%0 Journal Article %J Genome Biol %D 2019 %T Molecular evolutionary trends and feeding ecology diversification in the Hemiptera, anchored by the milkweed bug genome. %A Panfilio, Kristen A %A Vargas Jentzsch, Iris M %A Benoit, Joshua B %A Erezyilmaz, Deniz %A Suzuki, Yuichiro %A Colella, Stefano %A Robertson, Hugh M %A Poelchau, Monica F %A Waterhouse, Robert M %A Ioannidis, Panagiotis %A Weirauch, Matthew T %A Hughes, Daniel S T %A Murali, Shwetha C %A Werren, John H %A Jacobs, Chris G C %A Duncan, Elizabeth J %A Armisén, David %A Vreede, Barbara M I %A Baa-Puyoulet, Patrice %A Berger, Chloé S %A Chang, Chun-Che %A Chao, Hsu %A Chen, Mei-Ju M %A Chen, Yen-Ta %A Childers, Christopher P %A Chipman, Ariel D %A Cridge, Andrew G %A Crumière, Antonin J J %A Dearden, Peter K %A Didion, Elise M %A Dinh, Huyen %A Harshavardhan Doddapaneni %A Dolan, Amanda %A Dugan, Shannon %A Extavour, Cassandra G %A Febvay, Gérard %A Friedrich, Markus %A Ginzburg, Neta %A Yi Han %A Heger, Peter %A Holmes, Christopher J %A Horn, Thorsten %A Hsiao, Yi-Min %A Jennings, Emily C %A Johnston, J Spencer %A Jones, Tamsin E %A Jones, Jeffery W %A Khila, Abderrahman %A Koelzer, Stefan %A Kovacova, Viera %A Leask, Megan %A Lee, Sandra L %A Lee, Chien-Yueh %A Lovegrove, Mackenzie R %A Lu, Hsiao-Ling %A Lu, Yong %A Moore, Patricia J %A Munoz-Torres, Monica C %A Donna M Muzny %A Palli, Subba R %A Parisot, Nicolas %A Pick, Leslie %A Porter, Megan L %A Qu, Jiaxin %A Refki, Peter N %A Richter, Rose %A Rivera-Pomar, Rolando %A Rosendale, Andrew J %A Roth, Siegfried %A Sachs, Lena %A Santos, M Emília %A Seibert, Jan %A Sghaier, Essia %A Shukla, Jayendra N %A Stancliffe, Richard J %A Tidswell, Olivia %A Traverso, Lucila %A Van der Zee, Maurijn %A Viala, Sèverine %A Kim C Worley %A Zdobnov, Evgeny M %A Richard A Gibbs %A Stephen Richards %K Amino Acid Sequence %K Animals %K CYS2-HIS2 Zinc Fingers %K Evolution, Molecular %K Feeding Behavior %K Gene Dosage %K Gene Expression Profiling %K Gene Transfer, Horizontal %K Genes, Homeobox %K Genome, Insect %K Hemiptera %K Pigmentation %K Smell %K Transcription Factors %X

BACKGROUND: The Hemiptera (aphids, cicadas, and true bugs) are a key insect order, with high diversity for feeding ecology and excellent experimental tractability for molecular genetics. Building upon recent sequencing of hemipteran pests such as phloem-feeding aphids and blood-feeding bed bugs, we present the genome sequence and comparative analyses centered on the milkweed bug Oncopeltus fasciatus, a seed feeder of the family Lygaeidae.

RESULTS: The 926-Mb Oncopeltus genome is well represented by the current assembly and official gene set. We use our genomic and RNA-seq data not only to characterize the protein-coding gene repertoire and perform isoform-specific RNAi, but also to elucidate patterns of molecular evolution and physiology. We find ongoing, lineage-specific expansion and diversification of repressive C2H2 zinc finger proteins. The discovery of intron gain and turnover specific to the Hemiptera also prompted the evaluation of lineage and genome size as predictors of gene structure evolution. Furthermore, we identify enzymatic gains and losses that correlate with feeding biology, particularly for reductions associated with derived, fluid nutrition feeding.

CONCLUSIONS: With the milkweed bug, we now have a critical mass of sequenced species for a hemimetabolous insect order and close outgroup to the Holometabola, substantially improving the diversity of insect genomics. We thereby define commonalities among the Hemiptera and delve into how hemipteran genomes reflect distinct feeding ecologies. Given Oncopeltus's strength as an experimental model, these new sequence resources bolster the foundation for molecular research and highlight technical considerations for the analysis of medium-sized invertebrate genomes.

