1
|
Shi X, Li J, Liu T, Zhao H, Leng H, Sun K, Feng J. Divergence of cochlear transcriptomics between reference‑based and reference‑free transcriptome analyses among Rhinolophus ferrumequinum populations. PLoS One 2023; 18:e0288404. [PMID: 37432940 DOI: 10.1371/journal.pone.0288404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 06/26/2023] [Indexed: 07/13/2023] Open
Abstract
Differences in gene expression within tissues can lead to differences in tissue function. Understanding the transcriptome of a species helps elucidate the molecular mechanisms underlying phenotypic divergence. According to the presence or absence of a reference genome of for a studied species, transcriptome analyses can be divided into reference‑based and reference‑free methods, respectively. Presently, comparisons of complete transcriptome analysis results between those two methods are still rare. In this study, we compared the cochlear transcriptome analysis results of greater horseshoe bats (Rhinolophus ferrumequinum) from three lineages in China with different acoustic phenotypes using reference‑based and reference‑free methods to explore their differences in subsequent analysis. The results gained by reference-based results had lower false-positive rates and were more accurate because differentially expressed genes among the three populations obtained by this method had greater reliability and a higher annotation rate. Some phenotype-related enrichment terms, including those related to inorganic molecules and proton transmembrane channels, were also obtained only by the reference-based method. However, the reference‑based method might have the limitation of incomplete information acquisition. Thus, we believe that a combination of reference‑free and reference‑based methods is ideal for transcriptome analyses. The results of our study provided a reference for the selection of transcriptome analysis methods in the future.
Collapse
Affiliation(s)
- Xiaoxiao Shi
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, Jilin, China
| | - Jun Li
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, Jilin, China
| | - Tong Liu
- Department of Life Science, Jilin Agricultural University, Changchun, Jilin, China
| | - Hanbo Zhao
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural, Shenzhen, China
| | - Haixia Leng
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, Jilin, China
| | - Keping Sun
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, Jilin, China
- Key Laboratory of Vegetation Ecology, Ministry of Education, Changchun, Jilin, China
| | - Jiang Feng
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, Jilin, China
- Department of Life Science, Jilin Agricultural University, Changchun, Jilin, China
| |
Collapse
|
2
|
Krinos AI, Cohen NR, Follows MJ, Alexander H. Reverse engineering environmental metatranscriptomes clarifies best practices for eukaryotic assembly. BMC Bioinformatics 2023; 24:74. [PMID: 36869298 PMCID: PMC9983209 DOI: 10.1186/s12859-022-05121-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 12/21/2022] [Indexed: 03/05/2023] Open
Abstract
BACKGROUND Diverse communities of microbial eukaryotes in the global ocean provide a variety of essential ecosystem services, from primary production and carbon flow through trophic transfer to cooperation via symbioses. Increasingly, these communities are being understood through the lens of omics tools, which enable high-throughput processing of diverse communities. Metatranscriptomics offers an understanding of near real-time gene expression in microbial eukaryotic communities, providing a window into community metabolic activity. RESULTS Here we present a workflow for eukaryotic metatranscriptome assembly, and validate the ability of the pipeline to recapitulate real and manufactured eukaryotic community-level expression data. We also include an open-source tool for simulating environmental metatranscriptomes for testing and validation purposes. We reanalyze previously published metatranscriptomic datasets using our metatranscriptome analysis approach. CONCLUSION We determined that a multi-assembler approach improves eukaryotic metatranscriptome assembly based on recapitulated taxonomic and functional annotations from an in-silico mock community. The systematic validation of metatranscriptome assembly and annotation methods provided here is a necessary step to assess the fidelity of our community composition measurements and functional content assignments from eukaryotic metatranscriptomes.
Collapse
Affiliation(s)
- Arianna I Krinos
- MIT-WHOI Joint Program in Oceanography and Applied Ocean Science and Engineering, Cambridge and Woods Hole, MA, USA. .,Department of Biology, Woods Hole Oceanographic Institution, Woods Hole, MA, USA. .,Department of Earth, Atmospheric, and Planetary Science, Massachusetts Institute of Technology, Cambridge, MA, USA.
| | - Natalie R Cohen
- Skidaway Institute of Oceanography, University of Georgia, Savannah, GA, USA
| | - Michael J Follows
- Department of Earth, Atmospheric, and Planetary Science, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Harriet Alexander
- Department of Biology, Woods Hole Oceanographic Institution, Woods Hole, MA, USA.
| |
Collapse
|
3
|
Chakraborty S, Hossain A, Cao T, Gnanagobal H, Segovia C, Hill S, Monk J, Porter J, Boyce D, Hall JR, Bindea G, Kumar S, Santander J. Multi-Organ Transcriptome Response of Lumpfish ( Cyclopterus lumpus) to Aeromonas salmonicida Subspecies salmonicida Systemic Infection. Microorganisms 2022; 10:2113. [PMID: 36363710 PMCID: PMC9692985 DOI: 10.3390/microorganisms10112113] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 10/17/2022] [Accepted: 10/21/2022] [Indexed: 09/10/2023] Open
Abstract
Lumpfish is utilized as a cleaner fish to biocontrol sealice infestations in Atlantic salmon farms. Aeromonas salmonicida, a Gram-negative facultative intracellular pathogen, is the causative agent of furunculosis in several fish species, including lumpfish. In this study, lumpfish were intraperitoneally injected with different doses of A. salmonicida to calculate the LD50. Samples of blood, head-kidney, spleen, and liver were collected at different time points to determine the infection kinetics. We determined that A. salmonicida LD50 is 102 CFU per dose. We found that the lumpfish head-kidney is the primary target organ of A. salmonicida. Triplicate biological samples were collected from head-kidney, spleen, and liver pre-infection and at 3- and 10-days post-infection for RNA-sequencing. The reference genome-guided transcriptome assembly resulted in 6246 differentially expressed genes. The de novo assembly resulted in 403,204 transcripts, which added 1307 novel genes not identified by the reference genome-guided transcriptome. Differential gene expression and gene ontology enrichment analyses suggested that A. salmonicida induces lethal infection in lumpfish by uncontrolled and detrimental blood coagulation, complement activation, inflammation, DNA damage, suppression of the adaptive immune system, and prevention of cytoskeleton formation.
Collapse
Affiliation(s)
- Setu Chakraborty
- Marine Microbial Pathogenesis and Vaccinology Laboratory, Department of Ocean Sciences, Memorial University of Newfoundland, St. John’s, NL A1C 5S7, Canada
| | - Ahmed Hossain
- Marine Microbial Pathogenesis and Vaccinology Laboratory, Department of Ocean Sciences, Memorial University of Newfoundland, St. John’s, NL A1C 5S7, Canada
| | - Trung Cao
- Marine Microbial Pathogenesis and Vaccinology Laboratory, Department of Ocean Sciences, Memorial University of Newfoundland, St. John’s, NL A1C 5S7, Canada
| | - Hajarooba Gnanagobal
- Marine Microbial Pathogenesis and Vaccinology Laboratory, Department of Ocean Sciences, Memorial University of Newfoundland, St. John’s, NL A1C 5S7, Canada
| | - Cristopher Segovia
- Marine Microbial Pathogenesis and Vaccinology Laboratory, Department of Ocean Sciences, Memorial University of Newfoundland, St. John’s, NL A1C 5S7, Canada
| | - Stephen Hill
- Cold-Ocean Deep-Sea Research Facility, Department of Ocean Sciences, Memorial University of Newfoundland, St. John’s, NL A1C 5S7, Canada
| | - Jennifer Monk
- Dr. Joe Brown Aquatic Research Building, Department of Ocean Sciences, Memorial University of Newfoundland, St. John’s, NL A1C 5S7, Canada
| | - Jillian Porter
- Dr. Joe Brown Aquatic Research Building, Department of Ocean Sciences, Memorial University of Newfoundland, St. John’s, NL A1C 5S7, Canada
| | - Danny Boyce
- Dr. Joe Brown Aquatic Research Building, Department of Ocean Sciences, Memorial University of Newfoundland, St. John’s, NL A1C 5S7, Canada
| | - Jennifer R. Hall
- Aquatic Research Cluster, CREAIT Network, Department of Ocean Sciences, Memorial University of Newfoundland, St. John’s, NL A1C 5S7, Canada
| | - Gabriela Bindea
- INSERM, Laboratory of Integrative Cancer Immunology, 75006 Paris, France
- Equipe Labellisée Ligue Contre Le Cancer, 75013 Paris, France
- Centre de Recherche des Cordeliers, Sorbonne Université, Université de Paris, 75006 Paris, France
| | - Surendra Kumar
- Marine Microbial Pathogenesis and Vaccinology Laboratory, Department of Ocean Sciences, Memorial University of Newfoundland, St. John’s, NL A1C 5S7, Canada
- Ocean Frontier Institute, Department of Ocean Sciences, Memorial University of Newfoundland, St. John’s, NL A1C 5S7, Canada
| | - Javier Santander
- Marine Microbial Pathogenesis and Vaccinology Laboratory, Department of Ocean Sciences, Memorial University of Newfoundland, St. John’s, NL A1C 5S7, Canada
| |
Collapse
|
4
|
Powell AF, Feder A, Li J, Schmidt MHW, Courtney L, Alseekh S, Jobson EM, Vogel A, Xu Y, Lyon D, Dumschott K, McHale M, Sulpice R, Bao K, Lal R, Duhan A, Hallab A, Denton AK, Bolger ME, Fernie AR, Hind SR, Mueller LA, Martin GB, Fei Z, Martin C, Giovannoni JJ, Strickler SR, Usadel B. A Solanum lycopersicoides reference genome facilitates insights into tomato specialized metabolism and immunity. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 110:1791-1810. [PMID: 35411592 DOI: 10.1111/tpj.15770] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Revised: 03/10/2022] [Accepted: 03/27/2022] [Indexed: 06/14/2023]
Abstract
Wild relatives of tomato are a valuable source of natural variation in tomato breeding, as many can be hybridized to the cultivated species (Solanum lycopersicum). Several, including Solanum lycopersicoides, have been crossed to S. lycopersicum for the development of ordered introgression lines (ILs), facilitating breeding for desirable traits. Despite the utility of these wild relatives and their associated ILs, few finished genome sequences have been produced to aid genetic and genomic studies. Here we report a chromosome-scale genome assembly for S. lycopersicoides LA2951, which contains 37 938 predicted protein-coding genes. With the aid of this genome assembly, we have precisely delimited the boundaries of the S. lycopersicoides introgressions in a set of S. lycopersicum cv. VF36 × LA2951 ILs. We demonstrate the usefulness of the LA2951 genome by identifying several quantitative trait loci for phenolics and carotenoids, including underlying candidate genes, and by investigating the genome organization and immunity-associated function of the clustered Pto gene family. In addition, syntenic analysis of R2R3MYB genes sheds light on the identity of the Aubergine locus underlying anthocyanin production. The genome sequence and IL map provide valuable resources for studying fruit nutrient/quality traits, pathogen resistance, and environmental stress tolerance. We present a new genome resource for the wild species S. lycopersicoides, which we use to shed light on the Aubergine locus responsible for anthocyanin production. We also provide IL boundary mappings, which facilitated identifying novel carotenoid quantitative trait loci of which one was likely driven by an uncharacterized lycopene β-cyclase whose function we demonstrate.
Collapse
Affiliation(s)
| | - Ari Feder
- Boyce Thompson Institute, Ithaca, New York, 14853, USA
| | - Jie Li
- Department of Biochemistry and Metabolism, The John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Maximilian H-W Schmidt
- Institute for Biology I, BioSC, RWTH Aachen University, 52474, Aachen, Germany
- IBG-4 Bioinformatics, Forschungszentrum Jülich, 52428, Jülich, Germany
| | - Lance Courtney
- Boyce Thompson Institute, Ithaca, New York, 14853, USA
- Plant Biology Section, School of Integrative Plant Sciences, Cornell University, Ithaca, NY, 14853, USA
| | - Saleh Alseekh
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
- Center of Plant Systems Biology and Biotechnology, 4000, Plovdiv, Bulgaria
| | - Emma M Jobson
- Boyce Thompson Institute, Ithaca, New York, 14853, USA
| | - Alexander Vogel
- Institute for Biology I, BioSC, RWTH Aachen University, 52474, Aachen, Germany
| | - Yimin Xu
- Boyce Thompson Institute, Ithaca, New York, 14853, USA
| | - David Lyon
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Lab, Berkeley, CA, 94720, USA
| | - Kathryn Dumschott
- IBG-4 Bioinformatics, Forschungszentrum Jülich, 52428, Jülich, Germany
| | - Marcus McHale
- Plant Systems Biology Lab, Ryan Institute, National University of Ireland, H91 TK33, Galway, Ireland
| | - Ronan Sulpice
- Plant Systems Biology Lab, Ryan Institute, National University of Ireland, H91 TK33, Galway, Ireland
| | - Kan Bao
- Boyce Thompson Institute, Ithaca, New York, 14853, USA
| | - Rohit Lal
- Boyce Thompson Institute, Ithaca, New York, 14853, USA
| | - Asha Duhan
- Boyce Thompson Institute, Ithaca, New York, 14853, USA
| | - Asis Hallab
- IBG-4 Bioinformatics, Forschungszentrum Jülich, 52428, Jülich, Germany
| | - Alisandra K Denton
- Institute for Biology I, BioSC, RWTH Aachen University, 52474, Aachen, Germany
| | - Marie E Bolger
- IBG-4 Bioinformatics, Forschungszentrum Jülich, 52428, Jülich, Germany
| | - Alisdair R Fernie
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
- Center of Plant Systems Biology and Biotechnology, 4000, Plovdiv, Bulgaria
| | - Sarah R Hind
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | | | - Gregory B Martin
- Boyce Thompson Institute, Ithaca, New York, 14853, USA
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA, and
| | - Zhangjun Fei
- Boyce Thompson Institute, Ithaca, New York, 14853, USA
- US Department of Agriculture-Agricultural Research Service, Robert W. Holley Center for Agriculture and Health, Ithaca, NY, 14853, USA
| | - Cathie Martin
- Department of Biochemistry and Metabolism, The John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - James J Giovannoni
- Boyce Thompson Institute, Ithaca, New York, 14853, USA
- US Department of Agriculture-Agricultural Research Service, Robert W. Holley Center for Agriculture and Health, Ithaca, NY, 14853, USA
| | | | - Björn Usadel
- Institute for Biology I, BioSC, RWTH Aachen University, 52474, Aachen, Germany
- IBG-4 Bioinformatics, Forschungszentrum Jülich, 52428, Jülich, Germany
| |
Collapse
|
5
|
Shrestha AMS, B Guiao JE, R Santiago KC. Assembly-free rapid differential gene expression analysis in non-model organisms using DNA-protein alignment. BMC Genomics 2022; 23:97. [PMID: 35120462 PMCID: PMC8815227 DOI: 10.1186/s12864-021-08278-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2021] [Accepted: 12/22/2021] [Indexed: 11/16/2022] Open
Abstract
Background RNA-seq is being increasingly adopted for gene expression studies in a panoply of non-model organisms, with applications spanning the fields of agriculture, aquaculture, ecology, and environment. For organisms that lack a well-annotated reference genome or transcriptome, a conventional RNA-seq data analysis workflow requires constructing a de-novo transcriptome assembly and annotating it against a high-confidence protein database. The assembly serves as a reference for read mapping, and the annotation is necessary for functional analysis of genes found to be differentially expressed. However, assembly is computationally expensive. It is also prone to errors that impact expression analysis, especially since sequencing depth is typically much lower for expression studies than for transcript discovery. Results We propose a shortcut, in which we obtain counts for differential expression analysis by directly aligning RNA-seq reads to the high-confidence proteome that would have been otherwise used for annotation. By avoiding assembly, we drastically cut down computational costs – the running time on a typical dataset improves from the order of tens of hours to under half an hour, and the memory requirement is reduced from the order of tens of Gbytes to tens of Mbytes. We show through experiments on simulated and real data that our pipeline not only reduces computational costs, but has higher sensitivity and precision than a typical assembly-based pipeline. A Snakemake implementation of our workflow is available at: https://bitbucket.org/project_samar/samar. Conclusions The flip side of RNA-seq becoming accessible to even modestly resourced labs has been that the time, labor, and infrastructure cost of bioinformatics analysis has become a bottleneck. Assembly is one such resource-hungry process, and we show here that it can be avoided for quick and easy, yet more sensitive and precise, differential gene expression analysis in non-model organisms. Supplementary Information The online version contains supplementary material available at (10.1186/s12864-021-08278-7).
