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Kang JS, Yu JG, Xiang QP, Zhang XC. The Possible Earliest Allopolyploidization in Tracheophytes Revealed by Phylotranscriptomics and Morphology of Selaginellaceae. Mol Biol Evol 2024; 41:msae153. [PMID: 39101470 PMCID: PMC11299036 DOI: 10.1093/molbev/msae153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 07/15/2024] [Accepted: 07/19/2024] [Indexed: 08/06/2024] Open
Abstract
Selaginellaceae, originated in the Carboniferous and survived the Permian-Triassic mass extinction, is the largest family of lycophyte, which is sister to other tracheophytes. It stands out from tracheophytes by exhibiting extraordinary habitat diversity and lacking polyploidization. The organelle genome-based phylogenies confirmed the monophyly of Selaginella, with six or seven subgenera grouped into two superclades, but the phylogenetic positions of the enigmatic Selaginella sanguinolenta clade remained problematic. Here, we conducted a phylogenomic study on Selaginellaceae utilizing large-scale nuclear gene data from RNA-seq to elucidate the phylogeny and explore the causes of the phylogenetic incongruence of the S. sanguinolenta clade. Our phylogenetic analyses resolved three different positions of the S. sanguinolenta clade, which were supported by the sorted three nuclear gene sets, respectively. The results from the gene flow test, species network inference, and plastome-based phylogeny congruently suggested a probable hybrid origin of the S. sanguinolenta clade involving each common ancestor of the two superclades in Selaginellaceae. The hybrid hypothesis is corroborated by the evidence from rhizophore morphology and spore micromorphology. The chromosome observation and Ks distributions further suggested hybridization accompanied by polyploidization. Divergence time estimation based on independent datasets from nuclear gene sets and plastid genome data congruently inferred that allopolyploidization occurred in the Early Triassic. To our best knowledge, the allopolyploidization in the Mesozoic reported here represents the earliest record of tracheophytes. Our study revealed a unique triad of phylogenetic positions for a hybrid-originated group with comprehensive evidence and proposed a hypothesis for retaining both parental alleles through gene conversion.
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Affiliation(s)
- Jong-Soo Kang
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Ji-Gao Yu
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- China National Botanical Garden, Beijing 100093, China
| | - Qiao-Ping Xiang
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- China National Botanical Garden, Beijing 100093, China
| | - Xian-Chun Zhang
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- China National Botanical Garden, Beijing 100093, China
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de Paula LCB, Dios RDVP, Gudin FM, de Santis MD, Alvarez-Garcia DM, Antunes Júnior M, Freire BV, Marques FPDL, Lahr DJG, Nihei SS. Phylogenomic analysis of Tachinidae (Diptera: Calyptratae: Oestroidea): a transcriptomic approach to understanding the subfamily relationships. Cladistics 2024; 40:64-81. [PMID: 37837208 DOI: 10.1111/cla.12562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 08/25/2023] [Accepted: 09/13/2023] [Indexed: 10/15/2023] Open
Abstract
Tachinidae is the second most species-rich family of Diptera. It comprises four subfamilies, and all of its members have parasitoid habits. We present the first phylogenomic analysis of Tachinidae using transcriptomic data, based on 30 species. We constructed four datasets: three using translated data at the amino acid level (100% coverage, with 106 single-copy protein-coding genes; 75% coverage, with 1359 genes; and 50% coverage, with 1942 genes). The trees were estimated by analysing four matrices using maximum likelihood and maximum parsimony inferences, and only minor differences were found among them. Overall, our topologies are well resolved, with high node support. Polleniidae is corroborated as a sister group to Tachinidae. Within Tachinidae, our results confirm the hypothesis (Phasiinae + Dexiinae) + (Tachininae + Exoristinae). Phasiinae, Dexiinae and Exoristinae are recovered as monophyletic, and Tachininae as polyphyletic. Once again, the tribe Myiophasiini (Tachininae) composes a fifth lineage, clade sister to all the remaining Tachinidae. The Neotropical tribe Iceliini, formerly in Tachininae, is recovered within Exoristinae, sister to Winthemiini. In general, our results are congruent with recent phylogenetic studies that include tachinids, with the important confirmation of the subfamilial relationships and the existence of a fifth lineage of Tachinidae.
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Affiliation(s)
- Letícia Chiara Baldassio de Paula
- Department of Genetics, Institute of Biosciences, University of São Paulo, Rua do Matão, n 277, São Paulo, SP, 05508-090, Brazil
- Department of Zoology, Institute of Biosciences, University of São Paulo, Rua do Matão, Travessa 14, n 101, São Paulo, SP, 05508-090, Brazil
| | - Rodrigo de Vilhena Perez Dios
- Department of Zoology, Institute of Biosciences, University of São Paulo, Rua do Matão, Travessa 14, n 101, São Paulo, SP, 05508-090, Brazil
| | - Filipe Macedo Gudin
- Department of Zoology, Institute of Biosciences, University of São Paulo, Rua do Matão, Travessa 14, n 101, São Paulo, SP, 05508-090, Brazil
| | - Marcelo Domingos de Santis
- Department of Zoology, Institute of Biosciences, University of São Paulo, Rua do Matão, Travessa 14, n 101, São Paulo, SP, 05508-090, Brazil
- Zoologisches Forschungsmuseum Alexander Koenig, Leibniz-Institut zur Analyse des Biodiversitatswandels, Adenauerallee 127, D-53113, Bonn, Germany
| | - Deivys Moises Alvarez-Garcia
- Department of Zoology, Institute of Biosciences, University of São Paulo, Rua do Matão, Travessa 14, n 101, São Paulo, SP, 05508-090, Brazil
- Grupo de Investigación en Zoología y Ecología, Universidad de Sucre, Cra 28 # 5 - 267 Barrio Puerta Roja, Sincelejo, Colombia
| | - Manuel Antunes Júnior
- Department of Zoology, Institute of Biosciences, University of São Paulo, Rua do Matão, Travessa 14, n 101, São Paulo, SP, 05508-090, Brazil
| | - Beatriz Vieira Freire
- Department of Zoology, Institute of Biosciences, University of São Paulo, Rua do Matão, Travessa 14, n 101, São Paulo, SP, 05508-090, Brazil
| | - Fernando Portella de Luna Marques
- Department of Zoology, Institute of Biosciences, University of São Paulo, Rua do Matão, Travessa 14, n 101, São Paulo, SP, 05508-090, Brazil
| | - Daniel José Galafasse Lahr
- Department of Zoology, Institute of Biosciences, University of São Paulo, Rua do Matão, Travessa 14, n 101, São Paulo, SP, 05508-090, Brazil
| | - Silvio Shigueo Nihei
- Department of Zoology, Institute of Biosciences, University of São Paulo, Rua do Matão, Travessa 14, n 101, São Paulo, SP, 05508-090, Brazil
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Wei X, Xu D, Liu Z, Liu Q, Zhuo Z. SMRT Sequencing Technology Was Used to Construct the Batocera horsfieldi (Hope) Transcriptome and Reveal Its Features. INSECTS 2023; 14:625. [PMID: 37504630 PMCID: PMC10380457 DOI: 10.3390/insects14070625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2023] [Revised: 06/28/2023] [Accepted: 07/07/2023] [Indexed: 07/29/2023]
Abstract
Batocera horsfieldi (Hope) (Coleoptera: Cerambycidae) is an important forest pest in China that mainly infests timber and economic forests. This pest primarily causes plant tissue to necrotize, rot, and eventually die by feeding on the woody parts of tree trunks. To gain a deeper understanding of the genetic mechanism of B. horsfieldi, this study employed single-molecule real-time sequencing (SMRT) and Illumina RNA-seq technologies to conduct full-length transcriptome sequencing of the insect. Total RNA extracted from male and female adults was mixed and subjected to SMRT sequencing, generating a complete transcriptome. Transcriptome analysis, prediction of long non-coding RNA (lncRNA), coding sequences (CDs), analysis of simple sequence repeats (SSR), prediction of transcription factors, and functional annotation of transcripts were performed in this study. The collective 20,356,793 subreads (38.26 G, clean reads) were generated, including 432,091 circular consensus sequences and 395,851 full-length non-chimera reads. The full-length non-chimera reads (FLNC) were clustered and redundancies were removed, resulting in 39,912 consensus reads. SSR and ANGEL software v3.0 were used for predicting SSR and CDs. In addition, four tools were used for annotating 6058 lncRNAs, identifying 636 transcription factors. Furthermore, a total of 84,650 transcripts were functionally annotated in seven different databases. This is the first time that the full-length transcriptome of B. horsfieldi has been obtained using SMRT sequencing. This provides an important foundation for investigating the gene regulation underlying the interaction between B. horsfieldi and its host plants through gene editing in the future and provides a scientific basis for the prevention and control of B. horsfieldi.
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Affiliation(s)
- Xinju Wei
- College of Life Science, China West Normal University, Nanchong 637002, China
| | - Danping Xu
- College of Life Science, China West Normal University, Nanchong 637002, China
| | - Zhiqian Liu
- College of Life Science, China West Normal University, Nanchong 637002, China
| | - Quanwei Liu
- College of Life Science, China West Normal University, Nanchong 637002, China
| | - Zhihang Zhuo
- College of Life Science, China West Normal University, Nanchong 637002, China
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Bibliometric Analyses of Web of Science Illuminate Research Advances of Neuropterida. INSECTS 2022; 13:insects13050464. [PMID: 35621799 PMCID: PMC9147768 DOI: 10.3390/insects13050464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 05/01/2022] [Accepted: 05/12/2022] [Indexed: 02/04/2023]
Abstract
Neuropterida is a relatively primitive group of Holometabola. There are about 6500 extant species. Many species of this group are natural enemies and can prey on a variety of agricultural pests. In order to understand the leading research institutions, researchers and research contents, and to predict the future research directions of Neuropterida, the Web of Science core database, from January 1995 to September 2021, was searched with the theme of “Neuropterida or Neuroptera or Megaloptera or Raphidioptera or Lacewing”. The results showed that the United States and China published relatively more publications than other countries. In addition, researchers from these two countries had more cooperation with other countries. China Agricultural University ranked the highest in the number of publications and centrality in this field. In addition, it was found that the early research focused on the biological control of Neuropterida by analyzing the keyword burst, whereas the more recent research focused on the phylogeny of Neuropterida. As the first representative chromosome-level genome of Neuropterida has been published, the future research of Neuropterida will focus on the genomic studies and molecular mechanisms of their morphological characters, behavior, historical evolution and so on.
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Zhuang Y, Manzitto-Tripp EA. Co-expression network analyses of anthocyanin biosynthesis genes in Ruellia (Wild Petunias; Acanthaceae). BMC Ecol Evol 2022; 22:27. [PMID: 35260074 PMCID: PMC8905905 DOI: 10.1186/s12862-021-01955-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Accepted: 12/22/2021] [Indexed: 11/26/2022] Open
Abstract
Background Anthocyanins are major pigments contributing to flower coloration and as such knowledge of molecular architecture underlying the anthocyanin biosynthetic pathway (ABP) is key to understanding flower color diversification. To identify ABP structural genes and associated regulatory networks, we sequenced 16 transcriptomes generated from 10 species of Ruellia and then conducted co-expression analyses among resulting data. Results Complete coding sequences for 12 candidate structural loci representing eight genes plus nine candidate regulatory loci were assembled. Analysis of non-synonymous/synonymous (dn/ds) mutation rates indicated all identified loci are under purifying selection, suggesting overall selection to prevent the accumulation of deleterious mutations. Additionally, upstream enzymes have lower rates of molecular evolution compared to downstream enzymes. However, site-specific tests of selection yielded evidence for positive selection at several sites, including four in F3'H2 and five in DFR3, and these sites are located in protein binding regions. A species-level phylogenetic tree constructed using a newly implemented hybrid transcriptome–RADseq approach implicates several flower color transitions among the 10 species. We found evidence of both regulatory and structural mutations to F3′5'H in helping to explain the evolution of red flowers from purple-flowered ancestors. Conclusions Sequence comparisons and co-expression analyses of ABP loci revealed that mutations in regulatory loci are likely to play a greater role in flower color transitions in Ruellia compared to mutations in underlying structural genes. Supplementary Information The online version contains supplementary material available at 10.1186/s12862-021-01955-x.
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Affiliation(s)
- Yongbin Zhuang
- Department of Ecology and Evolutionary Biology, University of Colorado, UCB 334, Boulder, CO, 80309, USA.,Museum of Natural History, University of Colorado, UCB 350, Boulder, CO, 80309, USA.,College of Agronomy, Shandong Agricultural University, Taian, 271018, Shandong, China
| | - Erin A Manzitto-Tripp
- Department of Ecology and Evolutionary Biology, University of Colorado, UCB 334, Boulder, CO, 80309, USA. .,Museum of Natural History, University of Colorado, UCB 350, Boulder, CO, 80309, USA.
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Low-Coverage Whole Genomes Reveal the Higher Phylogeny of Green Lacewings. INSECTS 2021; 12:insects12100857. [PMID: 34680626 PMCID: PMC8539002 DOI: 10.3390/insects12100857] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 09/10/2021] [Accepted: 09/14/2021] [Indexed: 11/16/2022]
Abstract
Simple Summary Green lacewings (Chrysopidae) are one of the most commonly observed natural predators belonging to Neuroptera. They are widely distributed all over the world. The relationships among the three subfamilies of Chrysopidae have been controversial for a long time. We newly sequenced and analyzed the low-coverage genomes of five species (Apochrysa matsumurae, Chrysopa pallens, Chrysoperla furcifera, Italochrysa pardalina, Nothochrysa sinica), representing all three subfamilies, in order to reconstruct the higher phylogeny within this family. Our results suggested that Chrysopinae are a monophyletic sister group to the branch Apochrysinae + Nothochrysinae, and that Chrysopinae diverged from Apochrysinae + Nothochrysinae during the Early Cretaceous period (144–151 Ma), while Aporchrysinae diverged from Nothochrysinae around 117–133 Ma. Abstract Green lacewings are one of the largest families within Neuroptera and are widely distributed all over the world. Many species within this group are important natural predators that are widely used for the biological control of pests in agricultural ecosystems. Several proposed phylogenetic relationships among the three subfamilies of Chrysopidae have been extensively debated. To further understand the higher phylogeny as well as the evolutionary history of Chrysopidae, we newly sequenced and analyzed the low-coverage genomes of 5 species (Apochrysa matsumurae, Chrysopa pallens, Chrysoperla furcifera, Italochrysa pardalina, Nothochrysa sinica), representing 3 subfamilies of Chrysopidae. There are 2213 orthologs selected to reconstruct the phylogenetic tree. Phylogenetic reconstruction was performed using both concatenation and coalescent-based approaches, based on different data matrices. All the results suggested that Chrysopinae were a monophyletic sister group to the branch Apochrysinae + Nothochrysinae. These results were completely supported, except by the concatenation analyses of the nt data matrix, which suggested that Apochrysinae were a sister group to Chrysopinae + Nothchrysinae. The different topology from the nt data matrix may have been caused by the limited sampling of Chrysopidae. The divergence time showed that Chrysopinae diverged from Apochrysinae + Nothochrysinae during the Early Cretaceous period (144–151 Ma), while Aporchrysinae diverged from Nothochrysinae around 117–133 Ma. These results will improve our understanding of the higher phylogeny of Chrysopidae and lay a foundation for the utilization of natural predators.
