Chromosomal Rearrangement Inferred From Comparisons of 12 Drosophila Genomes
TLDR
The results provide estimated chromosomal evolution rates across this set of species on the basis of whole-genome synteny analysis, which are found to be higher than those previously reported.Abstract:
The availability of 12 complete genomes of various species of genus Drosophila provides a unique opportunity to analyze genome-scale chromosomal rearrangements among a group of closely related species. This article reports on the comparison of gene order between these 12 species and on the fixed rearrangement events that disrupt gene order. Three major themes are addressed: the conservation of syntenic blocks across species, the disruption of syntenic blocks (via chromosomal inversion events) and its relationship to the phylogenetic distribution of these species, and the rate of rearrangement events over evolutionary time. Comparison of syntenic blocks across this large genomic data set confirms that genetic elements are largely (95%) localized to the same Muller element across genus Drosophila species and paracentric inversions serve as the dominant mechanism for shuffling the order of genes along a chromosome. Gene-order scrambling between species is in accordance with the estimated evolutionary distances between them and we find it to approximate a linear process over time (linear to exponential with alternate divergence time estimates). We find the distribution of synteny segment sizes to be biased by a large number of small segments with comparatively fewer large segments. Our results provide estimated chromosomal evolution rates across this set of species on the basis of whole-genome synteny analysis, which are found to be higher than those previously reported. Identification of conserved syntenic blocks across these genomes suggests a large number of conserved blocks with varying levels of embryonic expression correlation in Drosophila melanogaster. On the other hand, an analysis of the disruption of syntenic blocks between species allowed the identification of fixed inversion breakpoints and estimates of breakpoint reuse and lineage-specific breakpoint event segregation.read more
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Highly evolvable malaria vectors: The genomes of 16 Anopheles mosquitoes
Daniel E. Neafsey,Robert M. Waterhouse,Mohammad Reza Abai,Sergey Aganezov,Max A. Alekseyev,James E. Allen,James Amon,Bruno Arcà,Peter Arensburger,Gleb N. Artemov,Lauren A. Assour,Hamidreza Basseri,Aaron M. Berlin,Bruce W. Birren,Stéphanie Blandin,Stéphanie Blandin,Andrew I. Brockman,Thomas R. Burkot,Austin Burt,Clara S. Chan,Cedric Chauve,Joanna C. Chiu,Mikkel B. Christensen,Carlo Costantini,Victoria L.M. Davidson,Elena Deligianni,Tania Dottorini,Vicky Dritsou,Stacey Gabriel,Wamdaogo M. Guelbeogo,Andrew Brantley Hall,Mira V. Han,Thaung Hlaing,Daniel S.T. Hughes,Daniel S.T. Hughes,Adam M. Jenkins,Xiaofang Jiang,Irwin Jungreis,Evdoxia G. Kakani,Evdoxia G. Kakani,Maryam Kamali,Petri Kemppainen,Ryan C. Kennedy,Ioannis K. Kirmitzoglou,Ioannis K. Kirmitzoglou,Lizette L. Koekemoer,Njoroge Laban,Nicholas Langridge,Mara K. N. Lawniczak,Manolis Lirakis,Neil F. Lobo,Ernesto Lowy,Robert M. MacCallum,Chunhong Mao,Gareth Maslen,Charles Mbogo,Jenny McCarthy,Kristin Michel,Sara N. Mitchell,Wendy Moore,Katherine A. Murphy,Anastasia N. Naumenko,Tony Nolan,Eva Maria Novoa,Samantha M. O’Loughlin,Chioma Oringanje,Mohammad Ali Oshaghi,Nazzy Pakpour,Philippos Aris Papathanos,Philippos Aris Papathanos,Ashley Peery,Michael Povelones,Anil Prakash,David P. Price,Ashok Rajaraman,Lisa J. Reimer,David C. Rinker,Antonis Rokas,Tanya L. Russell,N’Fale Sagnon,Maria