilicicola, using the Oxford Nanopore GridION sequencing platform. A total of 16 contigs were assembled and the genome of C. ilicicola isolate F018 was estimated to have 11 chromosomes. Currently, the C. ilicicola F018 genome represents the most contiguous assembly, which has the lowest contig number and the highest contig N50 among all Calonectria genome resources. Putative protein-coding sequences and secretory proteins were estimated to be 17,308 and 1,930 in the C. ilicicola F018 genome, respectively; and the prediction was close to other plant-pathogenic fungi, such as Fusarium species, within the Nectriaceae family. The availability of this high-quality genome resource is expected to facilitate research on fungal biology and genetics of C. ilicicola and to support advanced understanding of pathogen virulence and disease management.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Hsien-Hao Liu
- Department of Plant Pathology and Microbiology, National Taiwan University, Taipei City 10617, Taiwan
| | - Jie Wang
- Center for Genomics-Enabled Plant Science, Michigan State University, East Lansing, MI, U.S.A
| | - Ping-Hu Wu
- Department of Plant Pathology and Microbiology, National Taiwan University, Taipei City 10617, Taiwan
| | - Mei-Yeh Jade Lu
- NGS High Throughput Genomics Core, Biodiversity Research Center, Academia Sinica, Taipei City 11529, Taiwan
| | - Jeng-Yi Li
- NGS High Throughput Genomics Core, Biodiversity Research Center, Academia Sinica, Taipei City 11529, Taiwan
| | - Yuan-Min Shen
- Taichung District Agricultural Research and Extension Station, Council of Agriculture, Changhua County 51544, Taiwan
| | - Min-Nan Tzeng
- Kaohsiung District Agricultural Research and Extension Station, Council of Agriculture, Pingtung County 90846, Taiwan
| | - Chang-Hsin Kuo
- Department of Plant Medicine, National Chiayi University, Chiayi City 60004, Taiwan
| | - Ying-Hong Lin
- Department of Plant Medicine, National Pingtung University of Science and Technology, Pingtung 912301, Taiwan
- Plant Medicine Teaching Hospital, General Research Service Center, National Pingtung University of Science and Technology, Pingtung, Taiwan
| | - Hao-Xun Chang
- Department of Plant Pathology and Microbiology, National Taiwan University, Taipei City 10617, Taiwan
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Huang CF, Liu WY, Jade Lu MY, Chen YH, Ku MSB, Li WH. Whole genome duplication facilitated the evolution of C4 photosynthesis in Gynandropsis gynandra. Mol Biol Evol 2021; 38:4715-4731. [PMID: 34191030 PMCID: PMC8557433 DOI: 10.1093/molbev/msab200] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
In higher plants, whole-genome duplication (WGD) is thought to facilitate the evolution of C4 photosynthesis from C3 photosynthesis. To understand this issue, we used new and existing leaf-development transcriptomes to construct two coding sequence databases for C4Gynandropsis gynandra and C3Tarenaya hassleriana, which shared a WGD before their divergence. We compared duplicated genes in the two species and found that the WGD contributed to four aspects of the evolution of C4 photosynthesis in G. gynandra. First, G. gynandra has retained the duplicates of ALAAT (alanine aminotransferase) and GOGAT (glutamine oxoglutarate aminotransferase) for nitrogen recycling to establish a photorespiratory CO2 pump in bundle sheath (BS) cells for increasing photosynthesis efficiency, suggesting that G. gynandra experienced a C3–C4 intermediate stage during the C4 evolution. Second, G. gynandra has retained almost all known vein-development-related paralogous genes derived from the WGD event, likely contributing to the high vein complexity of G. gynandra. Third, the WGD facilitated the evolution of C4 enzyme genes and their recruitment into the C4 pathway. Fourth, several genes encoding photosystem I proteins were derived from the WGD and are upregulated in G. gynandra, likely enabling the NADH dehydrogenase-like complex to produce extra ATPs for the C4 CO2 concentration mechanism. Thus, the WGD apparently played an enabler role in the evolution of C4 photosynthesis in G. gynandra. Importantly, an ALAAT duplicate became highly expressed in BS cells in G. gynandra, facilitating nitrogen recycling and transition to the C4 cycle. This study revealed how WDG may facilitate C4 photosynthesis evolution.
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Affiliation(s)
- Chi-Fa Huang
- Biodiversity Research Center, Academia Sinica, Taipei, 11529, Taiwan
| | - Wen-Yu Liu
- Biodiversity Research Center, Academia Sinica, Taipei, 11529, Taiwan
| | - Mei-Yeh Jade Lu
- Biodiversity Research Center, Academia Sinica, Taipei, 11529, Taiwan
| | - Yi-Hua Chen
- Biodiversity Research Center, Academia Sinica, Taipei, 11529, Taiwan
| | - Maurice S B Ku
- Department of Bioagricultural Science, National Chiayi University, Chiayi, 600, Taiwan
| | - Wen-Hsiung Li
- Biodiversity Research Center, Academia Sinica, Taipei, 11529, Taiwan.,Department of Ecology and Evolution, University of Chicago, Chicago, 60637, USA
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Panibe JP, Wang L, Li J, Li MY, Lee YC, Wang CS, Ku MSB, Lu MYJ, Li WH. Chromosomal-level genome assembly of the semi-dwarf rice Taichung Native 1, an initiator of Green Revolution. Genomics 2021; 113:2656-2674. [PMID: 34111524 DOI: 10.1016/j.ygeno.2021.06.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 05/25/2021] [Accepted: 06/04/2021] [Indexed: 10/21/2022]
Abstract
Here we report the 409.5 Mb chromosome-level assembly of the first bred semi-dwarf rice, the Taichung Native 1 (TN1), which served as the template for the development of the Green Revolution (GR) cultivar IR8 "miracle rice". We sequenced the TN1 genome utilizing multiple platforms and produced PacBio long reads, Illumina paired-end reads, Illumina mate-pair reads and 10x Genomics linked reads. We used a hybrid approach to assemble the 226× coverage of sequences by a combination of de novo and reference-guided approaches. The assembled TN1 genome has an N50 scaffold size of 33.1 Mb with the longest measuring 45.5 Mb. We annotated 37,526 genes, in which 24,102 (64.23%) were assigned Blast2GO annotations. The genome has 4672 or 95.4% complete BUSCOs and a repeat content of 51.52%. We developed our own method of creating a GR pangenome using the orthologous relationships of the proteins of TN1, IR8, MH63 and IR64, identifying 16,999 core orthologue groups of Green Revolution. From the pangenome, we identified a set of shared and unique gene ontology terms for the accessory clusters, characterizing TN1, IR8, MH63 and IR64. This TN1 genome assembly and GR pangenome will be a resource for new genomic discoveries about Green Revolution, and for improving the disease and insect resistances and the yield of rice.
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Affiliation(s)
- Jerome P Panibe
- Institute of Molecular and Cellular Biology, National Tsing Hua University, Hsinchu 300, Taiwan; Bioinformatics Program, Taiwan International Graduate Program, Institute of Information Science, Academia Sinica, Taipei 115, Taiwan; Biodiversity Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Long Wang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, 210023 Nanjing, China
| | - Jengyi Li
- Biodiversity Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Meng-Yun Li
- Biodiversity Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Yi-Chen Lee
- Biodiversity Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Chang-Sheng Wang
- Department of Agronomy, National Chung-Hsing University, Taichung 40227, Taiwan
| | - Maurice S B Ku
- Department of Bioagricultutral Sciences, National Chiayi University, Chiayi 60004, Taiwan; School of Biological Sciences, Washington State University, Pullman 99164, WA, USA
| | - Mei-Yeh Jade Lu
- Biodiversity Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Wen-Hsiung Li
- Institute of Molecular and Cellular Biology, National Tsing Hua University, Hsinchu 300, Taiwan; Biodiversity Research Center, Academia Sinica, Taipei 115, Taiwan; Department of Ecology and Evolution, University of Chicago, Chicago, IL 60637, USA.