Collapse
Affiliation(s)
- Anish M S Shrestha
- Bioinformatics Lab, Advanced Research Institute for Informatics, Computing, and Networking (AdRIC), De La Salle University, Manila, Philippines. .,Department of Software Technology, College of Computer Studies, De La Salle University, Manila, Philippines.
| | - Joyce Emlyn B Guiao
- Bioinformatics Lab, Advanced Research Institute for Informatics, Computing, and Networking (AdRIC), De La Salle University, Manila, Philippines.,Department of Mathematics and Statistics, College of Science, De La Salle University, Manila, Philippines
| | - Kyle Christian R Santiago
- Bioinformatics Lab, Advanced Research Institute for Informatics, Computing, and Networking (AdRIC), De La Salle University, Manila, Philippines.,Department of Software Technology, College of Computer Studies, De La Salle University, Manila, Philippines
| |
Collapse
|
6
|
Resolving the microalgal gene landscape at the strain level: A novel hybrid transcriptome of Emiliania huxleyi CCMP3266. Appl Environ Microbiol 2021; 88:e0141821. [PMID: 34757817 DOI: 10.1128/aem.01418-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Microalgae are key ecological players with a complex evolutionary history. Genomic diversity, in addition to limited availability of high-quality genomes, challenge studies that aim to elucidate molecular mechanisms underlying microalgal ecophysiology. Here, we present a novel and comprehensive transcriptomic hybrid approach to generate a reference for genetic analyses, and resolve the microalgal gene landscape at the strain level. The approach is demonstrated for a strain of the coccolithophore microalga Emiliania huxleyi, which is a species complex with considerable genome variability. The investigated strain is commonly studied as a model for algal-bacterial interactions, and was therefore sequenced in the presence of bacteria to elicit the expression of interaction-relevant genes. We applied complementary PacBio Iso-Seq full-length cDNA, and poly(A)-independent Illumina total RNA sequencing, which resulted in a de novo assembled, near complete hybrid transcriptome. In particular, hybrid sequencing improved the reconstruction of long transcripts and increased the recovery of full-length transcript isoforms. To use the resulting hybrid transcriptome as a reference for genetic analyses, we demonstrate a method that collapses the transcriptome into a genome-like dataset, termed "synthetic genome" (sGenome). We used the sGenome as a reference to visually confirm the robustness of the CCMP3266 gene assembly, to conduct differential gene expression analysis, and to characterize novel E. huxleyi genes. The newly-identified genes contribute to our understanding of E. huxleyi genome diversification, and are predicted to play a role in microbial interactions. Our transcriptomic toolkit can be implemented in various microalgae to facilitate mechanistic studies on microalgal diversity and ecology. Importance Microalgae are key players in the ecology and biogeochemistry of our oceans. Efforts to implement genomic and transcriptomic tools in laboratory studies involving microalgae suffer from the lack of published genomes. In the case of coccolithophore microalgae, the problem has long been recognized; the model species Emiliania huxleyi is a species complex with genomes composed of a core, and a large variable portion. To study the role of the variable portion in niche adaptation, and specifically in microbial interactions, strain-specific genetic information is required. Here we present a novel transcriptomic hybrid approach, and generated strain-specific genome-like information. We demonstrate our approach on an E. huxleyi strain that is co-cultivated with bacteria. By constructing a "synthetic genome", we generated comprehensive gene annotations that enabled accurate analyses of gene expression patterns. Importantly, we unveiled novel genes in the variable portion of E. huxleyi that play putative roles in microbial interactions.
Collapse
|
7
|
Lee SG, Na D, Park C. Comparability of reference-based and reference-free transcriptome analysis approaches at the gene expression level. BMC Bioinformatics 2021; 22:310. [PMID: 34674628 PMCID: PMC8529712 DOI: 10.1186/s12859-021-04226-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2021] [Accepted: 06/01/2021] [Indexed: 11/10/2022] Open
Abstract
Background Lately, high-throughput RNA sequencing has been extensively used to elucidate the transcriptome landscape and dynamics of cell types of different species. In particular, for most non-model organisms lacking complete reference genomes with high-quality annotation of genetic information, reference-free (RF) de novo transcriptome analyses, rather than reference-based (RB) approaches, are widely used, and RF analyses have substantially contributed toward understanding the mechanisms regulating key biological processes and functions. To date, numerous bioinformatics studies have been conducted for assessing the workflow, production rate, and completeness of transcriptome assemblies within and between RF and RB datasets. However, the degree of consistency and variability of results obtained by analyzing gene expression levels through these two different approaches have not been adequately documented. Results In the present study, we evaluated the differences in expression profiles obtained with RF and RB approaches and revealed that the former tends to be satisfactorily replaced by the latter with respect to transcriptome repertoires, as well as from a gene expression quantification perspective. In addition, we urge cautious interpretation of these findings. Several genes that are lowly expressed, have long coding sequences, or belong to large gene families must be validated carefully, whenever gene expression levels are calculated using the RF method. Conclusions Our empirical results indicate important contributions toward addressing transcriptome-related biological questions in non-model organisms. Supplementary Information The online version contains supplementary material available at 10.1186/s12859-021-04226-0.
Collapse
Affiliation(s)
- Sung-Gwon Lee
- School of Biological Sciences and Technology, Chonnam National University, Gwangju, 61186, Republic of Korea
| | - Dokyun Na
- Department of Biomedical Engineering, Chung-Ang University, Seoul, 06974, Republic of Korea
| | - Chungoo Park
- School of Biological Sciences and Technology, Chonnam National University, Gwangju, 61186, Republic of Korea.
| |
Collapse
|
8
|
Bucchini F, Del Cortona A, Kreft Ł, Botzki A, Van Bel M, Vandepoele K. TRAPID 2.0: a web application for taxonomic and functional analysis of de novo transcriptomes. Nucleic Acids Res 2021; 49:e101. [PMID: 34197621 PMCID: PMC8464036 DOI: 10.1093/nar/gkab565] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 06/07/2021] [Accepted: 06/16/2021] [Indexed: 12/24/2022] Open
Abstract
Advances in high-throughput sequencing have resulted in a massive increase of RNA-Seq transcriptome data. However, the promise of rapid gene expression profiling in a specific tissue, condition, unicellular organism or microbial community comes with new computational challenges. Owing to the limited availability of well-resolved reference genomes, de novo assembled (meta)transcriptomes have emerged as popular tools for investigating the gene repertoire of previously uncharacterized organisms. Yet, despite their potential, these datasets often contain fragmented or contaminant sequences, and their analysis remains difficult. To alleviate some of these challenges, we developed TRAPID 2.0, a web application for the fast and efficient processing of assembled transcriptome data. The initial processing phase performs a global characterization of the input data, providing each transcript with several layers of annotation, comprising structural, functional, and taxonomic information. The exploratory phase enables downstream analyses from the web application. Available analyses include the assessment of gene space completeness, the functional analysis and comparison of transcript subsets, and the study of transcripts in an evolutionary context. A comparison with similar tools highlights TRAPID’s unique features. Finally, analyses performed within TRAPID 2.0 are complemented by interactive data visualizations, facilitating the extraction of new biological insights, as demonstrated with diatom community metatranscriptomes.
Collapse
Affiliation(s)
- François Bucchini
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium.,Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | - Andrea Del Cortona
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium.,Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | - Łukasz Kreft
- VIB Bioinformatics Core, VIB, 9052 Ghent, Belgium
| | | | - Michiel Van Bel
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium.,Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | - Klaas Vandepoele
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium.,Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium.,Bioinformatics Institute Ghent, Ghent University, 9052 Ghent, Belgium
| |
Collapse
|
9
|
Pabis K, Chiari Y, Sala C, Straka E, Giacconi R, Provinciali M, Li X, Brown-Borg H, Nowikovsky K, Valencak TG, Gundacker C, Garagnani P, Malavolta M. Elevated metallothionein expression in long-lived species mediates the influence of cadmium accumulation on aging. GeroScience 2021; 43:1975-1993. [PMID: 34117600 DOI: 10.1007/s11357-021-00393-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Accepted: 05/24/2021] [Indexed: 11/29/2022] Open
Abstract
Cadmium (Cd) accumulates with aging and is elevated in long-lived species. Metallothioneins (MTs), small cysteine-rich proteins involved in metal homeostasis and Cd detoxification, are known to be related to longevity. However, the relationship between Cd accumulation, the role of MTs, and aging is currently unclear. Specifically, we do not know if long-lived species evolved an efficient metal stress response by upregulating their MT levels to reduce the toxic effects of environmental pollutants, such as Cd, that accumulate over their longer life span. It is also unknown if the number of MT genes, their expression, or both protect the organisms from potentially damaging effects during aging. To address these questions, we reanalyzed several cross-species studies and obtained data on MT expression and Cd accumulation in long-lived mouse models. We confirmed a relationship between species maximum life span in captive mammals and their Cd content in liver and kidney. We found that although the number of MT genes does not affect longevity, gene expression and protein amount of specific MT paralogs are strongly related to life span in mammals. MT expression rather than gene number may influence the high Cd levels and longevity of some species. In support of this, we found that overexpression of MT-1 accelerated Cd accumulation in mice and that tissue Cd was higher in long-lived mouse strains with high MT expression. We conclude that long-lived species have evolved a more efficient stress response by upregulating the expression of MT genes in presence of Cd, which contributes to elevated tissue Cd levels.
Collapse
Affiliation(s)
- Kamil Pabis
- Center for Pathobiochemistry and Genetics, Institute of Medical Genetics, Medical University of Vienna, Währinger Strasse 10, 1090, Wien, Vienna, Austria
| | - Ylenia Chiari
- Department of Biology, George Mason University, Fairfax, VA, 22030, USA
| | - Claudia Sala
- Department of Physics and Astronomy, University of Bologna, 40126, Bologna, Italy
| | - Elisabeth Straka
- Center for Pathobiochemistry and Genetics, Institute of Medical Genetics, Medical University of Vienna, Währinger Strasse 10, 1090, Wien, Vienna, Austria
| | - Robertina Giacconi
- Advanced Technology Center for Aging Research, IRCCS INRCA, 60121, Ancona, Italy
| | - Mauro Provinciali
- Advanced Technology Center for Aging Research, IRCCS INRCA, 60121, Ancona, Italy
| | - Xinna Li
- Department of Pathology, University of Michigan School of Medicine, Ann Arbor, MI, 48109, USA
| | - Holly Brown-Borg
- Department of Biomedical Sciences, University of North Dakota School of Medicine and Health Sciences, Grand Forks, ND, 58203, USA
| | - Karin Nowikovsky
- Department of Internal Medicine I and Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
| | - Teresa G Valencak
- Department of Animal Science and Technology, College of Animal Sciences, Zhejiang University, Hangzhou, 310058, People's Republic of China
| | - Claudia Gundacker
- Center for Pathobiochemistry and Genetics, Institute of Medical Genetics, Medical University of Vienna, Währinger Strasse 10, 1090, Wien, Vienna, Austria
| | - Paolo Garagnani
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), and Interdepartmental Centre "L. Galvani" (CIG), University of Bologna, Bologna, Italy.,Division of Clinical Chemistry, Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Marco Malavolta
- Advanced Technology Center for Aging Research, IRCCS INRCA, 60121, Ancona, Italy.
| |
Collapse
|
10
|
Behera S, Voshall A, Moriyama EN. Plant Transcriptome Assembly: Review and Benchmarking. Bioinformatics 2021. [DOI: 10.36255/exonpublications.bioinformatics.2021.ch7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
|
11
|
Spillane JL, LaPolice TM, MacManes MD, Plachetzki DC. Signal, bias, and the role of transcriptome assembly quality in phylogenomic inference. BMC Ecol Evol 2021; 21:43. [PMID: 33726665 PMCID: PMC7968300 DOI: 10.1186/s12862-021-01772-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Accepted: 03/03/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Phylogenomic approaches have great power to reconstruct evolutionary histories, however they rely on multi-step processes in which each stage has the potential to affect the accuracy of the final result. Many studies have empirically tested and established methodology for resolving robust phylogenies, including selecting appropriate evolutionary models, identifying orthologs, or isolating partitions with strong phylogenetic signal. However, few have investigated errors that may be initiated at earlier stages of the analysis. Biases introduced during the generation of the phylogenomic dataset itself could produce downstream effects on analyses of evolutionary history. Transcriptomes are widely used in phylogenomics studies, though there is little understanding of how a poor-quality assembly of these datasets could impact the accuracy of phylogenomic hypotheses. Here we examined how transcriptome assembly quality affects phylogenomic inferences by creating independent datasets from the same input data representing high-quality and low-quality transcriptome assembly outcomes. RESULTS By studying the performance of phylogenomic datasets derived from alternative high- and low-quality assembly inputs in a controlled experiment, we show that high-quality transcriptomes produce richer phylogenomic datasets with a greater number of unique partitions than low-quality assemblies. High-quality assemblies also give rise to partitions that have lower alignment ambiguity and less compositional bias. In addition, high-quality partitions hold stronger phylogenetic signal than their low-quality transcriptome assembly counterparts in both concatenation- and coalescent-based analyses. CONCLUSIONS Our findings demonstrate the importance of transcriptome assembly quality in phylogenomic analyses and suggest that a portion of the uncertainty observed in such studies could be alleviated at the assembly stage.
