TY - JOUR A1 - Schwarte, Sandra A1 - Tiedemann, Ralph T1 - A Gene Duplication/Loss Event in the Ribulose-1,5-Bisphosphate-Carboxylase/Oxygenase (Rubisco) Small Subunit Gene Family among Accessions of Arabidopsis thaliana JF - Molecular biology and evolution N2 - Rubisco (ribulose-1,5-bisphosphate carboxylase/oxygenase; EC 4.1.1.39), the most abundant protein in nature, catalyzes the assimilation of CO(2) (worldwide about 10(11) t each year) by carboxylation of ribulose-1,5-bisphosphate. It is a hexadecamer consisting of eight large and eight small subunits. Although the Rubisco large subunit (rbcL) is encoded by a single gene on the multicopy chloroplast genome, the Rubisco small subunits (rbcS) are encoded by a family of nuclear genes. In Arabidopsis thaliana, the rbcS gene family comprises four members, that is, rbcS-1a, rbcS-1b, rbcS-2b, and rbcS-3b. We sequenced all Rubisco genes in 26 worldwide distributed A. thaliana accessions. In three of these accessions, we detected a gene duplication/loss event, where rbcS-1b was lost and substituted by a duplicate of rbcS-2b (called rbcS-2b*). By screening 74 additional accessions using a specific polymerase chain reaction assay, we detected five additional accessions with this duplication/loss event. In summary, we found the gene duplication/loss in 8 of 100 A. thaliana accessions, namely, Bch, Bu, Bur, Cvi, Fei, Lm, Sha, and Sorbo. We sequenced an about 1-kb promoter region for all Rubisco genes as well. This analysis revealed that the gene duplication/loss event was associated with promoter alterations (two insertions of 450 and 850 bp, one deletion of 730 bp) in rbcS-2b and a promoter deletion (2.3 kb) in rbcS-2b* in all eight affected accessions. The substitution of rbcS-1b by a duplicate of rbcS-2b (i.e., rbcS-2b*) might be caused by gene conversion. All four Rubisco genes evolve under purifying selection, as expected for central genes of the highly conserved photosystem of green plants. We inferred a single positive selected site, a tyrosine to aspartic acid substitution at position 72 in rbcS-1b. Exactly the same substitution compromises carboxylase activity in the cyanobacterium Anacystis nidulans. In A. thaliana, this substitution is associated with an inferred recombination. Functional implications of the substitution remain to be evaluated. KW - Arabidopsis thaliana KW - Arabidopsis lyrata KW - Rubisco KW - gene duplication KW - positive selection Y1 - 2011 U6 - https://doi.org/10.1093/molbev/msr008 SN - 0737-4038 VL - 28 IS - 6 SP - 1861 EP - 1876 PB - Oxford Univ. Press CY - Oxford ER - TY - GEN A1 - Gamba, Cristina A1 - Jones, Eppie R. A1 - Teasdale, Matthew D. A1 - McLaughlin, Russell L. A1 - González-Fortes, Gloria M. A1 - Mattiangeli, Valeria A1 - Domboróczki, László A1 - Kővári, Ivett A1 - Pap, Ildikó A1 - Anders, Alexandra A1 - Whittle, Alasdair A1 - Dani, János A1 - Raczky, Pál A1 - Higham, Thomas F. G. A1 - Hofreiter, Michael A1 - Bradley, Daniel G. A1 - Pinhasi, Ron T1 - Genome flux and stasis in a five millennium transect of European prehistory T2 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - The Great Hungarian Plain was a crossroads of cultural transformations that have shaped European prehistory. Here we analyse a 5,000-year transect of human genomes, sampled from petrous bones giving consistently excellent endogenous DNA yields, from 13 Hungarian Neolithic, Copper, Bronze and Iron Age burials including two to high (similar to 22x) and seven to similar to 1x coverage, to investigate the impact of these on Europe's genetic landscape. These data suggest genomic shifts with the advent of the Neolithic, Bronze and Iron Ages, with interleaved periods of genome stability. The earliest Neolithic context genome shows a European hunter-gatherer genetic signature and a restricted ancestral population size, suggesting direct contact between cultures after the arrival of the first farmers into Europe. The latest, Iron Age, sample reveals an eastern genomic influence concordant with introduced Steppe burial rites. We observe transition towards lighter pigmentation and surprisingly, no Neolithic presence of lactase persistence. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 1332 KW - ancient DNA KW - lactase-persistence KW - positive selection KW - patterns KW - sequence KW - farmers KW - pigmentation KW - homozygosity KW - ancestry KW - skin Y1 - 2014 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-437999 SN - 1866-8372 VL - 5 IS - 1332 ER - TY - JOUR A1 - Cornetti, Luca A1 - Valente, Luis M. A1 - Dunning, Luke T. A1 - Quan, Xueping A1 - Black, Richard A. A1 - Hebert, Olivier A1 - Savolainen, Vincent T1 - The Genome of the "Great Speciator" Provides Insights into Bird Diversification JF - Genome biology and evolution N2 - Among birds, white-eyes (genusZosterops) have diversified so extensively that Jared Diamond and Ernst Mayr referred to them as the 'great speciator." The Zosterops lineage exhibits some of the fastest rates of species diversification among vertebrates, and its members are the most prolific passerine island colonizers. We present a high-quality genome assembly for the silvereye (Zosterops lateralis), a white-eye species consisting of several subspecies distributed across multiple islands. We investigate the genetic basis of rapid diversification in white-eyes by conducting genomic analyses at varying taxonomic levels. First, we compare the silvereye genome with those of birds from different families and searched for genomic features that may be unique to Zosterops. Second, we compare the genomes of different species of white-eyes from Lifou island (South Pacific), using whole genome resequencing and restriction site associated DNA. Third, we contrast the genomes of two subspecies of silvereye