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Abstract
Phylogenomics, the study of phylogenetic relationships among taxa based on their genome sequences, has emerged as the preferred phylogenetic method because of the wealth of phylogenetic information contained in genome sequences. Genome sequencing, however, can be prohibitively expensive, especially for taxa with huge genomes and when many taxa need sequencing. Consequently, the less costly phylotranscriptomics has seen an increased use in recent years. Phylotranscriptomics reconstructs phylogenies using DNA sequences derived from transcriptomes, which are often orders of magnitude smaller than genomes. However, in the absence of corresponding genome sequences, comparative analyses of transcriptomes can be challenging and it is unclear whether phylotranscriptomics is as reliable as phylogenomics. Here, we respectively compare the phylogenomic and phylotranscriptomic trees of 22 mammals and 15 plants that have both sequenced nuclear genomes and publicly available RNA sequencing data from multiple tissues. We found that phylotranscriptomic analysis can be sensitive to orthologous gene identification. When a rigorous method for identifying orthologs is employed, phylogenomic and phylotranscriptomic trees are virtually identical to each other, regardless of the tissue of origin of the transcriptomes and whether the same tissue is used across species. These findings validate phylotranscriptomics, brighten its prospect, and illustrate the criticality of reliable ortholog detection in such practices.
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Affiliation(s)
- Seongmin Cheon
- School of Biological Sciences and Technology, Chonnam National University, Gwangju, Republic of Korea
| | - Jianzhi Zhang
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI
| | - Chungoo Park
- School of Biological Sciences and Technology, Chonnam National University, Gwangju, Republic of Korea
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Yang H, Xu D, Zhuo Z, Hu J, Lu B. Transcriptome and gene expression analysis of Rhynchophorus ferrugineus (Coleoptera: Curculionidae) during developmental stages. PeerJ 2020; 8:e10223. [PMID: 33194414 PMCID: PMC7643551 DOI: 10.7717/peerj.10223] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Accepted: 09/29/2020] [Indexed: 01/15/2023] Open
Abstract
Background Red palm weevil, Rhynchophorus ferrugineus Olivier, is one of the most destructive pests harming palm trees. However, genomic resources for R. ferrugineus are still lacking, limiting the ability to discover molecular and genetic means of pest control. Methods In this study, PacBio Iso-Seq and Illumina RNA-seq were used to generate transcriptome from three developmental stages of R. ferrugineus (pupa, 7th-instar larva, adult) to increase the understanding of the life cycle and molecular characteristics of the pest. Results Sequencing generated 625,983,256 clean reads, from which 63,801 full-length transcripts were assembled with N50 of 3,547 bp. Expression analyses revealed 8,583 differentially expressed genes (DEGs). Moreover, gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis revealed that these DEGs were mainly related to the peroxisome pathway which associated with metabolic pathways, material transportation and organ tissue formation. In summary, this work provides a valuable basis for further research on the growth and development, gene expression and gene prediction, and pest control of R. ferrugineus.
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Affiliation(s)
- Hongjun Yang
- College of Life Science, China West Normal University, Nanchong, Sichuan, China.,Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education, Key Laboratory of Germplasm Resources Biology of Tropical Special Ornamental Plants of Hainan Province, College of Forestry, Hainan University, Haikou, Hainan,China
| | - Danping Xu
- College of Life Science, China West Normal University, Nanchong, Sichuan, China
| | - Zhihang Zhuo
- College of Life Science, China West Normal University, Nanchong, Sichuan, China.,Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education, Key Laboratory of Germplasm Resources Biology of Tropical Special Ornamental Plants of Hainan Province, College of Forestry, Hainan University, Haikou, Hainan,China.,Key Laboratory of Integrated Pest Management on Crops in South China, Ministry of Agriculture, South China Agricultural University, Guangzhou, Guangdong, China
| | - Jiameng Hu
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education, Key Laboratory of Germplasm Resources Biology of Tropical Special Ornamental Plants of Hainan Province, College of Forestry, Hainan University, Haikou, Hainan,China
| | - Baoqian Lu
- Key Laboratory of Integrated Pest Management on Tropical Crops, Ministry of Agriculture China, Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, China
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Guo Q, Li D, Zhai Y, Gu Z. CCPRD: A Novel Analytical Framework for the Comprehensive Proteomic Reference Database Construction of NonModel Organisms. ACS OMEGA 2020; 5:15370-15384. [PMID: 32637811 PMCID: PMC7331046 DOI: 10.1021/acsomega.0c01278] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 06/09/2020] [Indexed: 06/11/2023]
Abstract
Protein reference databases are a critical part of producing efficient proteomic analyses. However, the method for constructing clean, efficient, and comprehensive protein reference databases of nonmodel organisms is lacking. Existing methods either do not have contamination control procedures, or these methods rely on a three-frame and/or six-frame translation that sharply increases the search space and the need for computational resources. Herein, we propose a framework for constructing a customized comprehensive proteomic reference database (CCPRD) from draft genomes and deep sequencing transcriptomes. Its effectiveness is demonstrated by incorporating the proteomes of nematocysts from endoparasitic cnidarian: myxozoans. By applying customized contamination removal procedures, contaminations in omic data were successfully identified and removed. This is an effective method that does not result in overdecontamination. This can be shown by comparing the CCPRD MS results with an artificially contaminated database and another database with removed contaminations in genomes and transcriptomes added back. CCPRD outperformed traditional frame-based methods by identifying 35.2-50.7% more peptides and 35.8-43.8% more proteins, with a maximum of 84.6% in size reduction. A BUSCO analysis showed that the CCPRD maintained a relatively high level of completeness compared to traditional methods. These results confirm the superiority of the CCPRD over existing methods in peptide and protein identification numbers, database size, and completeness. By providing a general framework for generating the reference database, the CCPRD, which does not need a high-quality genome, can potentially be applied to nonmodel organisms and significantly contribute to proteomic research.
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Affiliation(s)
- Qingxiang Guo
- Department of Aquatic
Animal Medicine, College of Fisheries, Huazhong
Agricultural University, Wuhan, Hubei Province 430070, PR China
- Hubei Engineering Technology Research
Center for Aquatic Animal Diseases Control and Prevention, Wuhan 430070, PR China
| | - Dan Li
- Department of Aquatic
Animal Medicine, College of Fisheries, Huazhong
Agricultural University, Wuhan, Hubei Province 430070, PR China
- Hubei Engineering Technology Research
Center for Aquatic Animal Diseases Control and Prevention, Wuhan 430070, PR China
| | - Yanhua Zhai
- Department of Aquatic
Animal Medicine, College of Fisheries, Huazhong
Agricultural University, Wuhan, Hubei Province 430070, PR China
- Hubei Engineering Technology Research
Center for Aquatic Animal Diseases Control and Prevention, Wuhan 430070, PR China
| | - Zemao Gu
- Department of Aquatic
Animal Medicine, College of Fisheries, Huazhong
Agricultural University, Wuhan, Hubei Province 430070, PR China
- Hubei Engineering Technology Research
Center for Aquatic Animal Diseases Control and Prevention, Wuhan 430070, PR China
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Yang H, Xu D, Zhuo Z, Hu J, Lu B. SMRT sequencing of the full-length transcriptome of the Rhynchophorus ferrugineus (Coleoptera: Curculionidae). PeerJ 2020; 8:e9133. [PMID: 32509454 PMCID: PMC7246026 DOI: 10.7717/peerj.9133] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Accepted: 04/14/2020] [Indexed: 12/23/2022] Open
Abstract
Background Red palm weevil Rhynchophorus ferrugineus (Coleoptera: Curculionidae) is one of the most destructive insects for palm trees in the world. However, its genome resources are still in the blank stage, which limits the study of molecular and growth development analysis. Methods In this study, we used PacBio Iso-Seq and Illumina RNA-seq to first generate transcriptome from three developmental stages of R. ferrugineus (pupa, 7th larva, female and male) to increase our understanding of the life cycle and molecular characteristics of R. ferrugineus. Results A total of 63,801 nonredundant full-length transcripts were generated with an average length of 2,964 bp from three developmental stages, including the 7th instar larva, pupa, female adult and male adult. These transcripts showed a high annotation rate in seven public databases, with 54,999 (86.20%) successfully annotated. Meanwhile, 2,184 alternative splicing (AS) events, 2,084 transcription factors (TFs), 66,230 simple sequence repeats (SSR) and 9,618 Long noncoding RNAs (lncRNAs) were identified. In summary, our results provide a new source of full-length transcriptional data and information for the further study of gene expression and genetics in R. ferrugineus.
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Affiliation(s)
- Hongjun Yang
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education, Key Laboratory of Germplasm Resources Biology of Tropical Special Ornamental Plants of Hainan Province, College of Forestry, Hainan University, Haikou, Hainan, China
| | - Danping Xu
- Sichuan Provincial Key Laboratory of Agricultural Products Processing and Preservative, College of Food Science, Sichuan Agricultural University, Yaan, Sichuan, China
| | - Zhihang Zhuo
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education, Key Laboratory of Germplasm Resources Biology of Tropical Special Ornamental Plants of Hainan Province, College of Forestry, Hainan University, Haikou, Hainan, China.,Key Laboratory of Integrated Pest Management on Crops in South China, Ministry of Agriculture, South China Agricultural University, Guangzhou, Guangdong, China
| | - Jiameng Hu
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education, Key Laboratory of Germplasm Resources Biology of Tropical Special Ornamental Plants of Hainan Province, College of Forestry, Hainan University, Haikou, Hainan, China
| | - Baoqian Lu
- Key Laboratory of Integrated Pest Management on Tropical Crops, Ministry of Agriculture China, Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, China
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Qiu F, Wang X, Zheng Y, Wang H, Liu X, Su X. Full-Length Transcriptome Sequencing and Different Chemotype Expression Profile Analysis of Genes Related to Monoterpenoid Biosynthesis in Cinnamomum porrectum. Int J Mol Sci 2019; 20:ijms20246230. [PMID: 31835605 PMCID: PMC6941020 DOI: 10.3390/ijms20246230] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Revised: 11/27/2019] [Accepted: 12/06/2019] [Indexed: 01/04/2023] Open
Abstract
Leaves of C. porrectum are rich in essential oils containing monoterpenes, sesquiterpenes and aromatic compounds, but the molecular mechanism of terpenoid biosynthesis in C. porrectum is still unclear. In this paper, the differences in the contents and compositions of terpenoids among three chemotypes were analyzed using gas chromatography mass spectrometry (GC/MS). Furthermore, the differential expression of gene transcripts in the leaf tissues of the three C. porrectum chemotypes were analyzed through a comparison of full-length transcriptomes and expression profiles. The essential oil of the three C. porrectum chemotypes leaves was mainly composed of monoterpenes. In the full-length transcriptome of C. porrectum, 104,062 transcripts with 306,337,921 total bp, an average length of 2944 bp, and an N50 length of 5449 bp, were obtained and 94025 transcripts were annotated. In the eucalyptol and linalool chemotype, the camphor and eucalyptol chemotype, and the camphor and linalool chemotype comparison groups, 21, 22 and 18 terpene synthase (TPS) unigenes were identified respectively. Three monoterpene synthase genes, CpTPS3, CpTPS5 and CpTPS9, were upregulated in the eucalyptol chemotype compared to the linalool chemotype and camphor chemotype. CpTPS1 was upregulated in the camphor chemotype compared to the linalool chemotype and the eucalyptol chemotype. CpTPS4 was upregulated in the linalool chemotype compared to the camphor chemotype and the eucalyptol chemotype. Different unigenes had different expression levels among the three chemotypes, but the unigene expression levels of the 2-C-methyl-D-erythritol 4phosphate (MEP) pathway were generally higher than those of the mevalonate acid (MVA) pathway. Quantitative reverse transcription PCR(qRT-PCR) further validated these expression levels. The present study provides new clues for the functional exploration of the terpenoid synthesis mechanism and key genes in different chemotypes of C. porrectum.
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Affiliation(s)
- Fengying Qiu
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China;
- Jiangxi Academy of Forestry, Camphor Engineering Technology Research Center for National Forestry and Grassland Administration, Nanchang 30032, China; (X.W.); (Y.Z.); (X.L.)
| | - Xindong Wang
- Jiangxi Academy of Forestry, Camphor Engineering Technology Research Center for National Forestry and Grassland Administration, Nanchang 30032, China; (X.W.); (Y.Z.); (X.L.)
| | - Yongjie Zheng
- Jiangxi Academy of Forestry, Camphor Engineering Technology Research Center for National Forestry and Grassland Administration, Nanchang 30032, China; (X.W.); (Y.Z.); (X.L.)
| | - Hongming Wang
- College of Bioengineering and Biotechnology, Tianshui Normal University, Tianshui 741000, China;
| | - Xinliang Liu
- Jiangxi Academy of Forestry, Camphor Engineering Technology Research Center for National Forestry and Grassland Administration, Nanchang 30032, China; (X.W.); (Y.Z.); (X.L.)
| | - Xiaohua Su
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China;
- Key Laboratory of Tree Breeding and Cultivation, National Forestry and Grassland Administration, Beijing 100091, China
- Correspondence: ; Tel.: +86-010-6288-9627
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12
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Yuan H, Chang H, Zhao L, Yang C, Huang Y. Sex- and tissue-specific transcriptome analyses and expression profiling of olfactory-related genes in Ceracris nigricornis Walker (Orthoptera: Acrididae). BMC Genomics 2019; 20:808. [PMID: 31694535 PMCID: PMC6836668 DOI: 10.1186/s12864-019-6208-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Accepted: 10/21/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The sophisticated insect olfactory system plays an important role in recognizing external odors and enabling insects to adapt to environment. Foraging, host seeking, mating, ovipositing and other forms of chemical communication are based on olfaction, which requires the participation of multiple olfactory genes. The exclusive evolutionary trend of the olfactory system in Orthoptera insects is an excellent model for studying olfactory evolution, but limited olfaction research is available for these species. The olfactory-related genes of Ceracris nigricornis Walker (Orthoptera: Acrididae), a severe pest of bamboos, have not yet been reported. RESULTS We sequenced and analyzed the transcriptomes from different tissues of C. nigricornis and obtained 223.76 Gb clean data that were assembled into 43,603 unigenes with an N50 length of 2235 bp. Among the transcripts, 66.79% of unigenes were annotated. Based on annotation and tBLASTn results, 112 candidate olfactory-related genes were identified for the first time, including 20 odorant-binding proteins (OBPs), 10 chemosensory-binding proteins (CSPs), 71 odorant receptors (ORs), eight ionotropic receptors (IRs) and three sensory neuron membrane proteins (SNMPs). The fragments per kilobase per million mapped fragments (FPKM) values showed that most olfactory-related differentially expressed genes (DEGs) were enriched in the antennae, and these results were confirmed by detecting the expression of olfactory-related genes with quantitative real-time PCR (qRT-PCR). Among these antennae-enriched genes, some were sex-biased, indicating their different roles in the olfactory system of C. nigricornis. CONCLUSIONS This study provides the first comprehensive list and expression profiles of olfactory-related genes in C. nigricornis and a foundation for functional studies of these olfactory-related genes at the molecular level.
