Hudson ME

References (3)

Title : The genomes of two key bumblebee species with primitive eusocial organization - Sadd_2015_Genome.Biol_16_76
Author(s) : Sadd BM , Barribeau SM , Bloch G , de Graaf DC , Dearden P , Elsik CG , Gadau J , Grimmelikhuijzen CJ , Hasselmann M , Lozier JD , Robertson HM , Smagghe G , Stolle E , Van Vaerenbergh M , Waterhouse RM , Bornberg-Bauer E , Klasberg S , Bennett AK , Camara F , Guigo R , Hoff K , Mariotti M , Munoz-Torres M , Murphy T , Santesmasses D , Amdam GV , Beckers M , Beye M , Biewer M , Bitondi MM , Blaxter ML , Bourke AF , Brown MJ , Buechel SD , Cameron R , Cappelle K , Carolan JC , Christiaens O , Ciborowski KL , Clarke DF , Colgan TJ , Collins DH , Cridge AG , Dalmay T , Dreier S , du Plessis L , Duncan E , Erler S , Evans J , Falcon T , Flores K , Freitas FC , Fuchikawa T , Gempe T , Hartfelder K , Hauser F , Helbing S , Humann FC , Irvine F , Jermiin LS , Johnson CE , Johnson RM , Jones AK , Kadowaki T , Kidner JH , Koch V , Kohler A , Kraus FB , Lattorff HM , Leask M , Lockett GA , Mallon EB , Antonio DS , Marxer M , Meeus I , Moritz RF , Nair A , Napflin K , Nissen I , Niu J , Nunes FM , Oakeshott JG , Osborne A , Otte M , Pinheiro DG , Rossie N , Rueppell O , Santos CG , Schmid-Hempel R , Schmitt BD , Schulte C , Simoes ZL , Soares MP , Swevers L , Winnebeck EC , Wolschin F , Yu N , Zdobnov EM , Aqrawi PK , Blankenburg KP , Coyle M , Francisco L , Hernandez AG , Holder M , Hudson ME , Jackson L , Jayaseelan J , Joshi V , Kovar C , Lee SL , Mata R , Mathew T , Newsham IF , Ngo R , Okwuonu G , Pham C , Pu LL , Saada N , Santibanez J , Simmons D , Thornton R , Venkat A , Walden KK , Wu YQ , Debyser G , Devreese B , Asher C , Blommaert J , Chipman AD , Chittka L , Fouks B , Liu J , O'Neill MP , Sumner S , Puiu D , Qu J , Salzberg SL , Scherer SE , Muzny DM , Richards S , Robinson GE , Gibbs RA , Schmid-Hempel P , Worley KC
Ref : Genome Biol , 16 :76 , 2015
Abstract : BACKGROUND: The shift from solitary to social behavior is one of the major evolutionary transitions. Primitively eusocial bumblebees are uniquely placed to illuminate the evolution of highly eusocial insect societies. Bumblebees are also invaluable natural and agricultural pollinators, and there is widespread concern over recent population declines in some species. High-quality genomic data will inform key aspects of bumblebee biology, including susceptibility to implicated population viability threats.
RESULTS: We report the high quality draft genome sequences of Bombus terrestris and Bombus impatiens, two ecologically dominant bumblebees and widely utilized study species. Comparing these new genomes to those of the highly eusocial honeybee Apis mellifera and other Hymenoptera, we identify deeply conserved similarities, as well as novelties key to the biology of these organisms. Some honeybee genome features thought to underpin advanced eusociality are also present in bumblebees, indicating an earlier evolution in the bee lineage. Xenobiotic detoxification and immune genes are similarly depauperate in bumblebees and honeybees, and multiple categories of genes linked to social organization, including development and behavior, show high conservation. Key differences identified include a bias in bumblebee chemoreception towards gustation from olfaction, and striking differences in microRNAs, potentially responsible for gene regulation underlying social and other traits.
CONCLUSIONS: These two bumblebee genomes provide a foundation for post-genomic research on these key pollinators and insect societies. Overall, gene repertoires suggest that the route to advanced eusociality in bees was mediated by many small changes in many genes and processes, and not by notable expansion or depauperation.
ESTHER : Sadd_2015_Genome.Biol_16_76
PubMedSearch : Sadd_2015_Genome.Biol_16_76
PubMedID: 25908251