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Fan WL, Yang LY, Hsieh JCH, Lin TC, Lu MYJ, Liao CT. Prognostic Genetic Biomarkers Based on Oncogenic Signaling Pathways for Outcome Prediction in Patients with Oral Cavity Squamous Cell Carcinoma. Cancers (Basel) 2021; 13:cancers13112709. [PMID: 34070941 PMCID: PMC8199274 DOI: 10.3390/cancers13112709] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 05/22/2021] [Accepted: 05/25/2021] [Indexed: 01/02/2023] Open
Abstract
Simple Summary A comprehensive analysis based on mutational signatures and oncogenic signaling pathways to identify a specific subgroup of patients that had a significantly negative impact on both disease-free and overall survival in oral cavity squamous cell carcinoma (OCSCC) from whole exome-sequencing data. This analysis has revealed a variety of biologically relevant candidate target genes. Thirty percent of 165 tumors had multiple targetable alterations in multiple pathways. This suggests the complex interplay and crosstalk of oncogenic signaling pathways play an important role on the outcome of patients with OCSCC, and the candidate genes and pathways identified may include prognostic genetic biomarkers or therapeutic targets for OCSCC. Abstract Mutational profiling of patients’ tumors has suggested that the development of oral cavity squamous cell carcinoma (OCSCC) is driven by multiple genes in multiple pathways. This study aimed to examine the association between genomic alterations and clinical outcomes in patients with advanced stages OCSCC to facilitate prognostic stratification. We re-analyzed our previous whole-exome sequencing data from 165 long-term follow-ups of stages III and IV patients with OCSCC. Their frequent mutations were mapped to 10 oncogenic signaling pathways. Clinicopathological risk factors, relapse, and survival were analyzed to identify the genetic factors associated with advanced OCSCC. Frequent genetic alterations included point mutations in TP53, FAT1, NOTCH1, CASP8, CDKN2A, HRAS, PIK3CA, KMT2B (also known as MLL4), and LINC00273; amplified segments in CCND1, EGFR, CTTN, and FGFR1; and lost segments in CDKN2A, ADAM3A, and CFHR1/CFHR4. Comprehensive analysis of genetic alterations revealed that subgroups based on mutational signatures had a significant negative impact on disease-free survival (p = 0.0005) and overall survival (p = 0.0024). Several important signaling pathways were identified to be frequently genetically altered in our cohort. A specific subgroup of patients with alterations in NOTCH, RTK/RAS/MAPK, and TGF-beta pathways that had a significantly negative impact on disease-free survival (p = 0.0009). Thirty percent of samples had multiple targetable mutations in multiple pathways, indicating opportunities for novel therapy.
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Affiliation(s)
- Wen-Lang Fan
- Genomic Medicine Core Laboratory, Linkou Chang Gung Memorial Hospital, Taoyuan 33382, Taiwan; (W.-L.F.); (T.-C.L.)
| | - Lan-Yan Yang
- Clinical Trial Center, Biostatistics and Informatics Unit, Linkou Chang Gung Memorial Hospital, Taoyuan 33382, Taiwan;
| | - Jason Chia-Hsun Hsieh
- Department of Internal Medicine, Division of Hematology-Oncology, New Taipei Municipal TuCheng Hospital, New Taipei City 236043, Taiwan;
- Medical Oncology, Linkou Chang Gung Memorial Hospital, Taoyuan 33382, Taiwan
- College of Medicine, Chang Gung University, Taoyuan 33382, Taiwan
| | - Tsung-Chieh Lin
- Genomic Medicine Core Laboratory, Linkou Chang Gung Memorial Hospital, Taoyuan 33382, Taiwan; (W.-L.F.); (T.-C.L.)
| | - Mei-Yeh Jade Lu
- Biodiversity Research Center, Academia Sinica, Taipei 11529, Taiwan;
| | - Chun-Ta Liao
- Department of Otorhinolaryngology, Head and Neck Surgery, Linkou Chang Gung Memorial Hospital and Chang Gung University, Taoyuan 33382, Taiwan
- Correspondence:
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9
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Lin CY, Lu MYJ, Yue JX, Li KL, Le Pétillon Y, Yong LW, Chen YH, Tsai FY, Lyu YF, Chen CY, Hwang SPL, Su YH, Yu JK. Molecular asymmetry in the cephalochordate embryo revealed by single-blastomere transcriptome profiling. PLoS Genet 2021; 16:e1009294. [PMID: 33382716 PMCID: PMC7806126 DOI: 10.1371/journal.pgen.1009294] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 01/13/2021] [Accepted: 11/24/2020] [Indexed: 12/13/2022] Open
Abstract
Studies in various animals have shown that asymmetrically localized maternal transcripts play important roles in axial patterning and cell fate specification in early embryos. However, comprehensive analyses of the maternal transcriptomes with spatial information are scarce and limited to a handful of model organisms. In cephalochordates (amphioxus), an early branching chordate group, maternal transcripts of germline determinants form a compact granule that is inherited by a single blastomere during cleavage stages. Further blastomere separation experiments suggest that other transcripts associated with the granule are likely responsible for organizing the posterior structure in amphioxus; however, the identities of these determinants remain unknown. In this study, we used high-throughput RNA sequencing of separated blastomeres to examine asymmetrically localized transcripts in two-cell and eight-cell stage embryos of the amphioxus Branchiostoma floridae. We identified 111 and 391 differentially enriched transcripts at the 2-cell stage and the 8-cell stage, respectively, and used in situ hybridization to validate the spatial distribution patterns for a subset of these transcripts. The identified transcripts could be categorized into two major groups: (1) vegetal tier/germ granule-enriched and (2) animal tier/anterior-enriched transcripts. Using zebrafish as a surrogate model system, we showed that overexpression of one animal tier/anterior-localized amphioxus transcript, zfp665, causes a dorsalization/anteriorization phenotype in zebrafish embryos by downregulating the expression of the ventral gene, eve1, suggesting a potential function of zfp665 in early axial patterning. Our results provide a global transcriptomic blueprint for early-stage amphioxus embryos. This dataset represents a rich platform to guide future characterization of molecular players in early amphioxus development and to elucidate conservation and divergence of developmental programs during chordate evolution.
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Affiliation(s)
- Che-Yi Lin
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, Taiwan
| | - Mei-Yeh Jade Lu
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Jia-Xing Yue
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Kun-Lung Li
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, Taiwan
| | - Yann Le Pétillon
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, Taiwan
| | - Luok Wen Yong
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, Taiwan
| | - Yi-Hua Chen
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Fu-Yu Tsai
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, Taiwan
- Department of Life Science, National Taiwan University, Taipei, Taiwan
| | - Yu-Feng Lyu
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, Taiwan
| | - Cheng-Yi Chen
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, Taiwan
| | - Sheng-Ping L. Hwang
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, Taiwan
| | - Yi-Hsien Su
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, Taiwan
- * E-mail: (Y-HS); (J-KY)
| | - Jr-Kai Yu
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, Taiwan
- Marine Research Station, Institute of Cellular and Organismic Biology, Academia Sinica, Yilan, Taiwan
- * E-mail: (Y-HS); (J-KY)
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10
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Yang HC, Chen CH, Wang JH, Liao HC, Yang CT, Chen CW, Lin YC, Kao CH, Lu MYJ, Liao JC. Analysis of genomic distributions of SARS-CoV-2 reveals a dominant strain type with strong allelic associations. Proc Natl Acad Sci U S A 2020; 117:30679-30686. [PMID: 33184173 PMCID: PMC7720151 DOI: 10.1073/pnas.2007840117] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causal agent of COVID 19, continues to evolve since its first emergence in December 2019. Using the complete sequences of 1,932 SARS-CoV-2 genomes, various clustering analyses consistently identified six types of the strains. Independent of the dendrogram construction, 13 signature variations in the form of single nucleotide variations (SNVs) in protein coding regions and one SNV in the 5' untranslated region (UTR) were identified and provided a direct interpretation for the six types (types I to VI). The six types of the strains and their underlying signature SNVs were validated in two subsequent analyses of 6,228 and 38,248 SARS-CoV-2 genomes which became available later. To date, type VI, characterized by the four signature SNVs C241T (5'UTR), C3037T (nsp3 F924F), C14408T (nsp12 P4715L), and A23403G (Spike D614G), with strong allelic associations, has become the dominant type. Since C241T is in the 5' UTR with uncertain significance and the characteristics can be captured by the other three strongly associated SNVs, we focus on the other three. The increasing frequency of the type VI haplotype 3037T-14408T-23403G in the majority of the submitted samples in various countries suggests a possible fitness gain conferred by the type VI signature SNVs. The fact that strains missing one or two of these signature SNVs fail to persist implies possible interactions among these SNVs. Later SNVs such as G28881A, G28882A, and G28883C have emerged with strong allelic associations, forming new subtypes. This study suggests that SNVs may become an important consideration in SARS-CoV-2 classification and surveillance.