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Affiliation(s)
- Hao Yuan
- College of Life Sciences, Shaanxi Normal University, Xi'an, 710062, China
| | - Huihui Chang
- College of Life Sciences, Shaanxi Normal University, Xi'an, 710062, China
| | - Lina Zhao
- College of Life Sciences, Shaanxi Normal University, Xi'an, 710062, China
| | - Chao Yang
- College of Life Sciences, Shaanxi Normal University, Xi'an, 710062, China.,Shaanxi Institute of Zoology, Xi'an, China
| | - Yuan Huang
- College of Life Sciences, Shaanxi Normal University, Xi'an, 710062, China.
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13
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Laumer CE. Inferring Ancient Relationships with Genomic Data: A Commentary on Current Practices. Integr Comp Biol 2019; 58:623-639. [PMID: 29982611 DOI: 10.1093/icb/icy075] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Contemporary phylogeneticists enjoy an embarrassment of riches, not only in the volumes of data now available, but also in the diversity of bioinformatic tools for handling these data. Here, I discuss a subset of these tools I consider well-suited to the task of inferring ancient relationships with coding sequence data in particular, encompassing data generation, orthology assignment, alignment and gene tree inference, supermatrix construction, and analysis under the best-fitting models applicable to large-scale datasets. Throughout, I compare and critique methods, considering both their theoretical principles and the details of their implementation, and offering practical tips on usage where appropriate. I also entertain different motivations for analyzing what are almost always originally DNA sequence data as codons, amino acids, and higher-order recodings. Although presented in a linear order, I see value in using the diversity of tools available to us to assess the sensitivity of clades of biological interest to different gene and taxon sets and analytical modes, which can be an indication of the presence of systematic error, of which a few forms remain poorly controlled by even the best available inference methods.
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Affiliation(s)
- Christopher E Laumer
- EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, EBML-EBI South Building, Hinxton CB10 1SD, UK
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14
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Wang Y, Zhou X, Wang L, Liu X, Yang D, Rokas A. Gene Selection and Evolutionary Modeling Affect Phylogenomic Inference of Neuropterida Based on Transcriptome Data. Int J Mol Sci 2019; 20:E1072. [PMID: 30832228 PMCID: PMC6429444 DOI: 10.3390/ijms20051072] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2018] [Revised: 02/18/2019] [Accepted: 02/26/2019] [Indexed: 11/30/2022] Open
Abstract
Neuropterida is a super order of Holometabola that consists of the orders Megaloptera (dobsonflies, fishflies, and alderflies), Neuroptera (lacewings) and Raphidioptera (snakeflies). Several proposed higher-level relationships within Neuropterida, such as the relationships between the orders or between the families, have been extensively debated. To further understand the evolutionary history of Neuropterida, we conducted phylogenomic analyses of all 13 published transcriptomes of the neuropterid species, as well as of a new transcriptome of the fishfly species Ctenochauliodes similis of Liu and Yang, 2006 (Megaloptera: Corydalidae: Chauliodinae) that we sequenced. Our phylogenomic data matrix contained 1392 ortholog genes from 22 holometabolan species representing six families from Neuroptera, two families from Raphidioptera, and two families from Megaloptera as the ingroup taxa, and nine orders of Holometabola as outgroups. Phylogenetic reconstruction was performed using both concatenation and coalescent-based approaches under a site-homogeneous model as well as under a site-heterogeneous model. Surprisingly, analyses using the site-homogeneous model strongly supported a paraphyletic Neuroptera, with Coniopterygidae assigned as the sister group of all other Neuropterida. In contrast, analyses using the site-heterogeneous model recovered Neuroptera as monophyletic. The monophyly of Neuroptera was also recovered in concatenation and coalescent-based analyses using genes with stronger phylogenetic signals [i.e., higher average bootstrap support (ABS) values and higher relative tree certainty including all conflicting bipartitions (RTCA) values] under the site-homogeneous model. The present study illustrated how both data selection and model selection influence phylogenomic analyses of large-scale data matrices comprehensively.
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Affiliation(s)
- Yuyu Wang
- College of Plant Protection, Hebei Agricultural University, Baoding 071001, China.
- Department of Entomology, China Agricultural University, Beijing 100193, China.
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA.
| | - Xiaofan Zhou
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA.
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou 510642, China.
| | - Liming Wang
- College of Plant Protection, Hebei Agricultural University, Baoding 071001, China.
| | - Xingyue Liu
- Department of Entomology, China Agricultural University, Beijing 100193, China.
| | - Ding Yang
- Department of Entomology, China Agricultural University, Beijing 100193, China.
| | - Antonis Rokas
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA.
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15
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Sheng Y, He M, Zhao F, Shao C, Miao M. Phylogenetic relationship analyses of complicated class Spirotrichea based on transcriptomes from three diverse microbial eukaryotes: Uroleptopsis citrina, Euplotes vannus and Protocruzia tuzeti. Mol Phylogenet Evol 2018; 129:338-345. [DOI: 10.1016/j.ympev.2018.06.025] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2018] [Accepted: 06/13/2018] [Indexed: 11/25/2022]
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16
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Majeed A, Singh A, Choudhary S, Bhardwaj P. RNAseq‐based phylogenetic reconstruction of Taxaceae and Cephalotaxaceae. Cladistics 2018; 35:461-468. [PMID: 34633712 DOI: 10.1111/cla.12362] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/15/2018] [Indexed: 11/29/2022] Open
Affiliation(s)
- Aasim Majeed
- Molecular Genetics Laboratory Department of Plant Sciences Central University of Punjab Mansa Road Bathinda 151001 India
| | - Amandeep Singh
- Molecular Genetics Laboratory Department of Plant Sciences Central University of Punjab Mansa Road Bathinda 151001 India
| | - Shruti Choudhary
- Molecular Genetics Laboratory Department of Plant Sciences Central University of Punjab Mansa Road Bathinda 151001 India
| | - Pankaj Bhardwaj
- Molecular Genetics Laboratory Department of Plant Sciences Central University of Punjab Mansa Road Bathinda 151001 India
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17
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Shen H, Jin D, Shu JP, Zhou XL, Lei M, Wei R, Shang H, Wei HJ, Zhang R, Liu L, Gu YF, Zhang XC, Yan YH. Large-scale phylogenomic analysis resolves a backbone phylogeny in ferns. Gigascience 2018; 7:1-11. [PMID: 29186447 PMCID: PMC5795342 DOI: 10.1093/gigascience/gix116] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2017] [Accepted: 11/17/2017] [Indexed: 11/30/2022] Open
Abstract
Background Ferns, originated about 360 million years ago, are the sister group of seed plants. Despite the remarkable progress in our understanding of fern phylogeny, with conflicting molecular evidence and different morphological interpretations, relationships among major fern lineages remain controversial. Results With the aim to obtain a robust fern phylogeny, we carried out a large-scale phylogenomic analysis using high-quality transcriptome sequencing data, which covered 69 fern species from 38 families and 11 orders. Both coalescent-based and concatenation-based methods were applied to both nucleotide and amino acid sequences in species tree estimation. The resulting topologies are largely congruent with each other, except for the placement of Angiopteris fokiensis, Cheiropleuria bicuspis, Diplaziopsis brunoniana, Matteuccia struthiopteris, Elaphoglossum mcclurei, and Tectaria subpedata. Conclusions Our result confirmed that Equisetales is sister to the rest of ferns, and Dennstaedtiaceae is sister to eupolypods. Moreover, our result strongly supported some relationships different from the current view of fern phylogeny, including that Marattiaceae may be sister to the monophyletic clade of Psilotaceae and Ophioglossaceae; that Gleicheniaceae and Hymenophyllaceae form a monophyletic clade sister to Dipteridaceae; and that Aspleniaceae is sister to the rest of the groups in eupolypods II. These results were interpreted with morphological traits, especially sporangia characters, and a new evolutionary route of sporangial annulus in ferns was suggested. This backbone phylogeny in ferns sets a foundation for further studies in biology and evolution in ferns, and therefore in plants.
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Affiliation(s)
- Hui Shen
- Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, 3888 Chenhua Road, Songjiang, Shanghai 201602, China.,Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, 3888 Chenhua Road, Songjiang, Shanghai 201602, China
| | - Dongmei Jin
- Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, 3888 Chenhua Road, Songjiang, Shanghai 201602, China.,Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, 3888 Chenhua Road, Songjiang, Shanghai 201602, China
| | - Jiang-Ping Shu
- Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, 3888 Chenhua Road, Songjiang, Shanghai 201602, China.,Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, 3888 Chenhua Road, Songjiang, Shanghai 201602, China
| | - Xi-Le Zhou
- Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, 3888 Chenhua Road, Songjiang, Shanghai 201602, China.,Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, 3888 Chenhua Road, Songjiang, Shanghai 201602, China
| | - Ming Lei
- Majorbio Bioinformatics Research Institute, Building 3, Lane 3399, Kangxin Road, International Medical Park, Pudong, Shanghai 201320, China
| | - Ran Wei
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, No. 20 Nanxincun, Xiangshan, Beijing 100093, China
| | - Hui Shang
- Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, 3888 Chenhua Road, Songjiang, Shanghai 201602, China.,Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, 3888 Chenhua Road, Songjiang, Shanghai 201602, China
| | - Hong-Jin Wei
- Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, 3888 Chenhua Road, Songjiang, Shanghai 201602, China.,Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, 3888 Chenhua Road, Songjiang, Shanghai 201602, China
| | - Rui Zhang
- Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, 3888 Chenhua Road, Songjiang, Shanghai 201602, China.,Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, 3888 Chenhua Road, Songjiang, Shanghai 201602, China
| | - Li Liu
- Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, 3888 Chenhua Road, Songjiang, Shanghai 201602, China.,Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, 3888 Chenhua Road, Songjiang, Shanghai 201602, China
| | - Yu-Feng Gu
- Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, 3888 Chenhua Road, Songjiang, Shanghai 201602, China.,Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, 3888 Chenhua Road, Songjiang, Shanghai 201602, China
| | - Xian-Chun Zhang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, No. 20 Nanxincun, Xiangshan, Beijing 100093, China
| | - Yue-Hong Yan
- Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, 3888 Chenhua Road, Songjiang, Shanghai 201602, China.,Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, 3888 Chenhua Road, Songjiang, Shanghai 201602, China
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18
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Matsuda T, Kozaki T, Ishii K, Gotoh T. Phylogeny of the spider mite sub-family Tetranychinae (Acari: Tetranychidae) inferred from RNA-Seq data. PLoS One 2018; 13:e0203136. [PMID: 30192794 PMCID: PMC6128517 DOI: 10.1371/journal.pone.0203136] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Accepted: 08/15/2018] [Indexed: 11/18/2022] Open
Abstract
Phylogenetic trees of spider mites were previously obtained using 18S and 28S rRNA genes. Because some of the bootstrap values were relatively low, these trees were unable to completely resolve the phylogeny. Here, we obtained RNA-Seq data for the 72 known species (73 strains) of spider mites to analyze the phylogeny of the sub-family Tetranychinae. The data were de novo assembled into a total alignment length of 790,047 bases corresponding to 264,133 amino acid residues in 652 genes. The sequence dataset was 200 times larger than the data used in the previous study. The new trees were much more robust and more clearly defined the clades of the tribes and the genera of the sub-family Tetranychinae. The tribe Tetranychini was polyphyletic because a monophyletic clade of Eurytetranychini was placed inside it. The six genera from which two or more species were sampled appeared to be monophyletic, but four genera (Schizotetranychus, Eotetranychus, Oligonychus and Tetranychus) appeared to be polyphyletic. These results strongly support the previous molecular inference of the polyphyletic tribes and genera, although the molecular phylogeny of the sub-family Tetranychinae does not fully agree with the current morphology-based taxonomy. The taxonomy of the sub-family Tetranychinae should be revised according to the molecular relationships revealed by this study.
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Affiliation(s)
- Tomoko Matsuda
- Faculty of Agriculture, Ibaraki University, Ami, Ibaraki, Japan
| | - Toshinori Kozaki
- Faculty of Agriculture, Tokyo University of Agriculture & Technology, Fuchu, Tokyo, Japan
| | - Kazuo Ishii
- Faculty of Agriculture, Tokyo University of Agriculture & Technology, Fuchu, Tokyo, Japan
| | - Tetsuo Gotoh
- Faculty of Agriculture, Ibaraki University, Ami, Ibaraki, Japan
- * E-mail:
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19
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Zhao L, Zhang X, Qiu Z, Huang Y. De Novo Assembly and Characterization of the Xenocatantops brachycerus Transcriptome. Int J Mol Sci 2018; 19:E520. [PMID: 29419810 PMCID: PMC5855742 DOI: 10.3390/ijms19020520] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2017] [Revised: 02/05/2018] [Accepted: 02/06/2018] [Indexed: 01/19/2023] Open
Abstract
Grasshoppers are common pests but also have high nutritional and commercial potential. Xenocatantops brachycerus Willemse (Orthoptera: Acrididae) is an economically important grasshopper species that is reared in China. Using the IlluminaHiSeqTM 4000 platform, three transcriptomes of the adult male, adult female, and nymph of X. brachycerus were sequenced. A total of 133,194,848 clean reads were obtained and de novo assembled into 43,187 unigenes with an average length of 964 bp (N50 of 1799 bp); of these, 24,717 (57.23%) unigenes matched known proteins. Based on these annotations, many putative transcripts related to X. brachycerus growth, development, environmental adaptability, and metabolism of nutritional components and bioactive components were identified. In addition, the expression profiles of all three transcriptome datasets were analyzed, and many differentially expressed genes were detected using RSEM and PossionDis. Unigenes. Unigenes with functions associated with growth and development exhibited higher transcript levels at the nymph stage, and unigenes associated with environmental adaptability showed increased transcription in the adults. These comprehensive X. brachycerus transcriptomic data will provide a useful molecular resource for gene prediction, molecular marker development, and studies on signaling pathways in this species and will serve as a reference for the efficient use of other grasshoppers.