V. Sharakhova,Terrance Shea,Felipe A. Simão,Felipe A. Simão,Frédéric Simard,Michel A. Slotman,Pradya Somboon,V. N. Stegniy,Claudio J. Struchiner,Claudio J. Struchiner,Gregg W.C. Thomas,Marta Tojo,Pantelis Topalis,Jose M. C. Tubio,Maria F. Unger,John Vontas,Catherine Walton,Craig S. Wilding,Judith H. Willis,Yi-Chieh Wu,Yi-Chieh Wu,Guiyun Yan,Evgeny M. Zdobnov,Evgeny M. Zdobnov,Xiaofan Zhou,Flaminia Catteruccia,Flaminia Catteruccia,George K. Christophides,Frank H. Collins,Robert S. Cornman,Andrea Crisanti,Andrea Crisanti,Martin J. Donnelly,Martin J. Donnelly,Scott J. Emrich,Michael C. Fontaine,Michael C. Fontaine,William M. Gelbart,Matthew W. Hahn,Immo A. Hansen,Paul I. Howell,Fotis C. Kafatos,Manolis Kellis,Daniel Lawson,Christos Louis,Shirley Luckhart,Marc A. T. Muskavitch,Marc A. T. Muskavitch,José M. C. Ribeiro,Michael A. Riehle,Igor V. Sharakhov,Zhijian Tu,Laurence J. Zwiebel,Nora J. Besansky +133 more
TL;DR: The authors investigated the genomic basis of vectorial capacity and explore new avenues for vector control, sequenced the genomes of 16 anopheline mosquito species from diverse locations spanning ~100 million years of evolution Comparative analyses show faster rates of gene gain and loss, elevated gene shuffling on the X chromosome, and more intron losses, relative to Drosophila.
Highly evolvable malaria vectors: The genomes of 16 Anopheles mosquitoes
Robert M. Waterhouse,Clara S. Chan,Irwin Jungreis,Eva Maria Novoa Pardo,Yi-Chieh Wu,Manolis Kellis +5 more
Journal ArticleDOI
Molecular traces of alternative social organization in a termite genome
Nicolas Terrapon,Nicolas Terrapon,Cai Li,Hugh M. Robertson,Lu Ji,Xuehong Meng,Warren Booth,Warren Booth,Zhensheng Chen,Christopher P. Childers,Karl M. Glastad,Kaustubh Gokhale,Johannes Gowin,Johannes Gowin,Wulfila Gronenberg,Russell A. Hermansen,Haofu Hu,Brendan G. Hunt,Ann Kathrin Huylmans,Ann Kathrin Huylmans,Sayed M.S. Khalil,Robert D. Mitchell,Monica Munoz-Torres,Julie A. Mustard,Hailin Pan,Justin T. Reese,Michael E. Scharf,Fengming Sun,Heiko Vogel,Jin Xiao,Wei Yang,Zhikai Yang,Zuoquan Yang,Jiajian Zhou,Jiwei Zhu,Colin S. Brent,Christine G. Elsik,Michael A. D. Goodisman,David A. Liberles,R. Michael Roe,Edward L. Vargo,Andreas Vilcinskas,Jun Wang,Erich Bornberg-Bauer,Judith Korb,Guojie Zhang,Juergen Liebig +46 more
TL;DR: The genome and stage-specific transcriptomes of the dampwood termite Zootermopsis nevadensis (Blattodea) are sequence and similarities in the number and expression of genes related to caste determination mechanisms support a hypothesized epigenetic regulation of caste differentiation.
A Comprehensive Map of Insulator Elements for the Drosophila Genome
Kevin P. White,Steven Henikoff,Lincoln Stein,Robert A. H. White,Steven Russell,Kami Ahmad,X. Feng,Jorja G. Henikoff,Carolyn A. Morrison,Parantu K. Shah,Christopher D. Brown,Nicolas Nègre,Pouya Kheradpour,Manolis Kellis +13 more
TL;DR: A map demarcating the boundaries of gene regulatory units and a framework for understanding insulator function during the development and evolution of Drosophila are provided.
Journal ArticleDOI
A Comprehensive Map of Insulator Elements for the Drosophila Genome
Nicolas Nègre,Christopher D. Brown,Parantu K. Shah,Pouya Kheradpour,Carolyn A. Morrison,Jorja G. Henikoff,X. Feng,Kami Ahmad,Steven Russell,Robert A. H. White,Lincoln Stein,Steven Henikoff,Manolis Kellis,Kevin P. White +13 more
TL;DR: In this paper, the genome-wide binding sites of 6 insulator-associated proteins (dCTCF, CP190, BEAF-32, Su(Hw), Mod(mdg4), and GAF) were studied to obtain the first comprehensive map of insulator elements in Drosophila embryos.
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