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Made available in DSpace on 2022-04-28T19:47:38Z (GMT). No. of bitstreams: 0 Previous issue date: 2021-01-01 Satellite DNAs (satDNAs) and transposable elements (TEs) are among the main components of constitutive heterochromatin (c-heterochromatin) and are related to their functionality, dynamics, and evolution. A peculiar case regarding the quantity and distribution of c-heterochromatin is observed in the genus of bees, Melipona, with species having a low amount of heterochromatin and species with high amount occupying almost all chromosomes. By combining low-pass genome sequencing and chromosomal analysis, we characterized the satDNAs and TEs of Melipona quadrifasciata (low c-heterochromatin) and Melipona scutellaris (high low c-heterochromatin) to understand c-heterochromatin composition and evolution. We identified 15 satDNA families and 20 TEs for both species. Significant variations in the repeat landscapes were observed between the species. In M. quadrifasciata, the repetitive fraction corresponded to only 3.78% of the genome library studied, whereas in M. scutellaris, it represented 54.95%. Massive quantitative and qualitative changes contributed to the differential amplification of c-heterochromatin, mainly due to the amplification of exclusive repetitions in M. scutellaris, as the satDNA MscuSat01-195 and the TE LTR/Gypsy_1 that represent 38.20 and 14.4% of its genome, respectively. The amplification of these two repeats is evident at the chromosomal level, with observation of their occurrence on most c-heterochromatin. Moreover, we detected repeats shared between species, revealing that they experienced mainly quantitative variations and varied in the organization on chromosomes and evolutionary patterns. Together, our data allow the discussion of patterns of evolution of repetitive DNAs and c-heterochromatin that occurred in a short period of time, after separation of the Michmelia and Melipona subgenera. Laboratório de Citogenética de Insetos Departamento de Biologia Geral Universidade Federal de Viçosa, Campus Viçosa, Av. P.H. Rolfs s/n Departamento de Biologia Geral E Aplicada Instituto de Biociências/IB UNESP–Universidade Estadual Paulista Departamento de Biologia Geral E Aplicada Instituto de Biociências/IB UNESP–Universidade Estadual Paulista

Made available in DSpace on 2020-12-12T01:26:10Z (GMT). No. of bitstreams: 0 Previous issue date: 2020-09-01 Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) A common characteristic of sex chromosomes is the accumulation of repetitive DNA, which accounts for their diversification and degeneration. In grasshoppers, the X0 sex-determining system in males is considered ancestral. However, in some species, derived variants like neo-XY in males evolved several times independently by Robertsonian translocation. This is the case of Ronderosia bergii, in which further large pericentromeric inversion in the neo-Y also took place, making this species particularly interesting for investigating sex chromosome evolution. Here, we characterized the satellite DNAs (satDNAs) and transposable elements (TEs) of the species to investigate the quantitative differences in repeat composition between male and female genomes putatively associated with sex chromosomes. We found a total of 53 satDNA families and 56 families of TEs. The satDNAs were 13.5% more abundant in males than in females, while TEs were just 1.02% more abundant in females. These results imply differential amplification of satDNAs on neo-Y chromosome and a minor role of TEs in sex chromosome differentiation. We showed highly differentiated neo-XY sex chromosomes owing to major amplification of satDNAs in neo-Y. Furthermore, chromosomal mapping of satDNAs suggests high turnover of neo-sex chromosomes in R. bergii at the intrapopulation level, caused by multiple paracentric inversions, amplifications, and transpositions. Finally, the species is an example of the action of repetitive DNAs in the generation of variability for sex chromosomes after the suppression of recombination, and helps understand sex chromosome evolution at the intrapopulation level. Departamento de Biologia Geral e Aplicada UNESP-Univ Estadual Paulista Instituto de Biociências/IB Department of Organismal Biology Uppsala University Evolutionary Biology Centre Department of Ecology and Genetics Uppsala University Evolutionary Biology Centre Departamento de Biologia Geral e Aplicada UNESP-Univ Estadual Paulista Instituto de Biociências/IB

To better understand the structure and variability of the 45S rDNA cistron and its evolutionary dynamics in grasshoppers, we performed a detailed analysis combining classical and molecular cytogenetic data with whole-genome sequencing in Abracris flavolienata, which shows extraordinary variability in the chromosomal distribution for this element. We found astonishing variability in the number and size of rDNA clusters at intra- and inter-population levels. Interestingly, FISH using distinct parts of 45S rDNA cistron (18S rDNA, 28S rDNA, and ITS1) as probes revealed a distinct number of clusters, suggesting independent mobility and amplification of the 45S rDNA components. This hypothesis is consistent with the higher genomic coverage of almost the entire cistron of 45S rDNA observed in A. flavolineata compared to other grasshoppers, besides coverage variability along the 45S rDNA cistron in the species. In addition, these differences in coverage for distinct components of the 45S rDNA cistron indicate emergence of pseudogenes evidenced by existence of truncated sequences, demonstrating the rDNA dynamics in the species. Although the chromosomal distribution of 18S rDNA was highly variable, the chromosomes 1, 3, 6, and 9 harbored rDNA clusters in all individuals with the occurrence of NOR activity in pair 9, suggesting ancestry or selective pressures to prevent pseudogenization of rDNA sequences in this chromosome pair. Additionally, small NORs and cryptic rDNA loci were observed. Finally, there was no evidence of enrichment and association of transposable elements, at least, inside or nearby rDNA cistron. These findings broaden our knowledge of rDNA dynamics, revealing an independent movement and amplification of segments of 45S rDNA cistron, which in A. flavolineata could be attributed to ectopic recombination. Fil: Ferretti, Ana B. S. M.. Universidade Estadual Paulista Julio de Mesquita Filho. Faculdade de Engenharia.; Brasil Fil: Ruiz Ruano, Francisco J.. Uppsala University; Suecia. Universidad de Granada; España Fil: Milani, Diogo. Universidade Estadual Paulista Julio de Mesquita Filho. Faculdade de Engenharia.; Brasil Fil: Loreto, Vilma. Universidade Federal de Pernambuco; Brasil Fil: Marti, Dardo Andrea. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Nordeste. Instituto de Biología Subtropical. Instituto de Biología Subtropical - Nodo Posadas | Universidad Nacional de Misiones. Instituto de Biología Subtropical. Instituto de Biología Subtropical - Nodo Posadas; Argentina Fil: Ramos, Érica Daniela. Universidade Estadual Paulista Julio de Mesquita Filho; Brasil Fil: Martins, Cesar. Universidade Estadual Paulista Julio de Mesquita Filho; Brasil Fil: Cabral de Mello, Diogo C.. Universidade Estadual Paulista Julio de Mesquita Filho; Brasil

