6
views
0
recommends
+1 Recommend
1 collections
    0
    shares
      • Record: found
      • Abstract: found
      • Article: found
      Is Open Access

      Amino acid synthesis loss in parasitoid wasps and other hymenopterans

      research-article

      Read this article at

      Bookmark
          There is no author summary for this article yet. Authors can add summaries to their articles on ScienceOpen to make them more accessible to a non-specialist audience.

          Abstract

          Insects utilize diverse food resources which can affect the evolution of their genomic repertoire, including leading to gene losses in different nutrient pathways. Here, we investigate gene loss in amino acid synthesis pathways, with special attention to hymenopterans and parasitoid wasps. Using comparative genomics, we find that synthesis capability for tryptophan, phenylalanine, tyrosine, and histidine was lost in holometabolous insects prior to hymenopteran divergence, while valine, leucine, and isoleucine were lost in the common ancestor of Hymenoptera. Subsequently, multiple loss events of lysine synthesis occurred independently in the Parasitoida and Aculeata. Experiments in the parasitoid Cotesia chilonis confirm that it has lost the ability to synthesize eight amino acids. Our findings provide insights into amino acid synthesis evolution, and specifically can be used to inform the design of parasitoid artificial diets for pest control.

          Related collections

          Most cited references95

          • Record: found
          • Abstract: found
          • Article: found
          Is Open Access

          Trimmomatic: a flexible trimmer for Illumina sequence data

          Motivation: Although many next-generation sequencing (NGS) read preprocessing tools already existed, we could not find any tool or combination of tools that met our requirements in terms of flexibility, correct handling of paired-end data and high performance. We have developed Trimmomatic as a more flexible and efficient preprocessing tool, which could correctly handle paired-end data. Results: The value of NGS read preprocessing is demonstrated for both reference-based and reference-free tasks. Trimmomatic is shown to produce output that is at least competitive with, and in many cases superior to, that produced by other tools, in all scenarios tested. Availability and implementation: Trimmomatic is licensed under GPL V3. It is cross-platform (Java 1.5+ required) and available at http://www.usadellab.org/cms/index.php?page=trimmomatic Contact: usadel@bio1.rwth-aachen.de Supplementary information: Supplementary data are available at Bioinformatics online.
            Bookmark
            • Record: found
            • Abstract: found
            • Article: found
            Is Open Access

            edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

            Summary: It is expected that emerging digital gene expression (DGE) technologies will overtake microarray technologies in the near future for many functional genomics applications. One of the fundamental data analysis tasks, especially for gene expression studies, involves determining whether there is evidence that counts for a transcript or exon are significantly different across experimental conditions. edgeR is a Bioconductor software package for examining differential expression of replicated count data. An overdispersed Poisson model is used to account for both biological and technical variability. Empirical Bayes methods are used to moderate the degree of overdispersion across transcripts, improving the reliability of inference. The methodology can be used even with the most minimal levels of replication, provided at least one phenotype or experimental condition is replicated. The software may have other applications beyond sequencing data, such as proteome peptide count data. Availability: The package is freely available under the LGPL licence from the Bioconductor web site (http://bioconductor.org). Contact: mrobinson@wehi.edu.au
              Bookmark
              • Record: found
              • Abstract: found
              • Article: not found

              HISAT: a fast spliced aligner with low memory requirements.

              HISAT (hierarchical indexing for spliced alignment of transcripts) is a highly efficient system for aligning reads from RNA sequencing experiments. HISAT uses an indexing scheme based on the Burrows-Wheeler transform and the Ferragina-Manzini (FM) index, employing two types of indexes for alignment: a whole-genome FM index to anchor each alignment and numerous local FM indexes for very rapid extensions of these alignments. HISAT's hierarchical index for the human genome contains 48,000 local FM indexes, each representing a genomic region of ∼64,000 bp. Tests on real and simulated data sets showed that HISAT is the fastest system currently available, with equal or better accuracy than any other method. Despite its large number of indexes, HISAT requires only 4.3 gigabytes of memory. HISAT supports genomes of any size, including those larger than 4 billion bases.
                Bookmark

                Author and article information

                Contributors
                Role: Reviewing Editor
                Role: Senior Editor
                Journal
                eLife
                Elife
                eLife
                eLife
                eLife Sciences Publications, Ltd
                2050-084X
                19 October 2020
                2020
                : 9
                : e59795
                Affiliations
                [1 ]State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University HangzhouChina
                [2 ]Department of Biology, University of Rochester RochesterUnited States
                [3 ]Division of Plant Sciences, College of Agriculture, Food and Natural Resources, University of Missouri ColumbiaUnited States
                Vanderbilt University United States
                University of Michigan United States
                Vanderbilt University United States
                Author notes
                [†]

                These authors contributed equally to this work.

                [‡]

                These authors also contributed equally to this work.

                Author information
                https://orcid.org/0000-0002-0203-0663
                https://orcid.org/0000-0002-4142-5852
                https://orcid.org/0000-0002-8352-2626
                https://orcid.org/0000-0003-4150-3408
                https://orcid.org/0000-0003-4937-8867
                https://orcid.org/0000-0002-8410-5250
                Article
                59795
                10.7554/eLife.59795
                7593089
                33074103
                5fc090ff-d2bb-47c6-a80e-a8688415fa48
                © 2020, Ye et al

                This article is distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use and redistribution provided that the original author and source are credited.

                History
                : 08 June 2020
                : 17 October 2020
                Funding
                Funded by: FundRef http://dx.doi.org/10.13039/501100001809, National Natural Science Foundation of China;
                Award ID: Major International (Regional) Joint Research Project of National Natural Science Foundation of China 31620103915
                Award Recipient :
                Funded by: FundRef http://dx.doi.org/10.13039/501100001809, National Natural Science Foundation of China;
                Award ID: Key Program of National Natural Science Foundation of China 31830074
                Award Recipient :
                Funded by: FundRef http://dx.doi.org/10.13039/501100001809, National Natural Science Foundation of China;
                Award ID: 31772238
                Award Recipient :
                Funded by: National Key Research and Development Program of China;
                Award ID: 2017YFD0200400
                Award Recipient :
                Funded by: National Key Research and Development Program of China;
                Award ID: 2017YFD0200904
                Award Recipient :
                Funded by: FundRef http://dx.doi.org/10.13039/100000001, National Science Foundation;
                Award ID: IOS-1456233
                Award Recipient :
                The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
                Categories
                Research Article
                Genetics and Genomics
                Custom metadata
                The synthesis capability of some amino acids is lost during the insect evolution, and hymenopteran parasitoids can make up for these deficiencies by altering free amino acid concentrations in host.

                Life sciences
                amino acid synthesis,trait loss,comparative genomics,genome sequencing,parasitoid wasps,cotesia chilonis,other

                Comments

                Comment on this article