TY  - JOUR
A1  - Adolfi, Mateus C.
A1  - Du, Kang
A1  - Kneitz, Susanne
A1  - Cabau, Cédric
A1  - Zahm, Margot
A1  - Klopp, Christophe
A1  - Feron, Romain
A1  - Paixão, Rômulo V.
A1  - Varela, Eduardo S.
A1  - de Almeida, Fernanda L.
A1  - de Oliveira, Marcos A.
A1  - Nóbrega, Rafael H.
A1  - Lopez-Roques, Céline
A1  - Iampietro, Carole
A1  - Lluch, Jérôme
A1  - Kloas, Werner
A1  - Wuertz, Sven
A1  - Schaefer, Fabian
A1  - Stöck, Matthias
A1  - Guiguen, Yann
A1  - Schartl, Manfred
T1  - A duplicated copy of id2b is an unusual sex-determining candidate gene on the Y chromosome of arapaima (Arapaima gigas)
JF  - Scientific Reports
N2  - Arapaima gigas is one of the largest freshwater fish species of high ecological and economic importance. Overfishing and habitat destruction are severe threats to the remaining wild populations. By incorporating a chromosomal Hi-C contact map, we improved the arapaima genome assembly to chromosome-level, revealing an unexpected high degree of chromosome rearrangements during evolution of the bonytongues (Osteoglossiformes). Combining this new assembly with pool-sequencing of male and female genomes, we identified id2bbY, a duplicated copy of the inhibitor of DNA binding 2b (id2b) gene on the Y chromosome as candidate male sex-determining gene. A PCR-test for id2bbY was developed, demonstrating that this gene is a reliable male-specific marker for genotyping. Expression analyses showed that this gene is expressed in juvenile male gonads. Its paralog, id2ba, exhibits a male-biased expression in immature gonads. Transcriptome analyses and protein structure predictions confirm id2bbY as a prime candidate for the master sex-determiner. Acting through the TGF beta signaling pathway, id2bbY from arapaima would provide the first evidence for a link of this family of transcriptional regulators to sex determination. Our study broadens our current understanding about the evolution of sex determination genetic networks and provide a tool for improving arapaima aquaculture for commercial and conservation purposes.
KW  - evolutionary genetics
KW  - genetic markers
KW  - genome
Y1  - 2021
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-265672
VL  - 11
IS  - 1
ER  - 
TY  - JOUR
A1  - Hurd, Paul J.
A1  - Grübel, Kornelia
A1  - Wojciechowski, Marek
A1  - Maleszka, Ryszard
A1  - Rössler, Wolfgang
T1  - Novel structure in the nuclei of honey bee brain neurons revealed by immunostaining
JF  - Scientific Reports
N2  - In the course of a screen designed to produce antibodies (ABs) with affinity to proteins in the honey bee brain we found an interesting AB that detects a highly specific epitope predominantly in the nuclei of Kenyon cells (KCs). The observed staining pattern is unique, and its unfamiliarity indicates a novel previously unseen nuclear structure that does not colocalize with the cytoskeletal protein f-actin. A single rod-like assembly, 3.7-4.1 mu m long, is present in each nucleus of KCs in adult brains of worker bees and drones with the strongest immuno-labelling found in foraging bees. In brains of young queens, the labelling is more sporadic, and the rod-like structure appears to be shorter (similar to 2.1 mu m). No immunostaining is detectable in worker larvae. In pupal stage 5 during a peak of brain development only some occasional staining was identified. Although the cellular function of this unexpected structure has not been determined, the unusual distinctiveness of the revealed pattern suggests an unknown and potentially important protein assembly. One possibility is that this nuclear assembly is part of the KCs plasticity underlying the brain maturation in adult honey bees. Because no labelling with this AB is detectable in brains of the fly Drosophila melanogaster and the ant Camponotus floridanus, we tentatively named this antibody AmBNSab (Apis mellifera Brain Neurons Specific antibody). Here we report our results to make them accessible to a broader community and invite further research to unravel the biological role of this curious nuclear structure in the honey bee central brain.
KW  - mushroom body calyx
KW  - synaptic complexes
KW  - bodies
KW  - insect
KW  - plasticity
KW  - insights
KW  - genome
KW  - model
KW  - proteins
KW  - methylation
KW  - biological techniques
KW  - cell biology
KW  - developmental biology
KW  - molecular biology
KW  - neuroscience
Y1  - 2021
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-260059
VL  - 11
ER  - 
TY  - JOUR
A1  - Biscotti, Maria Assunta
A1  - Gerdol, Marco
A1  - Canapa, Adriana
A1  - Forconi, Mariko
A1  - Olmo, Ettore
A1  - Pallavicini, Alberto
A1  - Barucca, Marco
A1  - Schartl, Manfred
T1  - The Lungfish Transcriptome: A Glimpse into Molecular Evolution Events at the Transition from Water to Land
JF  - Scientific Reports
N2  - Lungfish and coelacanths are the only living sarcopterygian fish. The phylogenetic relationship of lungfish to the last common ancestor of tetrapods and their close morphological similarity to their fossil ancestors make this species uniquely interesting. However their genome size, the largest among vertebrates, is hampering the generation of a whole genome sequence. To provide a partial solution to the problem, a high-coverage lungfish reference transcriptome was generated and assembled. The present findings indicate that lungfish, not coelacanths, are the closest relatives to land-adapted vertebrates. Whereas protein-coding genes evolve at a very slow rate, possibly reflecting a “living fossil” status, transposable elements appear to be active and show high diversity, suggesting a role for them in the remarkable expansion of the lungfish genome. Analyses of single genes and gene families documented changes connected to the water to land transition and demonstrated the value of the lungfish reference transcriptome for comparative studies of vertebrate evolution.
