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Zheng Y, Zhou Y, Huang Y, Wang H, Guo H, Yuan B, Zhang J. Transcriptome sequencing of black and white hair follicles in the giant panda. Integr Zool 2022; 18:552-568. [PMID: 35500067 DOI: 10.1111/1749-4877.12652] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
With the completion of the draft assembly of the giant panda genome sequence, RNA sequencing technology has been widely used in genetic research on giant pandas. We used RNA-seq to examine black and white hair follicle samples from adult pandas. By comparison with the giant panda genome, 75 963 SNP loci were labeled, 2 426 differentially expressed genes were identified, and 2 029 new genes were discovered, among which 631 were functionally annotated. A cluster analysis of the differentially expressed genes showed that they were mainly related to the Wnt signaling pathway, ECM-receptor interaction, the p53 signaling pathway and ribosome processing. The enrichment results showed that there were significant differences in the regulatory networks of hair follicles with different colors during the transitional stage of hair follicle resting growth, which may play a regulatory role in melanin synthesis during growth. In conclusion, our results provide new insights and more data support for research on the color formation in giant pandas. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Yi Zheng
- Department of Laboratory Animals, Jilin Provincial Key Laboratory of Animal Model, Jilin University, Changchun, China
| | - Yingmin Zhou
- Key Laboratory of SFGA on Conservation Biology of Rare Animals in The Giant Panda National Park, China
| | - Yijie Huang
- Department of Laboratory Animals, Jilin Provincial Key Laboratory of Animal Model, Jilin University, Changchun, China
| | - Haoqi Wang
- Department of Laboratory Animals, Jilin Provincial Key Laboratory of Animal Model, Jilin University, Changchun, China
| | - Haixiang Guo
- Department of Laboratory Animals, Jilin Provincial Key Laboratory of Animal Model, Jilin University, Changchun, China
| | - Bao Yuan
- Department of Laboratory Animals, Jilin Provincial Key Laboratory of Animal Model, Jilin University, Changchun, China
| | - Jiabao Zhang
- Department of Laboratory Animals, Jilin Provincial Key Laboratory of Animal Model, Jilin University, Changchun, China
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2
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Transcriptome Profiling across Five Tissues of Giant Panda. BIOMED RESEARCH INTERNATIONAL 2020; 2020:3852586. [PMID: 32851066 PMCID: PMC7436357 DOI: 10.1155/2020/3852586] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Revised: 05/03/2020] [Accepted: 06/01/2020] [Indexed: 11/18/2022]
Abstract
Gene differential expression studies can serve to explore and understand the laws and characteristics of animal life activities, and the difference in gene expression between different animal tissues has been well demonstrated and studied. However, for the world-famous rare and protected species giant panda (Ailuropoda melanoleuca), only the transcriptome of the blood and spleen has been reported separately. Here, in order to explore the transcriptome differences between the different tissues of the giant panda, transcriptome profiles of the heart, liver, spleen, lung, and kidney from five captive giant pandas were constructed with Illumina HiSeq 2500 platform. The comparative analysis of the intertissue gene expression patterns was carried out based on the generated RNA sequencing datasets. Analyses of Gene Ontology (GO) enrichment, Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment, and protein-protein interaction (PPI) network were performed according to the identified differentially expressed genes (DEGs). We generated 194.52 GB clean base data from twenty-five sequencing libraries and identified 18,701 genes, including 3492 novel genes. With corrected p value <0.05 and |log2FoldChange| >2, we finally obtained 921, 553, 574, 457, and 638 tissue-specific DEGs in the heart, liver, spleen, lung, and kidney, respectively. In addition, we identified TTN, CAV3, LDB3, TRDN, and ACTN2 in the heart; FGA, AHSG, and SERPINC1 in the liver; CD19, CD79B, and IL21R in the spleen; NKX2-4 and SFTPB in the lung; GC and HRG in the kidney as hub genes in the PPI network. The results of the analyses showed a similar gene expression pattern between the spleen and lung. This study provided for the first time the heart, liver, lung, and kidney's transcriptome resources of the giant panda, and it provided a valuable resource for further genetic research or other potential research.