Collapse
Affiliation(s)
- Jennifer L Spillane
- Molecular, Cellular, and Biomedical Sciences Department, University of New Hampshire, Durham, NH, 03824, USA.
- Hubbard Center for Genome Studies, University of New Hampshire, Durham, NH, 03824, USA.
| | - Troy M LaPolice
- Molecular, Cellular, and Biomedical Sciences Department, University of New Hampshire, Durham, NH, 03824, USA
- Hubbard Center for Genome Studies, University of New Hampshire, Durham, NH, 03824, USA
| | - Matthew D MacManes
- Molecular, Cellular, and Biomedical Sciences Department, University of New Hampshire, Durham, NH, 03824, USA
- Hubbard Center for Genome Studies, University of New Hampshire, Durham, NH, 03824, USA
| | - David C Plachetzki
- Molecular, Cellular, and Biomedical Sciences Department, University of New Hampshire, Durham, NH, 03824, USA.
- Hubbard Center for Genome Studies, University of New Hampshire, Durham, NH, 03824, USA.
| |
Collapse
|
12
|
Sun K, Gu L, Ma L, Duan Y. Atlas of ACE2 gene expression reveals novel insights into transmission of SARS-CoV-2. Heliyon 2021; 7:e05850. [PMID: 33392409 PMCID: PMC7762714 DOI: 10.1016/j.heliyon.2020.e05850] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 11/03/2020] [Accepted: 12/22/2020] [Indexed: 12/13/2022] Open
Abstract
The recent pandemic, COVID-19, is caused by a novel coronavirus, SARS-CoV-2, with elusive origin. SARS-CoV-2 infects mammalian cells via ACE2, a transmembrane protein. Therefore, the conservation and expression patterns of ACE2 may provide valuable insights into tracing the carriers of SARS-CoV-2. In this work, we analyzed the conservation of ACE2 and its expression pattern among various mammalian species that are close to human beings. We show that mammalian ACE2 gene is deeply conserved at both DNA and peptide levels, suggesting that a broad range of mammals can potentially host SARS-CoV-2. We further report that ACE2 expression in certain human tissues are consistent with clinical symptoms of COVID-19 patients. Furthermore, we have built the first atlas of ACE2 expression in various common mammals, which shows that ACE2 expresses in mammalian tissues in a species-specific manner. Most notably, we observe exceptionally high expression of ACE2 in external body parts of cats and dogs, suggesting that these household pet animals could be vulnerable to viral infections and/or may serve as intermediate hosts, thus yielding novel insights into the transmission of SARS-CoV-2.
Collapse
Affiliation(s)
- Kun Sun
- Shenzhen Bay Laboratory, Shenzhen, 518132, China
| | - Liuqi Gu
- Department of Ecology and Evolutionary Biology, The University of Kansas, Lawrence, KS, 66045, USA
- Beijing Huayuan Academy of Biotechnology, Beijing, 100192, China
| | - Li Ma
- Shenzhen Bay Laboratory, Shenzhen, 518132, China
| | - Yunfeng Duan
- Beijing Huayuan Academy of Biotechnology, Beijing, 100192, China
| |
Collapse
|
13
|
Ganesh S, Utebay B, Heit J, Coskun AF. Cellular sociology regulates the hierarchical spatial patterning and organization of cells in organisms. Open Biol 2020; 10:200300. [PMID: 33321061 PMCID: PMC7776581 DOI: 10.1098/rsob.200300] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Advances in single-cell biotechnology have increasingly revealed interactions of cells with their surroundings, suggesting a cellular society at the microscale. Similarities between cells and humans across multiple hierarchical levels have quantitative inference potential for reaching insights about phenotypic interactions that lead to morphological forms across multiple scales of cellular organization, namely cells, tissues and organs. Here, the functional and structural comparisons between how cells and individuals fundamentally socialize to give rise to the spatial organization are investigated. Integrative experimental cell interaction assays and computational predictive methods shape the understanding of societal perspective in the determination of the cellular interactions that create spatially coordinated forms in biological systems. Emerging quantifiable models from a simpler biological microworld such as bacterial interactions and single-cell organisms are explored, providing a route to model spatio-temporal patterning of morphological structures in humans. This analogical reasoning framework sheds light on structural patterning principles as a result of biological interactions across the cellular scale and up.
Collapse
Affiliation(s)
- Shambavi Ganesh
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA.,School of Electrical and Computer Engineering, Georgia Institute of Technology, Atlanta, GA, USA
| | - Beliz Utebay
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
| | - Jeremy Heit
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
| | - Ahmet F Coskun
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
| |
Collapse
|
14
|
Sheng M, She J, Xu W, Hong Y, Su Z, Zhang X. HpeNet: Co-expression Network Database for de novo Transcriptome Assembly of Paeonia lactiflora Pall. Front Genet 2020; 11:570138. [PMID: 33193666 PMCID: PMC7641121 DOI: 10.3389/fgene.2020.570138] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2020] [Accepted: 08/18/2020] [Indexed: 01/23/2023] Open
Abstract
The herbaceous peony (Paeonia lactiflora Pall.) is a well-known ornamental flowering and pharmaceutical plant found in China. Its high medicinal value has long been recognized by traditional Chinese medicine (as Radix paeoniae Alba and Radix paeoniae Rubra), and it has become economically valued for its oilseed in recent years; like other Paeonia species, it has been identified as a novel resource for the α-linolenic acid used in seed oil production. However, its genome has not yet been sequenced, and little transcriptome data on Paeonia lactiflora are available. To obtain a comprehensive transcriptome for Paeonia lactiflora, RNAs from 10 tissues of the Paeonia lactiflora Pall. cv Shaoyou17C were used for de novo assembly, and 416,062 unigenes were obtained. Using a homology search, it was found that 236,222 (approximately 57%) unigenes had at least one BLAST hit in one or more public data resources. The construction of co-expression networks is a feasible means for improving unigene annotation. Using in-house transcriptome data, we obtained a co-expression network covering 95.13% of the unigenes. Then we integrated co-expression network analyses and lipid-related pathway genes to study lipid metabolism in Paeonia lactiflora cultivars. Finally, we constructed the online database HpeNet (http://bioinformatics.cau.edu.cn/HpeNet) to integrate transcriptome data, gene information, the co-expression network, and so forth. The database can also be searched for gene details, gene functions, orthologous matches, and other data. Our online database may help the research community identify functional genes and perform research on Paeonia lactiflora more conveniently. We hope that de novo transcriptome assembly, combined with co-expression networks, can provide a feasible means to predict the gene function of species that do not have a reference genome.
Collapse
Affiliation(s)
- Minghao Sheng
- Beijing Agricultural Biotechnology Research Center, Beijing Engineering Research Center of Functional Floriculture, Beijing Academy of Agriculture and Forestry Science, Beijing, China.,State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Jiajie She
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Wenying Xu
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Yan Hong
- Beijing Agricultural Biotechnology Research Center, Beijing Engineering Research Center of Functional Floriculture, Beijing Academy of Agriculture and Forestry Science, Beijing, China
| | - Zhen Su
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Xiaodong Zhang
- Beijing Agricultural Biotechnology Research Center, Beijing Engineering Research Center of Functional Floriculture, Beijing Academy of Agriculture and Forestry Science, Beijing, China
| |
Collapse
|
15
|
Differential Gene Expression Between Polymorphic Zooids of the Marine Bryozoan Bugulina stolonifera. G3-GENES GENOMES GENETICS 2020; 10:3843-3857. [PMID: 32859685 PMCID: PMC7534450 DOI: 10.1534/g3.120.401348] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Bryozoans are a diverse phylum of marine and freshwater colonial invertebrates containing approximately 6,300 described living species. Bryozoans grow by budding new physiologically connected colony members (zooids) from a founding individual that forms from a metamorphosed larva. In some species these zooids come in different shapes and sizes and are specialized to serve different tasks within the colony. A complex interaction of genotype, environment, and developmental pathway shapes zooid fate, however, the specific mechanisms underlying the establishment of this division of labor remain unknown. Here, the first characterization of differential gene expression between polymorphic zooids of a bryozoan colony is presented. The development of different zooid types of lab-cultured Bugulina stolonifera colonies including feeding autozooids, avicularia (derived non-feeding zooids that are homologous to feeding autozooids but shaped like a bird’s beak), and rhizoids (a branching network of non-feeding anchoring zooids) was explored using RNA sequencing, de novo transcriptome assembly, and differential gene expression analyses. High throughput sequencing of cDNA libraries yielded an average of 14.9 ± 1.3 (SE) million high-quality paired-end reads per sample. Data for the first de novo transcriptome assemblies of B. stolonifera and the first characterization of genes involved in the formation and maintenance of zooid types within a bryozoan colony are presented. In a comparison between autozooid and avicularium tissues, 1,097 significant differentially expressed genes were uncovered. This work provides a much-needed foundation for understanding the mechanisms involved in the development of polymorphic zooids and the establishment of division of labor in bryozoans.
Collapse
|
16
|
Liu X, Hérault F, Diot C, Corre E. Development of a relevant strategy using de novo transcriptome assembly method for transcriptome comparisons between Muscovy and common duck species and their reciprocal inter-specific mule and hinny hybrids fed ad libitum and overfed. BMC Genomics 2020; 21:687. [PMID: 33008290 PMCID: PMC7531116 DOI: 10.1186/s12864-020-07099-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Accepted: 09/23/2020] [Indexed: 12/01/2022] Open
Abstract
Background Common Pekin and Muscovy ducks and their intergeneric hinny and mule hybrids have different abilities for fatty liver production. RNA-Seq analyses from the liver of these different genetic types fed ad libitum or overfed would help to identify genes with different response to overfeeding between them. However RNA-seq analyses from different species and comparison is challenging. The goal of this study was develop a relevant strategy for transcriptome analysis and comparison between different species. Results Transcriptomes were first assembled with a reference-based approach. Important mapping biases were observed when heterologous mapping were conducted on common duck reference genome, suggesting that this reference-based strategy was not suited to compare the four different genetic types. De novo transcriptome assemblies were then performed using Trinity and Oases. Assemblies of transcriptomes were not relevant when more than a single genetic type was considered. Finally, single genetic type transcriptomes were assembled with DRAP in a mega-transcriptome. No bias was observed when reads from the different genetic types were mapped on this mega-transcriptome and differences in gene expression between the four genetic types could be identified. Conclusions Analyses using both reference-based and de novo transcriptome assemblies point out a good performance of the de novo approach for the analysis of gene expression in different species. It also allowed the identification of differences in responses to overfeeding between Pekin and Muscovy ducks and hinny and mule hybrids.
Collapse
Affiliation(s)
- Xi Liu
- ABiMS Bioinformatics Facility, CNRS, Sorbonne Université, FR2424, Station Biologique, 29680, Roscoff, France
| | - Frédéric Hérault
- UMR PEGASE, INRAE, Institut Agro, 16 Le Clos, 35590, Saint-Gilles, France
| | - Christian Diot
- UMR PEGASE, INRAE, Institut Agro, 16 Le Clos, 35590, Saint-Gilles, France.
| | - Erwan Corre
- ABiMS Bioinformatics Facility, CNRS, Sorbonne Université, FR2424, Station Biologique, 29680, Roscoff, France.
| |
Collapse
|
17
|
Xu Z, Asakawa S. Physiological RNA dynamics in RNA-Seq analysis. Brief Bioinform 2020; 20:1725-1733. [PMID: 30010714 DOI: 10.1093/bib/bby045] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Revised: 04/24/2018] [Indexed: 02/06/2023] Open
Abstract
Physiological RNA dynamics cause problems in transcriptome analysis. Physiological RNA accumulation affects the analysis of RNA quantification, and physiological RNA degradation affects the analysis of the RNA sequence length, feature site and quantification. In the present article, we review the effects of physiological degradation and accumulation of RNA on analysing RNA sequencing data. Physiological RNA accumulation and degradation probably led to such phenomena as incorrect estimations of transcription quantification, differential expressions, co-expressions, RNA decay rates, alternative splicing, boundaries of transcription, novel genes, new single-nucleotide polymorphisms, small RNAs and gene fusion. Thus, the transcriptomic data obtained up to date warrant further scrutiny. New and improved techniques and bioinformatics software are needed to produce accurate data in transcriptome research.
Collapse
Affiliation(s)
- Zhongneng Xu
- Department of Ecology, Jinan University, Guangzhou 510632, China
| | - Shuichi Asakawa
- Department of Aquatic Bioscience, Graduate School of Agricultural and Life Science, The University of Tokyo, Tokyo 113-8657, Japan
| |
Collapse
|
18
|
Brand JN, Wiberg RAW, Pjeta R, Bertemes P, Beisel C, Ladurner P, Schärer L. RNA-Seq of three free-living flatworm species suggests rapid evolution of reproduction-related genes. BMC Genomics 2020; 21:462. [PMID: 32631219 PMCID: PMC7336406 DOI: 10.1186/s12864-020-06862-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Accepted: 06/22/2020] [Indexed: 01/03/2023] Open
Abstract
Background The genus Macrostomum consists of small free-living flatworms and contains Macrostomum lignano, which has been used in investigations of ageing, stem cell biology, bioadhesion, karyology, and sexual selection in hermaphrodites. Two types of mating behaviour occur within this genus. Some species, including M. lignano, mate via reciprocal copulation, where, in a single mating, both partners insert their male copulatory organ into the female storage organ and simultaneously donate and receive sperm. Other species mate via hypodermic insemination, where worms use a needle-like copulatory organ to inject sperm into the tissue of the partner. These contrasting mating behaviours are associated with striking differences in sperm and copulatory organ morphology. Here we expand the genomic resources within the genus to representatives of both behaviour types and investigate whether genes vary in their rate of evolution depending on their putative function. Results We present de novo assembled transcriptomes of three Macrostomum species, namely M. hystrix, a close relative of M. lignano that mates via hypodermic insemination, M. spirale, a more distantly related species that mates via reciprocal copulation, and finally M. pusillum, which represents a clade that is only distantly related to the other three species and also mates via hypodermic insemination. We infer 23,764 sets of homologous genes and annotate them using experimental evidence from M. lignano. Across the genus, we identify 521 gene families with conserved patterns of differential expression between juvenile vs. adult worms and 185 gene families with a putative expression in the testes that are restricted to the two reciprocally mating species. Further, we show that homologs of putative reproduction-related genes have a higher protein divergence across the four species than genes lacking such annotations and that they are more difficult to identify across the four species, indicating that these genes evolve more rapidly, while genes involved in neoblast function are more conserved. Conclusions This study improves the genus Macrostomum as a model system, by providing resources for the targeted investigation of gene function in a broad range of species. And we, for the first time, show that reproduction-related genes evolve at an accelerated rate in flatworms.
