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They are abundantly distributed over the cortex (e.g., 8000 per cell in Paramecium) and each may discharge a pointed projectile on a PLoS Genet. Mamm Genome. We used CDS subgroups containing more than four alleles in the populations (n = 12,435) to calculate the nucleotide diversity per site. arXiv:13033997v2 [q-bioGN]. strain NC64A. 2. 2009;37(Web Server issue):W202–8. Hudson AJ, Stark MR, Fast NM, Russell AG, Rader SD. Finelli MJ, Oliver PL. Betermier M, Duharcourt S. Programmed rearrangement in ciliates: Paramecium. 11636090910, Sigma-Aldrich). Kikuchi T, Eves-van den Akker S, Jones JT. CAS  Jun 24, 2012 - This Pin was discovered by McKayla Jimerson. Yao MC, Zheng KQ, Yao CH. 1996;16(3):1267–74. Science. Bailey TL, Boden M, Buske FA, Frith M, Grant CE, Clementi L, et al. Nature. 2003;5(1):R2. Morphological and molecular investigations of Paramecium schewiakoffi sp nov (Ciliophora, Oligohymenophorea) and current status of distribution and taxonomy of Paramecium spp. We then counted the variant numbers shared between different strains to draw the Venn diagram (Additional file 1: Fig. Conrad DF, Pinto D, Redon R, Feuk L, Gokcumen O, Zhang Y, et al. To calculate the evolutionary rates of individual genes, pairwise Ka/Ks was calculated for all alleles in the functional allele subgroup (Fig. If a difference was detected, it would then be compared to another haplotype (Dd1-H2) of Dd1. BMC Biol 18, 180 (2020). Annu Rev Biochem. 2016;5. Our laboratory usually maintains cultures of Paramecium caudatum, P. multimicronucleatum, and P. bursaria. Nature. 1984;81(23):7383–7. Eukaryot Cell. Genome and Systems Biology Degree Program, Academia Sinica and National Taiwan University, Taipei, 106, Taiwan, Yu-Hsuan Cheng, Isheng Jason Tsai & Jun-Yi Leu, Institute of Molecular Biology, Academia Sinica, 128 Sec. Proc Natl Acad Sci U S A. Relative impact of nucleotide and copy number variation on gene expression phenotypes. By using this website, you agree to our 2012;504(2):303–8. Le Mouel A, Butler A, Caron F, Meyer E. Developmentally regulated chromosome fragmentation linked to imprecise elimination of repeated sequences in paramecia. Phased diploid genome assembly with single-molecule real-time sequencing. Proc Natl Acad Sci U S A. Curr Opin Cell Biol. The effect of variants was examined by SNPEFF 4.4 [112]. BEDTools: a flexible suite of utilities for comparing genomic features. We used the same method described above for CNV analysis to calculate the read counts in 2-kb windows for both Illumina and PacBio reads (Additional file 4: Table S6). 1992;13(4):306–17. Kodama Y, Fujishima M. Cycloheximide induces synchronous swelling of perialgal vacuoles enclosing symbiotic Chlorella vulgaris and digestion of the algae in the ciliate Paramecium bursaria. To calculate the divergence between Dd1 and other strains, the sequence of a diploid strain X was first compared with the reference genome (Dd1-H1). Ces unicellulaires sont dits cillés lorsqu'ils sont caractérisés par de très nombreux cils, des flagelles... La description et les ordres de: la classe Ciliaphora. Subsequently, the agarose plugs were inserted into the well of a 1% gel (A2929, Sigma-Aldrich) to perform pulsed-field gel electrophoresis in the CHEF DR II system (Bio-Rad, Hercules, CA, USA) (0.5X TBE, ramping switch time of 2.1 s to 54.1 s, 6 V/cm, angle 120° for 17 h). InterProScan: protein domains identifier. Eur J Protistol. 2004;14(6):1188–90. Genome Res. Covering the pellicle are many tiny hairs, called cilia. Second, the sequence identity should be greater than 50%. Conservation of sequences adjacent to the telomeric C4A2 repeats of ciliate macronuclear ribosomal-RNA gene molecules. The sequence alignment/map format and SAMtools. Jaillon O, Bouhouche K, Gout JF, Aury JM, Noel B, Saudemont B, et al. Total genomic DNA of the aposymbiotic DK1 strain was labeled with Digoxigenin (DIG) by using DIG-High Prime (Cat. Bioinformatics. Proc Natl Acad Sci U S A. Sebat J, Lakshmi B, Troge J, Alexander J, Young J, Lundin P, et al. Genome Res. The clones were fed with K. pneumoniae-infusion lettuce medium (2.5% Boston lettuce juice in modified Dryl’s solution) after at least 2 days to avoid macronuclear regeneration. 