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Affiliation(s)
- Le Zhao
- College of Life Sciences, Shaanxi Normal University, Xi'an 710062, Shaanxi, China.
- School of Biological Sciences and Engineering, Shaanxi University of Technology, Hanzhong 723001, Shaanxi, China.
| | - Xinmei Zhang
- College of Life Sciences, Shaanxi Normal University, Xi'an 710062, Shaanxi, China.
| | - Zhongying Qiu
- College of Life Sciences, Shaanxi Normal University, Xi'an 710062, Shaanxi, China.
- School of Basic Medical Sciences, Xi'an Medical University, Xi'an 710021, Shaanxi, China.
| | - Yuan Huang
- College of Life Sciences, Shaanxi Normal University, Xi'an 710062, Shaanxi, China.
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20
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Rodgers R, Roach JL, Reid NM, Whitehead A, Duvernell DD. Phylogenomic analysis of Fundulidae (Teleostei: Cyprinodotiformes) using RNA-sequencing data. Mol Phylogenet Evol 2017; 121:150-157. [PMID: 29289545 DOI: 10.1016/j.ympev.2017.12.030] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Revised: 11/27/2017] [Accepted: 12/27/2017] [Indexed: 11/18/2022]
Abstract
Fishes of the New World cyprinodontiform family Fundulidae display a wide variety of tolerance to environmental conditions, making them a valuable model system for comparative, evolutionary, and environmental studies. Despite numerous attempts to resolve the phylogenetic relationships of family Fundulidae, the basal structure of the phylogeny remains unresolved. The lack of a robust and fully resolved phylogeny for family Fundulidae and its most speciose genus Fundulus is an impediment to future research. This study utilized novel RNA-sequencing data for phylogenetic inference among16 members of Fundulidae to better refine the basal nodes of the family and confront long-standing questions regarding (1) the monophyletic status of genus Fundulus, and validity of the Lucania and recently synonymized Adinia genera; (2) the relationship of the west coast endemic Fundulus parvipinnis and F. lima to other Fundulus species; and (3) the validity of subgeneric classifications. In addition, previously published nuclear gene sequences for 32 Fundulidae species were re-analyzed in combination with novel RNA-sequencing data. Maximum likelihood and Bayesian analyses generated identical phylogenies with strong statistical support at nearly all nodes, demonstrating the utility of RNA-sequencing data in constructing robust phylogenies not achievable by previous methods. While many past hypothesized evolutionary relationships for Fundulidae were reinforced, several alternative relationships are hypothesized at basal nodes resulting in a re-analysis of the deeper structure of family Fundulidae. These results reveal family Fundulidae as a paraphyletic grouping of members of genus Fundulus and Lucania and supports the previous synonymy of genus Adinia with genus Fundulus.
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Affiliation(s)
- Rachel Rodgers
- Biological Sciences, Southern Illinois University Edwardsville, Edwardsville, IL 62026, USA
| | - Jennifer L Roach
- Department of Environmental Toxicology, University of California, Davis, CA 95616, USA
| | - Noah M Reid
- Department of Environmental Toxicology, University of California, Davis, CA 95616, USA; Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269, USA
| | - Andrew Whitehead
- Department of Environmental Toxicology, University of California, Davis, CA 95616, USA
| | - David D Duvernell
- Biological Sciences, Southern Illinois University Edwardsville, Edwardsville, IL 62026, USA; Biological Sciences, Missouri University of Science and Technology, Rolla, MO 65401, USA.
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21
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Scott Chialvo CH, Chialvo P, Holland JD, Anderson TJ, Breinholt JW, Kawahara AY, Zhou X, Liu S, Zaspel JM. A phylogenomic analysis of lichen-feeding tiger moths uncovers evolutionary origins of host chemical sequestration. Mol Phylogenet Evol 2017; 121:23-34. [PMID: 29274497 DOI: 10.1016/j.ympev.2017.12.015] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2017] [Revised: 12/11/2017] [Accepted: 12/11/2017] [Indexed: 11/29/2022]
Abstract
Host species utilize a variety of defenses to deter feeding, including secondary chemicals. Some phytophagous insects have evolved tolerance to these chemical defenses, and can sequester secondary defense compounds for use against their own predators and parasitoids. While numerous studies have examined plant-insect interactions, little is known about lichen-insect interactions. Our study focused on reconstructing the evolution of lichen phenolic sequestration in the tiger moth tribe Lithosiini (Lepidoptera: Erebidae: Arctiinae), the most diverse lineage of lichen-feeding moths, with 3000 described species. We built an RNA-Seq dataset and examined the adult metabolome for the presence of lichen-derived phenolics. Using the transcriptomic dataset, we recover a well-resolved phylogeny of the Lithosiini, and determine that the metabolomes within species are more similar than those among species. Results from an initial ancestral state reconstruction suggest that the ability to sequester phenolics produced by a single chemical pathway preceded generalist sequestration of phenolics produced by multiple chemical pathways. We conclude that phenolics are consistently and selectively sequestered within Lithosiini. Furthermore, sequestration of compounds from a single chemical pathway may represent a synapomorphy of the tribe, and the ability to sequester phenolics produced by multiple pathways arose later. These findings expand on our understanding of the interactions between Lepidoptera and their lichen hosts.
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Affiliation(s)
- Clare H Scott Chialvo
- Department of Biological Sciences, PO Box 870344, University of Alabama, Tuscaloosa, AL 35487, USA.
| | - Pablo Chialvo
- Department of Biology, 320 Stanley Avenue, Lander University, Greenwood, SC 29649, USA
| | - Jeffrey D Holland
- Department of Entomology, 901 West State Street, Purdue University, West Lafayette, IN 47907, USA
| | - Timothy J Anderson
- Department of Entomology, 901 West State Street, Purdue University, West Lafayette, IN 47907, USA
| | - Jesse W Breinholt
- Florida Museum of Natural History, 3215 Hull Road, University of Florida, Gainesville, FL 32611, USA
| | - Akito Y Kawahara
- Florida Museum of Natural History, 3215 Hull Road, University of Florida, Gainesville, FL 32611, USA
| | - Xin Zhou
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, China Agricultural University, Beijing 100193, People's Republic of China; Department of Entomology, China Agricultural University, Beijing 100193, People's Republic of China
| | - Shanlin Liu
- China National GeneBank, 8/F, Beishan Industrial Zone, Yantian District, BGI-Shenzhen, People's Republic of China; BGI-Shenzhen, Beishan Industrial Zone, Yantian District, People's Republic of China
| | - Jennifer M Zaspel
- Department of Entomology, 901 West State Street, Purdue University, West Lafayette, IN 47907, USA; Milwaukee Public Museum, 800 W Wells St, Milwaukee, WI 53233, USA
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22
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Genome-Guided Phylo-Transcriptomic Methods and the Nuclear Phylogentic Tree of the Paniceae Grasses. Sci Rep 2017; 7:13528. [PMID: 29051622 PMCID: PMC5648822 DOI: 10.1038/s41598-017-13236-z] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Accepted: 09/20/2017] [Indexed: 11/23/2022] Open
Abstract
The past few years have witnessed a paradigm shift in molecular systematics from phylogenetic methods (using one or a few genes) to those that can be described as phylogenomics (phylogenetic inference with entire genomes). One approach that has recently emerged is phylo-transcriptomics (transcriptome-based phylogenetic inference). As in any phylogenetics experiment, accurate orthology inference is critical to phylo-transcriptomics. To date, most analyses have inferred orthology based either on pure sequence similarity or using gene-tree approaches. The use of conserved genome synteny in orthology detection has been relatively under-employed in phylogenetics, mainly due to the cost of sequencing genomes. While current trends focus on the quantity of genes included in an analysis, the use of synteny is likely to improve the quality of ortholog inference. In this study, we combine de novo transcriptome data and sequenced genomes from an economically important group of grass species, the tribe Paniceae, to make phylogenomic inferences. This method, which we call “genome-guided phylo-transcriptomics”, is compared to other recently published orthology inference pipelines, and benchmarked using a set of sequenced genomes from across the grasses. These comparisons provide a framework for future researchers to evaluate the costs and benefits of adding sequenced genomes to transcriptome data sets.
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23
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Carlson DE, Hedin M. Comparative transcriptomics of Entelegyne spiders (Araneae, Entelegynae), with emphasis on molecular evolution of orphan genes. PLoS One 2017; 12:e0174102. [PMID: 28379977 PMCID: PMC5381867 DOI: 10.1371/journal.pone.0174102] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2016] [Accepted: 03/04/2017] [Indexed: 11/18/2022] Open
Abstract
Next-generation sequencing technology is rapidly transforming the landscape of evolutionary biology, and has become a cost-effective and efficient means of collecting exome information for non-model organisms. Due to their taxonomic diversity, production of interesting venom and silk proteins, and the relative scarcity of existing genomic resources, spiders in particular are excellent targets for next-generation sequencing (NGS) methods. In this study, the transcriptomes of six entelegyne spider species from three genera (Cicurina travisae, C. vibora, Habronattus signatus, H. ustulatus, Nesticus bishopi, and N. cooperi) were sequenced and de novo assembled. Each assembly was assessed for quality and completeness and functionally annotated using gene ontology information. Approximately 100 transcripts with evidence of homology to venom proteins were discovered. After identifying more than 3,000 putatively orthologous genes across all six taxa, we used comparative analyses to identify 24 instances of positively selected genes. In addition, between ~ 550 and 1,100 unique orphan genes were found in each genus. These unique, uncharacterized genes exhibited elevated rates of amino acid substitution, potentially consistent with lineage-specific adaptive evolution. The data generated for this study represent a valuable resource for future phylogenetic and molecular evolutionary research, and our results provide new insight into the forces driving genome evolution in taxa that span the root of entelegyne spider phylogeny.
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Affiliation(s)
- David E. Carlson
- Department of Biology, San Diego State University, San Diego, California, United States of America
- Department of Ecology & Evolution, Stony Brook University, Stony Brook, New York, United States of America
| | - Marshal Hedin
- Department of Biology, San Diego State University, San Diego, California, United States of America
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24
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Resolving interspecific relationships within evolutionarily young lineages using RNA-seq data: An example from Pedicularis section Cyathophora (Orobanchaceae). Mol Phylogenet Evol 2017; 107:345-355. [DOI: 10.1016/j.ympev.2016.11.018] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Revised: 11/19/2016] [Accepted: 11/27/2016] [Indexed: 11/17/2022]
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25
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Shamim M, Kumar P, Kumar RR, Kumar M, Kumar RR, Singh KN. Assessing Fungal Biodiversity Using Molecular Markers. Fungal Biol 2017. [DOI: 10.1007/978-3-319-34106-4_15] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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26
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Prasad TSK, Mohanty AK, Kumar M, Sreenivasamurthy SK, Dey G, Nirujogi RS, Pinto SM, Madugundu AK, Patil AH, Advani J, Manda SS, Gupta MK, Dwivedi SB, Kelkar DS, Hall B, Jiang X, Peery A, Rajagopalan P, Yelamanchi SD, Solanki HS, Raja R, Sathe GJ, Chavan S, Verma R, Patel KM, Jain AP, Syed N, Datta KK, Khan AA, Dammalli M, Jayaram S, Radhakrishnan A, Mitchell CJ, Na CH, Kumar N, Sinnis P, Sharakhov IV, Wang C, Gowda H, Tu Z, Kumar A, Pandey A. Integrating transcriptomic and proteomic data for accurate assembly and annotation of genomes. Genome Res 2016; 27:133-144. [PMID: 28003436 PMCID: PMC5204337 DOI: 10.1101/gr.201368.115] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Accepted: 11/10/2016] [Indexed: 01/05/2023]
Abstract
Complementing genome sequence with deep transcriptome and proteome data could enable more accurate assembly and annotation of newly sequenced genomes. Here, we provide a proof-of-concept of an integrated approach for analysis of the genome and proteome of Anopheles stephensi, which is one of the most important vectors of the malaria parasite. To achieve broad coverage of genes, we carried out transcriptome sequencing and deep proteome profiling of multiple anatomically distinct sites. Based on transcriptomic data alone, we identified and corrected 535 events of incomplete genome assembly involving 1196 scaffolds and 868 protein-coding gene models. This proteogenomic approach enabled us to add 365 genes that were missed during genome annotation and identify 917 gene correction events through discovery of 151 novel exons, 297 protein extensions, 231 exon extensions, 192 novel protein start sites, 19 novel translational frames, 28 events of joining of exons, and 76 events of joining of adjacent genes as a single gene. Incorporation of proteomic evidence allowed us to change the designation of more than 87 predicted “noncoding RNAs” to conventional mRNAs coded by protein-coding genes. Importantly, extension of the newly corrected genome assemblies and gene models to 15 other newly assembled Anopheline genomes led to the discovery of a large number of apparent discrepancies in assembly and annotation of these genomes. Our data provide a framework for how future genome sequencing efforts should incorporate transcriptomic and proteomic analysis in combination with simultaneous manual curation to achieve near complete assembly and accurate annotation of genomes.