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3
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Du L, Liu Q, Shen F, Fan Z, Hou R, Yue B, Zhang X. Transcriptome analysis reveals immune-related gene expression changes with age in giant panda ( Ailuropoda melanoleuca) blood. Aging (Albany NY) 2020; 11:249-262. [PMID: 30641486 PMCID: PMC6339791 DOI: 10.18632/aging.101747] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Accepted: 12/26/2018] [Indexed: 12/24/2022]
Abstract
The giant panda (Ailuropoda melanoleuca), an endangered species endemic to western China, has long been threatened with extinction that is exacerbated by highly contagious and fatal diseases. Aging is the most well-defined risk factor for diseases and is associated with a decline in immune function leading to increased susceptibility to infection and reduced response to vaccination. Therefore, this study aimed to determine which genes and pathways show differential expression with age in blood tissues. We obtained 210 differentially expressed genes by RNA-seq, including 146 up-regulated and 64 down-regulated genes in old pandas (18-21yrs) compared to young pandas (2-6yrs). We identified ISG15, STAT1, IRF7 and DDX58 as the hub genes in the protein-protein interaction network. All of these genes were up-regulated with age and played important roles in response to pathogen invasion. Functional enrichment analysis indicated that up-regulated genes were mainly involved in innate immune response, while the down-regulated genes were mainly related to B cell activation. These may suggest that the innate immunity is relatively well preserved to compensate for the decline in the adaptive immune function. In conclusion, our findings will provide a foundation for future studies on the molecular mechanisms underlying immune changes associated with ageing.
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Affiliation(s)
- Lianming Du
- Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, College of Life Science, Sichuan University, Chengdu 610064, China.,Institute for Advanced Study, Chengdu University, Chengdu 610106, China
| | - Qin Liu
- Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, College of Life Science, Sichuan University, Chengdu 610064, China.,College of Life Sciences and Food Engineering, Yibin University, Yibin 644000, China
| | - Fujun Shen
- The Sichuan Key Laboratory for Conservation Biology of Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu 610081, China
| | - Zhenxin Fan
- Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, College of Life Science, Sichuan University, Chengdu 610064, China
| | - Rong Hou
- The Sichuan Key Laboratory for Conservation Biology of Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu 610081, China
| | - Bisong Yue
- Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, College of Life Science, Sichuan University, Chengdu 610064, China
| | - Xiuyue Zhang
- Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, College of Life Science, Sichuan University, Chengdu 610064, China
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4
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Fan H, Wu Q, Wei F, Yang F, Ng BL, Hu Y. Chromosome-level genome assembly for giant panda provides novel insights into Carnivora chromosome evolution. Genome Biol 2019; 20:267. [PMID: 31810476 PMCID: PMC6898958 DOI: 10.1186/s13059-019-1889-7] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 11/15/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Chromosome evolution is an important driver of speciation and species evolution. Previous studies have detected chromosome rearrangement events among different Carnivora species using chromosome painting strategies. However, few of these studies have focused on chromosome evolution at a nucleotide resolution due to the limited availability of chromosome-level Carnivora genomes. Although the de novo genome assembly of the giant panda is available, current short read-based assemblies are limited to moderately sized scaffolds, making the study of chromosome evolution difficult. RESULTS Here, we present a chromosome-level giant panda draft genome with a total size of 2.29 Gb. Based on the giant panda genome and published chromosome-level dog and cat genomes, we conduct six large-scale pairwise synteny alignments and identify evolutionary breakpoint regions. Interestingly, gene functional enrichment analysis shows that for all of the three Carnivora genomes, some genes located in evolutionary breakpoint regions are significantly enriched in pathways or terms related to sensory perception of smell. In addition, we find that the sweet receptor gene TAS1R2, which has been proven to be a pseudogene in the cat genome, is located in an evolutionary breakpoint region of the giant panda, suggesting that interchromosomal rearrangement may play a role in the cat TAS1R2 pseudogenization. CONCLUSIONS We show that the combined strategies employed in this study can be used to generate efficient chromosome-level genome assemblies. Moreover, our comparative genomics analyses provide novel insights into Carnivora chromosome evolution, linking chromosome evolution to functional gene evolution.