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Affiliation(s)
- Hsin-Chou Yang
- Institute of Statistical Science, Academia Sinica, Taipei 11529, Taiwan;
| | - Chun-Houh Chen
- Institute of Statistical Science, Academia Sinica, Taipei 11529, Taiwan
| | - Jen-Hung Wang
- Institute of Statistical Science, Academia Sinica, Taipei 11529, Taiwan
| | - Hsiao-Chi Liao
- Institute of Statistical Science, Academia Sinica, Taipei 11529, Taiwan
| | - Chih-Ting Yang
- Institute of Statistical Science, Academia Sinica, Taipei 11529, Taiwan
| | - Chia-Wei Chen
- Institute of Statistical Science, Academia Sinica, Taipei 11529, Taiwan
| | - Yin-Chun Lin
- Institute of Statistical Science, Academia Sinica, Taipei 11529, Taiwan
| | - Chiun-How Kao
- Institute of Statistical Science, Academia Sinica, Taipei 11529, Taiwan
- Department of Statistics, Tamkang University, New Taipei City 251301, Taiwan
| | - Mei-Yeh Jade Lu
- Biodiversity Research Center, Academia Sinica, Taipei 11529, Taiwan
| | - James C Liao
- Institute of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan
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11
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Wang WF, Lu MYJ, Cheng TJR, Tang YC, Teng YC, Hwa TY, Chen YH, Li MY, Wu MH, Chuang PC, Jou R, Wong CH, Li WH. Genomic Analysis of Mycobacterium tuberculosis Isolates and Construction of a Beijing Lineage Reference Genome. Genome Biol Evol 2020; 12:3890-3905. [PMID: 31971587 PMCID: PMC7058165 DOI: 10.1093/gbe/evaa009] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/14/2020] [Indexed: 12/03/2022] Open
Abstract
Tuberculosis (TB), an infectious disease caused by Mycobacterium tuberculosis, kills over 1 million people worldwide annually. Development of drug resistance (DR) in the pathogen is a major challenge for TB control. We conducted whole-genome analysis of seven Taiwan M. tuberculosis isolates: One drug susceptible (DS) and five DR Beijing lineage isolates and one DR Euro-American lineage isolate. Developing a new method for DR mutation identification and applying it to the next-generation sequencing (NGS) data from the 6 Beijing lineage isolates, we identified 13 known and 6 candidate DR mutations and provided experimental support for 4 of them. We assembled the genomes of one DS and two DR Beijing lineage isolates and the Euro-American lineage isolate using NGS data. Moreover, using both PacBio and NGS sequencing data, we obtained a high-quality assembly of an extensive DR Beijing lineage isolate. Comparative analysis of these five newly assembled genomes and two published complete genomes revealed a large number of genetic changes, including gene gains and losses, indels and translocations, suggesting rapid evolution of M. tuberculosis. We found the MazEF toxin–antitoxin system in all the seven isolates studied and several interesting mutations in MazEF proteins. Finally, we used the four assembled Beijing lineage genomes to construct a high-quality Beijing lineage reference genome that is DS and contains all the genes in the four genomes. It contains 212 genes not found in the standard reference H37Rv, which is Euro-American. It is therefore a better reference than H37Rv for the Beijing lineage, the predominant lineage in Asia.
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Affiliation(s)
- Woei-Fuh Wang
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan.,Center for Precision Medicine, China Medical University Hospital, Taichung, Taiwan
| | - Mei-Yeh Jade Lu
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | | | - Yi-Ching Tang
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Yu-Chuan Teng
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Teh-Yang Hwa
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Yi-Hua Chen
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Meng-Yun Li
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Mei-Hua Wu
- Tuberculosis Research Center, Centers for Disease Control, Taipei, Taiwan
| | - Pei-Chun Chuang
- Tuberculosis Research Center, Centers for Disease Control, Taipei, Taiwan
| | - Ruwen Jou
- Tuberculosis Research Center, Centers for Disease Control, Taipei, Taiwan
| | - Chi-Huey Wong
- Genome Research Center, Academia Sinica, Taipei, Taiwan
| | - Wen-Hsiung Li
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan.,Department of Ecology and Evolution, University of Chicago, Illinois
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12
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Gómez Luciano LB, Tsai IJ, Chuma I, Tosa Y, Chen YH, Li JY, Li MY, Lu MYJ, Nakayashiki H, Li WH. Blast Fungal Genomes Show Frequent Chromosomal Changes, Gene Gains and Losses, and Effector Gene Turnover. Mol Biol Evol 2019; 36:1148-1161. [PMID: 30835262 DOI: 10.1093/molbev/msz045] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Pyricularia is a fungal genus comprising several pathogenic species causing the blast disease in monocots. Pyricularia oryzae, the best-known species, infects rice, wheat, finger millet, and other crops. As past comparative and population genomics studies mainly focused on isolates of P. oryzae, the genomes of the other Pyricularia species have not been well explored. In this study, we obtained a chromosomal-level genome assembly of the finger millet isolate P. oryzae MZ5-1-6 and also highly contiguous assemblies of Pyricularia sp. LS, P. grisea, and P. pennisetigena. The differences in the genomic content of repetitive DNA sequences could largely explain the variation in genome size among these new genomes. Moreover, we found extensive gene gains and losses and structural changes among Pyricularia genomes, including a large interchromosomal translocation. We searched for homologs of known blast effectors across fungal taxa and found that most avirulence effectors are specific to Pyricularia, whereas many other effectors share homologs with distant fungal taxa. In particular, we discovered a novel effector family with metalloprotease activity, distinct from the well-known AVR-Pita family. We predicted 751 gene families containing putative effectors in 7 Pyricularia genomes and found that 60 of them showed differential expression in the P. oryzae MZ5-1-6 transcriptomes obtained under experimental conditions mimicking the pathogen infection process. In summary, this study increased our understanding of the structural, functional, and evolutionary genomics of the blast pathogen and identified new potential effector genes, providing useful data for developing crops with durable resistance.
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Affiliation(s)
- Luis B Gómez Luciano
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan.,Graduate Institute of Biotechnology, National Chung-Hsing University, Taichung, Taiwan.,Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program, Academia Sinica and National Chung-Hsing University, Taipei, Taiwan
| | | | - Izumi Chuma
- Obihiro University of Agriculture and Veterinary Medicine, Hokkaido, Japan
| | - Yukio Tosa
- Graduate School of Agricultural Science, Kobe University, Kobe, Japan
| | - Yi-Hua Chen
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Jeng-Yi Li
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Meng-Yun Li
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Mei-Yeh Jade Lu
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | | | - Wen-Hsiung Li
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan.,Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program, Academia Sinica and National Chung-Hsing University, Taipei, Taiwan.,Biotechnology Center, National Chung-Hsing University, Taichung, Taiwan.,Department of Ecology and Evolution, University of Chicago, Chicago, IL
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13
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Cho HY, Lu MYJ, Shih MC. The SnRK1-eIFiso4G1 signaling relay regulates the translation of specific mRNAs in Arabidopsis under submergence. New Phytol 2019; 222:366-381. [PMID: 30414328 DOI: 10.1111/nph.15589] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Accepted: 11/05/2018] [Indexed: 05/20/2023]
Abstract
Cellular responses to oxygen deprivation are essential for survival during energy crises in plants and animals. Hypoxia caused by submergence results in reprogramming of translation dynamic in plants, but the molecular mechanisms are not well understood. Here we show that Arabidopsis Snf1-related protein kinase 1 (SnRK1) phosphorylates the translation initiation factor eIFiso4G to regulate translation dynamic under submergence. In Arabidopsis, there are two eIFiso4G genes, eIFiso4G1 and eIFiso4G2, which belong to the eIF4G family. Both eIFiso4Gs were phosphorylated by SnRK1 under submergence. Interestingly, the eIFiso4G1 knockout mutant, but not the eIFiso4G2 mutant, became more sensitive to submergence, implying that eIFiso4G1 is involved in regulating submergence tolerance in Arabidopsis. Comparison of RNA sequences in the polysome fraction and the RNAs immunoprecipitated by eIFiso4G1 from Col-0 and the SnRK1 and eIFiso4G1 mutants revealed that lack of eIFiso4G1 phosphorylation disrupts the translation of specific mRNAs under submergence. Taken together, our findings suggest that the SnRK1-eIFiso4G1 relay controls the translation of an array of genes under hypoxia, including core hypoxia response genes and genes related to stress response and biosynthetic process.
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Affiliation(s)
- Hsing-Yi Cho
- Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program, Academia Sinica, National Chung-Hsing University, Taipei, 115, Taiwan
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, 115, Taiwan
- Graduate Institute of Biotechnology, National Chung-Hsing University, Taichung, 402, Taiwan
| | - Mei-Yeh Jade Lu
- Biodiversity Research Center, Academia Sinica, Taipei, 115, Taiwan
| | - Ming-Che Shih
- Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program, Academia Sinica, National Chung-Hsing University, Taipei, 115, Taiwan
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, 115, Taiwan
- Biotechnology Center, National Chung-Hsing University, Taichung, 402, Taiwan
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14
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Abstract
Degradome sequencing provides large amounts of data regarding RNA degradation. The degradome library construction described here is modified from the 5'-rapid amplification of cDNA ends (5'-RACE), and each degradome cDNA is sequenced by next-generation sequencing (NGS). Degradome profiles provide information confirming miRNA-mediated cleavage of target genes and allow the identification of novel targets. Furthermore, degradome sequencing provides additional information for the study of RNA processing, such as information regarding RNA-binding proteins. In this chapter, we describe a detailed optimized protocol for constructing a degradome library with high yield and quality, along with NGS and data mining procedures. We hope that the degradome approach will be applied to further studies of non-model organisms.
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Affiliation(s)
- Shih-Shun Lin
- Institute of Biotechnology, National Taiwan University, Taipei, Taiwan.
| | - Yihua Chen
- High Throughput Genomics Core, Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Mei-Yeh Jade Lu
- High Throughput Genomics Core, Biodiversity Research Center, Academia Sinica, Taipei, Taiwan.
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15
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Huang CF, Yu CP, Wu YH, Lu MYJ, Tu SL, Wu SH, Shiu SH, Ku MSB, Li WH. Elevated auxin biosynthesis and transport underlie high vein density in C 4 leaves. Proc Natl Acad Sci U S A 2017; 114:E6884-E6891. [PMID: 28761000 PMCID: PMC5565467 DOI: 10.1073/pnas.1709171114] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
High vein density, a distinctive trait of C4 leaves, is central to both C3-to-C4 evolution and conversion of C3 to C4-like crops. We tested the hypothesis that high vein density in C4 leaves is due to elevated auxin biosynthesis and transport in developing leaves. Up-regulation of genes in auxin biosynthesis pathways and higher auxin content were found in developing C4 leaves compared with developing C3 leaves. The same observation held for maize foliar (C4) and husk (C3) leaf primordia. Moreover, auxin content and vein density were increased in loss-of-function mutants of Arabidopsis MYC2, a suppressor of auxin biosynthesis. Treatment with an auxin biosynthesis inhibitor or an auxin transport inhibitor led to much fewer veins in new leaves. Finally, both Arabidopsis thaliana auxin efflux transporter pin1 and influx transporter lax2 mutants showed reduced vein numbers. Thus, development of high leaf vein density requires elevated auxin biosynthesis and transport.