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Affiliation(s)
- T S Keshava Prasad
- Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka 560066, India.,YU-IOB Center for Systems Biology and Molecular Medicine, Yenepoya University, Mangalore 575018, India.,NIMHANS-IOB Proteomics and Bioinformatics Laboratory, Neurobiology Research Centre, National Institute of Mental Health and Neuro Sciences, Bangalore, Karnataka 560029, India
| | - Ajeet Kumar Mohanty
- National Institute of Malaria Research, Field Station, Goa 403001, India.,Department of Zoology, Goa University, Taleigao Plateau, Goa 403206, India
| | - Manish Kumar
- Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka 560066, India.,Manipal University, Madhav Nagar, Manipal, Karnataka 576104, India
| | - Sreelakshmi K Sreenivasamurthy
- Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka 560066, India.,Manipal University, Madhav Nagar, Manipal, Karnataka 576104, India
| | - Gourav Dey
- Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka 560066, India.,Manipal University, Madhav Nagar, Manipal, Karnataka 576104, India
| | - Raja Sekhar Nirujogi
- Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka 560066, India.,Centre for Bioinformatics, Pondicherry University, Puducherry 605014, India
| | - Sneha M Pinto
- Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka 560066, India.,YU-IOB Center for Systems Biology and Molecular Medicine, Yenepoya University, Mangalore 575018, India
| | - Anil K Madugundu
- Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka 560066, India.,Centre for Bioinformatics, Pondicherry University, Puducherry 605014, India
| | - Arun H Patil
- Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka 560066, India.,School of Biotechnology, KIIT University, Bhubaneswar, Odisha 751024, India
| | - Jayshree Advani
- Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka 560066, India.,Manipal University, Madhav Nagar, Manipal, Karnataka 576104, India
| | - Srikanth S Manda
- Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka 560066, India.,Centre for Bioinformatics, Pondicherry University, Puducherry 605014, India
| | - Manoj Kumar Gupta
- Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka 560066, India.,Manipal University, Madhav Nagar, Manipal, Karnataka 576104, India
| | - Sutopa B Dwivedi
- Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka 560066, India
| | - Dhanashree S Kelkar
- Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka 560066, India
| | - Brantley Hall
- Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, USA
| | - Xiaofang Jiang
- Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, USA
| | - Ashley Peery
- Department of Entomology, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, USA
| | - Pavithra Rajagopalan
- Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka 560066, India.,School of Biotechnology, KIIT University, Bhubaneswar, Odisha 751024, India
| | - Soujanya D Yelamanchi
- Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka 560066, India.,School of Biotechnology, KIIT University, Bhubaneswar, Odisha 751024, India
| | - Hitendra S Solanki
- Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka 560066, India.,School of Biotechnology, KIIT University, Bhubaneswar, Odisha 751024, India
| | - Remya Raja
- Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka 560066, India
| | - Gajanan J Sathe
- Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka 560066, India.,Manipal University, Madhav Nagar, Manipal, Karnataka 576104, India
| | - Sandip Chavan
- Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka 560066, India.,Manipal University, Madhav Nagar, Manipal, Karnataka 576104, India
| | - Renu Verma
- Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka 560066, India.,School of Biotechnology, KIIT University, Bhubaneswar, Odisha 751024, India
| | - Krishna M Patel
- Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka 560066, India
| | - Ankit P Jain
- Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka 560066, India.,School of Biotechnology, KIIT University, Bhubaneswar, Odisha 751024, India
| | - Nazia Syed
- Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka 560066, India.,Department of Biochemistry and Molecular Biology, Pondicherry University, Puducherry 605014, India
| | - Keshava K Datta
- Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka 560066, India.,School of Biotechnology, KIIT University, Bhubaneswar, Odisha 751024, India
| | - Aafaque Ahmed Khan
- Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka 560066, India.,School of Biotechnology, KIIT University, Bhubaneswar, Odisha 751024, India
| | - Manjunath Dammalli
- Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka 560066, India.,Department of Biotechnology, Siddaganga Institute of Technology, Tumkur, Karnataka 572103, India
| | - Savita Jayaram
- Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka 560066, India.,Manipal University, Madhav Nagar, Manipal, Karnataka 576104, India
| | - Aneesha Radhakrishnan
- Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka 560066, India.,Department of Biochemistry and Molecular Biology, Pondicherry University, Puducherry 605014, India
| | - Christopher J Mitchell
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
| | - Chan-Hyun Na
- Department of Neurology, Johns Hopkins University, Baltimore, Maryland 21205, USA
| | - Nirbhay Kumar
- Department of Tropical Medicine, Tulane University School of Public Health and Tropical Medicine, New Orleans, Louisiana 70112, USA
| | - Photini Sinnis
- Malaria Research Institute, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland 21205, USA
| | - Igor V Sharakhov
- Department of Entomology, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, USA
| | - Charles Wang
- Center for Genomics and Department of Basic Sciences, School of Medicine, Loma Linda University, Loma Linda, California 92350, USA
| | - Harsha Gowda
- Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka 560066, India.,YU-IOB Center for Systems Biology and Molecular Medicine, Yenepoya University, Mangalore 575018, India
| | - Zhijian Tu
- Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, USA
| | - Ashwani Kumar
- National Institute of Malaria Research, Field Station, Goa 403001, India
| | - Akhilesh Pandey
- Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka 560066, India.,McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA.,Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA.,Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA.,Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
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27
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Shen XX, Salichos L, Rokas A. A Genome-Scale Investigation of How Sequence, Function, and Tree-Based Gene Properties Influence Phylogenetic Inference. Genome Biol Evol 2016; 8:2565-80. [PMID: 27492233 PMCID: PMC5010910 DOI: 10.1093/gbe/evw179] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/25/2016] [Indexed: 12/13/2022] Open
Abstract
Molecular phylogenetic inference is inherently dependent on choices in both methodology and data. Many insightful studies have shown how choices in methodology, such as the model of sequence evolution or optimality criterion used, can strongly influence inference. In contrast, much less is known about the impact of choices in the properties of the data, typically genes, on phylogenetic inference. We investigated the relationships between 52 gene properties (24 sequence-based, 19 function-based, and 9 tree-based) with each other and with three measures of phylogenetic signal in two assembled data sets of 2,832 yeast and 2,002 mammalian genes. We found that most gene properties, such as evolutionary rate (measured through the percent average of pairwise identity across taxa) and total tree length, were highly correlated with each other. Similarly, several gene properties, such as gene alignment length, Guanine-Cytosine content, and the proportion of tree distance on internal branches divided by relative composition variability (treeness/RCV), were strongly correlated with phylogenetic signal. Analysis of partial correlations between gene properties and phylogenetic signal in which gene evolutionary rate and alignment length were simultaneously controlled, showed similar patterns of correlations, albeit weaker in strength. Examination of the relative importance of each gene property on phylogenetic signal identified gene alignment length, alongside with number of parsimony-informative sites and variable sites, as the most important predictors. Interestingly, the subsets of gene properties that optimally predicted phylogenetic signal differed considerably across our three phylogenetic measures and two data sets; however, gene alignment length and RCV were consistently included as predictors of all three phylogenetic measures in both yeasts and mammals. These results suggest that a handful of sequence-based gene properties are reliable predictors of phylogenetic signal and could be useful in guiding the choice of phylogenetic markers.
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Affiliation(s)
- Xing-Xing Shen
- Department of Biological Sciences, Vanderbilt University
| | - Leonidas Salichos
- Department of Biological Sciences, Vanderbilt University Department of Molecular Biophysics and Biochemistry, Yale University
| | - Antonis Rokas
- Department of Biological Sciences, Vanderbilt University
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28
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Qiu Z, Liu F, Lu H, Huang Y. Characterization and analysis of a de novo transcriptome from the pygmy grasshopper Tetrix japonica. Mol Ecol Resour 2016; 17:381-392. [PMID: 27288670 DOI: 10.1111/1755-0998.12553] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2015] [Revised: 05/11/2016] [Accepted: 05/13/2016] [Indexed: 11/29/2022]
Abstract
The pygmy grasshopper Tetrix japonica is a common insect distributed throughout the world, and it has the potential for use in studies of body colour polymorphism, genomics and the biology of Tetrigoidea (Insecta: Orthoptera). However, limited biological information is available for this insect. Here, we conducted a de novo transcriptome study of adult and larval T. japonica to provide a better understanding of its gene expression and develop genomic resources for future work. We sequenced and explored the characteristics of the de novo transcriptome of T. japonica using Illumina HiSeq 2000 platform. A total of 107 608 206 paired-end clean reads were assembled into 61 141 unigenes using the trinity software; the mean unigene size was 771 bp, and the N50 length was 1238 bp. A total of 29 225 unigenes were functionally annotated to the NCBI nonredundant protein sequences (Nr), NCBI nonredundant nucleotide sequences (Nt), a manually annotated and reviewed protein sequence database (Swiss-Prot), Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases. A large number of putative genes that are potentially involved in pigment pathways, juvenile hormone (JH) metabolism and signalling pathways were identified in the T. japonica transcriptome. Additionally, 165 769 and 156 796 putative single nucleotide polymorphisms occurred in the adult and larvae transcriptomes, respectively, and a total of 3162 simple sequence repeats were detected in this assembly. This comprehensive transcriptomic data for T. japonica will provide a usable resource for gene predictions, signalling pathway investigations and molecular marker development for this species and other pygmy grasshoppers.
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Affiliation(s)
- Zhongying Qiu
- College of Life Sciences, Shaanxi Normal University, Xi'an, 710062, China
| | - Fei Liu
- College of Life Sciences, Shaanxi Normal University, Xi'an, 710062, China.,College of Life Sciences and Food Engineering, Shaanxi Xueqian Normal University, Xi'an, 710061, China
| | - Huimeng Lu
- Key Laboratory for Space Bioscience & Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Xi'an, 710072, China
| | - Yuan Huang
- College of Life Sciences, Shaanxi Normal University, Xi'an, 710062, China
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29
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Thomas T, De TD, Sharma P, Lata S, Saraswat P, Pandey KC, Dixit R. Hemocytome: deep sequencing analysis of mosquito blood cells in Indian malarial vector Anopheles stephensi. Gene 2016; 585:177-90. [PMID: 26915489 DOI: 10.1016/j.gene.2016.02.031] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Revised: 02/16/2016] [Accepted: 02/20/2016] [Indexed: 02/08/2023]
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30
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Sharma P, Das De T, Sharma S, Kumar Mishra A, Thomas T, Verma S, Kumari V, Lata S, Singh N, Valecha N, Chand Pandey K, Dixit R. Deep sequencing revealed molecular signature of horizontal gene transfer of plant like transcripts in the mosquito Anopheles culicifacies: an evolutionary puzzle. F1000Res 2015; 4:1523. [PMID: 26998230 PMCID: PMC4786938 DOI: 10.12688/f1000research.7534.1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 12/15/2015] [Indexed: 02/05/2023] Open
Abstract
In prokaryotes, horizontal gene transfer (HGT) has been regarded as an important evolutionary drive to acquire and retain beneficial genes for their survival in diverse ecologies. However, in eukaryotes, the functional role of HGTs remains questionable, although current genomic tools are providing increased evidence of acquisition of novel traits within non-mating metazoan species. Here, we provide another transcriptomic evidence for the acquisition of massive plant genes in the mosquito, Anopheles culicifacies. Our multiple experimental validations including genomic PCR, RT-PCR, real-time PCR, immuno-blotting and immuno-florescence microscopy, confirmed that plant like transcripts (PLTs) are of mosquito origin and may encode functional proteins. A comprehensive molecular analysis of the PLTs and ongoing metagenomic analysis of salivary microbiome provide initial clues that mosquitoes may have survival benefits through the acquisition of nuclear as well as chloroplast encoded plant genes. Our findings of PLTs further support the similar questionable observation of HGTs in other higher organisms, which is still a controversial and debatable issue in the community of evolutionists. We believe future understanding of the underlying mechanism of the feeding associated molecular responses may shed new insights in the functional role of PLTs in the mosquito.
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Affiliation(s)
- Punita Sharma
- Host-Parasite Interaction Biology Group, National Institute of Malaria Research, Delhi, India; Nano and Biotechnology Department, Guru Jambheshwar University, Haryana, India
| | - Tanwee Das De
- Host-Parasite Interaction Biology Group, National Institute of Malaria Research, Delhi, India
| | - Swati Sharma
- Host-Parasite Interaction Biology Group, National Institute of Malaria Research, Delhi, India
| | | | - Tina Thomas
- Host-Parasite Interaction Biology Group, National Institute of Malaria Research, Delhi, India
| | - Sonia Verma
- Host-Parasite Interaction Biology Group, National Institute of Malaria Research, Delhi, India
| | - Vandana Kumari
- Host-Parasite Interaction Biology Group, National Institute of Malaria Research, Delhi, India
| | - Suman Lata
- Host-Parasite Interaction Biology Group, National Institute of Malaria Research, Delhi, India
| | - Namita Singh
- Nano and Biotechnology Department, Guru Jambheshwar University, Haryana, India
| | - Neena Valecha
- Host-Parasite Interaction Biology Group, National Institute of Malaria Research, Delhi, India
| | - Kailash Chand Pandey
- Host-Parasite Interaction Biology Group, National Institute of Malaria Research, Delhi, India
| | - Rajnikant Dixit
- Host-Parasite Interaction Biology Group, National Institute of Malaria Research, Delhi, India
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31
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Wang Y, Zhou X, Yang D, Rokas A. A Genome-Scale Investigation of Incongruence in Culicidae Mosquitoes. Genome Biol Evol 2015; 7:3463-71. [PMID: 26608059 PMCID: PMC4700963 DOI: 10.1093/gbe/evv235] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Comparison of individual gene trees in several recent phylogenomic studies from diverse lineages has revealed a surprising amount of topological conflict or incongruence, but we still know relatively little about its distribution across the tree of life. To further our understanding of incongruence, the factors that contribute to it and how it can be ameliorated, we examined its distribution in a clade of 20 Culicidae mosquito species through the reconstruction and analysis of the phylogenetic histories of 2,007 groups of orthologous genes. Levels of incongruence were generally low, the three exceptions being the internodes concerned with the branching of Anopheles christyi, with the branching of the subgenus Anopheles as well as the already reported incongruence within the Anopheles gambiae species complex. Two of these incongruence events (A. gambiae species complex and A. christyi) are likely due to biological factors, whereas the third (subgenus Anopheles) is likely due to analytical factors. Similar to previous studies, the use of genes or internodes with high bootstrap support or internode certainty values, both of which were positively correlated with gene alignment length, substantially reduced the observed incongruence. However, the clade support values of the internodes concerned with the branching of the subgenus Anopheles as well as within the A. gambiae species complex remained very low. Based on these results, we infer that the prevalence of incongruence in Culicidae mosquitoes is generally low, that it likely stems from both analytical and biological factors, and that it can be ameliorated through the selection of genes with strong phylogenetic signal. More generally, selection of genes with strong phylogenetic signal may be a general empirical solution for reducing incongruence and increasing the robustness of inference in phylogenomic studies.
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Affiliation(s)
- Yuyu Wang
- Department of Entomology, China Agricultural University, Beijing, China Department of Biological Sciences, Vanderbilt University
| | - Xiaofan Zhou
- Department of Biological Sciences, Vanderbilt University
| | - Ding Yang
- Department of Entomology, China Agricultural University, Beijing, China
| | - Antonis Rokas
- Department of Biological Sciences, Vanderbilt University
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32
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Abstract
New phylogenomic analyses suggest that ants and Apoidea (hunting wasps and bees) are more closely related than we had previously believed.
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Affiliation(s)
- Bryan N Danforth
- Department of Entomology, Cornell University, Ithaca, NY 14853, USA.