Collapse
Affiliation(s)
- Jeremias N Brand
- Department of Environmental Sciences, Zoological Institute, University of Basel, Vesalgasse 1, 4051, Basel, Switzerland.
| | - R Axel W Wiberg
- Department of Environmental Sciences, Zoological Institute, University of Basel, Vesalgasse 1, 4051, Basel, Switzerland
| | - Robert Pjeta
- Institute of Zoology and Center of Molecular Biosciences Innsbruck, University of Innsbruck, Innsbruck, Austria
| | - Philip Bertemes
- Institute of Zoology and Center of Molecular Biosciences Innsbruck, University of Innsbruck, Innsbruck, Austria
| | - Christian Beisel
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Peter Ladurner
- Institute of Zoology and Center of Molecular Biosciences Innsbruck, University of Innsbruck, Innsbruck, Austria
| | - Lukas Schärer
- Department of Environmental Sciences, Zoological Institute, University of Basel, Vesalgasse 1, 4051, Basel, Switzerland
| |
Collapse
|
19
|
Höllbacher B, Balázs K, Heinig M, Uhlenhaut NH. Seq-ing answers: Current data integration approaches to uncover mechanisms of transcriptional regulation. Comput Struct Biotechnol J 2020; 18:1330-1341. [PMID: 32612756 PMCID: PMC7306512 DOI: 10.1016/j.csbj.2020.05.018] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 05/21/2020] [Accepted: 05/23/2020] [Indexed: 02/06/2023] Open
Abstract
Advancements in the field of next generation sequencing lead to the generation of ever-more data, with the challenge often being how to combine and reconcile results from different OMICs studies such as genome, epigenome and transcriptome. Here we provide an overview of the standard processing pipelines for ChIP-seq and RNA-seq as well as common downstream analyses. We describe popular multi-omics data integration approaches used to identify target genes and co-factors, and we discuss how machine learning techniques may predict transcriptional regulators and gene expression.
Collapse
Affiliation(s)
- Barbara Höllbacher
- Institute for Diabetes and Cancer IDC, Helmholtz Zentrum Muenchen (HMGU) and German Center for Diabetes Research (DZD), Munich 85764, Neuherberg, Germany.,Institute of Computational Biology ICB, Helmholtz Zentrum Muenchen (HMGU) and German Center for Diabetes Research (DZD), Munich 85764, Neuherberg, Germany.,Department of Informatics, TUM, Munich 85748, Garching, Germany
| | - Kinga Balázs
- Institute for Diabetes and Cancer IDC, Helmholtz Zentrum Muenchen (HMGU) and German Center for Diabetes Research (DZD), Munich 85764, Neuherberg, Germany
| | - Matthias Heinig
- Institute of Computational Biology ICB, Helmholtz Zentrum Muenchen (HMGU) and German Center for Diabetes Research (DZD), Munich 85764, Neuherberg, Germany.,Department of Informatics, TUM, Munich 85748, Garching, Germany
| | - N Henriette Uhlenhaut
- Institute for Diabetes and Cancer IDC, Helmholtz Zentrum Muenchen (HMGU) and German Center for Diabetes Research (DZD), Munich 85764, Neuherberg, Germany.,Metabolic Programming, TUM School of Life Sciences Weihenstephan, Munich 85354, Freising, Germany
| |
Collapse
|
20
|
Mashanov V, Akiona J, Khoury M, Ferrier J, Reid R, Machado DJ, Zueva O, Janies D. Active Notch signaling is required for arm regeneration in a brittle star. PLoS One 2020; 15:e0232981. [PMID: 32396580 PMCID: PMC7217437 DOI: 10.1371/journal.pone.0232981] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2019] [Accepted: 04/24/2020] [Indexed: 12/15/2022] Open
Abstract
Cell signaling pathways play key roles in coordinating cellular events in development. The Notch signaling pathway is highly conserved across all multicellular animals and is known to coordinate a multitude of diverse cellular events, including proliferation, differentiation, fate specification, and cell death. Specific functions of the pathway are, however, highly context-dependent and are not well characterized in post-traumatic regeneration. Here, we use a small-molecule inhibitor of the pathway (DAPT) to demonstrate that Notch signaling is required for proper arm regeneration in the brittle star Ophioderma brevispina, a highly regenerative member of the phylum Echinodermata. We also employ a transcriptome-wide gene expression analysis (RNA-seq) to characterize the downstream genes controlled by the Notch pathway in the brittle star regeneration. We demonstrate that arm regeneration involves an extensive cross-talk between the Notch pathway and other cell signaling pathways. In the regrowing arm, Notch regulates the composition of the extracellular matrix, cell migration, proliferation, and apoptosis, as well as components of the innate immune response. We also show for the first time that Notch signaling regulates the activity of several transposable elements. Our data also suggests that one of the possible mechanisms through which Notch sustains its activity in the regenerating tissues is via suppression of Neuralized1.
Collapse
Affiliation(s)
- Vladimir Mashanov
- Department of Biology, University of North Florida, Jacksonville, FL, United states of America
- Wake Forest Institute for Regenerative Medicine, Winston Salem, NC, United states of America
- * E-mail:
| | - Jennifer Akiona
- Department of Biology, University of North Florida, Jacksonville, FL, United states of America
| | - Maleana Khoury
- Department of Biology, University of North Florida, Jacksonville, FL, United states of America
| | - Jacob Ferrier
- University of North Carolina at Charlotte, Charlotte, NC, United states of America
| | - Robert Reid
- University of North Carolina at Charlotte, Charlotte, NC, United states of America
| | - Denis Jacob Machado
- University of North Carolina at Charlotte, Charlotte, NC, United states of America
| | - Olga Zueva
- Department of Biology, University of North Florida, Jacksonville, FL, United states of America
| | - Daniel Janies
- University of North Carolina at Charlotte, Charlotte, NC, United states of America
| |
Collapse
|
21
|
Rodríguez A, Mundy NI, Ibáñez R, Pröhl H. Being red, blue and green: the genetic basis of coloration differences in the strawberry poison frog (Oophaga pumilio). BMC Genomics 2020; 21:301. [PMID: 32293261 PMCID: PMC7158012 DOI: 10.1186/s12864-020-6719-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Accepted: 04/05/2020] [Indexed: 12/17/2022] Open
Abstract
Background Animal coloration is usually an adaptive attribute, under strong local selection pressures and often diversified among species or populations. The strawberry poison frog (Oophaga pumilio) shows an impressive array of color morphs across its distribution in Central America. Here we quantify gene expression and genetic variation to identify candidate genes involved in generating divergence in coloration between populations of red, green and blue O. pumilio from the Bocas del Toro archipelago in Panama. Results We generated a high quality non-redundant reference transcriptome by mapping the products of genome-guided and de novo transcriptome assemblies onto a re-scaffolded draft genome of O. pumilio. We then measured gene expression in individuals of the three color phenotypes and identified color-associated candidate genes by comparing differential expression results against a list of a priori gene sets for five different functional categories of coloration – pteridine synthesis, carotenoid synthesis, melanin synthesis, iridophore pathways (structural coloration), and chromatophore development. We found 68 candidate coloration loci with significant expression differences among the color phenotypes. Notable upregulated examples include pteridine synthesis genes spr, xdh and pts (in red and green frogs); carotenoid metabolism genes bco2 (in blue frogs), scarb1 (in red frogs), and guanine metabolism gene psat1 (in blue frogs). We detected significantly higher expression of the pteridine synthesis gene set in red and green frogs versus blue frogs. In addition to gene expression differences, we identified 370 outlier SNPs on 162 annotated genes showing signatures of diversifying selection, including eight pigmentation-associated genes. Conclusions Gene expression in the skin of the three populations of frogs with differing coloration is highly divergent. The strong signal of differential expression in pteridine genes is consistent with a major role of these genes in generating the coloration differences among the three morphs. However, the finding of differentially expressed genes across pathways and functional categories suggests that multiple mechanisms are responsible for the coloration differences, likely involving both pigmentary and structural coloration. In addition to regulatory differences, we found potential evidence of differential selection acting at the protein sequence level in several color-associated loci, which could contribute to the color polymorphism.
Collapse
Affiliation(s)
- Ariel Rodríguez
- Institute of Zoology, University of Veterinary Medicine of Hannover, Bünteweg 17, 30559, Hannover, Germany.
| | - Nicholas I Mundy
- Department of Zoology, University of Cambridge, Downing St, Cambridge, CB2 3EJ, England
| | - Roberto Ibáñez
- Smithsonian Tropical Research Institute, Apartado Postal, 0843-03092, Panamá, República de Panamá.,Sistema Nacional de Investigación, Secretaría Nacional de Ciencia, Tecnología e Innovación, Apartado, 0816-02852, Panamá, República de Panamá
| | - Heike Pröhl
- Institute of Zoology, University of Veterinary Medicine of Hannover, Bünteweg 17, 30559, Hannover, Germany
| |
Collapse
|
22
|
Trouern-Trend AJ, Falk T, Zaman S, Caballero M, Neale DB, Langley CH, Dandekar AM, Stevens KA, Wegrzyn JL. Comparative genomics of six Juglans species reveals disease-associated gene family contractions. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 102:410-423. [PMID: 31823432 DOI: 10.1111/tpj.14630] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2019] [Accepted: 11/01/2019] [Indexed: 06/10/2023]
Abstract
Juglans (walnuts), the most speciose genus in the walnut family (Juglandaceae), represents most of the family's commercially valuable fruit and wood-producing trees. It includes several species used as rootstock for their resistance to various abiotic and biotic stressors. We present the full structural and functional genome annotations of six Juglans species and one outgroup within Juglandaceae (Juglans regia, J. cathayensis, J. hindsii, J. microcarpa, J. nigra, J. sigillata and Pterocarya stenoptera) produced using BRAKER2 semi-unsupervised gene prediction pipeline and additional tools. For each annotation, gene predictors were trained using 19 tissue-specific J. regia transcriptomes aligned to the genomes. Additional functional evidence and filters were applied to multi-exonic and mono-exonic putative genes to yield between 27 000 and 44 000 high-confidence gene models per species. Comparison of gene models to the BUSCO embryophyta dataset suggested that, on average, genome annotation completeness was 85.6%. We utilized these high-quality annotations to assess gene family evolution within Juglans, and among Juglans and selected Eurosid species. We found notable contractions in several gene families in J. hindsii, including disease resistance-related wall-associated kinase (WAK), Catharanthus roseus receptor-like kinase (CrRLK1L) and others involved in abiotic stress response. Finally, we confirmed an ancient whole-genome duplication that took place in a common ancestor of Juglandaceae using site substitution comparative analysis.
Collapse
Affiliation(s)
| | - Taylor Falk
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, USA
| | - Sumaira Zaman
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, USA
| | - Madison Caballero
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, USA
| | - David B Neale
- Department of Plant Sciences, University of California Davis, Davis, CA, USA
| | - Charles H Langley
- Department of Evolution and Ecology, University of California Davis, Davis, CA, USA
| | - Abhaya M Dandekar
- Department of Plant Sciences, University of California Davis, Davis, CA, USA
| | - Kristian A Stevens
- Department of Evolution and Ecology, University of California Davis, Davis, CA, USA
- Department of Computer Science, University of California Davis, Davis, CA, USA
| | - Jill L Wegrzyn
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, USA
| |
Collapse
|
23
|
Khew CY, Harikrishna JA, Wee WY, Lau ET, Hwang SS. Transcriptional Sequencing and Gene Expression Analysis of Various Genes in Fruit Development of Three Different Black Pepper ( Piper nigrum L.) Varieties. Int J Genomics 2020; 2020:1540915. [PMID: 32399475 PMCID: PMC7210556 DOI: 10.1155/2020/1540915] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Revised: 01/30/2020] [Accepted: 03/13/2020] [Indexed: 11/18/2022] Open
Abstract
Black pepper (Piper nigrum) is a vital spice crop with uses ranging from culinary to pharmacological applications. However, limited genetic information has constrained the understanding of the molecular regulation of flower and fruit development in black pepper. In this study, a comparison among three different black pepper varieties, Semengok Aman (SA), Kuching (KC), and Semengok 1 (S1), with varying fruit characteristics was used to provide insight on the genetic regulation of flower and fruit development. Next-generation sequencing (NGS) technology was used to determine the flower and fruit transcriptomes by sequencing on an Illumina HiSeq 2500 platform followed by de novo assembly using SOAPdenovo-Trans. The high-quality assembly of 66,906 of unigenes included 64.4% of gene sequences (43,115) with similarity to one or more protein sequences from the GenBank database. Annotation with Blast2Go assigned 37,377 genes to one or more Gene Ontology terms. Of these genes, 5,874 genes were further associated with the biological pathways recorded in the KEGG database. Comparison of flower and fruit transcriptome data from the three different black pepper varieties revealed a large number of DEGs between flower and fruit of the SA variety. Gene Ontology (GO) enrichment analysis further supports functions of DEGs between flower and fruit in the categories of carbohydrate metabolic processes, embryo development, and DNA metabolic processes while the DEGs in fruit relate to biosynthetic process, secondary metabolic process, and catabolic process. The enrichment of DEGs in KEGG pathways was also investigated, and a large number of genes were found to belong to the nucleotide metabolism and carbohydrate metabolism categories. Gene expression profiling of flower formation-related genes reveals that other than regulating the flowering in black pepper, the flowering genes might also be implicated in the fruit development process. Transcriptional analysis of sugar transporter and carbohydrate metabolism genes in different fruit varieties suggested that the carbohydrate metabolism in black pepper fruit is developmentally regulated, and some genes might serve as potential genes for future crop quality improvement. Study on the piperine-related gene expression analysis suggested that lysine-derived products might present in all stages of fruit development, but the transportation was only active at the early stage of fruit development. These results indicate several candidate genes related to the development of flower and fruit in black pepper and provide a resource for future functional analysis and potentially for future crop improvement.