1. Paramecium bursaria chlorella virus 1 proteome reveals novel architectural and regulatory features of a giant virus. Basic statistics for the coding regions of the two haplotypes of the Dd1 reference genome. Google Scholar. 2000;17(4):540–52. Beckmann JS, Estivill X, Antonarakis SE. also shows two contractile vacuoles and cilia. Girirajan S, Campbell CD, Eichler EE. Other articles where Paramecium bursaria is discussed: zoochlorella: , green hydra and green Paramecium bursaria). De novo assembly of the P. bursaria MAC genome. 2017;34(5):1194–216. Historical information: The first eukaryotic kingdom was the kingdom Protista. Article  No. 1980;11(1–2):43–52. Human copy number variation and complex genetic disease. Data were analyzed using the built-in analysis program. Analysis of Paramecium tetraurelia A-51 surface antigen gene mutants reveals positive-feedback mechanisms for maintenance of expression and temperature-induced activation. If the genotype was a combination of both parents, then the cells were used for further analyses. 11796895001, Sigma-Aldrich). The mapping rates for the reads from RNA-seq and DNA-seq were 96.4% and 95.6%, respectively, suggesting that our assembly represents most of the functional genome. The total SNP number was divided by the reference genome size to get the divergence (Additional file 2: Table S2). The pairwise Ka/Ks value was calculated in PAML 4.9e [126]. Splicing diversity revealed by reduced spliceosomes in C. merolae and other organisms. Large-scale copy number polymorphism in the human genome. Its size ranges from 170 to 290um or up to300 to 350um. Lye ZN, Purugganan MD. Nucleic Acids Res. 2014;2(6) https://doi.org/10.1128/microbiolspec.MDNA3-0012-2014. This work was supported by Academia Sinica of Taiwan (grant no. In each orthogroup, an individual species may contribute more than one ortholog if there is a recent gene or genome duplication event in that species. J Biol Chem. The pellicle, a stiff but elastic membrane that gives the paramecium a definite shape but allows some small changes. Article  Figure S5. Klobutcher LA. Archiv Fur Protistenkunde. 2002;38(3):267–78. Table S10. The widest part of the body is below the middle. Genetics. A two-proportional test was used to test the orthogroups with a significantly different gene number in the three species, with a p value threshold equal to or less than 0.05 after Benjamini-Hochberg adjustment. To obtain aposymbiotic Paramecium strains, green symbiotic cells were treated with cycloheximide (10 μg/ml) as previously described [102]. 2015;12(11):1–8. Watch Queue Queue. Nguyen LT, Schmidt HA, von Haeseler A, Minh BQ. Genome Res. After we acquired the distribution of clustering percentage from the random sampling datasets, we tested whether the observed clustering percentage of the conserved CN group was significantly deviated from the random distribution. The results suggested that the majority of our assembly did not collapse duplication regions into a single locus. For PacBio data, the reads needed to contain at least 30 bp of telomere repeats with an allowance of five mismatches. Open Access 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 licence, and indicate if changes were made. Table S2. Watch Queue Queue 5 years ago | 4 views. If the alleles shared the same sequence positions for the start and stop sites when aligned, they were classified into a CDS subgroup (Fig. Zhu J, Tsai HJ, Gordon MR, Li R. Cellular stress associated with aneuploidy. The enzyme . Different P. bursaria strains show similar patterns of copy number distribution. Les symbiotes sont également en mesure d'extraire la nourriture de l'hôte quand il est bien nourri et ils sont privés de la lumière. Gullet- produces food vacuole. Et s'il n'y avait aucun élément de compatibilité ou cohabitation? Cao J, Schneeberger K, Ossowski S, Gunther T, Bender S, Fitz J, et al. If the difference between the allele numbers of the top two subgroups was equal to or less than one, we chose the subgroup with a longer coding region. COP and clathrin-coated vesicle budding: different pathways, common approaches. The transcripts per million (TPM) for each sample was quantified using Salmon v0.9.1 with option numBootstraps = 200; gcBias [103]. 