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Affiliation(s)
- Chi-Fa Huang
- Institute of Molecular and Cellular Biology, National Tsing Hua University, Hsinchu 300, Taiwan
- Biodiversity Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Chun-Ping Yu
- Biodiversity Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Yeh-Hua Wu
- Biodiversity Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Mei-Yeh Jade Lu
- Biodiversity Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Shih-Long Tu
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei 115, Taiwan
| | - Shu-Hsing Wu
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei 115, Taiwan
| | - Shin-Han Shiu
- Department of Plant Biology, Michigan State University, East Lansing, MI 48824;
| | - Maurice S B Ku
- Department of Bioagricultural Science, National Chiayi University, Chiayi 600, Taiwan;
- School of Biological Sciences, Washington State University, Pullman, WA 99164
| | - Wen-Hsiung Li
- Institute of Molecular and Cellular Biology, National Tsing Hua University, Hsinchu 300, Taiwan;
- Biodiversity Research Center, Academia Sinica, Taipei 115, Taiwan
- Department of Ecology and Evolution, University of Chicago, Chicago, IL 60637
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16
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Chen CK, Yu CP, Li SC, Wu SM, Lu MYJ, Chen YH, Chen DR, Ng CS, Ting CT, Li WH. Identification and evolutionary analysis of long non-coding RNAs in zebra finch. BMC Genomics 2017; 18:117. [PMID: 28143393 PMCID: PMC5282891 DOI: 10.1186/s12864-017-3506-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Accepted: 01/14/2017] [Indexed: 02/06/2023] Open
Abstract
Background Long non-coding RNAs (lncRNAs) are important in various biological processes, but very few studies on lncRNA have been conducted in birds. To identify IncRNAs expressed during feather development, we analyzed single-stranded RNA-seq (ssRNA-seq) data from the anterior and posterior dorsal regions during zebra finch (Taeniopygia guttata) embryonic development. Using published transcriptomic data, we further analyzed the evolutionary conservation of IncRNAs in birds and amniotes. Results A total of 1,081 lncRNAs, including 965 intergenic lncRNAs (lincRNAs), 59 intronic lncRNAs, and 57 antisense lncRNAs (lncNATs), were identified using our newly developed pipeline. These avian IncRNAs share similar characteristics with lncRNAs in mammals, such as shorter transcript length, lower exon number, lower average expression level and less sequence conservation than mRNAs. However, the proportion of lncRNAs overlapping with transposable elements in birds is much lower than that in mammals. We predicted the functions of IncRNAs based on the enriched functions of co-expressed protein-coding genes. Clusters of lncRNAs associated with natal down development were identified. The sequences and expression levels of candidate lncRNAs that shared conserved sequences among birds were validated by qPCR in both zebra finch and chicken. Finally, we identified three highly conserved lncRNAs that may be associated with natal down development. Conclusions Our study provides the first systematical identification of avian lncRNAs using ssRNA-seq analysis and offers a resource of embryonically expressed lncRNAs in zebra finch. We also predicted the biological function of identified lncRNAs. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3506-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Chih-Kuan Chen
- Institute of Ecology and Evolutionary Biology, National Taiwan University, Taipei, 10617, Taiwan.,Biodiversity Research Center, Academia Sinica, Taipei, 11529, Taiwan
| | - Chun-Ping Yu
- Biodiversity Research Center, Academia Sinica, Taipei, 11529, Taiwan
| | - Sung-Chou Li
- Department of Medical Research, Genomics and Proteomics Core Laboratory, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, 83301, Taiwan
| | - Siao-Man Wu
- Biodiversity Research Center, Academia Sinica, Taipei, 11529, Taiwan
| | - Mei-Yeh Jade Lu
- Biodiversity Research Center, Academia Sinica, Taipei, 11529, Taiwan
| | - Yi-Hua Chen
- Biodiversity Research Center, Academia Sinica, Taipei, 11529, Taiwan
| | - Di-Rong Chen
- Biodiversity Research Center, Academia Sinica, Taipei, 11529, Taiwan
| | - Chen Siang Ng
- Institute of Molecular and Cellular Biology & Department of Life Science, National Tsing Hua University, Hsinchu, 30013, Taiwan.
| | - Chau-Ti Ting
- Institute of Ecology and Evolutionary Biology, National Taiwan University, Taipei, 10617, Taiwan. .,Department of Life Science & Genome and Systems Biology Degree Program, National Taiwan University, Taipei, 10617, Taiwan. .,Research Center for Developmental Biology and Regenerative Medicine, National Taiwan University, Taipei, 10617, Taiwan.
| | - Wen-Hsiung Li
- Biodiversity Research Center, Academia Sinica, Taipei, 11529, Taiwan. .,Center for the Integrative and Evolutionary Galliformes Genomics (iEGG Center), National Chung Hsing University, Taichung, 40227, Taiwan. .,Department of Ecology and Evolution, University of Chicago, Chicago, IL, 60637, USA.
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17
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Tsai KJ, Lu MYJ, Yang KJ, Li M, Teng Y, Chen S, Ku MSB, Li WH. Assembling the Setaria italica L. Beauv. genome into nine chromosomes and insights into regions affecting growth and drought tolerance. Sci Rep 2016; 6:35076. [PMID: 27734962 PMCID: PMC5062080 DOI: 10.1038/srep35076] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Accepted: 09/23/2016] [Indexed: 12/23/2022] Open
Abstract
The diploid C4 plant foxtail millet (Setaria italica L. Beauv.) is an important crop in many parts of Africa and Asia for the vast consumption of its grain and ability to grow in harsh environments, but remains understudied in terms of complete genomic architecture. To date, there have been only two genome assembly and annotation efforts with neither assembly reaching over 86% of the estimated genome size. We have combined de novo assembly with custom reference-guided improvements on a popular cultivar of foxtail millet and have achieved a genome assembly of 477 Mbp in length, which represents over 97% of the estimated 490 Mbp. The assembly anchors over 98% of the predicted genes to the nine assembled nuclear chromosomes and contains more functional annotation gene models than previous assemblies. Our annotation has identified a large number of unique gene ontology terms related to metabolic activities, a region of chromosome 9 with several growth factor proteins, and regions syntenic with pearl millet or maize genomic regions that have been previously shown to affect growth. The new assembly and annotation for this important species can be used for detailed investigation and future innovations in growth for millet and other grains.
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Affiliation(s)
- Kevin J. Tsai
- Bioinformatics Program, Taiwan International Graduate Program, Institute of Information Science, Academia Sinica, Taipei, 11574 Taiwan
- Institute of Biomedical Informatics, National Yang-Ming University, Taipei, 11221 Taiwan
- Biodiversity Research Center, Academia Sinica, Taipei, 11574 Taiwan
| | - Mei-Yeh Jade Lu
- Biodiversity Research Center, Academia Sinica, Taipei, 11574 Taiwan
| | - Kai-Jung Yang
- Biodiversity Research Center, Academia Sinica, Taipei, 11574 Taiwan
| | - Mengyun Li
- Biodiversity Research Center, Academia Sinica, Taipei, 11574 Taiwan
| | - Yuchuan Teng
- Biodiversity Research Center, Academia Sinica, Taipei, 11574 Taiwan
| | - Shihmay Chen
- Biodiversity Research Center, Academia Sinica, Taipei, 11574 Taiwan
| | - Maurice S. B. Ku
- Department of Bioagricultural Science, National Chiayi University, Chiayi, 60004 Taiwan
- School of Biological Sciences, Washington State University, Pullman, WA 99164, USA
| | - Wen-Hsiung Li
- Biodiversity Research Center, Academia Sinica, Taipei, 11574 Taiwan
- Department of Ecology and Evolution, University of Chicago, Chicago, IL 60637 USA
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18
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Chen CK, Ng CS, Wu SM, Chen JJ, Cheng PL, Wu P, Lu MYJ, Chen DR, Chuong CM, Cheng HC, Ting CT, Li WH. Regulatory Differences in Natal Down Development between Altricial Zebra Finch and Precocial Chicken. Mol Biol Evol 2016; 33:2030-43. [PMID: 27189543 DOI: 10.1093/molbev/msw085] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Birds can be classified into altricial and precocial. The hatchlings of altricial birds are almost naked, whereas those of precocial birds are covered with natal down. This regulatory divergence is thought to reflect environmental adaptation, but the molecular basis of the divergence is unclear. To address this issue, we chose the altricial zebra finch and the precocial chicken as the model animals. We noted that zebra finch hatchlings show natal down growth suppressed anterior dorsal (AD) skin but partially down-covered posterior dorsal (PD) skin. Comparing the transcriptomes of AD and PD skins, we found that the feather growth promoter SHH (sonic hedgehog) was expressed higher in PD skin than in AD skin. Moreover, the data suggested that the FGF (fibroblast growth factor)/Mitogen-activated protein kinase (MAPK) signaling pathway is involved in natal down growth suppression and that FGF16 is a candidate upstream signaling suppressor. Ectopic expression of FGF16 on chicken leg skin showed downregulation of SHH, upregulation of the feather growth suppressor FGF10, and suppression of feather bud elongation, similar to the phenotype found in zebra finch embryonic AD skin. Therefore, we propose that FGF16-related signals suppress natal down elongation and cause the naked AD skin in zebra finch. Our study provides insights into the regulatory divergence in natal down formation between precocial and altricial birds.