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Affiliation(s)
- Huizhong Fan
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Qi Wu
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Fuwen Wei
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
| | - Fengtang Yang
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Bee Ling Ng
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Yibo Hu
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.
- University of Chinese Academy of Sciences, Beijing, China.
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China.
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5
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Srivastava A, Kumar Sarsani V, Fiddes I, Sheehan SM, Seger RL, Barter ME, Neptune-Bear S, Lindqvist C, Korstanje R. Genome assembly and gene expression in the American black bear provides new insights into the renal response to hibernation. DNA Res 2019; 26:37-44. [PMID: 30395234 PMCID: PMC6379037 DOI: 10.1093/dnares/dsy036] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2018] [Accepted: 10/04/2018] [Indexed: 12/16/2022] Open
Abstract
The prevalence of chronic kidney disease (CKD) is rising worldwide and 10-15% of the global population currently suffers from CKD and its complications. Given the increasing prevalence of CKD there is an urgent need to find novel treatment options. The American black bear (Ursus americanus) copes with months of lowered kidney function and metabolism during hibernation without the devastating effects on metabolism and other consequences observed in humans. In a biomimetic approach to better understand kidney adaptations and physiology in hibernating black bears, we established a high-quality genome assembly. Subsequent RNA-Seq analysis of kidneys comparing gene expression profiles in black bears entering (late fall) and emerging (early spring) from hibernation identified 169 protein-coding genes that were differentially expressed. Of these, 101 genes were downregulated and 68 genes were upregulated after hibernation. Fold changes ranged from 1.8-fold downregulation (RTN4RL2) to 2.4-fold upregulation (CISH). Most notable was the upregulation of cytokine suppression genes (SOCS2, CISH, and SERPINC1) and the lack of increased expression of cytokines and genes involved in inflammation. The identification of these differences in gene expression in the black bear kidney may provide new insights in the prevention and treatment of CKD.
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Affiliation(s)
| | | | - Ian Fiddes
- Genomics Institute, University of California, Santa Cruz, CA, USA
| | | | - Rita L Seger
- Animal and Veterinary Sciences Program, University of Maine, Orono, ME, USA
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6
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Mu Y, Huo J, Guan Y, Fan D, Xiao X, Wei J, Li Q, Mu P, Ao J, Chen X. An improved genome assembly for Larimichthys crocea reveals hepcidin gene expansion with diversified regulation and function. Commun Biol 2018; 1:195. [PMID: 30480097 PMCID: PMC6240063 DOI: 10.1038/s42003-018-0207-3] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Accepted: 10/25/2018] [Indexed: 12/11/2022] Open
Abstract
Larimichthys crocea (large yellow croaker) is a type of perciform fish well known for its peculiar physiological properties and economic value. Here, we constructed an improved version of the L. crocea genome assembly, which contained 26,100 protein-coding genes. Twenty-four pseudo-chromosomes of L. crocea were also reconstructed, comprising 90% of the genome assembly. This improved assembly revealed several expansions in gene families associated with olfactory detection, detoxification, and innate immunity. Specifically, six hepcidin genes (LcHamps) were identified in L. crocea, possibly resulting from lineage-specific gene duplication. All LcHamps possessed similar genomic structures and functional domains, but varied substantially with respect to expression pattern, transcriptional regulation, and biological function. LcHamp1 was associated specifically with iron metabolism, while LcHamp2s were functionally diverse, involving in antibacterial activity, antiviral activity, and regulation of intracellular iron metabolism. This functional diversity among gene copies may have allowed L. crocea to adapt to diverse environmental conditions.
