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gene duplication

Hila Behar, Sean W Graham, Harry Brumer
Carbohydrate-active enzymes (CAZymes) are central to the biosynthesis and modification of the plant cell wall. An ancient clade of bifunctional plant endo-glucanases (EG16 members) was recently revealed and proposed to represent a transitional group uniting plant xyloglucan endo-transglycosylase/hydrolase (XTH) gene products and bacterial mixed-linkage endo-glucanases in the phylogeny of Glycoside Hydrolase Family 16 (GH16). To gain broader insights into the distribution and frequency of EG16 and other GH16 members in plants, the Phytozome, Plaza, NCBI, and 1000 Plants databases were mined to build a comprehensive census among 1289 species spanning the broad phylogenetic diversity of multiple algae through recent plant lineages...
June 22, 2018: Plant Journal: for Cell and Molecular Biology
Mattia Vicario, Domenico Cieri, Marisa Brini, Tito Calì
The presynaptic protein alpha-synuclein (α-syn) is unequivocally linked to the development of Parkinson's disease (PD). Not only it is the major component of amyloid fibrils found in Lewy bodies but mutations and duplication/triplication in its gene are responsible for the onset of familial autosomal dominant forms of PD. Nevertheless, the precise mechanisms leading to neuronal degeneration are not fully understood. Several lines of evidence suggest that impaired autophagy clearance and mitochondrial dysfunctions such as bioenergetics and calcium handling defects and alteration in mitochondrial morphology might play a pivotal role in the etiology and progression of PD, and indicate the intriguing possibility that α-syn could be involved in the control of mitochondrial function both in physiological and pathological conditions...
2018: Frontiers in Neuroscience
Danijela Krgovic, Nadja Kokalj Vokac, Andreja Zagorac, Hojka Gregoric Kumperscak
Detection of copy number variations (CNVs) is a first-tier clinical diagnostic test for children with neurodevelopmental disorders (NDD), which reveals the genetic cause of the disorder in more than 20%. These are mostly known microdeletion/microduplication syndromes, but variants of unknown clinical significance (VOUS) and ambiguous CNVs can also be detected. An example of the last two are abnormalities in the DOCK8 gene. Conflicting interpretations of CNVs affecting DOCK8 can be found in the literature. Deletions were predicted to have a impact in carriers with variable clinical manifestations, where duplications have been proposed as benign variants...
June 21, 2018: Scientific Reports
Heleen Coenen, Tom Viaene, Michiel Vandenbussche, Koen Geuten
BACKGROUND: MADS-box genes are key regulators of plant reproductive development and members of most lineages of this gene family have been extensively studied. However, the function and diversification of the ancient TM8 lineage remains elusive to date. The available data suggest a possible function in flower development in tomato and fast evolution through numerous gene loss events in flowering plants. RESULTS: We show the broad conservation of TM8 within angiosperms and find that in contrast to other MADS-box gene lineages, no gene duplicates have been retained after major whole genome duplication events...
June 22, 2018: BMC Plant Biology
Pin Fee Chong, Hirotomo Saitsu, Yasunari Sakai, Toru Imagi, Ryoko Nakamura, Masaru Matsukura, Naomichi Matsumoto, Ryutaro Kira
SCN2A encodes the alpha-subunit of voltage-gated sodium channel, Nav1.2, which is highly expressed at an early stage of the postnatal brain. Genetic studies revealed that de novo heterozygous mutations of SCN2A caused severe developmental disorders in childhood, such as autism and epileptic encephalopathy. However, few reports have demonstrated the cases carrying segmental deletions at the SCN2A locus for those with epileptic disorders. In this study, we report a 1.8-year-old boy, who presented with West syndrome in infancy and developed the sequelae of psychomotor delay and autism...
June 13, 2018: Seizure: the Journal of the British Epilepsy Association
Yujuan Zhang, Donghua Li, Yanyan Wang, Rong Zhou, Linhai Wang, Yanxin Zhang, Jingyin Yu, Huihui Gong, Jun You, Xiurong Zhang
The NAM, ATAF1/2, and CUC2 (NAC) family constitutes a large family of plant-specific transcription factors, involved in many aspects of physiological processes and a variety of abiotic stresses. There is little information concerning the NAC family in Sesamum indicum. In this study, 87 sesame NAC genes were identified and phylogenetically clustered into 12 groups with Arabidopsis NAC genes. A total of 83 SiNAC genes were distributed non-randomly on the 16 linkage groups in sesame. Four and 49 SiNACs were found to be tandemly and segmentally duplicated, respectively...
2018: PloS One
Line Dahl Poulsen, Jeppe Vinther
RNA sequencing (RNA-seq) has become the preferred method for global quantification of bacterial gene expression. With the continued improvements in sequencing technology and data analysis tools, the most labor-intensive and expensive part of an RNA-seq experiment is the preparation of sequencing libraries, which is also essential for the quality of the data obtained. Here, we present a straightforward and inexpensive basic protocol for preparation of strand-specific RNA-seq libraries from bacterial RNA as well as a computational pipeline for the data analysis of sequencing reads...
