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https://www.readbyqxmd.com/read/28938719/population-wide-sampling-of-retrotransposon-insertion-polymorphisms-using-deep-sequencing-and-efficient-detection
#1
Qichao Yu, Wei Zhang, Xiaolong Zhang, Yongli Zeng, Yeming Wang, Yanhui Wang, Liqin Xu, Xiaoyun Huang, Nannan Li, Xinlan Zhou, Jie Lu, Xiaosen Guo, Guibo Li, Yong Hou, Shiping Liu, Bo Li
Active retrotransposons play important roles during evolution and continue to shape our genomes today, especially in genetic polymorphisms underlying a diverse set of diseases. However, studies of human retrotransposon insertion polymorphisms (RIPs) based on whole-genome deep sequencing at the population level have not been sufficiently undertaken, despite the obvious need for a thorough characterization of RIPs in the general population. Herein, we present a novel and efficient computational tool called Specific Insertions Detector (SID) for the detection of non-reference RIPs...
September 1, 2017: GigaScience
https://www.readbyqxmd.com/read/28938616/identification-of-potential-cancer-related-pseudogenes-in-lung-adenocarcinoma-based-on-cerna-hypothesis
#2
Yunzhen Wei, Zhiqiang Chang, Cheng Wu, Yinling Zhu, Kun Li, Yan Xu
Pseudogenes are initially regarded as non-functional genomic fossils resulted from inactivating gene mutations during evolution. Far from being silent, pseudogenes are proved to regulate the expression of protein-coding genes through function as microRNA sponge in vivo. The aim of our study was to propose an integrative systems biology approach to identify disease pseudogenes base on competitive endogenous RNA (ceRNA) hypothesis. Here, we applied our method to lung adenocarcinoma (LUAD) RNASeq data from TCGA and identified 33 candidate pseudogenes...
August 29, 2017: Oncotarget
https://www.readbyqxmd.com/read/28938601/mutation-profile-based-methods-for-understanding-selection-forces-in-cancer-somatic-mutations-a-comparative-analysis
#3
Zhan Zhou, Yangyun Zou, Gangbiao Liu, Jingqi Zhou, Jingcheng Wu, Shimin Zhao, Zhixi Su, Xun Gu
Human genes exhibit different effects on fitness in cancer and normal cells. Here, we present an evolutionary approach to measure the selection pressure on human genes, using the well-known ratio of the nonsynonymous to synonymous substitution rate in both cancer genomes (CN /CS ) and normal populations (pN /pS ). A new mutation-profile-based method that adopts sample-specific mutation rate profiles instead of conventional substitution models was developed. We found that cancer-specific selection pressure is quite different from the selection pressure at the species and population levels...
August 29, 2017: Oncotarget
https://www.readbyqxmd.com/read/28937979/molecular-genomic-characterization-of-tick-and-human-derived-severe-fever-with-thrombocytopenia-syndrome-virus-isolates-from-south-korea
#4
Seok-Min Yun, Su-Jin Park, Sun-Whan Park, WooYoung Choi, Hye Won Jeong, Young-Ki Choi, Won-Ja Lee
BACKGROUND: Severe fever with thrombocytopenia syndrome (SFTS) is an emerging tick-borne viral disease caused by the SFTS virus (SFTSV) from Bunyaviridae that is endemic in East Asia. However, the genetic and evolutionary characteristics shared between tick- and human-derived Korean SFTSV strains are still limited. METHODOLOGY/PRINCIPAL FINDINGS: In this study we identify, for the first time, the genome sequence of a tick (Haemaphysalis longicornis)-derived Korean SFTSV strain (designated as KAGWT) and compare this virus with recent human SFTSV isolates to identify the genetic variations and relationships among SFTSV strains...