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33
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Sharma P, Sharma S, Mishra AK, Thomas T, Das De T, Rohilla SL, Singh N, Pandey KC, Valecha N, Dixit R. Unraveling dual feeding associated molecular complexity of salivary glands in the mosquito Anopheles culicifacies. Biol Open 2015; 4:1002-15. [PMID: 26163527 PMCID: PMC4542284 DOI: 10.1242/bio.012294] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Mosquito salivary glands are well known to facilitate meal acquisition, however the fundamental question on how adult female salivary gland manages molecular responses during sugar versus blood meal uptake remains unanswered. To investigate these responses, we analyzed a total of 58.5 million raw reads generated from two independent RNAseq libraries of the salivary glands collected from 3–4 day-old sugar and blood fed Anopheles culicifacies mosquitoes. Comprehensive functional annotation analysis of 10,931 contigs unraveled that salivary glands may encode diverse nature of proteins in response to distinct physiological feeding status. Digital gene expression analysis and PCR validation indicated that first blood meal significantly alters the molecular architecture of the salivary glands. Comparative microscopic analysis also revealed that first blood meal uptake not only causes an alteration of at least 12–22% of morphological features of the salivary glands but also results in cellular changes e.g. apoptosis, confirming together that adult female salivary glands are specialized organs to manage meal specific responses. Unraveling the underlying mechanism of mosquito salivary gene expression, controlling dual feeding associated responses may provide a new opportunity to control vector borne diseases.
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Affiliation(s)
- Punita Sharma
- Host-Parasite Interaction Biology Group, National Institute of Malaria Research, Sector-8, Dwarka, Delhi 110077, India Nano and Biotechnology Department, Guru Jambheshwar University, Hisar, Haryana 125001, India
| | - Swati Sharma
- Host-Parasite Interaction Biology Group, National Institute of Malaria Research, Sector-8, Dwarka, Delhi 110077, India
| | | | - Tina Thomas
- Host-Parasite Interaction Biology Group, National Institute of Malaria Research, Sector-8, Dwarka, Delhi 110077, India
| | - Tanwee Das De
- Host-Parasite Interaction Biology Group, National Institute of Malaria Research, Sector-8, Dwarka, Delhi 110077, India
| | - Suman Lata Rohilla
- Host-Parasite Interaction Biology Group, National Institute of Malaria Research, Sector-8, Dwarka, Delhi 110077, India
| | - Namita Singh
- Nano and Biotechnology Department, Guru Jambheshwar University, Hisar, Haryana 125001, India
| | - Kailash C Pandey
- Host-Parasite Interaction Biology Group, National Institute of Malaria Research, Sector-8, Dwarka, Delhi 110077, India
| | - Neena Valecha
- Host-Parasite Interaction Biology Group, National Institute of Malaria Research, Sector-8, Dwarka, Delhi 110077, India
| | - Rajnikant Dixit
- Host-Parasite Interaction Biology Group, National Institute of Malaria Research, Sector-8, Dwarka, Delhi 110077, India
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34
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Abstract
Over the last three decades, transcriptomic studies of venom gland cells have continuously evolved, opening up new possibilities for exploring the molecular diversity of animal venoms, a prerequisite for the discovery of new drug candidates and molecular phylogenetics. The molecular complexity of animal venoms is much greater than initially thought. In this review, we describe the different technologies available for transcriptomic studies of venom, from the original individual cloning approaches to the more recent global Next Generation Sequencing strategies. Our understanding of animal venoms is evolving, with the discovery of complex and diverse bio-optimized cocktails of compounds, including mostly peptides and proteins, which are now beginning to be studied by academic and industrial researchers.
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Lyu MJA, Gowik U, Kelly S, Covshoff S, Mallmann J, Westhoff P, Hibberd JM, Stata M, Sage RF, Lu H, Wei X, Wong GKS, Zhu XG. RNA-Seq based phylogeny recapitulates previous phylogeny of the genus Flaveria (Asteraceae) with some modifications. BMC Evol Biol 2015; 15:116. [PMID: 26084484 PMCID: PMC4472175 DOI: 10.1186/s12862-015-0399-9] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2014] [Accepted: 05/29/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The genus Flaveria has been extensively used as a model to study the evolution of C4 photosynthesis as it contains C3 and C4 species as well as a number of species that exhibit intermediate types of photosynthesis. The current phylogenetic tree of the genus Flaveria contains 21 of the 23 known Flaveria species and has been previously constructed using a combination of morphological data and three non-coding DNA sequences (nuclear encoded ETS, ITS and chloroplast encoded trnL-F). RESULTS Here we developed a new strategy to update the phylogenetic tree of 16 Flaveria species based on RNA-Seq data. The updated phylogeny is largely congruent with the previously published tree but with some modifications. We propose that the data collection method provided in this study can be used as a generic method for phylogenetic tree reconstruction if the target species has no genomic information. We also showed that a "F. pringlei" genotype recently used in a number of labs may be a hybrid between F. pringlei (C3) and F. angustifolia (C3-C4). CONCLUSIONS We propose that the new strategy of obtaining phylogenetic sequences outlined in this study can be used to construct robust trees in a larger number of taxa. The updated Flaveria phylogenetic tree also supports a hypothesis of stepwise and parallel evolution of C4 photosynthesis in the Flavaria clade.
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Affiliation(s)
- Ming-Ju Amy Lyu
- CAS-MPG Partner Institute and Key Laboratory for Computational Biology, Shanghai Institutes for Biological Sciences, Shanghai, China.
| | - Udo Gowik
- Institute of Plant Molecular and Developmental Biology, Heinrich-Heine-University, Dusseldorf, Germany.
| | - Steve Kelly
- Department of Plant Sciences, University of Oxford, Oxford, UK.
| | - Sarah Covshoff
- Department of Plant Sciences, University of Cambridge, Cambridge, UK.
| | - Julia Mallmann
- Institute of Plant Molecular and Developmental Biology, Heinrich-Heine-University, Dusseldorf, Germany.
| | - Peter Westhoff
- Institute of Plant Molecular and Developmental Biology, Heinrich-Heine-University, Dusseldorf, Germany.
| | - Julian M Hibberd
- Department of Plant Sciences, University of Cambridge, Cambridge, UK.
| | - Matt Stata
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Canada.
| | - Rowan F Sage
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Canada.
| | - Haorong Lu
- BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen, 518083, China.
| | - Xiaofeng Wei
- BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen, 518083, China.
| | - Gane Ka-Shu Wong
- BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen, 518083, China.
- Department of Biological Sciences, University of Alberta, Edmonton, AB, T6G 2E9, Canada.
- Department of Medicine, University of Alberta, Edmonton, AB, T6G 2E1, Canada.
| | - Xin-Guang Zhu
- CAS-MPG Partner Institute and Key Laboratory for Computational Biology, Shanghai Institutes for Biological Sciences, Shanghai, China.
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Yang Y, Wang L, Han J, Tang X, Ma M, Wang K, Zhang X, Ren Q, Chen Q, Qiu Q. Comparative transcriptomic analysis revealed adaptation mechanism of Phrynocephalus erythrurus, the highest altitude Lizard living in the Qinghai-Tibet Plateau. BMC Evol Biol 2015; 15:101. [PMID: 26031664 PMCID: PMC4450828 DOI: 10.1186/s12862-015-0371-8] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2015] [Accepted: 04/29/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Organisms living at high altitudes must overcome three major environmental challenges: hypoxia, cold, and intense UV radiation. The molecular mechanisms that enable these challenges to be overcome have mainly been studied in endothermic organisms; relatively little attention has been paid to poikilothermic species. Here, we present deep transcriptome sequencing in two closely related lizards, the high altitude-dwelling Phrynocephalus erythrurus and the lowland-dwelling P. putjatia, to identify candidate genes under positive selection and to explore the convergent evolutionary adaptation of poikilothermic animals to high altitude life. RESULTS More than 70 million sequence reads were generated for each species via Illumina sequencing. De novo assembly produced 56,845 and 63,140 transcripts for P. erythrurus and P. putjatia, respectively. P. erythrurus had higher Ka/Ks ratios than P. putjatia, implying an accelerated evolutionary rate in the high altitude lizard lineage. 206 gene ontology (GO) categories with accelerated evolutionary rates and 43 candidate positively selected genes were detected along the P. erythrurus lineage. Some of these GO categories have functions associated with responses to hypoxia, energy metabolism and responses to UV damage. We also found that the high-altitude ranid frog R. kukunoris had higher Ka/Ks ratios than the closely related low-altitude frog R. chensinensis, and that the functional categories with accelerated evolutionary rates in R. kukunoris overlapped extensively with those detected along the P. erythrurus lineage. CONCLUSIONS The mechanisms of high altitude adaptation in P. erythrurus were tentatively inferred. By comparing two pairs of low- and high-altitude poikilothermic species, we found that similar functional categories had undergone positive selection in high altitude-dwelling Phrynocephalus and Rana lineages, indicating that similar mechanisms of adaptation to high altitude might have evolved in both genera. Our findings provide important guidance for future functional studies on high altitude adaptation in poikilothermic animals.
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Affiliation(s)
- Yongzhi Yang
- State Key Laboratory of Grassland Agro-ecosystem, School of Life Sciences, Lanzhou University, Lanzhou, Gansu, China.
| | - Lizhong Wang
- State Key Laboratory of Grassland Agro-ecosystem, School of Life Sciences, Lanzhou University, Lanzhou, Gansu, China.
| | - Jin Han
- State Key Laboratory of Grassland Agro-ecosystem, School of Life Sciences, Lanzhou University, Lanzhou, Gansu, China.
| | - Xiaolong Tang
- Institute of Biochemistry and Molecular Biology, School of Life Sciences, Lanzhou University, Lanzhou, Gansu, China.
| | - Ming Ma
- Institute of Biochemistry and Molecular Biology, School of Life Sciences, Lanzhou University, Lanzhou, Gansu, China.
| | - Kun Wang
- State Key Laboratory of Grassland Agro-ecosystem, School of Life Sciences, Lanzhou University, Lanzhou, Gansu, China.
| | - Xiao Zhang
- State Key Laboratory of Grassland Agro-ecosystem, School of Life Sciences, Lanzhou University, Lanzhou, Gansu, China.
| | - Qian Ren
- State Key Laboratory of Grassland Agro-ecosystem, School of Life Sciences, Lanzhou University, Lanzhou, Gansu, China.
| | - Qiang Chen
- Institute of Biochemistry and Molecular Biology, School of Life Sciences, Lanzhou University, Lanzhou, Gansu, China.
| | - Qiang Qiu
- State Key Laboratory of Grassland Agro-ecosystem, School of Life Sciences, Lanzhou University, Lanzhou, Gansu, China.
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Laumer CE, Hejnol A, Giribet G. Nuclear genomic signals of the 'microturbellarian' roots of platyhelminth evolutionary innovation. eLife 2015; 4:e05503. [PMID: 25764302 PMCID: PMC4398949 DOI: 10.7554/elife.05503] [Citation(s) in RCA: 114] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2014] [Accepted: 03/06/2015] [Indexed: 12/25/2022] Open
Abstract
Flatworms number among the most diverse invertebrate phyla and represent the most biomedically significant branch of the major bilaterian clade Spiralia, but to date, deep evolutionary relationships within this group have been studied using only a single locus (the rRNA operon), leaving the origins of many key clades unclear. In this study, using a survey of genomes and transcriptomes representing all free-living flatworm orders, we provide resolution of platyhelminth interrelationships based on hundreds of nuclear protein-coding genes, exploring phylogenetic signal through concatenation as well as recently developed consensus approaches. These analyses robustly support a modern hypothesis of flatworm phylogeny, one which emphasizes the primacy of the often-overlooked 'microturbellarian' groups in understanding the major evolutionary transitions within Platyhelminthes: perhaps most notably, we propose a novel scenario for the interrelationships between free-living and vertebrate-parasitic flatworms, providing new opportunities to shed light on the origins and biological consequences of parasitism in these iconic invertebrates.
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Affiliation(s)
- Christopher E Laumer
- Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, United States
| | - Andreas Hejnol
- Sars International Centre for Marine Molecular Biology, University of Bergen, Bergen, Norway
| | - Gonzalo Giribet
- Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, United States
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Cheng C, Jiao C, Singer SD, Gao M, Xu X, Zhou Y, Li Z, Fei Z, Wang Y, Wang X. Gibberellin-induced changes in the transcriptome of grapevine (Vitis labrusca × V. vinifera) cv. Kyoho flowers. BMC Genomics 2015; 16:128. [PMID: 25888129 PMCID: PMC4348105 DOI: 10.1186/s12864-015-1324-8] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2014] [Accepted: 02/04/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Gibberellins are well known for their growth control function in flower, fruit and seed development, and as such, exogenous gibberellic acid (GA) application plays an important role in viticulture. Unfortunately, the mechanism by which GA3 acts in the regulation of these complicated developmental processes in grape remains unclear. RESULTS In the present study, we demonstrated that application of GA3 to 'Kyoho' grapevine inflorescences at pre-bloom promoted flower opening, and induced fruit coloring as well as seed abortion. In an attempt to obtain a deeper understanding of the molecular mechanisms driving these responses to GA3 treatment, we performed large-scale transcriptome sequencing of grape flowers following GA3 treatment using Illumina sequencing technology. Global expression profiles of GA3-treated and untreated grape flowers were compared and a large number of GA3-responsive genes were identified. Gene ontology (GO) term classification and biochemical pathway analyses indicated that GA3 treatment caused changes in the levels of transcripts involved in cellular processes, reproduction, hormone and secondary metabolism, as well as the scavenging and detoxification of reactive oxygen species (ROS). These findings suggest that GA3-induced morphological alterations may be related to the control of hormone biosynthesis and signaling, regulation of transcription factors, alteration of secondary metabolites, and the stability of redox homeostasis. CONCLUSIONS Taken together, this comprehensive inflorescence transcriptome data set provides novel insight into the response of grape flowers to GA3 treatment, and also provides possible candidate genes or markers that could be used to guide future efforts in this field.
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Affiliation(s)
- Chenxia Cheng
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China. .,Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, Northwest A&F University, Yangling, 712100, Shaanxi, China. .,Department of Ornamental Horticulture, China Agricultural University, Beijing, 100193, China.
| | - Chen Jiao
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China. .,Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, Northwest A&F University, Yangling, 712100, Shaanxi, China.
| | - Stacy D Singer
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, T6G 2P5, Canada.
| | - Min Gao
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China. .,Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, Northwest A&F University, Yangling, 712100, Shaanxi, China.
| | - Xiaozhao Xu
- Institute for Horticultural Plants, China Agricultural University, Beijing, 100193, China.
| | - Yiming Zhou
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China.
| | - Zhi Li
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China. .,Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, Northwest A&F University, Yangling, 712100, Shaanxi, China.
| | - Zhangjun Fei
- Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, NY, 14853, USA. .,USDA Robert W. Holley Center for Agriculture and Health, Ithaca, NY, 14853, USA.
| | - Yuejin Wang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China. .,Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, Northwest A&F University, Yangling, 712100, Shaanxi, China.
| | - Xiping Wang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China. .,Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, Northwest A&F University, Yangling, 712100, Shaanxi, China.