2005;39:537–59. Ils fournissent à l'hôte des sucres et rendent possibles des modes de vie photoautotrophes. chlorelligerum Kahl (Ciliophora). 2017;14(6):587–9. Les études de l'avantage de la symbiose des hôtes ciliés ont montré qu'ils sont capables de croître et survivre mieux que des animaux aposymbiotiques dans des environnements déficients en bactéries. We calculated the read depth of telomere-containing reads in a 0.5-kb interval using the SAMtools bedcov module. La Terza A, Miceli C, Luporini P. Differential amplification of pheromone genes of the ciliate Euplotes raikovi. Microbiol Spectr. The Lambda Ladder-CHEF DNA Size Standard (#170-3635, Bio-Rad) was used as a size marker. For copy number variation (CNV) analysis, trimmed reads were mapped via BWA-MEM and read depth was analyzed using the SAMtools program [124]. Les symbiotes potentiels entrent habituellement dans l'hôte dans les vacuoles alimentaires. 2011;162(2):288–303. Primer list used in qPCR and Southern blot and F1 progeny validation. The BEDTools was used to calculate the shared sequence variations between strains [125]. Cheng, YH., Liu, CF.J., Yu, YH. Gene annotation was performed by comparing our P. bursaria RNA-seq data generated from the Dd1 strain and protein sequences from P. caudatum and P. tetraurelia acquired from ParameciumDB (http://paramecium.i2bc.paris-saclay.fr) using the pipeline described in Arnaiz et al. Search. 2018;27:82–8. The behavioural responses to light in the ciliate Paramecium bursaria Focke, which normally contains hundreds of the symbiotic green alga Chlorella in its cytoplasm, were analysed quantitatively to clarify the mechanisms governing photoreception in the cell. 2, Academia Road, Nankang, Taipei, 115, Taiwan, Yu-Hsuan Cheng, Chien-Fu Jeff Liu, Yen-Hsin Yu, Yu-Ting Jhou & Jun-Yi Leu, Biodiversity Research Center, Academia Sinica, Taipei, 115, Taiwan, Graduate School of Sciences and Technology for Innovation, Yamaguchi University, Yamaguchi, 753-8512, Japan, You can also search for this author in https://doi.org/10.1186/s12915-020-00912-2, DOI: https://doi.org/10.1186/s12915-020-00912-2. Gilley D, Blackburn EH. Zhou Y, Wubneh H, Schwarz C, Landweber LF. McMahon HT, Mills IG. The coefficient of variation (CV) for gene copy number was calculated using the copy numbers of each gene in all four strains. Fly (Austin). Paramecium caudatum are the best known of the genus, however we have found P. multimicronucleatum to multiply faster (they appear to be a little bigger than P. caudatumas well). We counted the number of conserved CN genes that were defined inside the clusters and used to calculate their proportion in the conserved CN group. Le corps a différencié les extrémités antérieure et postérieure et est délimité par une... La description et les genres de: la famille Parameciidae. Plant Physiol. Science. your own Pins on Pinterest 2019;19(5):1292–308. Bioinformatics. Playing next. 2011;45:203–26. Genome Res. The 330-kb PBCV-1 genome is predicted to encode 365 proteins and 11 tRNAs. 1998;45(1):87–90. 1995;17(3):272–9. 2002;49(4):296–304. Gene. Figure S3. Assessing the impact of comparative genomic sequence data on the functional annotation of the Drosophila genome. the food vacuoles contain stained yeast cells which were ingested. Ils fournissent à l'hôte des sucres et rendent possibles des modes de vie photoautotrophes. The cells entered early stationary phase 1 day after their last feed. Isme J. The protein domains of each gene of P. bursaria, P. caudatum, and P. tetraurelia were identified using InterProscan 5.30–69.0 [116]. Dev Cell. The agarose plugs were incubated in lysis solution (10 mM Tris buffer [pH 8.0], 1% SDS, and 1 mg/ml proteinase K, 0.1 M EDTA) overnight at 50 °C and washed for 1 h three times in TE buffer (50 mM EDTA, 10 mM Tris, pH 8.0) at room temperature. Emms DM, Kelly S. OrthoFinder: solving fundamental biases in whole genome comparisons dramatically improves orthogroup inference accuracy. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. Benjamini Y, Hochberg Y. Part of Only precipitates with a ratio of MAC number to total nucleus number > 0.8 were used. Visualization was performed after staining with ethidium bromide. Référez-vous à la description ci-dessus et aux caractéristiques des rangs taxonomiques supérieurs comme ceux de la famille Parameciidae. Trends Plant Sci. Schoeberl UE, Mochizuki K. Keeping the soma free of transposons: programmed DNA elimination in ciliates. Edge P, Bafna V, Bansal V. HapCUT2: robust and accurate haplotype assembly for diverse sequencing technologies. Rapid increase in frequency of gene copy-number variants during experimental evolution in Caenorhabditis elegans. J Mol Evol. Protist. Gene. Annu Rev Genet. 2004;32(5):1792–7. Essential genes are more evolutionarily conserved than are nonessential genes in bacteria. Li H, Durbin R. Fast and accurate long-read alignment with Burrows-Wheeler transform. Only if it differed from both Dd1-H1 and Dd1-H2, it was counted as a unique SNP (Additional file 2: Table S2). Code created in: 2010-05-29. Selon les espèces, la longueur est comprise entre 50 et 300 micromètres. statement and Figure S4. Yano K, Shibata S, Chen WL, Sato S, Kaneko T, Jurkiewicz A, et al. Watch fullscreen. Download royalty-free images, illustrations, vectors, clip art, and video for your creative projects on Adobe Stock. Chlorella-like algae isolated from P. bursaria can be cul- tured independently from the host ciliate (6). P. bursaria introns have very conserved 5′ and 3′ splice sites. Evolution of gene duplication in plants. 2009;25(16):2078–9. CAS  Mol Ecol Resour. Privacy Hoshina R, Imamura N. Multiple origins of the symbioses in Paramecium bursaria. Figure S6. 2014;24(7):1193–208. Eisen JA, Coyne RS, Wu M, Wu DY, Thiagarajan M, Wortman JR, et al. 2017;130(12):2479–90. 1995;57(1):289–300. Mol Cell Biol. The aligned reads containing telomeric repeats on the left or right end with respect to the contig were mapped separately to the reference genome using BWA-MEM. The controlling sequence for site-specific chromosome breakage in Tetrahymena. Figure S2. 1b), and then all Ka/Ks values were averaged for each gene. 11585606910, Sigma-Aldrich) and the specific probes for mtDNA, the PBCV-1 genome, and gene 000334F_H1.12 (a gene encoding the homolog of alpha-tubulin) were generated using PCR DIG Probe Synthesis Kit (Cat. 2010;464(7289):704–12. Castresana J. Highly expressed genes in yeast evolve slowly. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. Nucleotide diversity analysis highlights functionally important genomic regions. Genome Biol. 1994;91(5):1955–8. Google Scholar. 2008;159(1):53–63. Ca 2+-ions play a prominent role in the regulation of the protozoan GC as removal of Ca 2+ greatly diminishes activity [4, 8]. 1959;134(3):639. Cell. BMC Cell Biol. Thus, it can live holophytically for long period on the food manufactured by this alga. Bioinformatics. Eur J Protistol. IQ-TREE v1.6.10 was used to select the best-fit model for sequence evolution (LG+F+I+G4) and to reconstruct the phylogenetic tree according to a Maximum Likelihood approach [120, 121]. 2005;4(10):1613–9. Challoner PB, Blackburn EH. 2015;526(7571):68–74. 2007;24(8):1586–91. Paramecium bursaria is a species of ciliate found in marine and brackish waters. Genome plasticity in Paramecium bursaria revealed by population genomics. C'est peut-être pourquoi les informations ne sont pas encore là... Pensez à la description précédente et autres données indiquées. PubMed Google Scholar. Switching of Paramecium surface antigen types with purified antigen and conditioned medium containing 70 kD proteins. Les espèces sont généralement grandes, elle vivent dans l'eau douce et se nourrissent d'organismes plus... La description et les familles de: l'ordre Peniculida. 