June 2018: Current Protocols in Nucleic Acid Chemistry
Yoon-Sim Yap, Prabhakaran Munusamy, Cindy Lim, Claire H T Chan, Aldo Prawira, Sau-Yeen Loke, Swee-Ho Lim, Kong-Wee Ong, Wei-Sean Yong, Sarah B H Ng, Iain B H Tan, David F Callen, Jeffrey C T Lim, Aye-Aye Thike, Puay-Hoon Tan, Ann S G Lee
PURPOSE: The purpose of the study was to improve the understanding of NF1-associated breast cancer, given the increased risk of breast cancer in this tumour predisposition syndrome and the limited data. METHODS: We identified 18 women with NF1 and breast cancer at our institution. Clinical and pathologic characteristics of NF1-associated breast cancers were compared with 7132 breast cancers in patients without NF1 from our institutional database. Next generation sequencing was performed on DNA from blood and breast cancer specimens available...
June 21, 2018: Breast Cancer Research and Treatment
Margaret L I Hart, Ban L Vu, Quinten Bolden, Keith T Chen, Casey L Oakes, Lejla Zoronjic, Richard P Meisel
Gene duplication creates a second copy of a gene either in tandem to the ancestral locus or dispersed to another chromosomal location. When the ancestral copy of a dispersed duplicate is lost from the genome, it creates the appearance that the gene was "relocated" from the ancestral locus to the derived location. Gene relocations may be as common as canonical dispersed duplications in which both the ancestral and derived copies are retained. Relocated genes appear to be under more selective constraints than the derived copies of canonical duplications, and they are possibly as conserved as single-copy non-relocated genes...
June 21, 2018: Journal of Molecular Evolution
Thomas B Barton-Owen, David E K Ferrier, Ildikó M L Somorjai
The Pax3/7 transcription factor family is integral to developmental gene networks contributing to important innovations in vertebrate evolution, including the neural crest. The basal chordate lineage of amphioxus is ideally placed to understand the dynamics of the gene regulatory network evolution that produced these novelties. We report here the discovery that the cephalochordate lineage possesses two Pax3/7 genes, Pax3/7a and Pax3/7b. The tandem duplication is ancestral to all extant amphioxus, occurring in both Asymmetron and Branchiostoma, but originated after the split from the lineage leading to vertebrates...
June 20, 2018: Scientific Reports
Saleha Patel, Alice M Barkell, Deepti Gupta, Sarah L Strong, Shaun Bruton, Frederick W Muskett, Philip W Addis, Philip S Renshaw, Patrick M Slocombe, Carl Doyle, Alison Clargo, Richard J Taylor, Christine E Prosser, Alistair J Henry, Martyn K Robinson, Lorna C Waters, Gill Holdsworth, Mark David Carr
Dickkopf (Dkk) family proteins are important regulators of Wnt signalling pathways, which play key roles in many essential biological processes. Here we report the first detailed structural and dynamics study of a full-length mature Dkk protein (Dkk4, residues 19-224), including determination of the first atomic resolution structure for the N-terminal cysteine-rich domain (CRD1) conserved among Dkk proteins. We discovered that CRD1 has significant structural homology to the Dkk C-terminal cysteine-rich domain (CRD2), pointing to multiple gene duplication events during Dkk family evolution...
June 20, 2018: Journal of Biological Chemistry
Quentin Helleu, Mia T Levine
The heterochromatic genome compartment mediates strictly conserved cellular processes such as chromosome segregation, telomere integrity, and genome stability. Paradoxically, heterochromatic DNA sequence is wildly unconserved. Recent reports that many hybrid incompatibility genes encode heterochromatin proteins, together with the observation that inter-species hybrids suffer aberrant heterochromatin-dependent processes, suggest that heterochromatic DNA packaging requires species-specific innovations. Testing this model of co-evolution between fast-evolving heterochromatic DNA and its packaging proteins begins with defining the latter...
June 19, 2018: Molecular Biology and Evolution
Daniel J Leite, Luís Baudouin-Gonzalez, Sawa Iwasaki-Yokozawa, Jesus Lozano-Fernandez, Natascha Turetzek, Yasuko Akiyama-Oda, Nikola-Michael Prpic, Davide Pisani, Hiroki Oda, Prashant P Sharma, Alistair P McGregor
Homeobox genes are key toolkit genes that regulate the development of metazoans and changes in their regulation and copy number have contributed to the evolution of phenotypic diversity. We recently identified a whole genome duplication (WGD) event that occurred in an ancestor of spiders and scorpions (Arachnopulmonata), and that many homeobox genes, including two Hox clusters, appear to have been retained in arachnopulmonates. To better understand the consequences of this ancient WGD and the evolution of arachnid homeobox genes, we have characterised and compared the homeobox repertoires in a range of arachnids...