KW  - lungfish
KW  - transcriptome
KW  - genome
KW  - sarcopterygian fish
Y1  - 2016
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-167753
VL  - 6
IS  - 21571
ER  - 
TY  - JOUR
A1  - Benoit, Joshua B.
A1  - Adelman, Zach N.
A1  - Reinhardt, Klaus
A1  - Dolan, Amanda
A1  - Poelchau, Monica
A1  - Jennings, Emily C.
A1  - Szuter, Elise M.
A1  - Hagan, Richard W.
A1  - Gujar, Hemant
A1  - Shukla, Jayendra Nath
A1  - Zhu, Fang
A1  - Mohan, M.
A1  - Nelson, David R.
A1  - Rosendale, Andrew J.
A1  - Derst, Christian
A1  - Resnik, Valentina
A1  - Wernig, Sebastian
A1  - Menegazzi, Pamela
A1  - Wegener, Christian
A1  - Peschel, Nicolai
A1  - Hendershot, Jacob M.
A1  - Blenau, Wolfgang
A1  - Predel, Reinhard
A1  - Johnston, Paul R.
A1  - Ioannidis, Panagiotis
A1  - Waterhouse, Robert M.
A1  - Nauen, Ralf
A1  - Schorn, Corinna
A1  - Ott, Mark-Christoph
A1  - Maiwald, Frank
A1  - Johnston, J. Spencer
A1  - Gondhalekar, Ameya D.
A1  - Scharf, Michael E.
A1  - Raje, Kapil R.
A1  - Hottel, Benjamin A.
A1  - Armisén, David
A1  - Crumière, Antonin Jean Johan
A1  - Refki, Peter Nagui
A1  - Santos, Maria Emilia
A1  - Sghaier, Essia
A1  - Viala, Sèverine
A1  - Khila, Abderrahman
A1  - Ahn, Seung-Joon
A1  - Childers, Christopher
A1  - Lee, Chien-Yueh
A1  - Lin, Han
A1  - Hughes, Daniel S.T.
A1  - Duncan, Elizabeth J.
A1  - Murali, Shwetha C.
A1  - Qu, Jiaxin
A1  - Dugan, Shannon
A1  - Lee, Sandra L.
A1  - Chao, Hsu
A1  - Dinh, Huyen
A1  - Han, Yi
A1  - Doddapaneni, Harshavardhan
A1  - Worley, Kim C.
A1  - Muzny, Donna M.
A1  - Wheeler, David
A1  - Panfilio, Kristen A.
A1  - Jentzsch, Iris M. Vargas
A1  - Jentzsch, IMV
A1  - Vargo, Edward L.
A1  - Booth, Warren
A1  - Friedrich, Markus
A1  - Weirauch, Matthew T.
A1  - Anderson, Michelle A.E.
A1  - Jones, Jeffery W.
A1  - Mittapalli, Omprakash
A1  - Zhao, Chaoyang
A1  - Zhou, Jing-Jiang
A1  - Evans, Jay D.
A1  - Attardo, Geoffrey M.
A1  - Robertson, Hugh M.
A1  - Zdobnov, Evgeny M.
A1  - Ribeiro, Jose M.C.
A1  - Gibbs, Richard A.
A1  - Werren, John H.
A1  - Palli, Subba R.
A1  - Schal, Coby
A1  - Richards, Stephen
T1  - Unique features of a global human ectoparasite identified through sequencing of the bed bug genome
JF  - Nature Communications
N2  - The bed bug, Cimex lectularius, has re-established itself as a ubiquitous human ectoparasite throughout much of the world during the past two decades. This global resurgence is likely linked to increased international travel and commerce in addition to widespread insecticide resistance. Analyses of the C. lectularius sequenced genome (650 Mb) and 14,220 predicted protein-coding genes provide a comprehensive representation of genes that are linked to traumatic insemination, a reduced chemosensory repertoire of genes related to obligate hematophagy, host–symbiont interactions, and several mechanisms of insecticide resistance. In addition, we document the presence of multiple putative lateral gene transfer events. Genome sequencing and annotation establish a solid foundation for future research on mechanisms of insecticide resistance, human–bed bug and symbiont–bed bug associations, and unique features of bed bug biology that contribute to the unprecedented success of C. lectularius as a human ectoparasite.