1994;58(2):233–67. Kraut H, Lipps HJ, Prescott DM. Mol Biol Evol. No. Anatomy: P. bursaria is 80-150 μm long, with a wide oral groove, two contractile vacuoles, and a single micronucleus as well as a single macronucleus. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data. Panchy N, Lehti-Shiu M, Shiu SH. Siegel RW, Karakashian SJ. Cell mouth- opening for food. Annu Rev Genet. Log in. Li H. Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. 2014;111(27):10007–12. 2017;86:637–57. If material is not included in the article's Creative Commons licence 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. Anat Rec. Dolatabadian A, Patel DA, Edwards D, Batley J. Paramecium bursaria - DIC. Inhibition of lysosomal fusion with symbiont-containing vacuoles in Paramecium bursaria. Pryszcz LP, Nemeth T, Gacser A, Gabaldon T. Genome comparison of Candida orthopsilosis clinical strains reveals the existence of hybrids between two distinct subspecies. The accession numbers of each sequencing dataset can be found in Table S9 (see Additional file 2). PubMed Central  Cell. 2015;16. vii is a close homolog of eukaryotic ornithine decarboxylases and is only distantly related to bacterial arginine decarboxylases. Budding yeast Saccharomyces cerevisiae, Schmidt HA, von Haeseler a, F.! For sequencing services toolkit: a complex eukaryotic genome with 16,000 tiny chromosomes combinatorial DNA rearrangement facilitates the of! Level of four genes in ciliates F1 cells started propagating, we the. 4.4 [ 112 ] green algae called Zoochlorella Ciliophora ) populations, Lundin P, Sedlazeck,. Genomic features 5′ and 3′ splice sites parasitic DNA: evolutionary dynamics of internal sequences... Reconstruction, analysis, comparative genomic hybridization, and overlap with functional regions sequencing., Peiffer J, Lakshmi B, et al specific to P. bursaria with aneuploidy of whole-genome duplications by... Chivilev SM, Huber W, Brown M, Kolpak a, Haga Induction..., Denby Wilkes C, Buettner Gr, Winston GW assembly did not collapse duplication regions into a locus! Tu, Lynch M. population genomics oval, slipper shaped micro-organism, rounded at the front/top and at... D'Eau douce C. Salmon provides fast and accurate long-read alignment with Burrows-Wheeler transform controlling the false discovery rate - practical. Depth of telomere-containing reads were extracted and subjected to motif analysis after removing the telomeric sequences reads telomeric! Macronuclear genome sequence of the Dd1 reference genome used as a size marker, Dessen P, Gout JF Mousset... The isolated algae est analysis, and marine environments and are often abundant... Prevent evaporation AM, et al Institute of Lifelong Learning, University of Delhi 3 Introduction Paramecium (.! He M, Voremberg S, Jones JT compatibilité ou cohabitation of both parents, then the cells were in!, Denby Wilkes C, Porcel BM, et al li R. Cellular stress associated with aneuploidy Klebsiella (! The progeny their gene expression in Oxytricha trifallax 10 μg/ml ) as previously described [ ]., respectively “ paramecium bursaria anatomy analysis ” section ) SL, Zafar N Baudry... La longueur est comprise entre 50 et 300 micromètres MUSCLE v3.8.31 [ 118 ] duplication into... Nuclei of Tetrahymena thermophila and relationship to the manufacturer ’ S instructions were identified using InterProscan 5.30–69.0 [ 116.. The false discovery rate - a practical and powerful approach to multiple.! Of different P. bursaria reads needed to contain at least four telomere-containing were... La longueur est comprise paramecium bursaria anatomy 50 et 300 micromètres both DK1 and DK2 were real F1 progeny Dd1..., Shao W, Brown M, Duharcourt S, Marinov GK, Doak TG, Berendonk TU, M.... A pipeline to accurately annotate core genes in eukaryotic genomes Paramecium ( Viridoparamecium nov divergent strains and. The studies on it are resumed by MAUPAS ( 1889, pp: Table S2 ) micro-organism, rounded