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Affiliation(s)
- Yinnan Mu
- Institute of Oceanology, College of Animal Sciences, Fujian Agriculture and Forestry University, 350002, Fuzhou, China
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, State Oceanic Administration, 361005, Xiamen, China
| | - Jieying Huo
- Institute of Oceanology, College of Animal Sciences, Fujian Agriculture and Forestry University, 350002, Fuzhou, China
| | - Yanyun Guan
- Institute of Oceanology, College of Animal Sciences, Fujian Agriculture and Forestry University, 350002, Fuzhou, China
| | | | - Xiaoqiang Xiao
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, State Oceanic Administration, 361005, Xiamen, China
| | - Jingguang Wei
- College of Marine Sciences, South China Agricultural University, Guangzhou, China
| | - Qiuhua Li
- Institute of Oceanology, College of Animal Sciences, Fujian Agriculture and Forestry University, 350002, Fuzhou, China
| | - Pengfei Mu
- Institute of Oceanology, College of Animal Sciences, Fujian Agriculture and Forestry University, 350002, Fuzhou, China
| | - Jingqun Ao
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, State Oceanic Administration, 361005, Xiamen, China
| | - Xinhua Chen
- Institute of Oceanology, College of Animal Sciences, Fujian Agriculture and Forestry University, 350002, Fuzhou, China.
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, State Oceanic Administration, 361005, Xiamen, China.
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.
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7
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Gschloessl B, Dorkeld F, Berges H, Beydon G, Bouchez O, Branco M, Bretaudeau A, Burban C, Dubois E, Gauthier P, Lhuillier E, Nichols J, Nidelet S, Rocha S, Sauné L, Streiff R, Gautier M, Kerdelhué C. Draft genome and reference transcriptomic resources for the urticating pine defoliator Thaumetopoea pityocampa (Lepidoptera: Notodontidae). Mol Ecol Resour 2018; 18:602-619. [PMID: 29352511 DOI: 10.1111/1755-0998.12756] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Revised: 12/23/2017] [Accepted: 01/03/2018] [Indexed: 12/15/2022]
Abstract
The pine processionary moth Thaumetopoea pityocampa (Lepidoptera: Notodontidae) is the main pine defoliator in the Mediterranean region. Its urticating larvae cause severe human and animal health concerns in the invaded areas. This species shows a high phenotypic variability for various traits, such as phenology, fecundity and tolerance to extreme temperatures. This study presents the construction and analysis of extensive genomic and transcriptomic resources, which are an obligate prerequisite to understand their underlying genetic architecture. Using a well-studied population from Portugal with peculiar phenological characteristics, the karyotype was first determined and a first draft genome of 537 Mb total length was assembled into 68,292 scaffolds (N50 = 164 kb). From this genome assembly, 29,415 coding genes were predicted. To circumvent some limitations for fine-scale physical mapping of genomic regions of interest, a 3X coverage BAC library was also developed. In particular, 11 BACs from this library were individually sequenced to assess the assembly quality. Additionally, de novo transcriptomic resources were generated from various developmental stages sequenced with HiSeq and MiSeq Illumina technologies. The reads were de novo assembled into 62,376 and 63,175 transcripts, respectively. Then, a robust subset of the genome-predicted coding genes, the de novo transcriptome assemblies and previously published 454/Sanger data were clustered to obtain a high-quality and comprehensive reference transcriptome consisting of 29,701 bona fide unigenes. These sequences covered 99% of the cegma and 88% of the busco highly conserved eukaryotic genes and 84% of the busco arthropod gene set. Moreover, 90% of these transcripts could be localized on the draft genome. The described information is available via a genome annotation portal (http://bipaa.genouest.org/sp/thaumetopoea_pityocampa/).