Collapse
Affiliation(s)
- Choy Yuen Khew
- Department of Research and Quality Development, Malaysian Pepper Board, Lot 1115, Jalan Utama, Pending Industrial Area, 93450 KC, Sarawak, Malaysia
- School of Chemical Engineering and Science, Faculty of Engineering, Computing and Science, Swinburne University of Technology Sarawak Campus, Jalan Simpang Tiga, 93350 KC, Sarawak, Malaysia
| | - Jennifer Ann Harikrishna
- Centre for Research in Biotechnology for Agriculture (CEBAR), Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
| | - Wei Yee Wee
- Monash University Malaysia, Jalan Lagoon Selatan, 47500 Bandar Sunway, Selangor Darul Ehsan, Malaysia
| | - Ee Tiing Lau
- Department of Research and Quality Development, Malaysian Pepper Board, Lot 1115, Jalan Utama, Pending Industrial Area, 93450 KC, Sarawak, Malaysia
- School of Chemical Engineering and Science, Faculty of Engineering, Computing and Science, Swinburne University of Technology Sarawak Campus, Jalan Simpang Tiga, 93350 KC, Sarawak, Malaysia
| | - Siaw San Hwang
- School of Chemical Engineering and Science, Faculty of Engineering, Computing and Science, Swinburne University of Technology Sarawak Campus, Jalan Simpang Tiga, 93350 KC, Sarawak, Malaysia
| |
Collapse
|
24
|
Liu J, Deng JL, Tian Y. Transcriptome sequencing of the apricot (Prunus armeniaca L.) and identification of differentially expressed genes involved in drought stress. PHYTOCHEMISTRY 2020; 171:112226. [PMID: 31923721 DOI: 10.1016/j.phytochem.2019.112226] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 11/25/2019] [Accepted: 12/17/2019] [Indexed: 06/10/2023]
Abstract
Apricot (Prunus armeniaca L.) is an important fruit crop that is widely planted throughout the world. But drought affects both yield and quality of apricot. In order to study the effects of long-term drought on the molecular and physiological mechanisms of apricot, we used transcriptome sequencing and measured physiological indices. First, 322 million high-quality clean reads were obtained, and 74,892 unigenes were generated for the transcriptome. Among the assembled unigenes, 18,671 simple sequence repeats (SSRs) and 5581 differentially expressed genes (DEGs) were identified. The Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis of the DEGs revealed that starch and sucrose metabolism, plant-pathogen interaction and plant hormone signal transduction pathways are enriched. Additionally, we used quantitative real-time PCR (qRT-PCR) to confirm the RNA-seq results with 11 drought-related DEGs. Second, through the physiological analysis of apricot leaves under constant drought stress, and the results show the internal microstructure of apricot leaves changed to withstand drought stress. At the same time, plants exposed to long-term drought stress showed higher degree of membrane damage, which reduced photosynthesis in the damaged leaves. Our findings enrich the genome resources for apricot and refine our understanding of the molecular and physiological mechanisms of drought response in this fruit crop, providing insights into drought adaptation of the apricot.
Collapse
Affiliation(s)
- Jia Liu
- Horticulture Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, Sichuan, 610066, PR China; Southwestern Key Laboratory of Horticultural Crops Biology and Germplasm Enhancement, Ministry of Agriculture, Chengdu, Sichuan, 610066, PR China
| | - Jia Lin Deng
- Horticulture Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, Sichuan, 610066, PR China; Southwestern Key Laboratory of Horticultural Crops Biology and Germplasm Enhancement, Ministry of Agriculture, Chengdu, Sichuan, 610066, PR China.
| | - Yun Tian
- Horticulture Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, Sichuan, 610066, PR China; Southwestern Key Laboratory of Horticultural Crops Biology and Germplasm Enhancement, Ministry of Agriculture, Chengdu, Sichuan, 610066, PR China
| |
Collapse
|
25
|
Lim WK, Mathuru AS. Design, challenges, and the potential of transcriptomics to understand social behavior. Curr Zool 2020; 66:321-330. [PMID: 32684913 PMCID: PMC7357267 DOI: 10.1093/cz/zoaa007] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2019] [Accepted: 02/18/2020] [Indexed: 12/17/2022] Open
Abstract
Rapid advances in Ribonucleic Acid sequencing (or RNA-seq) technology for analyzing entire transcriptomes of desired tissue samples, or even of single cells at scale, have revolutionized biology in the past decade. Increasing accessibility and falling costs are making it possible to address many problems in biology that were once considered intractable, including the study of various social behaviors. RNA-seq is opening new avenues to understand long-standing questions on the molecular basis of behavioral plasticity and individual variation in the expression of a behavior. As whole transcriptomes are examined, it has become possible to make unbiased discoveries of underlying mechanisms with little or no necessity to predict genes involved in advance. However, researchers need to be aware of technical limitations and have to make specific decisions when applying RNA-seq to study social behavior. Here, we provide a perspective on the applications of RNA-seq and experimental design considerations for behavioral scientists who are unfamiliar with the technology but are considering using it in their research.
Collapse
Affiliation(s)
- Wen Kin Lim
- Science Division, Yale-NUS College, 12 College Avenue West, Singapore
| | - Ajay S Mathuru
- Science Division, Yale-NUS College, 12 College Avenue West, Singapore.,Institute of Molecular and Cell Biology (IMCB), 61 Biopolis Drive, Singapore.,Department of Physiology, Yong Loo Lin School of Medicine (YLL), National University of Singapore, Singapore
| |
Collapse
|
26
|
Carvajal-Lopez P, Von Borstel FD, Torres A, Rustici G, Gutierrez J, Romero-Vivas E. Microarray-Based Quality Assessment as a Supporting Criterion for de novo Transcriptome Assembly Selection. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2020; 17:198-206. [PMID: 30059314 DOI: 10.1109/tcbb.2018.2860997] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
RNA-Sequencing and de novo assembly have enabled the analysis of species with non-available reference transcriptomes, although intrinsic features (biological and technical) induce errors in the reconstruction. A strategy to resolve these errors consists of varying assembling process parameters to generate multiple reconstructions. However, the best assembly selection remains a challenge. Quantitative metrics for quality assessment have been inconsistent when compared with pertinent references. In this paper, a criterion for supporting assembly selection based on mapping DNA microarray hybridized probes to assembly sets is proposed. Mouse and fruit fly RNA-Seq datasets were assembled with standard de novo procedures. Quality assessment was estimated using quantitative metrics and the proposed criterion. The assembly that best mapped to the available reference transcriptomes of these model species provided the highest quality assembly. The hybridized probes identified the best assemblies, whereas quantitative metrics remained inconsistent. For example, subtle probe mapping difference of 0.25 percent, but statistically significant (ANOVA, p < 0.05), enabled the assembly selection that led to identify 3,719 more contigs and led to 1,049 further mapped contigs to the mouse reference transcriptome. The microarray data availability for non-model species makes the proposed criterion suitable for quality assessment of multiple de novo assembly strategies.
Collapse
|
27
|
Comparative Analysis of Strategies for De Novo Transcriptome Assembly in Prokaryotes: Streptomyces clavuligerus as a Case Study. High Throughput 2019; 8:ht8040020. [PMID: 31801255 PMCID: PMC6970227 DOI: 10.3390/ht8040020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 11/20/2019] [Accepted: 11/23/2019] [Indexed: 12/15/2022] Open
Abstract
The performance of software tools for de novo transcriptome assembly greatly depends on the selection of software parameters. Up to now, the development of de novo transcriptome assembly for prokaryotes has not been as remarkable as that for eukaryotes. In this contribution, Rockhopper2 was used to perform a comparative transcriptome analysis of Streptomyces clavuligerus exposed to diverse environmental conditions. The study focused on assessing the incidence of software parameters on software performance for the identification of differentially expressed genes as a final goal. For this, a statistical optimization was performed using the Transrate Assembly Score (TAS). TAS was also used for evaluating the software performance and for comparing it with related tools, e.g., Trinity. Transcriptome redundancy and completeness were also considered for this analysis. Rockhopper2 and Trinity reached a TAS value of 0.55092 and 0.58337, respectively. Trinity assembles transcriptomes with high redundancy, with 55.6% of transcripts having some duplicates. Additionally, we observed that the total number of differentially expressed genes (DEG) and their annotation greatly depends on the method used for removing redundancy and the tools used for transcript quantification. To our knowledge, this is the first work aimed at assessing de novo assembly software for prokaryotic organisms.
Collapse
|
28
|
Yohe LR, Davies KTJ, Simmons NB, Sears KE, Dumont ER, Rossiter SJ, Dávalos LM. Evaluating the performance of targeted sequence capture, RNA-Seq, and degenerate-primer PCR cloning for sequencing the largest mammalian multigene family. Mol Ecol Resour 2019; 20:140-153. [PMID: 31523924 DOI: 10.1111/1755-0998.13093] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2019] [Revised: 08/27/2019] [Accepted: 09/06/2019] [Indexed: 12/18/2022]
Abstract
Multigene families evolve from single-copy ancestral genes via duplication, and typically encode proteins critical to key biological processes. Molecular analyses of these gene families require high-confidence sequences, but the high sequence similarity of the members can create challenges for sequencing and downstream analyses. Focusing on the common vampire bat, Desmodus rotundus, we evaluated how different sequencing approaches performed in recovering the largest mammalian protein-coding multigene family: olfactory receptors (OR). Using the genome as a reference, we determined the proportion of intact protein-coding receptors recovered by: (a) amplicons from degenerate primers sequenced via Sanger technology, (b) RNA-Seq of the main olfactory epithelium, and (c) those genes captured with probes designed from transcriptomes of closely-related species. Our initial re-annotation of the high-quality vampire bat genome resulted in >400 intact OR genes, more than doubling the original estimate. Sanger-sequenced amplicons performed the poorest among the three approaches, detecting <33% of receptors in the genome. In contrast, the transcriptome reliably recovered >50% of the annotated genomic ORs, and targeted sequence capture recovered nearly 75% of annotated genes. Each sequencing approach assembled high-quality sequences, even if it did not recover all receptors in the genome. While some variation may be due to limitations of the study design (e.g., different individuals), variation among approaches was mostly caused by low coverage of some receptors rather than high rates of assembly error. Given this variability, we caution against using the counts of intact receptors per species to model the birth-death process of multigene families. Instead, our results support the use of orthologous sequences to explore and model the evolutionary processes shaping these genes.
Collapse
Affiliation(s)
- Laurel R Yohe
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY, USA.,Department of Geology and Geophysics, Yale University, Stony Brook, NY, USA
| | - Kalina T J Davies
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
| | - Nancy B Simmons
- Department of Mammalogy, Division of Vertebrate Zoology, American Museum of Natural History, New York, NY, USA
| | - Karen E Sears
- Department of Ecology and Evolutionary Biology, UCLA, Los Angeles, CA, USA
| | - Elizabeth R Dumont
- School of Natural Sciences, University of California Merced, Merced, CA, USA
| | - Stephen J Rossiter
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
| | - Liliana M Dávalos
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY, USA.,Consortium for Inter-Disciplinary Environmental Research, Stony Brook University, Stony Brook, NY, USA
| |
Collapse
|
29
|
Stark R, Grzelak M, Hadfield J. RNA sequencing: the teenage years. Nat Rev Genet 2019; 20:631-656. [DOI: 10.1038/s41576-019-0150-2] [Citation(s) in RCA: 679] [Impact Index Per Article: 135.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/18/2019] [Indexed: 12/12/2022]
|
30
|
Rey C, Veber P, Boussau B, Sémon M. CAARS: comparative assembly and annotation of RNA-Seq data. Bioinformatics 2019; 35:2199-2207. [PMID: 30452539 PMCID: PMC6596894 DOI: 10.1093/bioinformatics/bty903] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Revised: 09/13/2018] [Accepted: 11/16/2018] [Indexed: 02/05/2023] Open
Abstract
MOTIVATION RNA sequencing (RNA-Seq) is a widely used approach to obtain transcript sequences in non-model organisms, notably for performing comparative analyses. However, current bioinformatic pipelines do not take full advantage of pre-existing reference data in related species for improving RNA-Seq assembly, annotation and gene family reconstruction. RESULTS We built an automated pipeline named CAARS to combine novel data from RNA-Seq experiments with existing multi-species gene family alignments. RNA-Seq reads are assembled into transcripts by both de novo and assisted assemblies. Then, CAARS incorporates transcripts into gene families, builds gene alignments and trees and uses phylogenetic information to classify the genes as orthologs and paralogs of existing genes. We used CAARS to assemble and annotate RNA-Seq data in rodents and fishes using distantly related genomes as reference, a difficult case for this kind of analysis. We showed CAARS assemblies are more complete and accurate than those assembled by a standard pipeline consisting of de novo assembly coupled with annotation by sequence similarity on a guide species. In addition to annotated transcripts, CAARS provides gene family alignments and trees, annotated with orthology relationships, directly usable for downstream comparative analyses. AVAILABILITY AND IMPLEMENTATION CAARS is implemented in Python and Ocaml and is freely available at https://github.com/carinerey/caars. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Collapse
Affiliation(s)
- Carine Rey
- UnivLyon, Université Claude Bernard Lyon 1, ENS de Lyon, CNRS UMR, INSERM U1210, LBMC, F-69007, Lyon, France
| | - Philippe Veber
- UnivLyon, Université Claude Bernard Lyon 1, CNRS, UMR, LBBE, F-69100, Villeurbanne, France
| | - Bastien Boussau
- UnivLyon, Université Claude Bernard Lyon 1, CNRS, UMR, LBBE, F-69100, Villeurbanne, France
| | - Marie Sémon
- UnivLyon, Université Claude Bernard Lyon 1, ENS de Lyon, CNRS UMR, INSERM U1210, LBMC, F-69007, Lyon, France
| |
Collapse
|
31
|
Hsieh PH, Oyang YJ, Chen CY. Effect of de novo transcriptome assembly on transcript quantification. Sci Rep 2019; 9:8304. [PMID: 31165774 PMCID: PMC6549443 DOI: 10.1038/s41598-019-44499-3] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2018] [Accepted: 05/17/2019] [Indexed: 11/08/2022] Open
Abstract
Correct quantification of transcript expression is essential to understand the functional elements in different physiological conditions. For the organisms without the reference transcriptome, de novo transcriptome assembly must be carried out prior to quantification. However, a large number of erroneous contigs produced by the assemblers might result in unreliable estimation. In this regard, this study investigates how assembly quality affects the performance of quantification based on de novo transcriptome assembly. We examined the over-extended and incomplete contigs, and demonstrated that assembly completeness has a strong impact on the estimation of contig abundance. Then we investigated the behavior of the quantifiers with respect to sequence ambiguity which might be originally presented in the transcriptome or accidentally produced by assemblers. The results suggested that the quantifiers often over-estimate the expression of family-collapse contigs and under-estimate the expression of duplicated contigs. For organisms without reference transcriptome, it remains challenging to detect the inaccurate estimation on family-collapse contigs. On the contrary, we observed that the situation of under-estimation on duplicated contigs can be warned through analyzing the read proportion of estimated abundance (RPEA) of contigs in the connected component inferenced by the quantifiers. In addition, we suggest that the estimated quantification results on the connected component level have better accuracy over sequence level quantification. The analytic results conducted in this study provides valuable insights for future development of transcriptome assembly and quantification.