Made available in DSpace on 2019-10-06T15:24:24Z (GMT). No. of bitstreams: 0 Previous issue date: 2018-11-01 Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) Supernumerary (B) chromosomes are dispensable genomic elements occurring frequently among grasshoppers. Most B chromosomes are enriched with repetitive DNAs, including satellite DNAs (satDNAs) that could be implicated in their evolution. Although studied in some species, the specific ancestry of B chromosomes is difficult to ascertain and it was determined in only a few examples. Here we used bioinformatics and cytogenetics to characterize the composition and putative ancestry of B chromosomes in three grasshopper species, Rhammatocerus brasiliensis, Schistocerca rubiginosa, and Xyleus discoideus angulatus. Using the RepeatExplorer pipeline we searched for the most abundant satDNAs in Illumina sequenced reads, and then we generated probes used in fluorescent in situ hybridization (FISH) to determine chromosomal position. We used this information to infer ancestry and the events that likely occurred at the origin of B chromosomes. We found twelve, nine, and eighteen satDNA families in the genomes of R. brasiliensis, S. rubiginosa, and X. d. angulatus, respectively. Some satDNAs revealed clustered organization on A and B chromosomes varying in number of sites and position along chromosomes. We did not find specific satDNA occurring in the B chromosome. The satDNAs shared among A and B chromosomes support the idea of putative intraspecific ancestry from small autosomes in the three species, i.e., pair S11 in R. brasiliensis, pair S9 in S. rubiginosa, and pair S10 in X. d. angulatus. The possibility of involvement of other chromosomal pairs in B chromosome origin is also hypothesized. Finally, we discussed particular aspects in composition, origin, and evolution of the B chromosome for each species. Instituto de Biociências/IB Departamento de Biologia UNESP—Universidade Estadual Paulista Department of Evolutionary Biology Evolutionary Biology Center Uppsala University Instituto de Ciências Biológicas Laboratório de Biodiversidade e Genética de Insetos UPE—Universidade de Pernambuco Centro de Biociências/CB Departamento de Genética UFPE—Universidade Federal de Pernambuco Department of Entomology Texas A&M University 2475 TAMU Instituto de Biociências/IB Departamento de Biologia UNESP—Universidade Estadual Paulista FAPESP: 2015/16661-1 CNPq: 305300/2017-2

In the grasshopper Abracris flavolineata it was documented huge intrapopulation variation for 18S rDNA in individuals collected in six populations, but causes for this pattern was not understand yet. In this work we aimed to elucidate the molecular structure, evolutionary patterns of the rDNA 18S distribution and its causes in the genome of A. flavolineata. It was used a combination of classical cytogenetic techniques, mapping of18S rDNA through Fluorescence in situ hybridization (FISH) and genomics analyses from entire sequenced genome by Illumina hiseq 2000. It was analyzed 48 individuals collected in six distantly sampling places from Brazil and Argentina. FISH analyses confirmed the variability of 18S rDNA for all six populations that presented between 6-11 chomosomes labeled. Signals were observed in chromosomes 1, 3, 6 and 9 in all individuals and also it was noticed variation of cluster sizes. It was not found a fixed pattern at intra- or interpopulation levels in population from the same geographic region or between distant ones. Silver nitrate staning revealed Nocleolar Organizer Regions (NORs) in chromosome 9 of all individuals, indicating that the expression of the rDNA cluster in this chromosome could be under selection to be expressed, and also could represent ancestral placement of this sequence. It is a pattern also shared with congeneric species. In some individuals chromosome 10 presented NORs, however for some of them FISH signals in this bivalent was not observed, indicating cryptic loci in accordance with ‘dispersion-amplification-deletion’ model, suggested also for rDNA dispersion for other grasshoppers. Finally the reconstruction of entire 45S rDNA presented different coverages in the conserved genes (18S, 5.8S e 25S) and in the internal transcripts (ITS 1 e ITS 2) reveling that huge part of the copies are pseudogenes. The transposons Nimb and R2 are present in 45S rDNA, although apparently they are not able to transpose sequences. All data together suggests that the high amount of rDNA in A. flavolineata genome is caused by occurrence of pseudogene sequences that were moved random between chromosomes caused most parsimonialy by ectopic recombination, extra-chromosomal DNA or even by transposons not localized in the 45S cluster