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Affiliation(s)
- B Gschloessl
- CBGP, INRA, CIRAD, IRD, Montpellier SupAgro, Univ Montpellier, Montpellier, France
| | - F Dorkeld
- CBGP, INRA, CIRAD, IRD, Montpellier SupAgro, Univ Montpellier, Montpellier, France
| | - H Berges
- INRA-CNRGV, Castanet Tolosan Cedex, France
| | - G Beydon
- INRA-CNRGV, Castanet Tolosan Cedex, France
| | - O Bouchez
- INRA, US 1426, GeT-PlaGe, Genotoul, INRA Auzeville, Castanet Tolosan Cedex, France
| | - M Branco
- Forest Research Center (CEF), Instituto Superior de Agronomia (ISA), University of Lisbon (ULisboa), Lisboa, Portugal
| | - A Bretaudeau
- INRA, UMR Institut de Génétique, Environnement et Protection des Plantes (IGEPP), BioInformatics Platform for Agroecosystems Arthropods (BIPAA), Rennes, France.,INRIA, IRISA, GenOuest Core Facility, Rennes, France
| | - C Burban
- BIOGECO, INRA, Univ. Bordeaux, Cestas, France
| | - E Dubois
- Plateforme MGX-Montpellier GenomiX, c/o Institut de Génomique Fonctionnelle IGF-sud, UMR 5203 CNRS-U 661 INSERM-Université de Montpellier, Montpellier Cedex 05, France
| | - P Gauthier
- CBGP, IRD, CIRAD, INRA, Montpellier SupAgro, Univ Montpellier, Montpellier, France
| | - E Lhuillier
- INRA, US 1426, GeT-PlaGe, Genotoul, INRA Auzeville, Castanet Tolosan Cedex, France
| | - J Nichols
- Edinburgh Genomics, Ashworth Laboratories, The University of Edinburgh, Edinburgh, UK
| | - S Nidelet
- CBGP, INRA, CIRAD, IRD, Montpellier SupAgro, Univ Montpellier, Montpellier, France.,Plateforme MGX-Montpellier GenomiX, c/o Institut de Génomique Fonctionnelle IGF-sud, UMR 5203 CNRS-U 661 INSERM-Université de Montpellier, Montpellier Cedex 05, France
| | - S Rocha
- Forest Research Center (CEF), Instituto Superior de Agronomia (ISA), University of Lisbon (ULisboa), Lisboa, Portugal
| | - L Sauné
- CBGP, INRA, CIRAD, IRD, Montpellier SupAgro, Univ Montpellier, Montpellier, France
| | - R Streiff
- CBGP, INRA, CIRAD, IRD, Montpellier SupAgro, Univ Montpellier, Montpellier, France
| | - M Gautier
- CBGP, INRA, CIRAD, IRD, Montpellier SupAgro, Univ Montpellier, Montpellier, France
| | - C Kerdelhué
- CBGP, INRA, CIRAD, IRD, Montpellier SupAgro, Univ Montpellier, Montpellier, France
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8
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Zhang SV, Zhuo L, Hahn MW. AGOUTI: improving genome assembly and annotation using transcriptome data. Gigascience 2016; 5:31. [PMID: 27435057 PMCID: PMC4952227 DOI: 10.1186/s13742-016-0136-3] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Accepted: 07/04/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Genomes sequenced using short-read, next-generation sequencing technologies can have many errors and may be fragmented into thousands of small contigs. These incomplete and fragmented assemblies lead to errors in gene identification, such that single genes spread across multiple contigs are annotated as separate gene models. Such biases can confound inferences about the number and identity of genes within species, as well as gene gain and loss between species. RESULTS We present AGOUTI (Annotated Genome Optimization Using Transcriptome Information), a tool that uses RNA sequencing data to simultaneously combine contigs into scaffolds and fragmented gene models into single models. We show that AGOUTI improves both the contiguity of genome assemblies and the accuracy of gene annotation, providing updated versions of each as output. Running AGOUTI on both simulated and real datasets, we show that it is highly accurate and that it achieves greater accuracy and contiguity when compared with other existing methods. CONCLUSION AGOUTI is a powerful and effective scaffolder and, unlike most scaffolders, is expected to be more effective in larger genomes because of the commensurate increase in intron length. AGOUTI is able to scaffold thousands of contigs while simultaneously reducing the number of gene models by hundreds or thousands. The software is available free of charge under the MIT license.