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Affiliation(s)
- Chih-Kuan Chen
- Institute of Ecology and Evolutionary Biology, National Taiwan University, Taipei, Taiwan Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Chen Siang Ng
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan Institute of Molecular and Cellular Biology, National Tsing Hua University, Hsinchu, Taiwan
| | - Siao-Man Wu
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Jiun-Jie Chen
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Po-Liang Cheng
- Department of Life Science, National Chung Hsing University, Taichung, Taiwan
| | - Ping Wu
- Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles
| | - Mei-Yeh Jade Lu
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Di-Rong Chen
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Cheng-Ming Chuong
- Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles Center for the Integrative and Evolutionary Galliformes Genomics (iEGG Center), National Chung Hsing University, Taichung, Taiwan Research Center for Developmental Biology and Regenerative Medicine, National Taiwan University, Taipei, Taiwan
| | - Hsu-Chen Cheng
- Department of Life Science, National Chung Hsing University, Taichung, Taiwan Center for the Integrative and Evolutionary Galliformes Genomics (iEGG Center), National Chung Hsing University, Taichung, Taiwan
| | - Chau-Ti Ting
- Institute of Ecology and Evolutionary Biology, National Taiwan University, Taipei, Taiwan Research Center for Developmental Biology and Regenerative Medicine, National Taiwan University, Taipei, Taiwan Department of Life Science, National Taiwan University, Taipei, Taiwan
| | - Wen-Hsiung Li
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan Center for the Integrative and Evolutionary Galliformes Genomics (iEGG Center), National Chung Hsing University, Taichung, Taiwan Department of Ecology and Evolution, University of Chicago
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Ng CS, Chen CK, Fan WL, Wu P, Wu SM, Chen JJ, Lai YT, Mao CT, Lu MYJ, Chen DR, Lin ZS, Yang KJ, Sha YA, Tu TC, Chen CF, Chuong CM, Li WH. Transcriptomic analyses of regenerating adult feathers in chicken. BMC Genomics 2015; 16:756. [PMID: 26445093 PMCID: PMC4594745 DOI: 10.1186/s12864-015-1966-6] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Accepted: 09/30/2015] [Indexed: 11/13/2022] Open
Abstract
Background Feathers have diverse forms with hierarchical branching patterns and are an excellent model for studying the development and evolution of morphological traits. The complex structure of feathers allows for various types of morphological changes to occur. The genetic basis of the structural differences between different parts of a feather and between different types of feather is a fundamental question in the study of feather diversity, yet there is only limited relevant information for gene expression during feather development. Results We conducted transcriptomic analysis of five zones of feather morphologies from two feather types at different times during their regeneration after plucking. The expression profiles of genes associated with the development of feather structure were examined. We compared the gene expression patterns in different types of feathers and different portions of a feather and identified morphotype-specific gene expression patterns. Many candidate genes were identified for growth control, morphogenesis, or the differentiation of specific structures of different feather types. Conclusion This study laid the ground work for studying the evolutionary origin and diversification of feathers as abundant data were produced for the study of feather morphogenesis. It significantly increased our understanding of the complex molecular and cellular events in feather development processes and provided a foundation for future studies on the development of other skin appendages. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1966-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Chen Siang Ng
- Biodiversity Research Center, Academia Sinica, Taipei, 11529, Taiwan.
| | - Chih-Kuan Chen
- Biodiversity Research Center, Academia Sinica, Taipei, 11529, Taiwan. .,Institute of Ecology and Evolutionary Biology, National Taiwan University, Taipei, 10617, Taiwan.
| | - Wen-Lang Fan
- Biodiversity Research Center, Academia Sinica, Taipei, 11529, Taiwan. .,Whole-Genome Research Core Laboratory of Human Diseases, Chang Gung Memorial Hospital, Keelung, 20401, Taiwan.
| | - Ping Wu
- Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, USA.
| | - Siao-Man Wu
- Biodiversity Research Center, Academia Sinica, Taipei, 11529, Taiwan.
| | - Jiun-Jie Chen
- Biodiversity Research Center, Academia Sinica, Taipei, 11529, Taiwan.
| | - Yu-Ting Lai
- Biodiversity Research Center, Academia Sinica, Taipei, 11529, Taiwan.
| | - Chi-Tang Mao
- Biodiversity Research Center, Academia Sinica, Taipei, 11529, Taiwan.
| | - Mei-Yeh Jade Lu
- Biodiversity Research Center, Academia Sinica, Taipei, 11529, Taiwan.
| | - Di-Rong Chen
- Biodiversity Research Center, Academia Sinica, Taipei, 11529, Taiwan.
| | - Ze-Shiang Lin
- Biodiversity Research Center, Academia Sinica, Taipei, 11529, Taiwan.
| | - Kai-Jung Yang
- Biodiversity Research Center, Academia Sinica, Taipei, 11529, Taiwan.
| | - Yuan-An Sha
- Department of Animal Science, National Chung Hsing University, Taichung, 40227, Taiwan.
| | - Tsung-Che Tu
- Department of Animal Science, National Chung Hsing University, Taichung, 40227, Taiwan.
| | - Chih-Feng Chen
- Department of Animal Science, National Chung Hsing University, Taichung, 40227, Taiwan. .,Center for the Integrative and Evolutionary Galliformes Genomics (iEGG Center), National Chung Hsing University, Taichung, 40227, Taiwan.
| | - Cheng-Ming Chuong
- Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, USA. .,Center for the Integrative and Evolutionary Galliformes Genomics (iEGG Center), National Chung Hsing University, Taichung, 40227, Taiwan. .,Integrative Stem Cell Center, China Medical University, Taichung, 40402, Taiwan.
| | - Wen-Hsiung Li
- Biodiversity Research Center, Academia Sinica, Taipei, 11529, Taiwan. .,Center for the Integrative and Evolutionary Galliformes Genomics (iEGG Center), National Chung Hsing University, Taichung, 40227, Taiwan. .,Integrative Stem Cell Center, China Medical University, Taichung, 40402, Taiwan. .,Department of Ecology and Evolution, University of Chicago, Chicago, IL, 60637, USA.
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Shiao MS, Chang JM, Fan WL, Lu MYJ, Notredame C, Fang S, Kondo R, Li WH. Expression Divergence of Chemosensory Genes between Drosophila sechellia and Its Sibling Species and Its Implications for Host Shift. Genome Biol Evol 2015; 7:2843-58. [PMID: 26430061 PMCID: PMC4684695 DOI: 10.1093/gbe/evv183] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Drosophila sechellia relies exclusively on the fruits of Morinda citrifolia, which are toxic to most insects, including its sibling species Drosophila melanogaster and Drosophila simulans. Although several odorant binding protein (Obp) genes and olfactory receptor (Or) genes have been suggested to be associated with the D. sechellia host shift, a broad view of how chemosensory genes have contributed to this shift is still lacking. We therefore studied the transcriptomes of antennae, the main organ responsible for detecting food resource and oviposition, of D. sechellia and its two sibling species. We wanted to know whether gene expression, particularly chemosensory genes, has diverged between D. sechellia and its two sibling species. Using a very stringent definition of differential gene expression, we found a higher percentage of chemosensory genes differentially expressed in the D. sechellia lineage (7.8%) than in the D. simulans lineage (5.4%); for upregulated chemosensory genes, the percentages were 8.8% in D. sechellia and 5.2% in D. simulans. Interestingly, Obp50a exhibited the highest upregulation, an approximately 100-fold increase, and Or85c--previously reported to be a larva-specific gene--showed approximately 20-fold upregulation in D. sechellia. Furthermore, Ir84a (ionotropic receptor 84a), which has been proposed to be associated with male courtship behavior, was significantly upregulated in D. sechellia. We also found expression divergence in most of the chemosensory gene families between D. sechellia and the two sibling species. Our observations suggest that the host shift of D. sechellia was associated with the enrichment of differentially expressed, particularly upregulated, chemosensory genes.