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Krishnan R, Kumar V, Ananth V, Singh S, Nair AS, Dhar PK. Computational identification of novel microRNAs and their targets in the malarial vector, Anopheles stephensi. SYSTEMS AND SYNTHETIC BIOLOGY 2015; 9:11-7. [PMID: 25972985 DOI: 10.1007/s11693-014-9159-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Revised: 12/10/2014] [Accepted: 12/15/2014] [Indexed: 11/28/2022]
Abstract
MicroRNAs are a ~22 nucleotide small non-coding RNAs found in animals, plants and viruses. They regulate key cellular processes by enhancing, degrading or silencing protein coding targets. Currently most of the data on miRNA is available from Drosophila . Given their important post-transcriptional role in several organisms, there is a need to understand the miRNA mediated processes in normal and abnormal conditions. Here we report four novel microRNAs ast - mir - 2502, ast - mir - 2559, ast - mir - 3868 and ast - mir - 9891 in Anopheles stephensi identified from a set of 3,052 transcriptome sequences, showing average minimum free energy of -31.8 kcal/mol of duplex formation with mRNA indicating their functional relevance. Phylogenetic study shows conservation of sequence signatures within the Class Insecta. Furthermore, 26 potential targets of these four miRNAs have been predicted that play an important role in the mosquito life-cycle. This work leads to novel leads and experimental possibilities for improved understanding of gene regulatory processes in mosquito.
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Affiliation(s)
- Remya Krishnan
- Department of Computational Biology and Bioinformatics, University of Kerala, Trivandrum, Kerala India
| | - Vinod Kumar
- Department of Computational Biology and Bioinformatics, University of Kerala, Trivandrum, Kerala India
| | - Vivek Ananth
- Synthetic Biology Group, Department of Life Sciences, School of Natural Sciences, Shiv Nadar University, Greater Noida, U.P. India
| | - Shailja Singh
- Synthetic Biology Group, Department of Life Sciences, School of Natural Sciences, Shiv Nadar University, Greater Noida, U.P. India ; Department of Parasitology and Mycology, Institut Pasteur, Paris, France
| | - Achuthsankar S Nair
- Department of Computational Biology and Bioinformatics, University of Kerala, Trivandrum, Kerala India
| | - Pawan K Dhar
- Department of Computational Biology and Bioinformatics, University of Kerala, Trivandrum, Kerala India ; Synthetic Biology Group, Department of Life Sciences, School of Natural Sciences, Shiv Nadar University, Greater Noida, U.P. India
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40
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Gong W, He S, Tian J, Sun J, Pan Z, Jia Y, Sun G, Du X. Comparison of the transcriptome between two cotton lines of different fiber color and quality. PLoS One 2014; 9:e112966. [PMID: 25401744 PMCID: PMC4234635 DOI: 10.1371/journal.pone.0112966] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2014] [Accepted: 10/16/2014] [Indexed: 01/27/2023] Open
Abstract
To understand the mechanism of fiber development and pigmentation formation, the mRNAs of two cotton lines were sequenced: line Z128 (light brown fiber) was a selected mutant from line Z263 (dark brown fiber). The primary walls of the fiber cell in both Z263 and Z128 contain pigments; more pigments were laid in the lumen of the fiber cell in Z263 compared with that in Z128. However, Z263 contained less cellulose than Z128. A total of 71,895 unigenes were generated: 13,278 (20.26%) unigenes were defined as differentially expressed genes (DEGs) by comparing the library of Z128 with that of Z263; 5,345 (8.16%) unigenes were up-regulated and 7,933 (12.10%) unigenes were down-regulated. qRT-PCR and comparative transcriptional analysis demonstrated that the pigmentation formation in brown cotton fiber was possibly the consequence of an interaction between oxidized tannins and glycosylated anthocyanins. Furthermore, our results showed the pigmentation related genes not only regulated the fiber color but also influenced the fiber quality at the fiber elongation stage (10 DPA). The highly expressed flavonoid gene in the fiber elongation stage could be related to the fiber quality. DEGs analyses also revealed that transcript levels of some fiber development genes (Ca2+/CaM, reactive oxygen, ethylene and sucrose phosphate synthase) varied dramatically between these two cotton lines.
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Affiliation(s)
- Wenfang Gong
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Shoupu He
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Jiahuan Tian
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Junling Sun
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Zhaoe Pan
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Yinhua Jia
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Gaofei Sun
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
- Department of Computer Science and Information Engineering, Anyang Institute of Technology, Anyang, China
| | - Xiongming Du
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
- * E-mail:
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Breinholt JW, Kawahara AY. Phylotranscriptomics: saturated third codon positions radically influence the estimation of trees based on next-gen data. Genome Biol Evol 2014; 5:2082-92. [PMID: 24148944 PMCID: PMC3845638 DOI: 10.1093/gbe/evt157] [Citation(s) in RCA: 87] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Recent advancements in molecular sequencing techniques have led to a surge in the number of phylogenetic studies that incorporate large amounts of genetic data. We test the assumption that analyzing large number of genes will lead to improvements in tree resolution and branch support using moths in the superfamily Bombycoidea, a group with some interfamilial relationships that have been difficult to resolve. Specifically, we use a next-gen data set that included 19 taxa and 938 genes (∼1.2M bp) to examine how codon position and saturation might influence resolution and node support among three key families. Maximum likelihood, parsimony, and species tree analysis using gene tree parsimony, on different nucleotide and amino acid data sets, resulted in largely congruent topologies with high bootstrap support compared with prior studies that included fewer loci. However, for a few shallow nodes, nucleotide and amino acid data provided high support for conflicting relationships. The third codon position was saturated and phylogenetic analysis of this position alone supported a completely different, potentially misleading sister group relationship. We used the program RADICAL to assess the number of genes needed to fix some of these difficult nodes. One such node originally needed a total of 850 genes but only required 250 when synonymous signal was removed. Our study shows that, in order to effectively use next-gen data to correctly resolve difficult phylogenetic relationships, it is necessary to assess the effects of synonymous substitutions and third codon positions.
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Cázares-Raga FE, Chávez-Munguía B, González-Calixto C, Ochoa-Franco AP, Gawinowicz MA, Rodríguez MH, Hernández-Hernández FC. Morphological and proteomic characterization of midgut of the malaria vector Anopheles albimanus at early time after a blood feeding. J Proteomics 2014; 111:100-12. [PMID: 25132141 DOI: 10.1016/j.jprot.2014.07.037] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2014] [Revised: 07/16/2014] [Accepted: 07/29/2014] [Indexed: 01/27/2023]
Abstract
The midgut of anopheline mosquito is the entry of Plasmodium, the causative agent of malaria.When the mosquito feeds on parasite infected host, Plasmodium parasites reach the midgut and must confront digestive enzymes, the innate immune response and go across the peritrophic matrix (PM), a thick extracellular sheath secreted by the mosquito midgut epithelial cells. Then, to continue its development, the parasite must reach the salivary glands to achieve transmission to a vertebrate host. We report here the morphological and biochemical descriptions of the midgut changes after a blood meal in Anopheles albimanus. Before blood feeding, midgut epithelial cells contained numerous electrondense vesicles distributed in the central to apical side. These vesicles were secreted to the luminal side of the midgut after a blood meal. At early times after blood ingest, the PM is formed near microvilli as a granulous amorphous material and after it consolidates forming a highly organized fibrillar structure, constituted by layers of electrondense and electronlucent regions. Proteomic comparative analysis of sugar and blood fed midguts showed several molecules that modify their abundance after blood intake; these include innate immunity, cytoskeletal, stress response, signaling, and digestive, detoxifying and metabolism enzymes. Biological significance In the midgut of mosquitoes during bloodfeeding, many simultaneous processes occur, including digestion, innate immune activities, cytoskeleton modifications, construction of a peritrophic matrix and hormone production, between others. Mechanical forces are very intense during bloodfeeding and epithelial and muscular cells must resist the stress, modifying the actin cytoskeleton and coordinating intracellular responses by signaling. Microorganisms present in midgut contents reproduce and interact with epithelial cells triggering innate immune response. When infectious agents are present in the blood meal they must traverse the peritrophic matrix, an envelope formed from secretion products of epithelial cells, and evade the immune system in order to reach the epithelium and continue their journey towards salivary glands, in preparation for the transmission to the new hosts. During all these processes, proteins of mosquitoes are modified in order to deal with mechanical and biological challenges, and the aim of this work is to study these changes.
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Affiliation(s)
- F E Cázares-Raga
- Depto. de Infectómica y Patogénesis Molecular, Centro de Investigación y de Estudios Avanzados del IPN, Mexico, D.F., Mexico
| | - B Chávez-Munguía
- Depto. de Infectómica y Patogénesis Molecular, Centro de Investigación y de Estudios Avanzados del IPN, Mexico, D.F., Mexico
| | - C González-Calixto
- Depto. de Infectómica y Patogénesis Molecular, Centro de Investigación y de Estudios Avanzados del IPN, Mexico, D.F., Mexico
| | - A P Ochoa-Franco
- Depto. de Infectómica y Patogénesis Molecular, Centro de Investigación y de Estudios Avanzados del IPN, Mexico, D.F., Mexico
| | - M A Gawinowicz
- Herbert Irving Comprehensive Cancer Center, Columbia University, NY, USA
| | - M H Rodríguez
- Centro de Investigación sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Cuernavaca, Morelos, Mexico
| | - F C Hernández-Hernández
- Depto. de Infectómica y Patogénesis Molecular, Centro de Investigación y de Estudios Avanzados del IPN, Mexico, D.F., Mexico.
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Kagale S, Robinson SJ, Nixon J, Xiao R, Huebert T, Condie J, Kessler D, Clarke WE, Edger PP, Links MG, Sharpe AG, Parkin IAP. Polyploid evolution of the Brassicaceae during the Cenozoic era. THE PLANT CELL 2014; 26:2777-91. [PMID: 25035408 PMCID: PMC4145113 DOI: 10.1105/tpc.114.126391] [Citation(s) in RCA: 120] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2014] [Revised: 06/07/2014] [Accepted: 06/19/2014] [Indexed: 05/18/2023]
Abstract
The Brassicaceae (Cruciferae) family, owing to its remarkable species, genetic, and physiological diversity as well as its significant economic potential, has become a model for polyploidy and evolutionary studies. Utilizing extensive transcriptome pyrosequencing of diverse taxa, we established a resolved phylogeny of a subset of crucifer species. We elucidated the frequency, age, and phylogenetic position of polyploidy and lineage separation events that have marked the evolutionary history of the Brassicaceae. Besides the well-known ancient α (47 million years ago [Mya]) and β (124 Mya) paleopolyploidy events, several species were shown to have undergone a further more recent (∼7 to 12 Mya) round of genome multiplication. We identified eight whole-genome duplications corresponding to at least five independent neo/mesopolyploidy events. Although the Brassicaceae family evolved from other eudicots at the beginning of the Cenozoic era of the Earth (60 Mya), major diversification occurred only during the Neogene period (0 to 23 Mya). Remarkably, the widespread species divergence, major polyploidy, and lineage separation events during Brassicaceae evolution are clustered in time around epoch transitions characterized by prolonged unstable climatic conditions. The synchronized diversification of Brassicaceae species suggests that polyploid events may have conferred higher adaptability and increased tolerance toward the drastically changing global environment, thus facilitating species radiation.
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Affiliation(s)
- Sateesh Kagale
- Agriculture and Agri-Food Canada, Saskatoon SK S7N 0X2, Canada National Research Council Canada, Saskatoon SK S7N 0W9, Canada
| | | | - John Nixon
- Agriculture and Agri-Food Canada, Saskatoon SK S7N 0X2, Canada
| | - Rong Xiao
- Agriculture and Agri-Food Canada, Saskatoon SK S7N 0X2, Canada
| | - Terry Huebert
- Agriculture and Agri-Food Canada, Saskatoon SK S7N 0X2, Canada
| | - Janet Condie
- National Research Council Canada, Saskatoon SK S7N 0W9, Canada
| | - Dallas Kessler
- Plant Gene Resources of Canada, Saskatoon SK S7N 0X2, Canada
| | - Wayne E Clarke
- Agriculture and Agri-Food Canada, Saskatoon SK S7N 0X2, Canada
| | - Patrick P Edger
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720
| | - Matthew G Links
- Agriculture and Agri-Food Canada, Saskatoon SK S7N 0X2, Canada
| | - Andrew G Sharpe
- National Research Council Canada, Saskatoon SK S7N 0W9, Canada
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Mathias DK, Jardim JG, Parish LA, Armistead JS, Trinh HV, Kumpitak C, Sattabongkot J, Dinglasan RR. Differential roles of an Anopheline midgut GPI-anchored protein in mediating Plasmodium falciparum and Plasmodium vivax ookinete invasion. INFECTION GENETICS AND EVOLUTION 2014; 28:635-47. [PMID: 24929123 DOI: 10.1016/j.meegid.2014.05.025] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2014] [Revised: 05/19/2014] [Accepted: 05/23/2014] [Indexed: 12/14/2022]
Abstract
Novel strategies to directly thwart malaria transmission are needed to maintain the gains achieved by current control measures. Transmission-blocking interventions (TBIs), namely vaccines and drugs targeting parasite or mosquito molecules required for vector-stage parasite development, have been recognized as promising approaches for preventing malaria transmission. However, the number of TBI targets is limited and their degree of conservation among the major vector-parasite systems causing human disease is unclear. Therefore, discovery and characterization of novel proteins involved in vector-stage parasite development of Plasmodium falciparum and Plasmodium vivax is paramount. We mined the recent Anopheles gambiae midgut lipid raft proteome for putative mosquito-derived TBI targets and characterized a secreted glycoconjugate of unknown function, AgSGU. We analyzed molecular variation in this protein among a range of anopheline mosquitoes, determined its transcriptomic and proteomic profiles, and conducted both standard and direct membrane feeding assays with P. falciparum (lab/field) and P. vivax (field) in An. gambiae and Anopheles dirus. We observed that α-AgSGU antibodies significantly reduced midgut infection intensity for both lab and field isolates of P. falciparum in An. gambiae and An. dirus. However, no transmission-reducing effects were noted when comparable concentrations of antibodies were included in P. vivax-infected blood meals. Although antibodies against AgSGU exhibit transmission-reducing activity, the high antibody titer required for achieving 80% reduction in oocyst intensity precludes its consideration as a malaria mosquito-based TBI candidate. However, our results suggest that P. falciparum and P. vivax ookinetes use a different repertoire of midgut surface glycoproteins for invasion and that α-AgSGU antibodies, as well as antibodies to other mosquito-midgut microvillar surface proteins, may prove useful as tools for interrogating Plasmodium-mosquito interactions.