%B Genome Biol %V 20 %P 64 %8 2019 Apr 02 %G eng %N 1 %1 https://www.ncbi.nlm.nih.gov/pubmed/30935422?dopt=Abstract %R 10.1186/s13059-019-1660-0 %0 Journal Article %J BMC Biol %D 2017 %T The house spider genome reveals an ancient whole-genome duplication during arachnid evolution. %A Schwager, Evelyn E %A Sharma, Prashant P %A Clarke, Thomas %A Leite, Daniel J %A Wierschin, Torsten %A Pechmann, Matthias %A Akiyama-Oda, Yasuko %A Esposito, Lauren %A Bechsgaard, Jesper %A Bilde, Trine %A Buffry, Alexandra D %A Chao, Hsu %A Dinh, Huyen %A Harshavardhan Doddapaneni %A Dugan, Shannon %A Eibner, Cornelius %A Extavour, Cassandra G %A Funch, Peter %A Garb, Jessica %A Gonzalez, Luis B %A Gonzalez, Vanessa L %A Griffiths-Jones, Sam %A Yi Han %A Hayashi, Cheryl %A Hilbrant, Maarten %A Hughes, Daniel S T %A Janssen, Ralf %A Lee, Sandra L %A Maeso, Ignacio %A Murali, Shwetha C %A Donna M Muzny %A Nunes da Fonseca, Rodrigo %A Paese, Christian L B %A Qu, Jiaxin %A Ronshaugen, Matthew %A Schomburg, Christoph %A Schönauer, Anna %A Stollewerk, Angelika %A Torres-Oliva, Montserrat %A Turetzek, Natascha %A Vanthournout, Bram %A Werren, John H %A Wolff, Carsten %A Worley, Kim C %A Bucher, Gregor %A Richard A Gibbs %A Coddington, Jonathan %A Oda, Hiroki %A Stanke, Mario %A Ayoub, Nadia A %A Prpic, Nikola-Michael %A Flot, Jean-François %A Posnien, Nico %A Richards, Stephen %A McGregor, Alistair P %K Animals %K Evolution, Molecular %K Female %K Gene Duplication %K Genome %K Male %K Spiders %K Synteny %X

BACKGROUND: The duplication of genes can occur through various mechanisms and is thought to make a major contribution to the evolutionary diversification of organisms. There is increasing evidence for a large-scale duplication of genes in some chelicerate lineages including two rounds of whole genome duplication (WGD) in horseshoe crabs. To investigate this further, we sequenced and analyzed the genome of the common house spider Parasteatoda tepidariorum.

RESULTS: We found pervasive duplication of both coding and non-coding genes in this spider, including two clusters of Hox genes. Analysis of synteny conservation across the P. tepidariorum genome suggests that there has been an ancient WGD in spiders. Comparison with the genomes of other chelicerates, including that of the newly sequenced bark scorpion Centruroides sculpturatus, suggests that this event occurred in the common ancestor of spiders and scorpions, and is probably independent of the WGDs in horseshoe crabs. Furthermore, characterization of the sequence and expression of the Hox paralogs in P. tepidariorum suggests that many have been subject to neo-functionalization and/or sub-functionalization since their duplication.

CONCLUSIONS: Our results reveal that spiders and scorpions are likely the descendants of a polyploid ancestor that lived more than 450 MYA. Given the extensive morphological diversity and ecological adaptations found among these animals, rivaling those of vertebrates, our study of the ancient WGD event in Arachnopulmonata provides a new comparative platform to explore common and divergent evolutionary outcomes of polyploidization events across eukaryotes.