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Affiliation(s)
- Meng-Shin Shiao
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan Research Center, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Jia-Ming Chang
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003, Barcelona, Spain Universitat Pompeu Fabra (UPF), Barcelona, Spain Institute of Human Genetics (IGH), UPR 1142, CNRS, Montpellier, France
| | - Wen-Lang Fan
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan Whole-Genome Research Core Laboratory of Human Diseases, Chang Gung Memorial Hospital, Keelung, Taiwan
| | - Mei-Yeh Jade Lu
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Cedric Notredame
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003, Barcelona, Spain Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Shu Fang
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Rumi Kondo
- Graduate School of Humanities and Sciences, Ochanomizu University, Tokyo, Japan
| | - Wen-Hsiung Li
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan Department of Ecology and Evolution, University of Chicago
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Ng CS, Wu P, Fan WL, Yan J, Chen CK, Lai YT, Wu SM, Mao CT, Chen JJ, Lu MYJ, Ho MR, Widelitz RB, Chen CF, Chuong CM, Li WH. Genomic organization, transcriptomic analysis, and functional characterization of avian α- and β-keratins in diverse feather forms. Genome Biol Evol 2014; 6:2258-73. [PMID: 25152353 PMCID: PMC4202321 DOI: 10.1093/gbe/evu181] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Feathers are hallmark avian integument appendages, although they were also present on theropods. They are composed of flexible corneous materials made of α- and β-keratins, but their genomic organization and their functional roles in feathers have not been well studied. First, we made an exhaustive search of α- and β-keratin genes in the new chicken genome assembly (Galgal4). Then, using transcriptomic analysis, we studied α- and β-keratin gene expression patterns in five types of feather epidermis. The expression patterns of β-keratin genes were different in different feather types, whereas those of α-keratin genes were less variable. In addition, we obtained extensive α- and β-keratin mRNA in situ hybridization data, showing that α-keratins and β-keratins are preferentially expressed in different parts of the feather components. Together, our data suggest that feather morphological and structural diversity can largely be attributed to differential combinations of α- and β-keratin genes in different intrafeather regions and/or feather types from different body parts. The expression profiles provide new insights into the evolutionary origin and diversification of feathers. Finally, functional analysis using mutant chicken keratin forms based on those found in the human α-keratin mutation database led to abnormal phenotypes. This demonstrates that the chicken can be a convenient model for studying the molecular biology of human keratin-based diseases.
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Affiliation(s)
- Chen Siang Ng
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Ping Wu
- Department of Pathology, Keck School of Medicine, University of Southern California
| | - Wen-Lang Fan
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Jie Yan
- Department of Pathology, Keck School of Medicine, University of Southern California Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, China
| | - Chih-Kuan Chen
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan Institute of Ecology and Evolutionary Biology, National Taiwan University, Taipei, Taiwan
| | - Yu-Ting Lai
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Siao-Man Wu
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Chi-Tang Mao
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan Molecular Biology of Agricultural Sciences, Taiwan International Graduate Program, Academia Sinica, Taipei, Taiwan Graduate Institute of Biotechnology, National Chung Hsing University, Taichung, Taiwan
| | - Jun-Jie Chen
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Mei-Yeh Jade Lu
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Meng-Ru Ho
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Randall B Widelitz
- Department of Pathology, Keck School of Medicine, University of Southern California
| | - Chih-Feng Chen
- Department of Animal Science, National Chung Hsing University, Taichung, Taiwan Center for the Integrative and Evolutionary Galliformes Genomics (iEGG Center), National Chung Hsing University, Taichung, Taiwan
| | - Cheng-Ming Chuong
- Department of Pathology, Keck School of Medicine, University of Southern California Center for the Integrative and Evolutionary Galliformes Genomics (iEGG Center), National Chung Hsing University, Taichung, Taiwan
| | - Wen-Hsiung Li
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan Department of Ecology and Evolution, University of Chicago
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Fan WL, Ng CS, Chen CF, Lu MYJ, Chen YH, Liu CJ, Wu SM, Chen CK, Chen JJ, Mao CT, Lai YT, Lo WS, Chang WH, Li WH. Genome-wide patterns of genetic variation in two domestic chickens. Genome Biol Evol 2013; 5:1376-92. [PMID: 23814129 PMCID: PMC3730349 DOI: 10.1093/gbe/evt097] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Domestic chickens are excellent models for investigating the genetic basis of phenotypic diversity, as numerous phenotypic changes in physiology, morphology, and behavior in chickens have been artificially selected. Genomic study is required to study genome-wide patterns of DNA variation for dissecting the genetic basis of phenotypic traits. We sequenced the genomes of the Silkie and the Taiwanese native chicken L2 at ∼23- and 25-fold average coverage depth, respectively, using Illumina sequencing. The reads were mapped onto the chicken reference genome (including 5.1% Ns) to 92.32% genome coverage for the two breeds. Using a stringent filter, we identified ∼7.6 million single-nucleotide polymorphisms (SNPs) and 8,839 copy number variations (CNVs) in the mapped regions; 42% of the SNPs have not found in other chickens before. Among the 68,906 SNPs annotated in the chicken sequence assembly, 27,852 were nonsynonymous SNPs located in 13,537 genes. We also identified hundreds of shared and divergent structural and copy number variants in intronic and intergenic regions and in coding regions in the two breeds. Functional enrichments of identified genetic variants were discussed. Radical nsSNP-containing immunity genes were enriched in the QTL regions associated with some economic traits for both breeds. Moreover, genetic changes involved in selective sweeps were detected. From the selective sweeps identified in our two breeds, several genes associated with growth, appetite, and metabolic regulation were identified. Our study provides a framework for genetic and genomic research of domestic chickens and facilitates the domestic chicken as an avian model for genomic, biomedical, and evolutionary studies.
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Affiliation(s)
- Wen-Lang Fan
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
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Abstract
Abstract
Background
Antennae of fruit flies are the major organs responsible for detecting environmental volatiles, e.g., egg-laying substrates. An adult antenna contains many sensilla full of olfactory sensory neurons, where olfactory receptor (Or) genes are expressed. Each sensory neuron only expresses up to three receptors, making it difficult to estimate expression levels by conventional methods. In this study, we applied Illumina RNA sequencing (RNA-seq) to study the expression levels of Or and other genes in fly antennae.
Results
RNA from approximately 1,200 pairs of adult antennae from each sex of Drosophila melanogaster was used to obtain the antennal transcriptome of each sex. We detected approximately 12,000 genes expressed in antennae of either sex. The most highly expressed genes included pheromone-binding genes, transmembrane transporter genes, and sensory reception genes. Among the 61 annotated Or genes, we observed 53 and 54 genes (approximately 90%) expressed (fragments per kilobase of exon per million fragments mapped (FPKM) > 0.05) in male and female antennae, respectively; approximately 25 genes were expressed with FPKM > 15. Compared to previous studies, which extracted RNA from the whole body or head and used microarrays, antenna-specific transcriptomes obtained by RNA-seq provided more reliable estimates of gene expression levels and revealed many lowly expressed genes. Ninty-one genes, including one odorant-binding protein (Obp) gene and four Or genes, were differentially expressed between male and female antennae. These sexually biased genes were enriched on the X chromosome and showed enrichment in different gene ontology categories for male and female flies. The present and previous data together suggest that a gene family with putative immune response functions is related to pheromone detection and involved in the courtship behavior of male flies.
Conclusions
Tissue-specific RNA-seq is powerful for detecting lowly expressed genes. Our study provides new insight into the expression of olfactory-related genes in Drosophila antennae.
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Schaefke B, Emerson JJ, Wang TY, Lu MYJ, Hsieh LC, Li WH. Inheritance of gene expression level and selective constraints on trans- and cis-regulatory changes in yeast. Mol Biol Evol 2013; 30:2121-33. [PMID: 23793114 DOI: 10.1093/molbev/mst114] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Gene expression evolution can be caused by changes in cis- or trans-regulatory elements or both. As cis and trans regulation operate through different molecular mechanisms, cis and trans mutations may show different inheritance patterns and may be subjected to different selective constraints. To investigate these issues, we obtained and analyzed gene expression data from two Saccharomyces cerevisiae strains and their hybrid, using high-throughput sequencing. Our data indicate that compared with other types of genes, those with antagonistic cis-trans interactions are more likely to exhibit over- or underdominant inheritance of expression level. Moreover, in accordance with previous studies, genes with trans variants tend to have a dominant inheritance pattern, whereas cis variants are enriched for additive inheritance. In addition, cis regulatory differences contribute more to expression differences between species than within species, whereas trans regulatory differences show a stronger association between divergence and polymorphism. Our data indicate that in the trans component of gene expression differences genes subjected to weaker selective constraints tend to have an excess of polymorphism over divergence compared with those subjected to stronger selective constraints. In contrast, in the cis component, this difference between genes under stronger and weaker selective constraint is mostly absent. To explain these observations, we propose that purifying selection more strongly shapes trans changes than cis changes and that positive selection may have significantly contributed to cis regulatory divergence.