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Affiliation(s)
- Derrick K Mathias
- W. Harry Feinstone Department of Molecular Microbiology & Immunology, Johns Hopkins Bloomberg School of Public Health & Malaria Research Institute, Baltimore, MD 21205, USA.
| | - Juliette G Jardim
- W. Harry Feinstone Department of Molecular Microbiology & Immunology, Johns Hopkins Bloomberg School of Public Health & Malaria Research Institute, Baltimore, MD 21205, USA.
| | - Lindsay A Parish
- W. Harry Feinstone Department of Molecular Microbiology & Immunology, Johns Hopkins Bloomberg School of Public Health & Malaria Research Institute, Baltimore, MD 21205, USA.
| | - Jennifer S Armistead
- W. Harry Feinstone Department of Molecular Microbiology & Immunology, Johns Hopkins Bloomberg School of Public Health & Malaria Research Institute, Baltimore, MD 21205, USA.
| | - Hung V Trinh
- W. Harry Feinstone Department of Molecular Microbiology & Immunology, Johns Hopkins Bloomberg School of Public Health & Malaria Research Institute, Baltimore, MD 21205, USA.
| | | | | | - Rhoel R Dinglasan
- W. Harry Feinstone Department of Molecular Microbiology & Immunology, Johns Hopkins Bloomberg School of Public Health & Malaria Research Institute, Baltimore, MD 21205, USA.
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Kamali M, Marek PE, Peery A, Antonio-Nkondjio C, Ndo C, Tu Z, Simard F, Sharakhov IV. Multigene phylogenetics reveals temporal diversification of major African malaria vectors. PLoS One 2014; 9:e93580. [PMID: 24705448 PMCID: PMC3976319 DOI: 10.1371/journal.pone.0093580] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2013] [Accepted: 03/05/2014] [Indexed: 12/21/2022] Open
Abstract
The major vectors of malaria in sub-Saharan Africa belong to subgenus Cellia. Yet, phylogenetic relationships and temporal diversification among African mosquito species have not been unambiguously determined. Knowledge about vector evolutionary history is crucial for correct interpretation of genetic changes identified through comparative genomics analyses. In this study, we estimated a molecular phylogeny using 49 gene sequences for the African malaria vectors An. gambiae, An. funestus, An. nili, the Asian malaria mosquito An. stephensi, and the outgroup species Culex quinquefasciatus and Aedes aegypti. To infer the phylogeny, we identified orthologous sequences uniformly distributed approximately every 5 Mb in the five chromosomal arms. The sequences were aligned and the phylogenetic trees were inferred using maximum likelihood and neighbor-joining methods. Bayesian molecular dating using a relaxed log normal model was used to infer divergence times. Trees from individual genes agreed with each other, placing An. nili as a basal clade that diversified from the studied malaria mosquito species 47.6 million years ago (mya). Other African malaria vectors originated more recently, and independently acquired traits related to vectorial capacity. The lineage leading to An. gambiae diverged 30.4 mya, while the African vector An. funestus and the Asian vector An. stephensi were the most closely related sister taxa that split 20.8 mya. These results were supported by consistently high bootstrap values in concatenated phylogenetic trees generated individually for each chromosomal arm. Genome-wide multigene phylogenetic analysis is a useful approach for discerning historic relationships among malaria vectors, providing a framework for the correct interpretation of genomic changes across species, and comprehending the evolutionary origins of this ubiquitous and deadly insect-borne disease.
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Affiliation(s)
- Maryam Kamali
- Department of Entomology, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, United States of America
| | - Paul E Marek
- Department of Entomology, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, United States of America
| | - Ashley Peery
- Department of Entomology, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, United States of America
| | | | - Cyrille Ndo
- Malaria Research Laboratory, OCEAC, Yaounde, Cameroon; MIVEGEC (UMR IRD224-CNRS5290-UM1-UM2), Institut de Recherche pour le Développement (IRD), Montpellier, France; Faculty of Medicine and Pharmaceutical Sciences, University of Douala, Douala, Cameroon
| | - Zhijian Tu
- Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, United States of America
| | - Frederic Simard
- MIVEGEC (UMR IRD224-CNRS5290-UM1-UM2), Institut de Recherche pour le Développement (IRD), Montpellier, France
| | - Igor V Sharakhov
- Department of Entomology, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, United States of America
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Lin J, Chen G, Gu L, Shen Y, Zheng M, Zheng W, Hu X, Zhang X, Qiu Y, Liu X, Jiang C. Phylogenetic affinity of tree shrews to Glires is attributed to fast evolution rate. Mol Phylogenet Evol 2013; 71:193-200. [PMID: 24333622 DOI: 10.1016/j.ympev.2013.12.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2013] [Revised: 11/25/2013] [Accepted: 12/02/2013] [Indexed: 11/26/2022]
Abstract
Previous phylogenetic analyses have led to incongruent evolutionary relationships between tree shrews and other suborders of Euarchontoglires. What caused the incongruence remains elusive. In this study, we identified 6845 orthologous genes between seventeen placental mammals. Tree shrews and Primates were monophyletic in the phylogenetic trees derived from the first or/and second codon positions whereas tree shrews and Glires formed a monophyly in the trees derived from the third or all codon positions. The same topology was obtained in the phylogeny inference using the slowly and fast evolving genes, respectively. This incongruence was likely attributed to the fast substitution rate in tree shrews and Glires. Notably, sequence GC content only was not informative to resolve the controversial phylogenetic relationships between tree shrews, Glires, and Primates. Finally, estimation in the confidence of the tree selection strongly supported the phylogenetic affiliation of tree shrews to Primates as a monophyly.
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Affiliation(s)
- Jiannan Lin
- Shanghai Tenth People's Hospital, Shanghai Key Laboratory of Signaling and Disease Research, The School of Life Sciences and Technology, Tongji University, Shanghai 200120, China.
| | - Guangfeng Chen
- Shanghai Tenth People's Hospital, Tongji University School of Medicine, 301 Yanchangzhong Rd, Shanghai 200072, China.
| | - Liang Gu
- Shanghai Tenth People's Hospital, Shanghai Key Laboratory of Signaling and Disease Research, The School of Life Sciences and Technology, Tongji University, Shanghai 200120, China.
| | - Yuefeng Shen
- Shanghai Tenth People's Hospital, Shanghai Key Laboratory of Signaling and Disease Research, The School of Life Sciences and Technology, Tongji University, Shanghai 200120, China.
| | - Meizhu Zheng
- Shanghai Tenth People's Hospital, Shanghai Key Laboratory of Signaling and Disease Research, The School of Life Sciences and Technology, Tongji University, Shanghai 200120, China.
| | - Weisheng Zheng
- Shanghai Tenth People's Hospital, Shanghai Key Laboratory of Signaling and Disease Research, The School of Life Sciences and Technology, Tongji University, Shanghai 200120, China.
| | - Xinjie Hu
- Shanghai Tenth People's Hospital, Shanghai Key Laboratory of Signaling and Disease Research, The School of Life Sciences and Technology, Tongji University, Shanghai 200120, China.
| | - Xiaobai Zhang
- Shanghai Tenth People's Hospital, Shanghai Key Laboratory of Signaling and Disease Research, The School of Life Sciences and Technology, Tongji University, Shanghai 200120, China.
| | - Yu Qiu
- Shanghai Tenth People's Hospital, Tongji University School of Medicine, 301 Yanchangzhong Rd, Shanghai 200072, China.
| | - Xiaoqing Liu
- Shanghai Tenth People's Hospital, Tongji University School of Medicine, 301 Yanchangzhong Rd, Shanghai 200072, China.
| | - Cizhong Jiang
- Shanghai Tenth People's Hospital, Shanghai Key Laboratory of Signaling and Disease Research, The School of Life Sciences and Technology, Tongji University, Shanghai 200120, China.
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Bazinet AL, Cummings MP, Mitter KT, Mitter CW. Can RNA-Seq resolve the rapid radiation of advanced moths and butterflies (Hexapoda: Lepidoptera: Apoditrysia)? An exploratory study. PLoS One 2013; 8:e82615. [PMID: 24324810 PMCID: PMC3853519 DOI: 10.1371/journal.pone.0082615] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2013] [Accepted: 10/23/2013] [Indexed: 11/19/2022] Open
Abstract
Recent molecular phylogenetic studies of the insect order Lepidoptera have robustly resolved family-level divergences within most superfamilies, and most divergences among the relatively species-poor early-arising superfamilies. In sharp contrast, relationships among the superfamilies of more advanced moths and butterflies that comprise the mega-diverse clade Apoditrysia (ca. 145,000 spp.) remain mostly poorly supported. This uncertainty, in turn, limits our ability to discern the origins, ages and evolutionary consequences of traits hypothesized to promote the spectacular diversification of Apoditrysia. Low support along the apoditrysian "backbone" probably reflects rapid diversification. If so, it may be feasible to strengthen resolution by radically increasing the gene sample, but case studies have been few. We explored the potential of next-generation sequencing to conclusively resolve apoditrysian relationships. We used transcriptome RNA-Seq to generate 1579 putatively orthologous gene sequences across a broad sample of 40 apoditrysians plus four outgroups, to which we added two taxa from previously published data. Phylogenetic analysis of a 46-taxon, 741-gene matrix, resulting from a strict filter that eliminated ortholog groups containing any apparent paralogs, yielded dramatic overall increase in bootstrap support for deeper nodes within Apoditrysia as compared to results from previous and concurrent 19-gene analyses. High support was restricted mainly to the huge subclade Obtectomera broadly defined, in which 11 of 12 nodes subtending multiple superfamilies had bootstrap support of 100%. The strongly supported nodes showed little conflict with groupings from previous studies, and were little affected by changes in taxon sampling, suggesting that they reflect true signal rather than artifacts of massive gene sampling. In contrast, strong support was seen at only 2 of 11 deeper nodes among the "lower", non-obtectomeran apoditrysians. These represent a much harder phylogenetic problem, for which one path to resolution might include further increase in gene sampling, together with improved orthology assignments.
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Affiliation(s)
- Adam L. Bazinet
- Laboratory of Molecular Evolution, Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland, United States of America
| | - Michael P. Cummings
- Laboratory of Molecular Evolution, Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland, United States of America
| | - Kim T. Mitter
- Department of Entomology, University of Maryland, College Park, Maryland, United States of America
| | - Charles W. Mitter
- Department of Entomology, University of Maryland, College Park, Maryland, United States of America
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48
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Integrating phylogenetics, phylogeography and population genetics through genomes and evolutionary theory. Mol Phylogenet Evol 2013; 69:1172-85. [DOI: 10.1016/j.ympev.2013.06.006] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2013] [Revised: 06/06/2013] [Accepted: 06/12/2013] [Indexed: 11/22/2022]
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49
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Rinker DC, Zhou X, Pitts RJ. Antennal transcriptome profiles of anopheline mosquitoes reveal human host olfactory specialization in Anopheles gambiae. BMC Genomics 2013; 14:749. [PMID: 24182346 PMCID: PMC3833343 DOI: 10.1186/1471-2164-14-749] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2013] [Accepted: 10/22/2013] [Indexed: 01/29/2023] Open
Abstract
BACKGROUND Two sibling members of the Anopheles gambiae species complex display notable differences in female blood meal preferences. An. gambiae s.s. has a well-documented preference for feeding upon human hosts, whereas An. quadriannulatus feeds on vertebrate/mammalian hosts, with only opportunistic feeding upon humans. Because mosquito host-seeking behaviors are largely driven by the sensory modality of olfaction, we hypothesized that hallmarks of these divergent host seeking phenotypes will be in evidence within the transcriptome profiles of the antennae, the mosquito's principal chemosensory appendage. RESULTS To test this hypothesis, we have sequenced antennal mRNA of non-bloodfed females from each species and observed a number of distinct quantitative and qualitative differences in their chemosensory gene repertoires. In both species, these gene families show higher rates of sequence polymorphisms than the overall rates in their respective transcriptomes, with potentially important divergences between the two species. Moreover, quantitative differences in odorant receptor transcript abundances have been used to model potential distinctions in volatile odor receptivity between the two sibling species of anophelines. CONCLUSION This analysis suggests that the anthropophagic behavior of An. gambiae s.s. reflects the differential distribution of olfactory receptors in the antenna, likely resulting from a co-option and refinement of molecular components common to both species. This study improves our understanding of the molecular evolution of chemoreceptors in closely related anophelines and suggests possible mechanisms that underlie the behavioral distinctions in host seeking that, in part, account for the differential vectorial capacity of these mosquitoes.
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Affiliation(s)
- David C Rinker
- Center for Human Genetics Research, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Xiaofan Zhou
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, USA
| | - Ronald Jason Pitts
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, USA
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50
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Wen J, Xiong Z, Nie ZL, Mao L, Zhu Y, Kan XZ, Ickert-Bond SM, Gerrath J, Zimmer EA, Fang XD. Transcriptome sequences resolve deep relationships of the grape family. PLoS One 2013; 8:e74394. [PMID: 24069307 PMCID: PMC3775763 DOI: 10.1371/journal.pone.0074394] [Citation(s) in RCA: 80] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2013] [Accepted: 08/01/2013] [Indexed: 01/26/2023] Open
Abstract
Previous phylogenetic studies of the grape family (Vitaceae) yielded poorly resolved deep relationships, thus impeding our understanding of the evolution of the family. Next-generation sequencing now offers access to protein coding sequences very easily, quickly and cost-effectively. To improve upon earlier work, we extracted 417 orthologous single-copy nuclear genes from the transcriptomes of 15 species of the Vitaceae, covering its phylogenetic diversity. The resulting transcriptome phylogeny provides robust support for the deep relationships, showing the phylogenetic utility of transcriptome data for plants over a time scale at least since the mid-Cretaceous. The pros and cons of transcriptome data for phylogenetic inference in plants are also evaluated.
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Affiliation(s)
- Jun Wen
- Department of Botany, National Museum of Natural History, MRC166, Smithsonian Institution, Washington, D.C., United States of America
| | | | - Ze-Long Nie
- Key Laboratory of Biodiversity and Biogeography, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
| | | | | | - Xian-Zhao Kan
- College of Life Sciences, Anhui Normal University, Wuhu, Anhui, China
| | - Stefanie M. Ickert-Bond
- UA Museum of the North Herbarium and Department of Biology and Wildlife, University of Alaska Fairbanks, Fairbanks, Alaska, United States of America
| | - Jean Gerrath
- Department of Biology, University of Northern Iowa, Cedar Falls, Iowa, United States of America
| | - Elizabeth A. Zimmer
- Department of Botany, National Museum of Natural History, MRC166, Smithsonian Institution, Washington, D.C., United States of America
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