University of Nebraska - Lincoln DigitalCommons@University of Nebraska - Lincoln Biochemistry -- Faculty Publications Biochemistry, Department of 2015 Drosophila Muller F Elements Maintain a Distinct Set of Genomic Properties Over 40 Million Years of Evolution Wilson Leung Washington University in St. Louis Cheryl Bailey University of Nebraska-Lincoln Participating Students and Faculty of the Genomics Education Partnership Follow this and additional works at: http://digitalcommons.unl.edu/biochemfacpub Part of the Biochemistry Commons, Biotechnology Commons, and the Other Biochemistry, Biophysics, and Structural Biology Commons Leung, Wilson; Bailey, Cheryl; and Participating Students and Faculty of the Genomics Education Partnership, "Drosophila Muller F Elements Maintain a Distinct Set of Genomic Properties Over 40 Million Years of Evolution" (2015). Biochemistry -- Faculty Publications. 199. http://digitalcommons.unl.edu/biochemfacpub/199 This Article is brought to you for free and open access by the Biochemistry, Department of at DigitalCommons@University of Nebraska - Lincoln. It has been accepted for inclusion in Biochemistry -- Faculty Publications by an authorized administrator of DigitalCommons@University of Nebraska - Lincoln. INVESTIGATION Drosophila Muller F Elements Maintain a Distinct Set of Genomic Properties Over 40 Million Years of Evolution Wilson Leung and Participating Students and Faculty of the Genomics Education Partnership1 ABSTRACT The Muller F element (4.2 Mb, ~80 protein-coding genes) is an unusual autosome of Drosophila KEYWORDS melanogaster; it is mostly heterochromatic with a low recombination rate. To investigatehowtheseproperties codon bias impact the evolution of repeats and genes, we manually improved the sequence and annotated the genes on the evolution of D. erecta, D. mojavensis,andD. grimshawi F elements and euchromatic domains from the Muller D element. We heterochro- find that F elements have greater transposon density (25–50%) than euchromatic reference regions (3–11%). Among matin theFelements,D. grimshawi has the lowest transposon density (particularly DINE-1: 2% vs. 11–27%). F element genes gene size have larger coding spans, more coding exons, larger introns, and lower codon bias. Comparison of the Effective melting Number of Codons with the Codon Adaptation Index shows that, in contrast to the other species, codon bias in characteristics D. grimshawi F element genes can be attributed primarily to selection instead of mutational biases, suggesting transposons that density and types of transposons affect the degree of local heterochromatin formation. F element genes have lower estimated DNA melting temperatures than D element genes, potentially facilitating transcription through heterochromatin. Most F element genes (~90%) have remained on that element, but the F element has smaller syntenic blocks than genome averages (3.4–3.6 vs. 8.4–8.8 genes per block), indicating greater rates of inversion despite lower rates of recombination. Overall, the F element has maintained characteristics that are distinct from other autosomes in the Drosophila lineage, illuminating the constraints imposed by a heterochromatic milieu. Classically, chromatin has been demarcated into two major types based With an estimated size of 4.2 Mb overall, the Drosophila melanogaster on the staining patterns in interphase nuclei. Regions that remain Muller F element, (also known as the dot chromosome, or the fourth densely stained throughout the cell cycle are classified as heterochro- chromosome in that species) is unusual in that it appears entirely het- matin, whereas regions that stain weakly during interphase are clas- erochromatic by most criteria, but the distal 1.3 Mb has a gene density sified as euchromatin (Heitz 1928). Heterochromatic regions generally and fraction of active genes (~50% in S2 cells) that are similar to the are late replicating and have lower rates of recombination, lower gene euchromatic regions of the D. melanogaster genome (Riddle et al. 2009, density, greater repeat density, greater levels of histone 3 lysine 9 di- 2012). Insertion of a PEV reporter (hsp70-driven white)inmostcases and tri-methylation (H3K9me2/3), and associated Heterochromatin results in a variegating phenotype (partial silencing; see Supplemental Protein 1a (HP1a) compared with euchromatic regions (reviewed in Text in File S1), indicating that even this distal region of the F element is Grewal and Elgin 2007). packaged as heterochromatin (Sun et al. 2004; Riddle et al. 2008). Sub- sequent high-resolution mapping of the chromatin landscape of the F Copyright © 2015 Leung et al. element supports this conclusion (Riddle et al. 2012). These character- doi: 10.1534/g3.114.015966 istics of the F element have made