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Chang YM, Liu WY, Shih ACC, Shen MN, Lu CH, Lu MYJ, Yang HW, Wang TY, Chen SCC, Chen SM, Li WH, Ku MS. Characterizing regulatory and functional differentiation between maize mesophyll and bundle sheath cells by transcriptomic analysis. Plant Physiol 2012; 160:165-77. [PMID: 22829318 PMCID: PMC3440195 DOI: 10.1104/pp.112.203810] [Citation(s) in RCA: 114] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2012] [Accepted: 07/23/2012] [Indexed: 05/18/2023]
Abstract
To study the regulatory and functional differentiation between the mesophyll (M) and bundle sheath (BS) cells of maize (Zea mays), we isolated large quantities of highly homogeneous M and BS cells from newly matured second leaves for transcriptome profiling by RNA sequencing. A total of 52,421 annotated genes with at least one read were found in the two transcriptomes. Defining a gene with more than one read per kilobase per million mapped reads as expressed, we identified 18,482 expressed genes; 14,972 were expressed in M cells, including 53 M-enriched transcription factor (TF) genes, whereas 17,269 were expressed in BS cells, including 214 BS-enriched TF genes. Interestingly, many TF gene families show a conspicuous BS preference in expression. Pathway analyses reveal differentiation between the two cell types in various functional categories, with the M cells playing more important roles in light reaction, protein synthesis and folding, tetrapyrrole synthesis, and RNA binding, while the BS cells specialize in transport, signaling, protein degradation and posttranslational modification, major carbon, hydrogen, and oxygen metabolism, cell division and organization, and development. Genes coding for several transporters involved in the shuttle of C(4) metabolites and BS cell wall development have been identified, to our knowledge, for the first time. This comprehensive data set will be useful for studying M/BS differentiation in regulation and function.
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Affiliation(s)
- Yao-Ming Chang
- Biodiversity Research Center (Y.-M.C., W.-Y.L., M.-N.S., M.-Y.J.L., T.-Y.W., W.-H.L.), Genomics Research Center (Y.-M.C., W.-Y.L., S.M.C., W.-H.L.), and Institute of Information Science (A.C.-C.S., C.-H.L.), Academia Sinica, Taipei, Taiwan 115; Institute of Bioagricultural Science, National Chiayi University, Chiayi, Taiwan 600 (H.-W.Y., M.S.B.K.); Department of Ecology and Evolution, University of Chicago, Chicago, Illinois 60637 (S.C.-C.C., W.-H.L.); and School of Biological Sciences, Washington State University, Pullman, Washington 99164–4238 (M.S.B.K.)
| | - Wen-Yu Liu
- Biodiversity Research Center (Y.-M.C., W.-Y.L., M.-N.S., M.-Y.J.L., T.-Y.W., W.-H.L.), Genomics Research Center (Y.-M.C., W.-Y.L., S.M.C., W.-H.L.), and Institute of Information Science (A.C.-C.S., C.-H.L.), Academia Sinica, Taipei, Taiwan 115; Institute of Bioagricultural Science, National Chiayi University, Chiayi, Taiwan 600 (H.-W.Y., M.S.B.K.); Department of Ecology and Evolution, University of Chicago, Chicago, Illinois 60637 (S.C.-C.C., W.-H.L.); and School of Biological Sciences, Washington State University, Pullman, Washington 99164–4238 (M.S.B.K.)
| | - Arthur Chun-Chieh Shih
- Biodiversity Research Center (Y.-M.C., W.-Y.L., M.-N.S., M.-Y.J.L., T.-Y.W., W.-H.L.), Genomics Research Center (Y.-M.C., W.-Y.L., S.M.C., W.-H.L.), and Institute of Information Science (A.C.-C.S., C.-H.L.), Academia Sinica, Taipei, Taiwan 115; Institute of Bioagricultural Science, National Chiayi University, Chiayi, Taiwan 600 (H.-W.Y., M.S.B.K.); Department of Ecology and Evolution, University of Chicago, Chicago, Illinois 60637 (S.C.-C.C., W.-H.L.); and School of Biological Sciences, Washington State University, Pullman, Washington 99164–4238 (M.S.B.K.)
| | - Meng-Ni Shen
- Biodiversity Research Center (Y.-M.C., W.-Y.L., M.-N.S., M.-Y.J.L., T.-Y.W., W.-H.L.), Genomics Research Center (Y.-M.C., W.-Y.L., S.M.C., W.-H.L.), and Institute of Information Science (A.C.-C.S., C.-H.L.), Academia Sinica, Taipei, Taiwan 115; Institute of Bioagricultural Science, National Chiayi University, Chiayi, Taiwan 600 (H.-W.Y., M.S.B.K.); Department of Ecology and Evolution, University of Chicago, Chicago, Illinois 60637 (S.C.-C.C., W.-H.L.); and School of Biological Sciences, Washington State University, Pullman, Washington 99164–4238 (M.S.B.K.)
| | - Chen-Hua Lu
- Biodiversity Research Center (Y.-M.C., W.-Y.L., M.-N.S., M.-Y.J.L., T.-Y.W., W.-H.L.), Genomics Research Center (Y.-M.C., W.-Y.L., S.M.C., W.-H.L.), and Institute of Information Science (A.C.-C.S., C.-H.L.), Academia Sinica, Taipei, Taiwan 115; Institute of Bioagricultural Science, National Chiayi University, Chiayi, Taiwan 600 (H.-W.Y., M.S.B.K.); Department of Ecology and Evolution, University of Chicago, Chicago, Illinois 60637 (S.C.-C.C., W.-H.L.); and School of Biological Sciences, Washington State University, Pullman, Washington 99164–4238 (M.S.B.K.)
| | - Mei-Yeh Jade Lu
- Biodiversity Research Center (Y.-M.C., W.-Y.L., M.-N.S., M.-Y.J.L., T.-Y.W., W.-H.L.), Genomics Research Center (Y.-M.C., W.-Y.L., S.M.C., W.-H.L.), and Institute of Information Science (A.C.-C.S., C.-H.L.), Academia Sinica, Taipei, Taiwan 115; Institute of Bioagricultural Science, National Chiayi University, Chiayi, Taiwan 600 (H.-W.Y., M.S.B.K.); Department of Ecology and Evolution, University of Chicago, Chicago, Illinois 60637 (S.C.-C.C., W.-H.L.); and School of Biological Sciences, Washington State University, Pullman, Washington 99164–4238 (M.S.B.K.)
| | - Hui-Wen Yang
- Biodiversity Research Center (Y.-M.C., W.-Y.L., M.-N.S., M.-Y.J.L., T.-Y.W., W.-H.L.), Genomics Research Center (Y.-M.C., W.-Y.L., S.M.C., W.-H.L.), and Institute of Information Science (A.C.-C.S., C.-H.L.), Academia Sinica, Taipei, Taiwan 115; Institute of Bioagricultural Science, National Chiayi University, Chiayi, Taiwan 600 (H.-W.Y., M.S.B.K.); Department of Ecology and Evolution, University of Chicago, Chicago, Illinois 60637 (S.C.-C.C., W.-H.L.); and School of Biological Sciences, Washington State University, Pullman, Washington 99164–4238 (M.S.B.K.)
| | - Tzi-Yuan Wang
- Biodiversity Research Center (Y.-M.C., W.-Y.L., M.-N.S., M.-Y.J.L., T.-Y.W., W.-H.L.), Genomics Research Center (Y.-M.C., W.-Y.L., S.M.C., W.-H.L.), and Institute of Information Science (A.C.-C.S., C.-H.L.), Academia Sinica, Taipei, Taiwan 115; Institute of Bioagricultural Science, National Chiayi University, Chiayi, Taiwan 600 (H.-W.Y., M.S.B.K.); Department of Ecology and Evolution, University of Chicago, Chicago, Illinois 60637 (S.C.-C.C., W.-H.L.); and School of Biological Sciences, Washington State University, Pullman, Washington 99164–4238 (M.S.B.K.)
| | - Sean C.-C. Chen
- Biodiversity Research Center (Y.-M.C., W.-Y.L., M.-N.S., M.-Y.J.L., T.-Y.W., W.-H.L.), Genomics Research Center (Y.-M.C., W.-Y.L., S.M.C., W.-H.L.), and Institute of Information Science (A.C.-C.S., C.-H.L.), Academia Sinica, Taipei, Taiwan 115; Institute of Bioagricultural Science, National Chiayi University, Chiayi, Taiwan 600 (H.-W.Y., M.S.B.K.); Department of Ecology and Evolution, University of Chicago, Chicago, Illinois 60637 (S.C.-C.C., W.-H.L.); and School of Biological Sciences, Washington State University, Pullman, Washington 99164–4238 (M.S.B.K.)
| | - Stella Maris Chen
- Biodiversity Research Center (Y.-M.C., W.-Y.L., M.-N.S., M.-Y.J.L., T.-Y.W., W.-H.L.), Genomics Research Center (Y.-M.C., W.-Y.L., S.M.C., W.-H.L.), and Institute of Information Science (A.C.-C.S., C.-H.L.), Academia Sinica, Taipei, Taiwan 115; Institute of Bioagricultural Science, National Chiayi University, Chiayi, Taiwan 600 (H.-W.Y., M.S.B.K.); Department of Ecology and Evolution, University of Chicago, Chicago, Illinois 60637 (S.C.-C.C., W.-H.L.); and School of Biological Sciences, Washington State University, Pullman, Washington 99164–4238 (M.S.B.K.)
| | - Wen-Hsiung Li
- Biodiversity Research Center (Y.-M.C., W.-Y.L., M.-N.S., M.-Y.J.L., T.-Y.W., W.-H.L.), Genomics Research Center (Y.-M.C., W.-Y.L., S.M.C., W.-H.L.), and Institute of Information Science (A.C.-C.S., C.-H.L.), Academia Sinica, Taipei, Taiwan 115; Institute of Bioagricultural Science, National Chiayi University, Chiayi, Taiwan 600 (H.-W.Y., M.S.B.K.); Department of Ecology and Evolution, University of Chicago, Chicago, Illinois 60637 (S.C.-C.C., W.-H.L.); and School of Biological Sciences, Washington State University, Pullman, Washington 99164–4238 (M.S.B.K.)
| | - Maurice S.B. Ku
- Biodiversity Research Center (Y.-M.C., W.-Y.L., M.-N.S., M.-Y.J.L., T.-Y.W., W.-H.L.), Genomics Research Center (Y.-M.C., W.-Y.L., S.M.C., W.-H.L.), and Institute of Information Science (A.C.-C.S., C.-H.L.), Academia Sinica, Taipei, Taiwan 115; Institute of Bioagricultural Science, National Chiayi University, Chiayi, Taiwan 600 (H.-W.Y., M.S.B.K.); Department of Ecology and Evolution, University of Chicago, Chicago, Illinois 60637 (S.C.-C.C., W.-H.L.); and School of Biological Sciences, Washington State University, Pullman, Washington 99164–4238 (M.S.B.K.)