%B BMC Biol %V 15 %P 62 %8 2017 Jul 31 %G eng %N 1 %1 https://www.ncbi.nlm.nih.gov/pubmed/28756775?dopt=Abstract %R 10.1186/s12915-017-0399-x %0 Journal Article %J PLoS Biol %D 2014 %T The first myriapod genome sequence reveals conservative arthropod gene content and genome organisation in the centipede Strigamia maritima. %A Chipman, Ariel D %A Ferrier, David E K %A Brena, Carlo %A Qu, Jiaxin %A Hughes, Daniel S T %A Schröder, Reinhard %A Torres-Oliva, Montserrat %A Znassi, Nadia %A Jiang, Huaiyang %A Almeida, Francisca C %A Alonso, Claudio R %A Apostolou, Zivkos %A Aqrawi, Peshtewani %A Arthur, Wallace %A Barna, Jennifer C J %A Blankenburg, Kerstin P %A Brites, Daniela %A Capella-Gutiérrez, Salvador %A Coyle, Marcus %A Dearden, Peter K %A Du Pasquier, Louis %A Duncan, Elizabeth J %A Ebert, Dieter %A Eibner, Cornelius %A Erikson, Galina %A Evans, Peter D %A Extavour, Cassandra G %A Francisco, Liezl %A Gabaldón, Toni %A Gillis, William J %A Goodwin-Horn, Elizabeth A %A Green, Jack E %A Griffiths-Jones, Sam %A Grimmelikhuijzen, Cornelis J P %A Gubbala, Sai %A Guigó, Roderic %A Yi Han %A Hauser, Frank %A Havlak, Paul %A Hayden, Luke %A Helbing, Sophie %A Holder, Michael %A Hui, Jerome H L %A Hunn, Julia P %A Hunnekuhl, Vera S %A Jackson, Laronda %A Javaid, Mehwish %A Jhangiani, Shalini N %A Jiggins, Francis M %A Jones, Tamsin E %A Kaiser, Tobias S %A Kalra, Divya %A Kenny, Nathan J %A Korchina, Viktoriya %A Kovar, Christie L %A Kraus, F Bernhard %A Lapraz, François %A Lee, Sandra L %A Lv, Jie %A Mandapat, Christigale %A Manning, Gerard %A Mariotti, Marco %A Mata, Robert %A Mathew, Tittu %A Neumann, Tobias %A Newsham, Irene %A Ngo, Dinh N %A Ninova, Maria %A Okwuonu, Geoffrey %A Ongeri, Fiona %A Palmer, William J %A Patil, Shobha %A Patraquim, Pedro %A Pham, Christopher %A Pu, Ling-Ling %A Putman, Nicholas H %A Rabouille, Catherine %A Ramos, Olivia Mendivil %A Rhodes, Adelaide C %A Robertson, Helen E %A Robertson, Hugh M %A Ronshaugen, Matthew %A Rozas, Julio %A Saada, Nehad %A Sánchez-Gracia, Alejandro %A Steven E Scherer %A Schurko, Andrew M %A Siggens, Kenneth W %A Simmons, DeNard %A Stief, Anna %A Stolle, Eckart %A Telford, Maximilian J %A Tessmar-Raible, Kristin %A Thornton, Rebecca %A Van der Zee, Maurijn %A von Haeseler, Arndt %A Williams, James M %A Willis, Judith H %A Wu, Yuanqing %A Zou, Xiaoyan %A Lawson, Daniel %A Donna M Muzny %A Worley, Kim C %A Richard A Gibbs %A Akam, Michael %A Richards, Stephen %K Animals %K Arthropods %K Circadian Rhythm Signaling Peptides and Proteins %K DNA Methylation %K Evolution, Molecular %K Female %K Genome %K Genome, Mitochondrial %K Hormones %K Male %K Multigene Family %K Phylogeny %K Polymorphism, Genetic %K Protein Kinases %K Receptors, Odorant %K RNA, Untranslated %K Selenoproteins %K Sex Chromosomes %K Synteny %K Transcription Factors %X

Myriapods (e.g., centipedes and millipedes) display a simple homonomous body plan relative to other arthropods. All members of the class are terrestrial, but they attained terrestriality independently of insects. Myriapoda is the only arthropod class not represented by a sequenced genome. We present an analysis of the genome of the centipede Strigamia maritima. It retains a compact genome that has undergone less gene loss and shuffling than previously sequenced arthropods, and many orthologues of genes conserved from the bilaterian ancestor that have been lost in insects. Our analysis locates many genes in conserved macro-synteny contexts, and many small-scale examples of gene clustering. We describe several examples where S. maritima shows different solutions from insects to similar problems. The insect olfactory receptor gene family is absent from S. maritima, and olfaction in air is likely effected by expansion of other receptor gene families. For some genes S. maritima has evolved paralogues to generate coding sequence diversity, where insects use alternate splicing. This is most striking for the Dscam gene, which in Drosophila generates more than 100,000 alternate splice forms, but in S. maritima is encoded by over 100 paralogues. We see an intriguing linkage between the absence of any known photosensory proteins in a blind organism and the additional absence of canonical circadian clock genes. The phylogenetic position of myriapods allows us to identify where in arthropod phylogeny several particular molecular mechanisms and traits emerged. For example, we conclude that juvenile hormone signalling evolved with the emergence of the exoskeleton in the arthropods and that RR-1 containing cuticle proteins evolved in the lineage leading to Mandibulata. We also identify when various gene expansions and losses occurred. The genome of S. maritima offers us a unique glimpse into the ancestral arthropod genome, while also displaying many adaptations to its specific life history.

%B PLoS Biol %V 12 %P e1002005 %8 2014 Nov %G eng %N 11 %1 https://www.ncbi.nlm.nih.gov/pubmed/25423365?dopt=Abstract %R 10.1371/journal.pbio.1002005