Collapse
Affiliation(s)
- Ping-Han Hsieh
- Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, Taipei, 10617, Taiwan
| | - Yen-Jen Oyang
- Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, Taipei, 10617, Taiwan
- Department of Computer Science and Information Engineering, National Taiwan University, Taipei, 10617, Taiwan
| | - Chien-Yu Chen
- Department of Bio-Industrial Mechatronics Engineering, National Taiwan University, Taipei, 10617, Taiwan.
- Genome and Systems Biology Program, National Taiwan University and Academia sinica, Taipei, 10617, Taiwan.
| |
Collapse
|
32
|
Ng WL, Wu W, Zou P, Zhou R. Comparative transcriptomics sheds light on differential adaptation and species diversification between two Melastoma species and their F 1 hybrid. AOB PLANTS 2019; 11:plz019. [PMID: 31037213 PMCID: PMC6481908 DOI: 10.1093/aobpla/plz019] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Accepted: 03/27/2019] [Indexed: 06/09/2023]
Abstract
Variation in gene expression has been shown to promote adaptive divergence, and can lead to speciation. The plant genus Melastoma, thought to have diversified through adaptive radiation, provides an excellent model for the study of gene expressional changes during adaptive differentiation and following interspecific hybridization. In this study, we performed RNA-seq on M. candidum, M. sanguineum and their F1 hybrid, to investigate the role of gene expression in species diversification within the genus. Reference transcriptomes were assembled using combined data from both parental species, resulting in 50 519 and 48 120 transcripts for the leaf and flower petal, after removing redundancy. Differential expression analysis uncovered 3793 and 2116 differentially expressed (DE) transcripts, most of which are between M. candidum and M. sanguineum. Differential expression was observed for genes related to light responses, as well as genes that regulate the development of leaf trichomes, a trait that among others is thought to protect plants against sunlight, suggesting the differential adaptation of the species to sunlight intensity. The analysis of positively selected genes between the two species also revealed possible differential adaptation to other abiotic stresses such as drought and temperature. In the hybrid, almost all possible modes of expression were observed at the DE transcripts, although at most transcripts, the expression levels were similar to that of either parent instead of being intermediate. A small number of transgressively expressed transcripts that matched genes known to promote plant growth and adaptation to stresses in new environments were also found, possibly explaining the vigour observed in the hybrid. The findings in this study provided insights into the role of gene expression in the diversification of Melastoma, which we believe is an important example for more cross-taxa comparisons in the future.
Collapse
Affiliation(s)
- Wei Lun Ng
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
- China-ASEAN College of Marine Sciences, Xiamen University Malaysia, Sepang, Selangor, Malaysia
| | - Wei Wu
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Peishan Zou
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Renchao Zhou
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
| |
Collapse
|
33
|
Todd EV, Liu H, Lamm MS, Thomas JT, Rutherford K, Thompson KC, Godwin JR, Gemmell NJ. Female Mimicry by Sneaker Males Has a Transcriptomic Signature in Both the Brain and the Gonad in a Sex-Changing Fish. Mol Biol Evol 2019; 35:225-241. [PMID: 29136184 DOI: 10.1093/molbev/msx293] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Phenotypic plasticity represents an elegant adaptive response of individuals to a change in their environment. Bluehead wrasses (Thalassoma bifasciatum) exhibit astonishing sexual plasticity, including female-to-male sex change and discrete male morphs that differ strikingly in behavior, morphology, and gonadal investment. Using RNA-seq transcriptome profiling, we examined the genes and physiological pathways underlying flexible behavioral and gonadal differences among female, dominant (bourgeois) male, and female-mimic (sneaker) male blueheads. For the first time in any organism, we find that female mimicry by sneaker males has a transcriptional signature in both the brain and the gonad. Sneaker males shared striking similarity in neural gene expression with females, supporting the idea that males with alternative reproductive phenotypes have "female-like brains." Sneaker males also overexpressed neuroplasticity genes, suggesting that their opportunistic reproductive strategy requires a heightened capacity for neuroplasticity. Bourgeois males overexpressed genes associated with socio-sexual behaviors (e.g., isotocin), but also neuroprotective genes and biomarkers of oxidative stress and aging, indicating a hitherto unexplored cost to these males of attaining the reproductively privileged position at the top of the social hierarchy. Our novel comparison of testicular transcriptomes in a fish with male sexual polymorphism associates greater gonadal investment by sneaker males with overexpression of genes involved in cell proliferation and sperm quality control. We propose that morphological female-mimicry by sneaker male teleosts entails pervasive downregulation of androgenesis genes, consistent with low androgen production in males lacking well-developed secondary sexual characters.
Collapse
Affiliation(s)
- Erica V Todd
- Department of Anatomy, University of Otago, Dunedin, New Zealand
| | - Hui Liu
- Department of Anatomy, University of Otago, Dunedin, New Zealand
| | - Melissa S Lamm
- Department of Biological Sciences and WM Keck Center for Behavioral Biology, North Carolina State University, Raleigh, NC
| | - Jodi T Thomas
- Department of Anatomy, University of Otago, Dunedin, New Zealand
| | - Kim Rutherford
- Department of Anatomy, University of Otago, Dunedin, New Zealand
| | - Kelly C Thompson
- Department of Biological Sciences and WM Keck Center for Behavioral Biology, North Carolina State University, Raleigh, NC
| | - John R Godwin
- Department of Biological Sciences and WM Keck Center for Behavioral Biology, North Carolina State University, Raleigh, NC
| | - Neil J Gemmell
- Department of Anatomy, University of Otago, Dunedin, New Zealand
| |
Collapse
|
34
|
Yang H, Jaime M, Polihronakis M, Kanegawa K, Markow T, Kaneshiro K, Oliver B. Re-annotation of eight Drosophila genomes. Life Sci Alliance 2018; 1:e201800156. [PMID: 30599046 PMCID: PMC6305970 DOI: 10.26508/lsa.201800156] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Revised: 12/15/2018] [Accepted: 12/16/2018] [Indexed: 12/11/2022] Open
Abstract
The sequenced genomes of the Drosophila phylogeny are a central resource for comparative work supporting the understanding of the Drosophila melanogaster non-mammalian model system. These have also facilitated evolutionary studies on the selected and random differences that distinguish the thousands of extant species of Drosophila. However, full utility has been hampered by uneven genome annotation. We have generated a large expression profile dataset for nine species of Drosophila and trained a transcriptome assembly approach on D. melanogaster that best matched the extensively curated annotation. We then applied this to the other species to add more than 10000 transcript models per species. We also developed new orthologs to facilitate cross-species comparisons. We validated the new annotation of the distantly related Drosophila grimshawi with an extensive collection of newly sequenced cDNAs. This re-annotation will facilitate understanding both the core commonalities and the species differences in this important group of model organisms, and suggests a strategy for annotating the many forthcoming genomes covering the tree of life.
Collapse
Affiliation(s)
- Haiwang Yang
- Section of Developmental Genomics, Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Maria Jaime
- Section of Developmental Genomics, Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Maxi Polihronakis
- Drosophila Species Stock Center, Division of Biological Sciences, University of California San Diego, La Jolla, CA, USA
| | - Kelvin Kanegawa
- Hawaiian Drosophila Research Stock Center, Pacific Biosciences Research Center, University of Hawai'i at Manoa, Honolulu, HI, USA
| | - Therese Markow
- National Laboratory of Genomics for Biodiversity (LANGEBIO), Irapuato, Guanajuato, Mexico.,Drosophila Species Stock Center, Division of Biological Sciences, University of California San Diego, La Jolla, CA, USA
| | - Kenneth Kaneshiro
- Hawaiian Drosophila Research Stock Center, Pacific Biosciences Research Center, University of Hawai'i at Manoa, Honolulu, HI, USA
| | - Brian Oliver
- Section of Developmental Genomics, Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| |
Collapse
|
35
|
Swenson JD, Klomp J, Fisher RA, Crow KD. How the Devil Ray Got Its Horns: The Evolution and Development of Cephalic Lobes in Myliobatid Stingrays (Batoidea: Myliobatidae). Front Ecol Evol 2018. [DOI: 10.3389/fevo.2018.00181] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
|
36
|
Wang R, Liu P, Fan J, Li L. Comparative transcriptome analysis two genotypes of Acer truncatum Bunge seeds reveals candidate genes that influences seed VLCFAs accumulation. Sci Rep 2018; 8:15504. [PMID: 30341360 PMCID: PMC6195533 DOI: 10.1038/s41598-018-33999-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Accepted: 10/06/2018] [Indexed: 12/30/2022] Open
Abstract
The Acer truncatum Bunge is a particular widespread forest tree species in northern China. VLCFAs are important to eukaryotes survival and play diverse roles throughout the development. So far, there are reports that the Acer truncatum seeds fatty acid (FA) rich in VLCFAs, but little is known about the physiological mechanism responsible for the biosynthesis. A total of approximately 37.07 Gbp was generated, it was comprehensive enough to determine the majority of the regulation VLCFAs biosynthesis genes. The 97,053 different unigenes were assembled and identified, and large numbers of EST-SSRs were determined. The expression profiles of crucial genes (KCS, KCR, HCD and ECR) involved in VLCFAs elongation of fatty acids were also studied. To our knowledge, the present study provides the first comprehensive of the transcriptome of Acer truncatum seeds. This transcriptome dataset have been made publicly available NCBI, we believe that it may provide new resource for future high-throughput gene expression of Acer truncatum seeds growth and development and will provide theoretical basic information for improving the yield of VLCFAs, especially nervonic acid.
Collapse
Affiliation(s)
- Rongkai Wang
- College of Forestry, Northwest A&F University, Yangling, 712100, China
| | - Pei Liu
- College of Forestry, Northwest A&F University, Yangling, 712100, China
| | - Jinshuan Fan
- College of Forestry, Northwest A&F University, Yangling, 712100, China
| | - Lingli Li
- College of Forestry, Northwest A&F University, Yangling, 712100, China.
| |
Collapse
|
37
|
Kaczor-Urbanowicz KE, Kim Y, Li F, Galeev T, Kitchen RR, Gerstein M, Koyano K, Jeong SH, Wang X, Elashoff D, Kang SY, Kim SM, Kim K, Kim S, Chia D, Xiao X, Rozowsky J, Wong DTW. Novel approaches for bioinformatic analysis of salivary RNA sequencing data for development. Bioinformatics 2018; 34:1-8. [PMID: 28961734 DOI: 10.1093/bioinformatics/btx504] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Accepted: 08/08/2017] [Indexed: 01/05/2023] Open
Abstract
Motivation Analysis of RNA sequencing (RNA-Seq) data in human saliva is challenging. Lack of standardization and unification of the bioinformatic procedures undermines saliva's diagnostic potential. Thus, it motivated us to perform this study. Results We applied principal pipelines for bioinformatic analysis of small RNA-Seq data of saliva of 98 healthy Korean volunteers including either direct or indirect mapping of the reads to the human genome using Bowtie1. Analysis of alignments to exogenous genomes by another pipeline revealed that almost all of the reads map to bacterial genomes. Thus, salivary exRNA has fundamental properties that warrant the design of unique additional steps while performing the bioinformatic analysis. Our pipelines can serve as potential guidelines for processing of RNA-Seq data of human saliva. Availability and implementation Processing and analysis results of the experimental data generated by the exceRpt (v4.6.3) small RNA-seq pipeline (github.gersteinlab.org/exceRpt) are available from exRNA atlas (exrna-atlas.org). Alignment to exogenous genomes and their quantification results were used in this paper for the analyses of small RNAs of exogenous origin. Contact dtww@ucla.edu.
Collapse
Affiliation(s)
- Karolina Elzbieta Kaczor-Urbanowicz
- Center for Oral/Head & Neck Oncology Research, School of Dentistry, Division of Oral Biology & Medicine University of California at Los Angeles, Los Angeles, CA 90095, USA
| | - Yong Kim
- Center for Oral/Head & Neck Oncology Research, School of Dentistry, Division of Oral Biology & Medicine University of California at Los Angeles, Los Angeles, CA 90095, USA
| | - Feng Li
- Center for Oral/Head & Neck Oncology Research, School of Dentistry, Division of Oral Biology & Medicine University of California at Los Angeles, Los Angeles, CA 90095, USA
| | - Timur Galeev
- Department of Molecular Biophysics and Biochemistry, Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA
| | - Rob R Kitchen
- Department of Molecular Biophysics and Biochemistry, Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA
| | - Mark Gerstein
- Department of Molecular Biophysics and Biochemistry, Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA.,The Department of Computer Science, Yale University, New Haven, CT 06520
| | - Kikuye Koyano
- Department of Integrative Biology and Physiology, University of California at Los Angeles, Los Angeles, CA 90095-1570, USA
| | - Sung-Hee Jeong
- Department of Oral Medicine, School of Dentistry, Pusan National University, Beomeo-ri, Mulgeum-eup, Yangsan-si, Gyeongsangnam-do 626-770, Korea
| | - Xiaoyan Wang
- Department of Biostatistics, University of California at Los Angeles, Los Angeles, CA 90024, USA
| | - David Elashoff
- Department of Biostatistics, University of California at Los Angeles, Los Angeles, CA 90024, USA
| | - So Young Kang
- Department of Pathology & Translational Genomics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Gangnam-gu, Seoul, Korea
| | - Su Mi Kim
- Department of Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Gangnam-gu, Seoul, Korea
| | - Kyoung Kim
- Department of Pathology & Translational Genomics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Gangnam-gu, Seoul, Korea
| | - Sung Kim
- Department of Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Gangnam-gu, Seoul, Korea
| | - David Chia
- Department of Pathology & Laboratory Medicine, University of California at Los Angeles, Los Angeles, CA 90095, USA
| | - Xinshu Xiao
- Department of Integrative Biology and Physiology, University of California at Los Angeles, Los Angeles, CA 90095-1570, USA
| | - Joel Rozowsky
- Department of Molecular Biophysics and Biochemistry,Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA
| | - David T W Wong
- Center for Oral/Head & Neck Oncology Research, School of Dentistry, Division of Oral Biology & Medicine University of California at Los Angeles, Los Angeles, CA 90095, USA
| |
Collapse
|
38
|
MacManes MD. The Oyster River Protocol: a multi-assembler and kmer approach for de novo transcriptome assembly. PeerJ 2018; 6:e5428. [PMID: 30083482 PMCID: PMC6078068 DOI: 10.7717/peerj.5428] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Accepted: 07/21/2018] [Indexed: 11/24/2022] Open
Abstract
Characterizing transcriptomes in non-model organisms has resulted in a massive increase in our understanding of biological phenomena. This boon, largely made possible via high-throughput sequencing, means that studies of functional, evolutionary, and population genomics are now being done by hundreds or even thousands of labs around the world. For many, these studies begin with a de novo transcriptome assembly, which is a technically complicated process involving several discrete steps. The Oyster River Protocol (ORP), described here, implements a standardized and benchmarked set of bioinformatic processes, resulting in an assembly with enhanced qualities over other standard assembly methods. Specifically, ORP produced assemblies have higher Detonate and TransRate scores and mapping rates, which is largely a product of the fact that it leverages a multi-assembler and kmer assembly process, thereby bypassing the shortcomings of any one approach. These improvements are important, as previously unassembled transcripts are included in ORP assemblies, resulting in a significant enhancement of the power of downstream analysis. Further, as part of this study, I show that assembly quality is unrelated with the number of reads generated, above 30 million reads. Code Availability: The version controlled open-source code is available at https://github.com/macmanes-lab/Oyster_River_Protocol. Instructions for software installation and use, and other details are available at http://oyster-river-protocol.rtfd.org/.