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Affiliation(s)
- Simo V. Zhang
- />School of Informatics and Computing, Indiana University, Bloomington, IN 47405 USA
| | - Luting Zhuo
- />School of Informatics and Computing, Indiana University, Bloomington, IN 47405 USA
| | - Matthew W. Hahn
- />School of Informatics and Computing, Indiana University, Bloomington, IN 47405 USA
- />Department of Biology, Indiana University, Bloomington, IN 47405 USA
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9
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Santos LN, Silva ES, Santos AS, De Sá PH, Ramos RT, Silva A, Cooper PJ, Barreto ML, Loureiro S, Pinheiro CS, Alcantara-Neves NM, Pacheco LGC. De novo assembly and characterization of the Trichuris trichiura adult worm transcriptome using Ion Torrent sequencing. Acta Trop 2016; 159:132-41. [PMID: 27038556 DOI: 10.1016/j.actatropica.2016.03.036] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Revised: 03/23/2016] [Accepted: 03/30/2016] [Indexed: 12/26/2022]
Abstract
Infection with helminthic parasites, including the soil-transmitted helminth Trichuris trichiura (human whipworm), has been shown to modulate host immune responses and, consequently, to have an impact on the development and manifestation of chronic human inflammatory diseases. De novo derivation of helminth proteomes from sequencing of transcriptomes will provide valuable data to aid identification of parasite proteins that could be evaluated as potential immunotherapeutic molecules in near future. Herein, we characterized the transcriptome of the adult stage of the human whipworm T. trichiura, using next-generation sequencing technology and a de novo assembly strategy. Nearly 17.6 million high-quality clean reads were assembled into 6414 contiguous sequences, with an N50 of 1606bp. In total, 5673 protein-encoding sequences were confidentially identified in the T. trichiura adult worm transcriptome; of these, 1013 sequences represent potential newly discovered proteins for the species, most of which presenting orthologs already annotated in the related species T. suis. A number of transcripts representing probable novel non-coding transcripts for the species T. trichiura were also identified. Among the most abundant transcripts, we found sequences that code for proteins involved in lipid transport, such as vitellogenins, and several chitin-binding proteins. Through a cross-species expression analysis of gene orthologs shared by T. trichiura and the closely related parasites T. suis and T. muris it was possible to find twenty-six protein-encoding genes that are consistently highly expressed in the adult stages of the three helminth species. Additionally, twenty transcripts could be identified that code for proteins previously detected by mass spectrometry analysis of protein fractions of the whipworm somatic extract that present immunomodulatory activities. Five of these transcripts were amongst the most highly expressed protein-encoding sequences in the T. trichiura adult worm. Besides, orthologs of proteins demonstrated to have potent immunomodulatory properties in related parasitic helminths were also predicted from the T. trichiura de novo assembled transcriptome.
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Affiliation(s)
- Leonardo N Santos
- Institute of Health Sciences, Federal University of Bahia, Salvador, BA, Brazil
| | - Eduardo S Silva
- Institute of Health Sciences, Federal University of Bahia, Salvador, BA, Brazil
| | - André S Santos
- Institute of Health Sciences, Federal University of Bahia, Salvador, BA, Brazil
| | - Pablo H De Sá
- Institute of Biological Sciences, Federal University of Pará, Belém, PA, Brazil
| | - Rommel T Ramos
- Institute of Biological Sciences, Federal University of Pará, Belém, PA, Brazil
| | - Artur Silva
- Institute of Biological Sciences, Federal University of Pará, Belém, PA, Brazil
| | - Philip J Cooper
- Institute of Infection and Immunity, St. George's University of London, London, UK; Centro de Investigacion en Enfermedades Infecciosas y Cronicas, Pontificia Universidad Catolica del Ecuador, Quito, Ecuador
| | - Maurício L Barreto
- Institute of Public Health, Federal University of Bahia, Salvador, BA, Brazil; Centro de Pesquisas Gonçalo Muniz, FIOCRUZ-BA, Salvador, BA, Brazil
| | - Sebastião Loureiro
- Institute of Public Health, Federal University of Bahia, Salvador, BA, Brazil
| | - Carina S Pinheiro
- Institute of Health Sciences, Federal University of Bahia, Salvador, BA, Brazil
| | | | - Luis G C Pacheco
- Institute of Health Sciences, Federal University of Bahia, Salvador, BA, Brazil.
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