title: Transcription factors, chromatin proteins and the diversification of Hemiptera.
abstract: Availability of complete genomes provides a means to explore the evolution of enormous developmental, morphological, and behavioral diversity among insects. Hemipterans in particular show great diversity of both morphology and life history within a single order. To better understand the role of transcription regulators in the diversification of hemipterans, using sequence profile searches and hidden Markov models we computationally analyzed transcription factors (TFs) and chromatin proteins (CPs) in the recently available Rhodnius prolixus genome along with 13 other insect and 4 non-insect arthropod genomes. We generated a comprehensive collection of TFs and CPs across arthropods including 303 distinct types of domains in TFs and 139 in CPs. This, along with the availability of two hemipteran genomes, R. prolixus and Acyrthosiphon pisum, helped us identify possible determinants for their dramatic morphological and behavioral divergence. We identified five domain families (i.e. Pipsqueak, SAZ/MADF, THAP, FLYWCH and BED finger) as having undergone differential patterns of lineage-specific expansion in hemipterans or within hemipterans relative to other insects. These expansions appear to be at least in part driven by transposons, with the DNA-binding domains of transposases having provided the raw material for emergence of new TFs. Our analysis suggests that while R. prolixus probably retains a state closer to the ancestral hemipteran, A. pisum represents a highly derived state, with the emergence of asexual reproduction potentially favoring genome duplication and transposon expansion. Both hemipterans are predicted to possess active DNA methylation systems. However, in the course of their divergence, aphids seem to have expanded the ancestral hemipteran DNA methylation along with a distinctive linkage to the histone methylation system, as suggested by expansion of SET domain methylases, including those fused to methylated CpG recognition domains. Thus, differential use of DNA methylation and histone methylation might have played a role in emergence of polyphenism and cyclic parthenogenesis from the ancestral hemipteran.
authors.affiliation: National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA; Laboratório de Química e Função de Proteínas e Peptídeos, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, RJ, Brazil; Instituto Nacional de Ciência e Tecnologia em Entomologia Molecular (INCT-EM), Rio de Janeiro, RJ, Brazil. Electronic address: nwvidal@gmail.com.
authors.forename: Newton M
authors.initials: NM
authors.lastname: Vidal
authors.affiliation: National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA; Laboratório de Química e Função de Proteínas e Peptídeos, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, RJ, Brazil. Electronic address: analauragrazziotin@gmail.com.
authors.forename: Ana Laura
authors.initials: AL
authors.lastname: Grazziotin
authors.affiliation: National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA. Electronic address: lakshmin@ncbi.nlm.nih.gov.
authors.forename: Lakshminarayan M
authors.initials: LM
authors.lastname: Iyer
authors.affiliation: National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA. Electronic address: aravind@ncbi.nlm.nih.gov.
authors.forename: L
authors.initials: L
authors.lastname: Aravind
authors.affiliation: Laboratório de Química e Função de Proteínas e Peptídeos, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, RJ, Brazil; Instituto Nacional de Ciência e Tecnologia em Entomologia Molecular (INCT-EM), Rio de Janeiro, RJ, Brazil. Electronic address: thiago.venancio@gmail.com.
authors.forename: Thiago M
authors.initials: TM
authors.lastname: Venancio
mesh_terms: D000818:Animals; D001042:Aphids / Q000235:genetics; D001181:Arthropods / Q000235:genetics; D005075:Biological Evolution; D002843:Chromatin / Q000737:chemistry / Q000235:genetics*; D019175:DNA Methylation; D004251:DNA Transposable Elements; D049750:Genome, Insect; D006430:Hemiptera / Q000033:anatomy & histology / Q000145:classification / Q000235:genetics*; D006657:Histones; D008390:Markov Chains; D010802:Phylogeny; D020543:Proteome / Q000235:genetics; D012100:Reproduction, Asexual / Q000235:genetics; D012239:Rhodnius / Q000235:genetics; D014157:Transcription Factors / Q000235:genetics*
chemical_list: D002843:Chromatin; D004251:DNA Transposable Elements; D006657:Histones; D020543:Proteome; D014157:Transcription Factors
keywords: Genome evolution; Insect development; Lineage-specific expansion; Rhodnius prolixus; Transcription factor; Transposable element