Collapse
Affiliation(s)
- Matthew D MacManes
- Department of Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, NH, USA
| |
Collapse
|
39
|
Venturini L, Caim S, Kaithakottil GG, Mapleson DL, Swarbreck D. Leveraging multiple transcriptome assembly methods for improved gene structure annotation. Gigascience 2018; 7:5057872. [PMID: 30052957 PMCID: PMC6105091 DOI: 10.1093/gigascience/giy093] [Citation(s) in RCA: 80] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Accepted: 07/20/2018] [Indexed: 01/22/2023] Open
Abstract
Background The performance of RNA sequencing (RNA-seq) aligners and assemblers varies greatly across different organisms and experiments, and often the optimal approach is not known beforehand. Results Here, we show that the accuracy of transcript reconstruction can be boosted by combining multiple methods, and we present a novel algorithm to integrate multiple RNA-seq assemblies into a coherent transcript annotation. Our algorithm can remove redundancies and select the best transcript models according to user-specified metrics, while solving common artifacts such as erroneous transcript chimerisms. Conclusions We have implemented this method in an open-source Python3 and Cython program, Mikado, available on GitHub.
Collapse
Affiliation(s)
- Luca Venturini
- Earlham Institute, Norwich Research Park, NR47UZ, Norwich, United Kingdom
| | - Shabhonam Caim
- Earlham Institute, Norwich Research Park, NR47UZ, Norwich, United Kingdom
- Quadram Institute Biosciences, Norwich Research Park, NR47UA, Norwich, United Kingdom
| | | | | | - David Swarbreck
- Earlham Institute, Norwich Research Park, NR47UZ, Norwich, United Kingdom
| |
Collapse
|
40
|
Macrander J, Panda J, Janies D, Daly M, Reitzel AM. Venomix: a simple bioinformatic pipeline for identifying and characterizing toxin gene candidates from transcriptomic data. PeerJ 2018; 6:e5361. [PMID: 30083468 PMCID: PMC6074769 DOI: 10.7717/peerj.5361] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Accepted: 07/09/2018] [Indexed: 12/12/2022] Open
Abstract
The advent of next-generation sequencing has resulted in transcriptome-based approaches to investigate functionally significant biological components in a variety of non-model organism. This has resulted in the area of “venomics”: a rapidly growing field using combined transcriptomic and proteomic datasets to characterize toxin diversity in a variety of venomous taxa. Ultimately, the transcriptomic portion of these analyses follows very similar pathways after transcriptome assembly often including candidate toxin identification using BLAST, expression level screening, protein sequence alignment, gene tree reconstruction, and characterization of potential toxin function. Here we describe the Python package Venomix, which streamlines these processes using common bioinformatic tools along with ToxProt, a publicly available annotated database comprised of characterized venom proteins. In this study, we use the Venomix pipeline to characterize candidate venom diversity in four phylogenetically distinct organisms, a cone snail (Conidae; Conus sponsalis), a snake (Viperidae; Echis coloratus), an ant (Formicidae; Tetramorium bicarinatum), and a scorpion (Scorpionidae; Urodacus yaschenkoi). Data on these organisms were sampled from public databases, with each original analysis using different approaches for transcriptome assembly, toxin identification, or gene expression quantification. Venomix recovered numerically more candidate toxin transcripts for three of the four transcriptomes than the original analyses and identified new toxin candidates. In summary, we show that the Venomix package is a useful tool to identify and characterize the diversity of toxin-like transcripts derived from transcriptomic datasets. Venomix is available at: https://bitbucket.org/JasonMacrander/Venomix/.
Collapse
Affiliation(s)
- Jason Macrander
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC, United States of America.,Department of Evolution, Ecology, and Organismal Biology, Ohio State University, Columbus, OH, United States of America
| | - Jyothirmayi Panda
- College of Computing and Informatics, University of North Carolina at Charlotte, Charlotte, NC, United States of America
| | - Daniel Janies
- College of Computing and Informatics, University of North Carolina at Charlotte, Charlotte, NC, United States of America.,Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, NC, United States of America
| | - Marymegan Daly
- Department of Evolution, Ecology, and Organismal Biology, Ohio State University, Columbus, OH, United States of America
| | - Adam M Reitzel
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC, United States of America
| |
Collapse
|
41
|
Wang S, Gribskov M. Comprehensive evaluation of de novo transcriptome assembly programs and their effects on differential gene expression analysis. Bioinformatics 2018; 33:327-333. [PMID: 28172640 DOI: 10.1093/bioinformatics/btw625] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Revised: 09/08/2016] [Accepted: 09/23/2016] [Indexed: 02/02/2023] Open
Abstract
Motivation With the decreased cost of RNA-Seq, an increasing number of non-model organisms have been sequenced. Due to the lack of reference genomes, de novo transcriptome assembly is required. However, there is limited systematic research evaluating the quality of de novo transcriptome assemblies and how the assembly quality influences downstream analysis. Results We used two authentic RNA-Seq datasets from Arabidopsis thaliana, and produced transcriptome assemblies using eight programs with a series of k-mer sizes (from 25 to 71), including BinPacker, Bridger, IDBA-tran, Oases-Velvet, SOAPdenovo-Trans, SSP, Trans-ABySS and Trinity. We measured the assembly quality in terms of reference genome base and gene coverage, transcriptome assembly base coverage, number of chimeras and number of recovered full-length transcripts. SOAPdenovo-Trans performed best in base coverage, while Trans-ABySS performed best in gene coverage and number of recovered full-length transcripts. In terms of chimeric sequences, BinPacker and Oases-Velvet were the worst, while IDBA-tran, SOAPdenovo-Trans, Trans-ABySS and Trinity produced fewer chimeras across all single k-mer assemblies. In differential gene expression analysis, about 70% of the significantly differentially expressed genes (DEG) were the same using reference genome and de novo assemblies. We further identify four reasons for the differences in significant DEG between reference genome and de novo transcriptome assemblies: incomplete annotation, exon level differences, transcript fragmentation and incorrect gene annotation, which we suggest that de novo assembly is beneficial even when a reference genome is available. Availability and Implementation Software used in this study are publicly available at the authors' websites. Contact gribskov@purdue.edu Supplimentary Information Supplementary data are available at Bioinformatics online.
Collapse
Affiliation(s)
- Sufang Wang
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
| | - Michael Gribskov
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA.,Department of Computer Science, Purdue University, West Lafayette, IN, USA
| |
Collapse
|
42
|
Immune-Related Functional Differential Gene Expression in Koi Carp ( Cyprinus carpio) after Challenge with Aeromonas sobria. Int J Mol Sci 2018; 19:ijms19072107. [PMID: 30036965 PMCID: PMC6073842 DOI: 10.3390/ijms19072107] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Revised: 07/03/2018] [Accepted: 07/16/2018] [Indexed: 11/16/2022] Open
Abstract
In order to understand the molecular basis underlying the host immune response of koi carp (Cyprinus carpio), Illumina HiSeqTM 2000 is used to analyze the muscle and spleen transcriptome of koi carp infected with Aeromonas sobria (A. sobria). De novo assembly of paired-end reads yielded 69,480 unigenes, of which the total length, average length, N50, and GC content are 70,120,028 bp, 1037 bp, 1793 bp, and 45.77%, respectively. Annotation is performed by comparison against various databases, yielding 42,229 (non-redundant protein sequence (NR): 60.78%), 59,255 (non-redundant nucleotide (NT): 85.28%), 35,900 (Swiss-Prot: 51.67%), 11,772 (clusters of orthologous groups (COG): 16.94%), 33,057 (Kyoto Encyclopedia of Genes and Genomes (KEGG): 47.58%), 18,764 (Gene Ontology (GO): 27.01%), and 32,085 (Interpro: 46.18%) unigenes. Comparative analysis of the expression profiles between bacterial challenge fish and control fish identifies 7749 differentially expressed genes (DEGs) from the muscle and 7846 DEGs from the spleen. These DEGs are further categorized with KEGG. Enrichment analysis of the DEGs and unigenes reveals major immune-related functions, including up-regulation of genes related with Toll-like receptor signaling, complement and coagulation cascades, and antigen processing and presentation. The results from RNA-Seq data are also validated and confirmed the consistency of the expression levels of seven immune-related genes after 24 h post infection with qPCR. Microsatellites (11,534), including di-to hexa nucleotide repeat motifs, are also identified. Altogether, this work provides valuable insights into the underlying immune mechanisms elicited during bacterial infection in koi carp that may aid in the future development of disease control measures in protection against A. sobria.
Collapse
|
43
|
Martinez B, Khudyakov J, Rutherford K, Crocker DE, Gemmell N, Ortiz RM. Adipose transcriptome analysis provides novel insights into molecular regulation of prolonged fasting in northern elephant seal pups. Physiol Genomics 2018; 50:495-503. [PMID: 29625017 DOI: 10.1152/physiolgenomics.00002.2018] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The physiological and cellular adaptations to extreme fasting in northern elephant seals ( Mirounga angustirostris, NES) are remarkable and may help to elucidate endocrine mechanisms that regulate lipid metabolism and energy homeostasis in mammals. Recent studies have highlighted the importance of thyroid hormones in the maintenance of a lipid-based metabolism during prolonged fasting in weaned NES pups. To identify additional molecular regulators of fasting, we used a transcriptomics approach to examine changes in global gene expression profiles before and after 6-8 wk of fasting in weaned NES pups. We produced a de novo assembly and identified 98 unique protein-coding genes that were differentially expressed between early and late fasting. Most of the downregulated genes were associated with lipid, carbohydrate, and protein metabolism. A number of downregulated genes were also associated with maintenance of the extracellular matrix, consistent with tissue remodeling during weight loss and the multifunctional nature of blubber tissue, which plays both metabolic and structural roles in marine mammals. Using this data set, we predict potential mechanisms by which NES pups sustain metabolism and regulate adipose stores throughout the fast, and provide a valuable resource for additional studies of extreme metabolic adaptations in mammals.
Collapse
Affiliation(s)
- Bridget Martinez
- Department of Molecular & Cellular Biology, University of California, Merced, California.,Department of Medicine, St. George's University School of Medicine, St. George, Grenada.,Department of Anatomy, University of Otago , Dunedin , New Zealand.,Department of Physics and Engineering, Los Alamos National Laboratory , Los Alamos, New Mexico
| | - Jane Khudyakov
- Department of Biological Sciences, University of the Pacific , Stockton, California
| | - Kim Rutherford
- Department of Anatomy, University of Otago , Dunedin , New Zealand
| | - Daniel E Crocker
- Department of Biology, Sonoma State University , Rohnert Park, California
| | - Neil Gemmell
- Department of Anatomy, University of Otago , Dunedin , New Zealand
| | - Rudy M Ortiz
- Department of Molecular & Cellular Biology, University of California, Merced, California
| |
Collapse
|
44
|
San-Jose LM, Roulin A. Genomics of coloration in natural animal populations. Philos Trans R Soc Lond B Biol Sci 2018; 372:rstb.2016.0337. [PMID: 28533454 DOI: 10.1098/rstb.2016.0337] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/15/2017] [Indexed: 12/28/2022] Open
Abstract
Animal coloration has traditionally been the target of genetic and evolutionary studies. However, until very recently, the study of the genetic basis of animal coloration has been mainly restricted to model species, whereas research on non-model species has been either neglected or mainly based on candidate approaches, and thereby limited by the knowledge obtained in model species. Recent high-throughput sequencing technologies allow us to overcome previous limitations, and open new avenues to study the genetic basis of animal coloration in a broader number of species and colour traits, and to address the general relevance of different genetic structures and their implications for the evolution of colour. In this review, we highlight aspects where genome-wide studies could be of major utility to fill in the gaps in our understanding of the biology and evolution of animal coloration. The new genomic approaches have been promptly adopted to study animal coloration although substantial work is still needed to consider a larger range of species and colour traits, such as those exhibiting continuous variation or based on reflective structures. We argue that a robust advancement in the study of animal coloration will also require large efforts to validate the functional role of the genes and variants discovered using genome-wide tools.This article is part of the themed issue 'Animal coloration: production, perception, function and application'.