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Chen HL, Chen YC, Lu MYJ, Chang JJ, Wang HTC, Ke HM, Wang TY, Ruan SK, Wang TY, Hung KY, Cho HY, Lin WT, Shih MC, Li WH. A highly efficient β-glucosidase from the buffalo rumen fungus Neocallimastix patriciarum W5. Biotechnol Biofuels 2012; 5:24. [PMID: 22515264 PMCID: PMC3403894 DOI: 10.1186/1754-6834-5-24] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2011] [Accepted: 04/19/2012] [Indexed: 05/07/2023]
Abstract
BACKGROUND Cellulose, which is the most abundant renewable biomass on earth, is a potential bio-resource of alternative energy. The hydrolysis of plant polysaccharides is catalyzed by microbial cellulases, including endo-β-1,4-glucanases, cellobiohydrolases, cellodextrinases, and β-glucosidases. Converting cellobiose by β-glucosidases is the key factor for reducing cellobiose inhibition and enhancing the efficiency of cellulolytic enzymes for cellulosic ethanol production. RESULTS In this study, a cDNA encoding β-glucosidase was isolated from the buffalo rumen fungus Neocallimastix patriciarum W5 and is named NpaBGS. It has a length of 2,331 bp with an open reading frame coding for a protein of 776 amino acid residues, corresponding to a theoretical molecular mass of 85.1 kDa and isoelectric point of 4.4. Two GH3 catalytic domains were found at the N and C terminals of NpaBGS by sequence analysis. The cDNA was expressed in Pichia pastoris and after protein purification, the enzyme displayed a specific activity of 34.5 U/mg against cellobiose as the substrate. Enzymatic assays showed that NpaBGS was active on short cello-oligosaccharides from various substrates. A weak activity in carboxymethyl cellulose (CMC) digestion indicated that the enzyme might also have the function of an endoglucanase. The optimal activity was detected at 40°C and pH 5 ~ 6, showing that the enzyme prefers a weak acid condition. Moreover, its activity could be enhanced at 50°C by adding Mg2+ or Mn2+ ions. Interestingly, in simultaneous saccharification and fermentation (SSF) experiments using Saccharomyces cerevisiae BY4741 or Kluyveromyces marxianus KY3 as the fermentation yeast, NpaBGS showed advantages in cell growth, glucose production, and ethanol production over the commercial enzyme Novo 188. Moreover, we showed that the KY3 strain engineered with the NpaNGS gene can utilize 2 % dry napiergrass as the sole carbon source to produce 3.32 mg/ml ethanol when Celluclast 1.5 L was added to the SSF system. CONCLUSION Our characterizations of the novel β-glucosidase NpaBGS revealed that it has a preference of weak acidity for optimal yeast fermentation and an optimal temperature of ~40°C. Since NpaBGS performs better than Novo 188 under the living conditions of fermentation yeasts, it has the potential to be a suitable enzyme for SSF.
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Affiliation(s)
- Hsin-Liang Chen
- Biodiversity Research Center, Academia Sinica, Taipei, 115, Taiwan
| | - Yo-Chia Chen
- Department of Biological Science & Technology, National Pingtung University of Science & Technology, Neipu Hsiang, Pingtung, 91201, Taiwan
| | - Mei-Yeh Jade Lu
- Biodiversity Research Center, Academia Sinica, Taipei, 115, Taiwan
| | - Jui-Jen Chang
- Biodiversity Research Center, Academia Sinica, Taipei, 115, Taiwan
- Genomics Research Center, Academia Sinica, Taipei, 115, Taiwan
| | | | - Huei-Mien Ke
- Biodiversity Research Center, Academia Sinica, Taipei, 115, Taiwan
- Program in Microbial Genomics, National Chung-Hsing University, Taichung, 402, Taiwan
| | - Tzi-Yuan Wang
- Biodiversity Research Center, Academia Sinica, Taipei, 115, Taiwan
| | - Sz-Kai Ruan
- Biodiversity Research Center, Academia Sinica, Taipei, 115, Taiwan
| | - Tao-Yuan Wang
- Biodiversity Research Center, Academia Sinica, Taipei, 115, Taiwan
| | - Kuo-Yen Hung
- Genomics Research Center, Academia Sinica, Taipei, 115, Taiwan
| | - Hsing-Yi Cho
- Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program, National Chung-Hsing University – Academia Sinica, Taipei, 115, Taiwan
- Graduate Institute of Biotechnology, National Chung-Hsing University, Taichung, 402, Taiwan
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, 115, Taiwan
| | - Wan-Ting Lin
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, 115, Taiwan
| | - Ming-Che Shih
- Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program, National Chung-Hsing University – Academia Sinica, Taipei, 115, Taiwan
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, 115, Taiwan
- Biotechnology Center, National Chung-Hsing University, Taichung, 402, Taiwan
| | - Wen-Hsiung Li
- Biodiversity Research Center, Academia Sinica, Taipei, 115, Taiwan
- Genomics Research Center, Academia Sinica, Taipei, 115, Taiwan
- Biotechnology Center, National Chung-Hsing University, Taichung, 402, Taiwan
- Department of Ecology and Evolution, University of Chicago, Chicago, IL, 60637, USA
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Shiao MS, Chang AYF, Liao BY, Ching YH, Lu MYJ, Chen SM, Li WH. Transcriptomes of mouse olfactory epithelium reveal sexual differences in odorant detection. Genome Biol Evol 2012; 4:703-12. [PMID: 22511034 PMCID: PMC3381674 DOI: 10.1093/gbe/evs039] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
To sense numerous odorants and chemicals, animals have evolved a large number of olfactory receptor genes (Olfrs) in their genome. In particular, the house mouse has ∼1,100 genes in the Olfr gene family. This makes the mouse a good model organism to study Olfr genes and olfaction-related genes. To date, whether male and female mice possess the same ability in detecting environmental odorants is still unknown. Using the next generation sequencing technology (paired-end mRNA-seq), we detected 1,088 expressed Olfr genes in both male and female olfactory epithelium. We found that not only Olfr genes but also odorant-binding protein (Obp) genes have evolved rapidly in the mouse lineage. Interestingly, Olfr genes tend to express at a higher level in males than in females, whereas the Obp genes clustered on the X chromosome show the opposite trend. These observations may imply a more efficient odorant-transporting system in females, whereas a more active Olfr gene expressing system in males. In addition, we detected the expression of two genes encoding major urinary proteins, which have been proposed to bind and transport pheromones or act as pheromones in mouse urine. This observation suggests a role of main olfactory system (MOS) in pheromone detection, contrary to the view that only accessory olfactory system (AOS) is involved in pheromone detection. This study suggests the sexual differences in detecting environmental odorants in MOS and demonstrates that mRNA-seq provides a powerful tool for detecting genes with low expression levels and with high sequence similarities.
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Affiliation(s)
- Meng-Shin Shiao
- Genomics Research Center, Academia Sinica, Taipei, Taiwan, ROC
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Abstract
Gene expression is regulated both by cis elements, which are DNA segments closely linked to the genes they regulate, and by trans factors, which are usually proteins capable of diffusing to unlinked genes. Understanding the patterns and sources of regulatory variation is crucial for understanding phenotypic and genome evolution. Here, we measure genome-wide allele-specific expression by deep sequencing to investigate the patterns of cis and trans expression variation between two strains of Saccharomyces cerevisiae. We propose a statistical modeling framework based on the binomial distribution that simultaneously addresses normalization of read counts derived from different parents and estimating the cis and trans expression variation parameters. We find that expression polymorphism in yeast is common for both cis and trans, though trans variation is more common. Constraint in expression evolution is correlated with other hallmarks of constraint, including gene essentiality, number of protein interaction partners, and constraint in amino acid substitution, indicating that both cis and trans polymorphism are clearly under purifying selection, though trans variation appears to be more sensitive to selective constraint. Comparing interspecific expression divergence between S. cerevisiae and S. paradoxus to our intraspecific variation suggests a significant departure from a neutral model of molecular evolution. A further examination of correlation between polymorphism and divergence within each category suggests that cis divergence is more frequently mediated by positive Darwinian selection than is trans divergence.
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Affiliation(s)
- J J Emerson
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan
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