June 19, 2018: Molecular Biology and Evolution
Antonio Benítez-Burraco, Montserrat Barcos-Martínez, Isabel Espejo-Portero, Maite Fernández-Urquiza, Raúl Torres-Ruiz, Sandra Rodríguez-Perales, Ma Salud Jiménez-Romero
The chromosome 1q21.1 duplication syndrome (OMIM# 612475) is characterized by head anomalies, mild facial dysmorphisms, and cognitive problems, including autistic features, mental retardation, developmental delay, and learning disabilities. Speech and language development are sometimes impaired, but no detailed characterization of language problems in this condition has been provided to date. We report in detail on the cognitive and language phenotype of a child who presents with a duplication in 1q21.1 (arr[hg19] 1q21...
2018: Frontiers in Pediatrics
Gabriel C Dworschak, Hartmut Engels, Jessica Becker, Lukas Soellner, Thomas Eggermann, Florian Kipfmueller, Andreas Müller, Heiko Reutter, Martina Kreiß
Background: Congenital diaphragmatic hernia (CDH) is a rare defect of the diaphragm commonly associated with high morbidity and mortality due to lung hypoplasia and pulmonary hypertension. Although in 70% of patients the etiology of a CDH remains unknown, a multitude of causative chromosomal aberrations has been identified. Case presentation: We describe the first case of isolated 11p15 duplication with CDH. The 18.6 Mb large duplication affected 285 RefSeq genes and included the Beckwith-Wiedemann (BWS)-associated imprinting control region 2 (ICR2, KCNQ1OT1 TSS DMR), whereas the ICR1 ( H19 TSS DMR) was not affected...
2018: Frontiers in Pediatrics
Narjara Lopes de Abreu, Ruy José Válka Alves, Sérgio Ricardo Sodré Cardoso, Yann J K Bertrand, Filipe Sousa, Climbiê Ferreira Hall, Bernard E Pfeil, Alexandre Antonelli
Background: Current evidence suggests that for more robust estimates of species tree and divergence times, several unlinked genes are required. However, most phylogenetic trees for non-model organisms are based on single sequences or just a few regions, using traditional sequencing methods. Techniques for massive parallel sequencing or next generation sequencing (NGS) are an alternative to traditional methods that allow access to hundreds of DNA regions. Here we use this approach to resolve the phylogenetic incongruence found in Polystachya Hook...
2018: PeerJ
Jie Chen, Chu-Ze Shen, Yan-Ping Guo, Guang-Yuan Rao
There are several types of capitulum in the Asteraceae due to different combinations of florets varying in corolla shape and stamen development. Previous studies have shown that the formation of ray florets on a radiate capitulum may be related to the parallel co-option of CYC2 -like genes among independent Asteraceae lineages. The present work tests that hypothesis and attempts to shed light on the pattern of evolution of the Asteraceae capitulum and floral heteromorphism under the regulation of CYC2 -like genes...
2018: Frontiers in Plant Science
Surasak Puvabanditsin, Vidya Puthenpura, Seyni Gueye-Ndiaye, Michele Takyi, Adaora Madubuko, Lauren Walzer, Rajeev Mehta
We report a term female infant with congenital heart block and total anomalous of pulmonary venous return. The results of single nucleotide polymorphism oligonucleotide microarray analysis showed an interstitial duplication of approximately 818 Kb, which involved 11 genes, including the entire LAMB3 gene which is known to associate with cardiac conduction defect. Our report adds to the collective knowledge that the cardiac conduction defect is a clinical feature of chromosome 1q32.2 duplication.
May 2018: Annals of Pediatric Cardiology
Venugopal S Vineeth, Usha R Dutta, Karthik Tallapakka, Aneek Das Bhowmik, Ashwin Dalal
Rett syndrome is a neurodevelopmental disorder affecting the nervous, musculoskeletal and gastroenteric systems. Affected individuals show normal neonatal development for 6-18 months followed by sudden growth arrest, psychomotor retardation and a broad spectrum of clinical features. Sequence variants in MECP2 gene have been identified as the major genetic etiology accounting for 90-95% of patients. Apart from MECP2, pathogenic sequence variants and copy number variants of FOXG1 gene lead to congenital type of Rett syndrome which is a more severe form and characterised by absence of early normal development as seen in classical Rett syndrome...
June 16, 2018: Gene
Jin Zhang, Yu Li, Bobin Liu, Lijuan Wang, Li Zhang, Jianjun Hu, Jun Chen, Huanquan Zheng, Mengzhu Lu
BACKGROUND: Rab proteins form the largest family of the Ras superfamily of small GTP-binding proteins and regulate intracellular trafficking pathways. However, the function of the Rab proteins in woody species is still an open question. RESULTS: Here, a total of 67 PtRabs were identified in Populus trichocarpa and categorized into eight subfamilies (RabA-RabH). Based on their chromosomal distribution and duplication blocks in the Populus genome, a total of 27 PtRab paralogous pairs were identified and all of them were generated by whole-genome duplication events...
June 18, 2018: BMC Plant Biology
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