Blog
About

1,378
views
0
recommends
+1 Recommend
1 collections
    0
    shares
      • Record: found
      • Abstract: found
      • Article: found
      Is Open Access

      Hemimetabolous genomes reveal molecular basis of termite eusociality

      1 , 12 , 1 , 12 , 2 , 12 , 1 , 1 , 3 , 4 , 3 , 3 , 3 , 5 , 6 , 5 , 6 , 3 , 7 , 3 , 8 , 1 , 1 , 3 , 1 , 1 , 5 , 5 , 3 , 3 , 7 , 9 , 4 , 3 , 5 , 10 , 3 , 11 , 9 , 7 , 3 , 10 , 3 , 9 , * , 5 , 6 , * , 1 , *

      Nature ecology & evolution

      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

          Around 150 million years ago, eusocial termites evolved from within the cockroaches, 50 million years before eusocial Hymenoptera, such as bees and ants, appeared. Here, we report the 2-Gb genome of the German cockroach, Blattella germanica, and the 1.3-Gb genome of the drywood termite Cryptotermes secundus. We show evolutionary signatures of termite eusociality by comparing the genomes and transcriptomes of three termites and the cockroach against the background of 16 other eusocial and non-eusocial insects. Dramatic adaptive changes in genes underlying the production and perception of pheromones confirm the importance of chemical communication in the termites. These are accompanied by major changes in gene regulation and the molecular evolution of caste determination. Many of these results parallel molecular mechanisms of eusocial evolution in Hymenoptera. However, the specific solutions are remarkably different, thus revealing a striking case of convergence in one of the major evolutionary transitions in biological complexity.

          Related collections

          Most cited references 93

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

          Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2

          In comparative high-throughput sequencing assays, a fundamental task is the analysis of count data, such as read counts per gene in RNA-seq, for evidence of systematic changes across experimental conditions. Small replicate numbers, discreteness, large dynamic range and the presence of outliers require a suitable statistical approach. We present DESeq2, a method for differential analysis of count data, using shrinkage estimation for dispersions and fold changes to improve stability and interpretability of estimates. This enables a more quantitative analysis focused on the strength rather than the mere presence of differential expression. The DESeq2 package is available at http://www.bioconductor.org/packages/release/bioc/html/DESeq2.html. Electronic supplementary material The online version of this article (doi:10.1186/s13059-014-0550-8) contains supplementary material, which is available to authorized users.
            Bookmark
            • Record: found
            • Abstract: found
            • Article: found
            Is Open Access

            MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

            We report a major update of the MAFFT multiple sequence alignment program. This version has several new features, including options for adding unaligned sequences into an existing alignment, adjustment of direction in nucleotide alignment, constrained alignment and parallel processing, which were implemented after the previous major update. This report shows actual examples to explain how these features work, alone and in combination. Some examples incorrectly aligned by MAFFT are also shown to clarify its limitations. We discuss how to avoid misalignments, and our ongoing efforts to overcome such limitations.
              Bookmark
              • Record: found
              • Abstract: found
              • Article: found
              Is Open Access

              BEDTools: a flexible suite of utilities for comparing genomic features

              Motivation: Testing for correlations between different sets of genomic features is a fundamental task in genomics research. However, searching for overlaps between features with existing web-based methods is complicated by the massive datasets that are routinely produced with current sequencing technologies. Fast and flexible tools are therefore required to ask complex questions of these data in an efficient manner. Results: This article introduces a new software suite for the comparison, manipulation and annotation of genomic features in Browser Extensible Data (BED) and General Feature Format (GFF) format. BEDTools also supports the comparison of sequence alignments in BAM format to both BED and GFF features. The tools are extremely efficient and allow the user to compare large datasets (e.g. next-generation sequencing data) with both public and custom genome annotation tracks. BEDTools can be combined with one another as well as with standard UNIX commands, thus facilitating routine genomics tasks as well as pipelines that can quickly answer intricate questions of large genomic datasets. Availability and implementation: BEDTools was written in C++. Source code and a comprehensive user manual are freely available at http://code.google.com/p/bedtools Contact: aaronquinlan@gmail.com; imh4y@virginia.edu Supplementary information: Supplementary data are available at Bioinformatics online.
                Bookmark