it an ideal platform for elucidating 1A listing of all authors appears at the end of this article. factors that are involved in heterochromatin formation and for exploring Manuscript received October 18, 2014; accepted for publication February 20, their impact on genes that are embedded in a heterochromatic domain 2015; published Early Online March 4, 2015. This is an open-access article distributed under the terms of the Creative (Elgin and Reuter 2013). Commons Attribution Unported License (http://creativecommons.org/licenses/ Immunofluorescent staining of polytene chromosomes with anti- by/3.0/), which permits unrestricted use, distribution, and reproduction in any bodies directed against H3K9me2 shows that, similar to D. melanogaster, medium, provided the original work is properly cited. the F elements of D. erecta, D. mojavensis,andD. grimshawi also are Supporting information is available online at http://www.g3journal.org/lookup/ suppl/doi:10.1534/g3.114.015966/-/DC1 enriched in H3K9me2 (Figure 1, left). These enrichment patterns indicate Corresponding author: Sarah C. R. Elgin, Washington University in St. Louis, Campus that the F element has maintained its heterochromatic properties in Box 1137, One Brookings Drive, St. Louis, MO 63130-4899. E-mail: [email protected] species (i.e., D. mojavensis and D. grimshawi) that last shared a common Volume 5 | May 2015 | 719 Figure 1 The Drosophila F element has maintained its heterochromatic properties in four different Drosophila species. (Left) Immunofluorescent stain- ing of polytene chromosomes using H3K9me2-specific antibodies shows that the D. melanogaster, D. erecta, D. mojavensis, and D. grimshawi F ele- ments (colored arrows) are enriched in H3K9me2 (a mark of heterochroma- tin). (Right) Phylogenetic tree of the Drosophila genomes sequenced by the Drosophila 12 Genomes Consor- tium (Powell 1997). The colored stars next to the species names in the phy- logenetic tree denote the species an- alyzed in this study; the same color scheme is used in this and subsequent figures. ancestor with D. melanogaster about 40 million years ago (Powell 1997; codon bias, the selective pressure experienced by F element genes, and Figure 1, right). the frequency of gene movement? To investigate the evolution of this unusual domain, we performed Our analyses show that F element genes in both the Sophophora and comparative analyses of the repeat and gene characteristics of the F Drosophila clades have maintained a set of distinct characteristics (larger element in four Drosophila species. The Drosophila 12 Genomes Con- gene size, lower codon bias, lower melting temperature) compared with sortium (Drosophila 12 Genomes Consortium et al. 2007) and the genes on other autosomes. Most of the D. melanogaster F element genes modENCODE project (Kharchenko et al. 2011) have produced a large (~90%) have remained on the same Muller element in all four collection of genomic datasets for D. melanogaster and 11 other Dro- Drosophila species, but there have been a large number of inver- sophila species. Previous analyses of the evolution of these Drosophila sions. F elements of the species in the Drosophila clade (i.e., D. mojavensis species have relied primarily on the Comparative Analysis Freeze 1 and D. grimshawi) exhibit different repeat distributions and gene (CAF1) draft assembly and computational (GLEAN-R) gene predic- characteristics compared to the species in the melanogaster subgroup tions (Drosophila 12 Genomes Consortium et al. 2007). Most of these (i.e., D. melanogaster and D. erecta). F element genes generally exhibit analyses only focused on the Muller elements A–E and the properties lower codon bias and weaker positive selection compared to genes in of the F element generally have not been examined carefully. the euchromatic reference regions; these characteristics are least pro- In this study, we have built on these genomic resources by per- nounced in D. grimshawi, which also has a much lower density of the forming manual sequence improvement and gene annotation of the Drosophila INterspersed Element 1 (DINE-1) transposon. Despite D. erecta, D. mojavensis,andD. grimshawi F elements and euchromatic these differences, our analyses show that F element genes in all four reference regions derived from the Muller D elements. The D element species generally share a common set of characteristics that presum- analysis regions (referred to as “base”)arelocatedproximaltotheperi- ably reflect the local environment and could contribute to their ability centric heterochromatin so that they have a similar topological position to function in a heterochromatic domain. in the nucleus as the F element. To identify characteristics that are associated with the proximity to pericentric or telomeric