that differ in plumage color. In accordance with theory, we show that white-eyes have high rates of substitutions, gene duplication, and positive selection relative to other birds. Below genus level, we find that genomic differentiation accumulates rapidly and reveals contrasting demographic histories between sympatric species on Lifou, indicative of past interspecific interactions. Finally, we highlight genes possibly involved in color polymorphism between the subspecies of silvereye. By providing the first whole-genome sequence resources for white-eyes and by conducting analyses at different taxonomic levels, we provide genomic evidence underpinning this extraordinary bird radiation. KW - genome evolution KW - positive selection KW - gene duplication KW - phylogenomics KW - demography KW - morphological divergence Y1 - 2015 U6 - https://doi.org/10.1093/gbe/evv168 SN - 1759-6653 VL - 7 IS - 9 SP - 2680 EP - 2691 PB - Oxford Univ. Press CY - Oxford ER - TY - GEN A1 - Siska, Veronika A1 - Jones, Eppie Ruth A1 - Jeon, Sungwon A1 - Bhak, Youngjune A1 - Kim, Hak-Min A1 - Cho, Yun Sung A1 - Kim, Hyunho A1 - Lee, Kyusang A1 - Veselovskaya, Elizaveta A1 - Balueva, Tatiana A1 - Gallego-Llorente, Marcos A1 - Hofreiter, Michael A1 - Bradley, Daniel G. A1 - Eriksson, Anders A1 - Pinhasi, Ron A1 - Bhak, Jong A1 - Manica, Andrea T1 - Genome-wide data from two early Neolithic East Asian individuals dating to 7700 years ago T2 - Postprints der Universität Potsdam Mathematisch-Naturwissenschaftliche Reihe N2 - Ancient genomes have revolutionized our understanding of Holocene prehistory and, particularly, the Neolithic transition in western Eurasia. In contrast, East Asia has so far received little attention, despite representing a core region at which the Neolithic transition took place independently similar to 3 millennia after its onset in the Near East. We report genome-wide data from two hunter-gatherers from Devil's Gate, an early Neolithic cave site (dated to similar to 7.7 thousand years ago) located in East Asia, on the border between Russia and Korea. Both of these individuals are genetically most similar to geographically close modern populations from the Amur Basin, all speaking Tungusic languages, and, in particular, to the Ulchi. The similarity to nearby modern populations and the low levels of additional genetic material in the Ulchi imply a high level of genetic continuity in this region during the Holocene, a pattern that markedly contrasts with that reported for Europe. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 791 KW - Mitochondrial-DNA analysis KW - positive selection KW - jomon skeletons KW - ancient DNA KW - pigmentation KW - population KW - admixture KW - edar KW - gene KW - polymorohism Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-439977 SN - 1866-8372 IS - 791 ER - TY - JOUR A1 - Kolora, Sree Rohit Raj A1 - Weigert, Anne A1 - Saffari, Amin A1 - Kehr, Stephanie A1 - Walter Costa, Maria Beatriz A1 - Spröer, Cathrin A1 - Indrischek, Henrike A1 - Chintalapati, Manjusha A1 - Lohse, Konrad A1 - Doose, Gero A1 - Overmann, Jörg A1 - Bunk, Boyke A1 - Bleidorn, Christoph A1 - Grimm-Seyfarth, Annegret A1 - Henle, Klaus A1 - Nowick, Katja A1 - Faria, Rui A1 - Stadler, Peter F. A1 - Schlegel, Martin T1 - Divergent evolution in the genomes of closely related lacertids, Lacerta viridis and L. bilineata, and implications for speciation JF - GigaScience N2 - Background Lacerta viridis and Lacerta bilineata are sister species of European green lizards (eastern and western clades, respectively) that, until recently, were grouped together as the L. viridis complex. Genetic incompatibilities were observed between lacertid populations through crossing experiments, which led to the delineation of two separate species within the L. viridis complex. The population history of these sister species and processes driving divergence are unknown. We constructed the first high-quality de novo genome assemblies for both L. viridis and L. bilineata through Illumina and PacBio sequencing, with annotation support provided from transcriptome sequencing of several tissues. To estimate gene flow between the two species and identify factors involved in reproductive isolation, we studied their evolutionary history, identified genomic rearrangements, detected signatures of selection on non-coding RNA, and on protein-coding genes. Findings Here we show that gene flow was primarily unidirectional from L. bilineata to L. viridis after their split at least 1.15 million years ago. We detected positive selection of the non-coding repertoire; mutations in transcription factors; accumulation of divergence through inversions; selection on genes involved in neural development, reproduction, and behavior, as well as in ultraviolet-response, possibly driven by sexual selection, whose contribution to reproductive isolation between these lacertid species needs to be further evaluated. Conclusion The combination of short and long sequence reads resulted in one of the most complete lizard genome assemblies. The characterization of a diverse array of genomic features provided valuable insights into the demographic history of divergence among European green lizards, as well as key species differences, some of which are candidates that could have played a role in speciation. In addition, our study generated valuable genomic resources that can be used to address conservation-related issues in lacertids. KW - sister species KW - PacBio and Illumina KW - de novo hybrid assembly KW - transcripts KW - noncoding RNA KW - zinc fingers KW - positive selection KW - UV response KW - inversions KW - gene flow Y1 - 2018 U6 - https://doi.org/10.1093/gigascience/giy160 SN - 2047-217X VL - 8 IS - 2 PB - Oxford Univ. Press CY - Oxford ER -