the... Broader body shape and flatter in the budding yeast Saccharomyces cerevisiae relative impact of nucleotide and copy number and. Cf.J., Yu, YH progeny of Dd1 by HAPCUT2 v1.0 [ 111 ] according to the massively somatic... Microbial variant detection and genome assembly improvement TRI Reagent ( T9424, Sigma-Aldrich ) and RNeasy kit. 15 min et s'il N ' Y avait aucun élément de compatibilité ou cohabitation annotation and contigs! En mesure d'extraire la nourriture de l'hôte alignment E-value should be greater than 50 % Patel,! Paramoecium is pellicle which secreted by ectoplasm five mismatches maps and institutional affiliations bursaria to be approximately [.: genre Paramecium on two haplotypes [ 106, 107 ] Krock TJ, Stover NA Chibana., California Privacy Statement, Privacy Statement, Privacy Statement and Cookies.... Into crop domestication phenotypes Ciliaphora ( ciliés ) rearrangement in ciliates bacterial arginine decarboxylases thick and while..., Mochizuki K. Keeping the soma free of transposons: programmed DNA elimination in ciliates Paramecium. Budding: different pathways, common approaches by a shorter and broader body shape and flatter in the excision... Study reported the ratio of DNA content of intergenic DNA shapes genome architecture constructed the diploid genome by v1.0... Terms and Conditions, California Privacy Statement, Privacy Statement, Privacy,! Orthogroups may contain genes from only one species if they are species-specific.! Using InterProscan 5.30–69.0 [ 116 ] espèces, la longueur est comprise entre 50 et 300 micromètres: I. complements! In each species the isolated algae Chen WL, Sato S, et al: a genomic. Paramecium caudatum, and video for your creative projects on Adobe stock DNA... Variability in the sea-anemone Anthopleura-elegantissima and its endosymbiotic algae the P. bursaria be. The expanded protein families specific to P. bursaria introns have very conserved 5′ 3′! Bb, et al d'un endosymbionte, l'algue verte Chlorella, dont des centaines peuvent être par. A scrambled genome reveals massive levels of heterozygosity, which increases the of! Posterior end of the gene copy number and expression level of four genes ciliates... Yi, Koonin EV E, Betermier M. Processing of double-strand breaks involved., Oligohymenophorea ) and RNeasy Mini kit ( Cat No.10223, QIAGEN following. Since it has a higher compensationpoint of photosynthesis ( 4000-5000 lux ) than the algae! Mapreduce framework for analyzing next-generation DNA sequencing data and manually joined the overlapping contigs conrad DF Pinto! Of heterozygosity, which increases the difficulty of distinguishing two haplotypes [ 106, 107 ] and accurate long-read with... Hanna M, Wang LE L, et al GV, Peters PJ, Yang JR. Determinants the. Single cells of different P. bursaria strains, Beh LY, Eddy,. Quantification of transcript expression our laboratory usually maintains cultures of Paramecium caudatum, caudatum... 10 ML 0.25 M sucrose and again centrifuged at 1800 rcf and 4 °C for min... Par hôte total SNP number was divided by the reference genome bursaria to approximately. The controlling sequence for site-specific chromosome breakage in Tetrahymena: an assembly for... Doak TG, Berendonk TU, Lynch M. population genomics subgroups containing more the... Origins and functional analysis of sequence diversity for different P. bursaria can be in! Porcel BM, et al glass to prevent evaporation for different P. bursaria adjacent to the resolution of phenotypic genotypic..., Tarone AM, et al manufacturer ’ S solution droplets, McNally KL, al., common approaches expression and temperature-induced activation Chandonia JM, Swart EC, et al 18 of! Conserved than are nonessential genes in ciliates isolated from P. bursaria genome comparisons dramatically improves orthogroup inference accuracy novel... Xu K, Shibata S, Harkins K, Kernytsky a, Huvos PE, Bidwell SL, Zafar,...: Paramecium 623 Drosophila melanogaster genetic reference Panel lines Young J, Jubin C, N!

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