Collapse
Affiliation(s)
- Luis M San-Jose
- Department of Ecology and Evolution, University of Lausanne, Building Le Biophore, 1015 Lausanne, Switzerland
| | - Alexandre Roulin
- Department of Ecology and Evolution, University of Lausanne, Building Le Biophore, 1015 Lausanne, Switzerland
| |
Collapse
|
45
|
Dylus DV, Czarkwiani A, Blowes LM, Elphick MR, Oliveri P. Developmental transcriptomics of the brittle star Amphiura filiformis reveals gene regulatory network rewiring in echinoderm larval skeleton evolution. Genome Biol 2018; 19:26. [PMID: 29490679 PMCID: PMC5831733 DOI: 10.1186/s13059-018-1402-8] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Accepted: 02/01/2018] [Indexed: 12/13/2022] Open
Abstract
Background Amongst the echinoderms the class Ophiuroidea is of particular interest for its phylogenetic position, ecological importance and developmental and regenerative biology. However, compared to other echinoderms, notably echinoids (sea urchins), relatively little is known about developmental changes in gene expression in ophiuroids. To address this issue, we have generated and assembled a large RNAseq data set of four key stages of development in the brittle star Amphiura filiformis and a de novo reference transcriptome of comparable quality to that of a model echinoderm—the sea urchin Strongylocentrotus purpuratus. Furthermore, we provide access to the new data via a web interface: http://www.echinonet.eu/shiny/Amphiura_filiformis/. Results We have identified highly conserved genes associated with the development of a biomineralised skeleton. We also identify important class-specific characters, including the independent duplication of the msp130 class of genes in different echinoderm classes and the unique occurrence of spicule matrix (sm) genes in echinoids. Using a new quantification pipeline for our de novo transcriptome, validated with other methodologies, we find major differences between brittle stars and sea urchins in the temporal expression of many transcription factor genes. This divergence in developmental regulatory states is more evident in early stages of development when cell specification begins, rather than when cells initiate differentiation. Conclusions Our findings indicate that there has been a high degree of gene regulatory network rewiring and clade-specific gene duplication, supporting the hypothesis of a convergent evolution of larval skeleton development in echinoderms. Electronic supplementary material The online version of this article (10.1186/s13059-018-1402-8) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- David V Dylus
- Research Department of Genetics, Evolution and Environment, University College London, Darwin Building, Gower Street, London, WC1E 6BT, UK.,CoMPLEX/SysBio, UCL, Gower Street, London, WC1E 6BT, UK.,Present address: Department of Computational Biology, UNIL, Genopode, 1005, Lausanne, Switzerland
| | - Anna Czarkwiani
- Research Department of Genetics, Evolution and Environment, University College London, Darwin Building, Gower Street, London, WC1E 6BT, UK
| | - Liisa M Blowes
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London, E1 4NS, UK.,Present address: Centre for Cell Biology & Cutaneous Research, Blizard Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, E1 2AT, UK
| | - Maurice R Elphick
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London, E1 4NS, UK
| | - Paola Oliveri
- Research Department of Genetics, Evolution and Environment, University College London, Darwin Building, Gower Street, London, WC1E 6BT, UK. .,Centre for Life's Origins and Evolution (CLOE), UCL, Gower Street, London, WC1E 6BT, UK.
| |
Collapse
|
46
|
Yang Y, Wang Y, Jia L, Yang G, Xu X, Zhai H, He S, Li J, Dai X, Qin N, Zhu C, Liu Q. Involvement of an ABI-like protein and a Ca2+-ATPase in drought tolerance as revealed by transcript profiling of a sweetpotato somatic hybrid and its parents Ipomoea batatas (L.) Lam. and I. triloba L. PLoS One 2018; 13:e0193193. [PMID: 29466419 PMCID: PMC5821372 DOI: 10.1371/journal.pone.0193193] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Accepted: 02/06/2018] [Indexed: 12/14/2022] Open
Abstract
Previously, we obtained the sweetpotato somatic hybrid KT1 from a cross between sweetpotato (Ipomoea batatas (L.) Lam.) cv. Kokei No. 14 and its drought-tolerant wild relative I. triloba L. KT1 not only inherited the thick storage root characteristic of Kokei No. 14 but also the drought-tolerance trait of I. triloba L. The aim of this study was to explore the molecular mechanism of the drought tolerance of KT1. Four-week-old in vitro-grown plants of KT1, Kokei No. 14, and I. triloba L. were subjected to a simulated drought stress treatment (30% PEG6000) for 0, 6, 12 and 24 h. Total RNA was extracted from samples at each time point, and then used for transcriptome sequencing. The gene transcript profiles of KT1 and its parents were compared to identify differentially expressed genes, and drought-related modules were screened by a weighted gene co-expression network analysis. The functions of ABI-like protein and Ca2+-ATPase, two proteins screened from the cyan and light yellow modules, were analyzed in terms of their potential roles in drought tolerance in KT1 and its parents. These analyses of the drought responses of KT1 and its somatic donors at the transcriptional level provide new annotations for the molecular mechanism of drought tolerance in the somatic hybrid KT1 and its parents.
Collapse
Affiliation(s)
- Yufeng Yang
- Food Crop Institute, Henan Academy of Agricultural Sciences, Zhengzhou, China
- Key Laboratory of Sweetpotato Biology and Biotechnology, Ministry of Agriculture, China Agricultural University, Beijing, China
| | - Yannan Wang
- Food Crop Institute, Henan Academy of Agricultural Sciences, Zhengzhou, China
- Key Laboratory of Sweetpotato Biology and Biotechnology, Ministry of Agriculture, China Agricultural University, Beijing, China
| | - Licong Jia
- Key Laboratory of Sweetpotato Biology and Biotechnology, Ministry of Agriculture, China Agricultural University, Beijing, China
| | - Guohong Yang
- Food Crop Institute, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Xinzhi Xu
- Food Crop Institute, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Hong Zhai
- Key Laboratory of Sweetpotato Biology and Biotechnology, Ministry of Agriculture, China Agricultural University, Beijing, China
| | - Shaozhen He
- Key Laboratory of Sweetpotato Biology and Biotechnology, Ministry of Agriculture, China Agricultural University, Beijing, China
| | - Junxia Li
- Food Crop Institute, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Xiaodong Dai
- Food Crop Institute, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Na Qin
- Food Crop Institute, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Cancan Zhu
- Food Crop Institute, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Qingchang Liu
- Key Laboratory of Sweetpotato Biology and Biotechnology, Ministry of Agriculture, China Agricultural University, Beijing, China
- * E-mail:
| |
Collapse
|
47
|
Taheri S, Lee Abdullah T, Yusop MR, Hanafi MM, Sahebi M, Azizi P, Shamshiri RR. Mining and Development of Novel SSR Markers Using Next Generation Sequencing (NGS) Data in Plants. Molecules 2018; 23:E399. [PMID: 29438290 PMCID: PMC6017569 DOI: 10.3390/molecules23020399] [Citation(s) in RCA: 83] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2017] [Revised: 01/11/2018] [Accepted: 01/13/2018] [Indexed: 11/17/2022] Open
Abstract
Microsatellites, or simple sequence repeats (SSRs), are one of the most informative and multi-purpose genetic markers exploited in plant functional genomics. However, the discovery of SSRs and development using traditional methods are laborious, time-consuming, and costly. Recently, the availability of high-throughput sequencing technologies has enabled researchers to identify a substantial number of microsatellites at less cost and effort than traditional approaches. Illumina is a noteworthy transcriptome sequencing technology that is currently used in SSR marker development. Although 454 pyrosequencing datasets can be used for SSR development, this type of sequencing is no longer supported. This review aims to present an overview of the next generation sequencing, with a focus on the efficient use of de novo transcriptome sequencing (RNA-Seq) and related tools for mining and development of microsatellites in plants.
Collapse
Affiliation(s)
- Sima Taheri
- Department of Crop Science, Faculty of Agriculture, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia.
| | - Thohirah Lee Abdullah
- Department of Crop Science, Faculty of Agriculture, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia.
| | - Mohd Rafii Yusop
- Department of Crop Science, Faculty of Agriculture, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia.
- Laboratory of Climate-Smart Food Crop Production, Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia.
| | - Mohamed Musa Hanafi
- Laboratory of Climate-Smart Food Crop Production, Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia.
- Laboratory of Plantation Science and Technology, Institute of Plantation Studies, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia.
- Department of Land Management, Faculty of Agriculture, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia.
| | - Mahbod Sahebi
- Laboratory of Climate-Smart Food Crop Production, Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia.
| | - Parisa Azizi
- Laboratory of Climate-Smart Food Crop Production, Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia.
| | - Redmond Ramin Shamshiri
- Smart Farming Technology Research Center, Department of Biological and Agricultural Engineering, Faculty of Engineering, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia.
| |
Collapse
|
48
|
Krabbenhoft TJ, Turner TF. Comparative transcriptomics of cyprinid minnows and carp in a common wild setting: a resource for ecological genomics in freshwater communities. DNA Res 2018; 25:11-23. [PMID: 28985264 PMCID: PMC5824830 DOI: 10.1093/dnares/dsx034] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Accepted: 08/12/2017] [Indexed: 12/30/2022] Open
Abstract
Comparative transcriptomics can now be conducted on organisms in natural settings, which has greatly enhanced understanding of genome–environment interactions. Here, we demonstrate the utility and potential pitfalls of comparative transcriptomics of wild organisms, with an example from three cyprinid fish species (Teleostei:Cypriniformes). We present extensively filtered and annotated transcriptome assemblies that provide a valuable resource for studies of genome evolution (e.g. polyploidy), ecological and morphological diversification, speciation, and shared and unique responses to environmental variation in cyprinid fishes. Our results and analyses address the following points: (i) ‘essential developmental genes’ are shown to be ubiquitously expressed in a diverse suite of tissues across later ontogenetic stages (i.e. juveniles and adults), making these genes are useful for assessing the quality of transcriptome assemblies, (ii) the influence of microbiomes and other exogenous DNA, (iii) potentially novel, species-specific genes, and (iv) genomic rearrangements (e.g. whole genome duplication). The data we present provide a resource for future comparative work in cypriniform fishes and other taxa across a variety of sub-disciplines, including stress response, morphological diversification, community ecology, ecotoxicology, and climate change.
Collapse
Affiliation(s)
- Trevor J Krabbenhoft
- Department of Biology and Museum of Southwestern Biology, University of New Mexico, Albuquerque, NM 87131, USA
| | - Thomas F Turner
- Department of Biology and Museum of Southwestern Biology, University of New Mexico, Albuquerque, NM 87131, USA
| |
Collapse
|
49
|
Chen M, Henry N, Almsaeed A, Zhou X, Wegrzyn J, Ficklin S, Staton M. New extension software modules to enhance searching and display of transcriptome data in Tripal databases. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2018; 2017:4049442. [PMID: 29220446 PMCID: PMC5532966 DOI: 10.1093/database/bax052] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Accepted: 06/20/2017] [Indexed: 01/16/2023]
Abstract
Tripal is an open source software package for developing biological databases with a focus on genetic and genomic data. It consists of a set of core modules that deliver essential functions for loading and displaying data records and associated attributes including organisms, sequence features and genetic markers. Beyond the core modules, community members are encouraged to contribute extension modules to build on the Tripal core and to customize Tripal for individual community needs. To expand the utility of the Tripal software system, particularly for RNASeq data, we developed two new extension modules. Tripal Elasticsearch enables fast, scalable searching of the entire content of a Tripal site as well as the construction of customized advanced searches of specific data types. We demonstrate the use of this module for searching assembled transcripts by functional annotation. A second module, Tripal Analysis Expression, houses and displays records from gene expression assays such as RNA sequencing. This includes biological source materials (biomaterials), gene expression values and protocols used to generate the data. In the case of an RNASeq experiment, this would reflect the individual organisms and tissues used to produce sequencing libraries, the normalized gene expression values derived from the RNASeq data analysis and a description of the software or code used to generate the expression values. The module will load data from common flat file formats including standard NCBI Biosample XML. Data loading, display options and other configurations can be controlled by authorized users in the Drupal administrative backend. Both modules are open source, include usage documentation, and can be found in the Tripal organization’s GitHub repository. Database URL: Tripal Elasticsearch module:https://github.com/tripal/tripal_elasticsearch Tripal Analysis Expression module:https://github.com/tripal/tripal_analysis_expression
Collapse
Affiliation(s)
- Ming Chen
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN, USA.,Department of Genome Science and Technology, University of Tennessee, Knoxville, TN, USA
| | - Nathan Henry
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN, USA
| | - Abdullah Almsaeed
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN, USA
| | - Xiao Zhou
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN, USA
| | - Jill Wegrzyn
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, USA
| | - Stephen Ficklin
- Department of Horticulture, Washington State University, Pullman, WA, USA
| | - Margaret Staton
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN, USA
| |
Collapse
|
50
|
de Busserolles F, Cortesi F, Helvik JV, Davies WIL, Templin RM, Sullivan RKP, Michell CT, Mountford JK, Collin SP, Irigoien X, Kaartvedt S, Marshall J. Pushing the limits of photoreception in twilight conditions: The rod-like cone retina of the deep-sea pearlsides. SCIENCE ADVANCES 2017; 3:eaao4709. [PMID: 29134201 PMCID: PMC5677336 DOI: 10.1126/sciadv.aao4709] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Accepted: 10/17/2017] [Indexed: 06/07/2023]
Abstract
Most vertebrates have a duplex retina comprising two photoreceptor types, rods for dim-light (scotopic) vision and cones for bright-light (photopic) and color vision. However, deep-sea fishes are only active in dim-light conditions; hence, most species have lost their cones in favor of a simplex retina composed exclusively of rods. Although the pearlsides, Maurolicus spp., have such a pure rod retina, their behavior is at odds with this simplex visual system. Contrary to other deep-sea fishes, pearlsides are mostly active during dusk and dawn close to the surface, where light levels are intermediate (twilight or mesopic) and require the use of both rod and cone photoreceptors. This study elucidates this paradox by demonstrating that the pearlside retina does not have rod photoreceptors only; instead, it is composed almost exclusively of transmuted cone photoreceptors. These transmuted cells combine the morphological characteristics of a rod photoreceptor with a cone opsin and a cone phototransduction cascade to form a unique photoreceptor type, a rod-like cone, specifically tuned to the light conditions of the pearlsides' habitat (blue-shifted light at mesopic intensities). Combining properties of both rods and cones into a single cell type, instead of using two photoreceptor types that do not function at their full potential under mesopic conditions, is likely to be the most efficient and economical solution to optimize visual performance. These results challenge the standing paradigm of the function and evolution of the vertebrate duplex retina and emphasize the need for a more comprehensive evaluation of visual systems in general.
Collapse
Affiliation(s)
- Fanny de Busserolles
- Queensland Brain Institute, The University of Queensland, Brisbane, Queensland 4072, Australia
- Red Sea Research Center, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Fabio Cortesi
- Queensland Brain Institute, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Jon Vidar Helvik
- Department of Biology, University of Bergen, Bergen 5020, Norway
| | - Wayne I. L. Davies
- The Oceans Institute, The University of Western Australia, Crawley, Western Australia 6009, Australia
- School of Biological Science, The University of Western Australia, Crawley, Western Australia 6009, Australia
- Lions Eye Institute, The University of Western Australia, Crawley, Western Australia 6009, Australia
| | - Rachel M. Templin
- Queensland Brain Institute, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Robert K. P. Sullivan
- Queensland Brain Institute, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Craig T. Michell
- Red Sea Research Center, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
- Department of Environmental and Biological Sciences, University of Eastern Finland, Yliopistokatu 7, FI-80101 Joensuu, Finland
| | - Jessica K. Mountford
- The Oceans Institute, The University of Western Australia, Crawley, Western Australia 6009, Australia
- School of Biological Science, The University of Western Australia, Crawley, Western Australia 6009, Australia
- Lions Eye Institute, The University of Western Australia, Crawley, Western Australia 6009, Australia
| | - Shaun P. Collin
- The Oceans Institute, The University of Western Australia, Crawley, Western Australia 6009, Australia
- School of Biological Science, The University of Western Australia, Crawley, Western Australia 6009, Australia
- Lions Eye Institute, The University of Western Australia, Crawley, Western Australia 6009, Australia
| | - Xabier Irigoien
- Red Sea Research Center, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
- Marine Research, AZTI - Tecnalia, Herrera Kaia, Portualdea z/g, 20110 Pasaia (Gipuzkoa), Spain
- IKERBASQUE, Basque Foundation for Science, Bilbao, Spain
| | - Stein Kaartvedt
- Red Sea Research Center, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
- Department of Biosciences, University of Oslo, Oslo 0316, Norway
| | - Justin Marshall
- Queensland Brain Institute, The University of Queensland, Brisbane, Queensland 4072, Australia
| |
Collapse
|