Title : Finding the missing honey bee genes: lessons learned from a genome upgrade - Elsik_2014_BMC.Genomics_15_86
Author(s) : Elsik CG , Worley KC , Bennett AK , Beye M , Camara F , Childers CP , de Graaf DC , Debyser G , Deng J , Devreese B , Elhaik E , Evans JD , Foster LJ , Graur D , Guigo R , Hoff KJ , Holder ME , Hudson ME , Hunt GJ , Jiang H , Joshi V , Khetani RS , Kosarev P , Kovar CL , Ma J , Maleszka R , Moritz RF , Munoz-Torres MC , Murphy TD , Muzny DM , Newsham IF , Reese JT , Robertson HM , Robinson GE , Rueppell O , Solovyev V , Stanke M , Stolle E , Tsuruda JM , Vaerenbergh MV , Waterhouse RM , Weaver DB , Whitfield CW , Wu Y , Zdobnov EM , Zhang L , Zhu D , Gibbs RA
Ref : BMC Genomics , 15 :86 , 2014
Abstract : BACKGROUND: The first generation of genome sequence assemblies and annotations have had a significant impact upon our understanding of the biology of the sequenced species, the phylogenetic relationships among species, the study of populations within and across species, and have informed the biology of humans. As only a few Metazoan genomes are approaching finished quality (human, mouse, fly and worm), there is room for improvement of most genome assemblies. The honey bee (Apis mellifera) genome, published in 2006, was noted for its bimodal GC content distribution that affected the quality of the assembly in some regions and for fewer genes in the initial gene set (OGSv1.0) compared to what would be expected based on other sequenced insect genomes.
RESULTS: Here, we report an improved honey bee genome assembly (Amel_4.5) with a new gene annotation set (OGSv3.2), and show that the honey bee genome contains a number of genes similar to that of other insect genomes, contrary to what was suggested in OGSv1.0. The new genome assembly is more contiguous and complete and the new gene set includes ~5000 more protein-coding genes, 50% more than previously reported. About 1/6 of the additional genes were due to improvements to the assembly, and the remaining were inferred based on new RNAseq and protein data.
CONCLUSIONS: Lessons learned from this genome upgrade have important implications for future genome sequencing projects. Furthermore, the improvements significantly enhance genomic resources for the honey bee, a key model for social behavior and essential to global ecology through pollination.
ESTHER : Elsik_2014_BMC.Genomics_15_86
PubMedSearch : Elsik_2014_BMC.Genomics_15_86
PubMedID: 24479613

Title : Genome of the long-living sacred lotus (Nelumbo nucifera Gaertn.) - Ming_2013_Genome.Biol_14_R41
Author(s) : Ming R , VanBuren R , Liu Y , Yang M , Han Y , Li LT , Zhang Q , Kim MJ , Schatz MC , Campbell M , Li J , Bowers JE , Tang H , Lyons E , Ferguson AA , Narzisi G , Nelson DR , Blaby-Haas CE , Gschwend AR , Jiao Y , Der JP , Zeng F , Han J , Min XJ , Hudson KA , Singh R , Grennan AK , Karpowicz SJ , Watling JR , Ito K , Robinson SA , Hudson ME , Yu Q , Mockler TC , Carroll A , Zheng Y , Sunkar R , Jia R , Chen N , Arro J , Wai CM , Wafula E , Spence A , Xu L , Zhang J , Peery R , Haus MJ , Xiong W , Walsh JA , Wu J , Wang ML , Zhu YJ , Paull RE , Britt AB , Du C , Downie SR , Schuler MA , Michael TP , Long SP , Ort DR , Schopf JW , Gang DR , Jiang N , Yandell M , dePamphilis CW , Merchant SS , Paterson AH , Buchanan BB , Li S , Shen-Miller J
Ref : Genome Biol , 14 :R41 , 2013
Abstract : BACKGROUND: Sacred lotus is a basal eudicot with agricultural, medicinal, cultural and religious importance. It was domesticated in Asia about 7,000 years ago, and cultivated for its rhizomes and seeds as a food crop. It is particularly noted for its 1,300-year seed longevity and exceptional water repellency, known as the lotus effect. The latter property is due to the nanoscopic closely packed protuberances of its self-cleaning leaf surface, which have been adapted for the manufacture of a self-cleaning industrial paint, Lotusan. RESULTS: The genome of the China Antique variety of the sacred lotus was sequenced with Illumina and 454 technologies, at respective depths of 101x and 5.2x. The final assembly has a contig N50 of 38.8 kbp and a scaffold N50 of 3.4 Mbp, and covers 86.5% of the estimated 929 Mbp total genome size. The genome notably lacks the paleo-triplication observed in other eudicots, but reveals a lineage-specific duplication. The genome has evidence of slow evolution, with a 30% slower nucleotide mutation rate than observed in grape. Comparisons of the available sequenced genomes suggest a minimum gene set for vascular plants of 4,223 genes. Strikingly, the sacred lotus has 16 COG2132 multi-copper oxidase family proteins with root-specific expression; these are involved in root meristem phosphate starvation, reflecting adaptation to limited nutrient availability in an aquatic environment. CONCLUSIONS: The slow nucleotide substitution rate makes the sacred lotus a better resource than the current standard, grape, for reconstructing the pan-eudicot genome, and should therefore accelerate comparative analysis between eudicots and monocots.
ESTHER : Ming_2013_Genome.Biol_14_R41
PubMedSearch : Ming_2013_Genome.Biol_14_R41
PubMedID: 23663246
Gene_locus related to this paper: nelnu-a0a1u8aj84 , nelnu-a0a1u8bpe4 , nelnu-a0a1u7z9m9 , nelnu-a0a1u7ywy5 , nelnu-a0a1u8aik2 , nelnu-a0a1u7zmb5 , nelnu-a0a1u8a7m7 , nelnu-a0a1u8b0n9 , nelnu-a0a1u8b461 , nelnu-a0a1u7zzj3 , nelnu-a0a1u8ave7 , nelnu-a0a1u7yn26