                Author and article information

                Journal
                101698577
                46074
                Nat Ecol Evol
                Nat Ecol Evol
                Nature ecology & evolution
                2397-334X
                16 April 2019
                05 February 2018
                March 2018
                25 April 2019
                : 2
                : 3
                : 557-566
                Affiliations
                [1 ]Institute for Evolution and Biodiversity, University of Münster, Münster, Germany.
                [2 ]Department of Entomology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
                [3 ]Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, Houston, TX, USA.
                [4 ]USDA-ARS, National Agricultural Library, Beltsville, MD, USA.
                [5 ]Evolutionary Biology & Ecology, University of Freiburg, Freiburg, Germany.
                [6 ]Behavioral Biology, University of Osnabrück, Osnabrück, Germany.
                [7 ]Ecology and Evolution, University of Copenhagen, Copenhagen, Denmark.
                [8 ]Institute of Science and Technology Austria, Klosterneuburg, Austria.
                [9 ]Institut de Biologia Evolutiva, CSIC-University Pompeu Fabra, Barcelona, Spain.
                [10 ]Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, USA.
                [11 ]China National GeneBank, Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, China.
                [12 ]These authors contributed equally: Mark C. Harrison, Evelien Jongepier and Hugh M. Robertson.
                Author notes

                Author contributions

                E.B.-B. conceived, managed and coordinated the project; M.C.H., E.J. and H.M.R. are joint first authors. J.K. conceived and managed the C. secundus sequencing project, and coordinated termite-related analyses; S.R. conceived and managed the B. germanica sequencing project; S.R., S.D., S.L.L., H.C., H.V.D., H.D., Y.H., J.Q., S.C.M., D.S.T.H., K.C.W., D.M.M. and R.A.G. carried out B. germanica library construction, genome sequencing and assembly; C.S. and A.W-.K. provided biological material through full-sib mating for B. germanica; X.B. and C.S. co-managed the B. germanica analysis; M.P. and C.P.C. implemented Web Apollo data traces; S.O. and M.P. provided biological material for M. natalensis; C.G., J.G., J.M.M.-K., A.M., F.S., H.H. and J.K. coordinated and carried out DNA and RNA sequencing for C. secundus; M-D.P., X.B. and G.Y. coordinated transcriptome sequencing of B. germanica; L.M. performed automated gene prediction on C. secundus; E.J. and N.A. improved assembly and annotation for B. germanica & C. secundus, and compared and analysed genome sizes and quality. E.J., N.A. and L.P.M.K. analysed TEs; M.C.H. analysed CpG patterns and signatures of selection; T.B-F., E.J., C.K., L.P.M.K. and A.L-E. performed orthology and phylogenetic analyses; L.P.M.K., E.J., H.M.R. and M.C.H. analysed gene family evolution; A.L-E., E.J. and M.C.H. analysed transcriptomes and performed differential expression analyses; T.B.-F. and A.L-E. carried out orthoMCL clustering; H.M.R. corrected gene models for chemoreceptors; C.K. and E.J. corrected gene models for desaturases and elongases; A-K.H. and M.C.H. corrected gene models for cytochrome P450s; E.B.-B. and M.C.H drafted and wrote the manuscript; X.B., M.-D.P. and J.K. contributed to sections of the manuscript; E.J., L.P.M.K., A.L-E., C.K. and M.C.H. wrote and organized the Supplementary Information; L.P.M.K., N.A., A.L-E., M.C.H. and E.B.-B. prepared figures for the manuscript. All authors read, corrected and commented on the manuscript.

                [* ] Correspondence and requests for materials should be addressed to X.B. or J.K. or E.B.-B. xavier.belles@ 123456ibe.upf-csic.es ; judith.korb@ 123456biologie.uni-freiburg.de ; ebb@ 123456uni-muenster.de
                Article
                NIHMS1022840
                10.1038/s41559-017-0459-1
                6482461
                29403074

                This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

                Reprints and permissions information is available at www.nature.com/reprints.

                Categories
                Article

                Comments

                Comment on this article