KW  - human ectoparasite
KW  - bed bug
KW  - Cimex lectularius
KW  - genome
Y1  - 2016
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-166221
VL  - 7
IS  - 10165
ER  - 
TY  - JOUR
A1  - Matos, I
A1  - Machado, M. P.
A1  - Schartl, M.
A1  - Coelho, M. M.
T1  - Gene expression dosage regulation in an allopolyploid fish
JF  - PLoS ONE
N2  - How allopolyploids are able not only to cope but profit from their condition is a question that remains elusive, but is of great importance within the context of successful allopolyploid evolution. One outstanding example of successful allopolyploidy is the endemic Iberian cyprinid Squalius alburnoides. Previously, based on the evaluation of a few genes, it was reported that the transcription levels between diploid and triploid S. alburnoides were similar. If this phenomenon occurs on a full genomic scale, a wide functional "diploidization'' could be related to the success of these polyploids. We generated RNA-seq data from whole juvenile fish and from adult livers, to perform the first comparative quantitative transcriptomic analysis between diploid and triploid individuals of a vertebrate allopolyploid. Together with an assay to estimate relative expression per cell, it was possible to infer the relative sizes of transcriptomes. This showed that diploid and triploid S. alburnoides hybrids have similar liver transcriptome sizes. This in turn made it valid to directly compare the S. alburnoides RNA-seq transcript data sets and obtain a profile of dosage responses across the S. alburnoides transcriptome. We found that 64% of transcripts in juveniles' samples and 44% in liver samples differed less than twofold between diploid and triploid hybrids (similar expression). Yet, respectively 29% and 15% of transcripts presented accurate dosage compensation (PAA/PA expression ratio of 1 instead of 1.5). Therefore, an exact functional diploidization of the triploid genome does not occur, but a significant down regulation of gene expression in triploids was observed. However, for those genes with similar expression levels between diploids and triploids, expression is not globally strictly proportional to gene dosage nor is it set to a perfect diploid level. This quantitative expression flexibility may be a strong contributor to overcome the genomic shock, and be an immediate evolutionary advantage of allopolyploids.
KW  - RNA-Seq
KW  - balance hypothesis
KW  - hybrids
KW  - genome
KW  - maize
KW  - Squalius alburnoides
KW  - cell size
KW  - evolution
KW  - heterosis
KW  - complex
Y1  - 2015
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-143565
VL  - 10
IS  - 3
ER  - 
TY  - JOUR
A1  - Garcia, Tzintzuni I.
A1  - Matos, Isa
A1  - Shen, Yingjia
A1  - Pabuwal, Vagmita
A1  - Coelho, Maria Manuela
A1  - Wakamatsu, Yuko
A1  - Schartl, Manfred
A1  - Walter, Ronald B.
T1  - Novel Method for Analysis of Allele Specific Expression in Triploid Oryzias latipes Reveals Consistent Pattern of Allele Exclusion
JF  - PLOS ONE
N2  - Assessing allele-specific gene expression (ASE) on a large scale continues to be a technically challenging problem. Certain biological phenomena, such as X chromosome inactivation and parental imprinting, affect ASE most drastically by completely shutting down the expression of a whole set of alleles. Other more subtle effects on ASE are likely to be much more complex and dependent on the genetic environment and are perhaps more important to understand since they may be responsible for a significant amount of biological diversity. Tools to assess ASE in a diploid biological system are becoming more reliable. Non-diploid systems are, however, not uncommon. In humans full or partial polyploid states are regularly found in both healthy (meiotic cells, polynucleated cell types) and diseased tissues (trisomies, non-disjunction events, cancerous tissues). In this work we have studied ASE in the medaka fish model system. We have developed a method for determining ASE in polyploid organisms from RNAseq data and we have implemented this method in a software tool set. As a biological model system we have used nuclear transplantation to experimentally produce artificial triploid medaka composed of three different haplomes. We measured ASE in RNA isolated from the livers of two adult, triploid medaka fish that showed a high degree of similarity. The majority of genes examined (82%) shared expression more or less evenly among the three alleles in both triploids. The rest of the genes (18%) displayed a wide range of ASE levels. Interestingly the majority of genes (78%) displayed generally consistent ASE levels in both triploid individuals. A large contingent of these genes had the same allele entirely suppressed in both triploids. When viewed in a chromosomal context, it is revealed that these genes are from large sections of 4 chromosomes and may be indicative of some broad scale suppression of gene expression.
KW  - RNA-SEQ data
KW  - copy-number alteration
KW  - squalius alburnoides
KW  - gene expression
KW  - medaka
KW  - variant detection
KW  - transplantation
KW  - genome
KW  - generation
KW  - evolution
Y1  - 2014
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-116000
SN  - 1932-6203
VL  - 9
IS  - 6
ER  -