September 22, 2017: PLoS Neglected Tropical Diseases
https://www.readbyqxmd.com/read/28937654/genome-wide-analysis-of-cca1-like-proteins-in-soybean-and-functional-characterization-of-gmmyb138a
#5
Shaomin Bian, Donghao Jin, Ruihua Li, Xin Xie, Guoli Gao, Weikang Sun, Yuejia Li, Lulu Zhai, Xuyan Li
Plant CIRCADIAN CLOCK ASSOCIATED1 (CCA1)-like proteins are a class of single-repeat MYELOBLASTOSIS ONCOGENE (MYB) transcription factors generally featured by a highly conserved motif SHAQK(Y/F)F, which play important roles in multiple biological processes. Soybean is an important grain legume for seed protein and edible vegetable oil. However, essential understandings regarding CCA1-like proteins are very limited in soybean. In this study, 54 CCA1-like proteins were identified by data mining of soybean genome...
September 22, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28935753/mechanisms-of-transmission-ratio-distortion-at-hybrid-sterility-loci-within-and-between-mimulus-species
#6
Rachel E Kerwin, Andrea L Sweigart
Hybrid incompatibilities are a common correlate of genomic divergence and a potentially important contributor to reproductive isolation. However, we do not yet have a detailed understanding of how hybrid incompatibility loci function and evolve within their native species, or why they are dysfunctional in hybrids. Here, we explore these issues for a well-studied, two-locus hybrid incompatibility between hybrid male sterility 1 (hms1) and hybrid male sterility 2 (hms2) in the closely related yellow monkeyflower species Mimulus guttatus and M...
September 21, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28935583/role-of-elasmobranchs-and-holocephalans-in-understanding-peptide-evolution-in-the-vertebrates-lessons-learned-from-gonadotropin-releasing-hormone-gnrh-and-corticotropin-releasing-factor-crf-phylogenies
#7
REVIEW
David A Lovejoy, Ola M Michalec, David W Hogg, David I Wosnick
The cartilaginous fishes (Class Chondrichthyes) comprise two morphologically distinct subclasses; Elasmobranchii and Holocephali. Evidence indicates early divergence of these subclasses, suggesting monophyly of their lineage. However, such a phylogenetic understanding is not yet developed within two highly conserved peptide lineages, GnRH and CRF. Various GnRH forms exist across the Chondrichthyes. Although 4-7 immunoreactive forms have been described in Elasmobranchii, only one has been elucidated in Holocephali...
September 18, 2017: General and Comparative Endocrinology
https://www.readbyqxmd.com/read/28935117/the-role-of-krab-zfps-in-transposable-element-repression-and-mammalian-evolution
#8
REVIEW
Peng Yang, Yixuan Wang, Todd S Macfarlan
Kruppel-associated box zinc-finger proteins (KRAB-ZFPs) make up the largest family of transcription factors in humans. These proteins emerged in the last common ancestor of coelacanth and tetrapods, and have expanded and diversified in the mammalian lineage. Although their mechanism of transcriptional repression has been well studied for over a decade, the DNA-binding activities and the biological functions of these proteins have been largely unexplored. Recent large-scale ChIP-seq studies and loss-of-function experiments have revealed that KRAB-ZFPs play a major role in the recognition and transcriptional silencing of transposable elements (TEs), consistent with an 'arms race model' of KRAB-ZFP evolution against invading TEs...
September 18, 2017: Trends in Genetics: TIG
https://www.readbyqxmd.com/read/28934931/mitochondrial-genomes-of-african-pangolins-and-insights-into-evolutionary-patterns-and-phylogeny-of-the-family-manidae
#9
Zelda du Toit, Morné du Plessis, Desiré L Dalton, Raymond Jansen, J Paul Grobler, Antoinette Kotzé
BACKGROUND: This study used next generation sequencing to generate the mitogenomes of four African pangolin species; Temminck's ground pangolin (Smutsia temminckii), giant ground pangolin (S. gigantea), white-bellied pangolin (Phataginus tricuspis) and black-bellied pangolin (P. tetradactyla). RESULTS: The results indicate that the mitogenomes of the African pangolins are 16,558 bp for S. temminckii, 16,540 bp for S. gigantea, 16,649 bp for P. tetradactyla and 16,565 bp for P...
September 21, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28934927/evolution-and-expression-analysis-reveal-the-potential-role-of-the-hd-zip-gene-family-in-regulation-of-embryo-abortion-in-grapes-vitis-vinifera-l
#10
Zhiqian Li, Chen Zhang, Yurui Guo, Weili Niu, Yuejin Wang, Yan Xu
BACKGROUND: The HD-Zip family has a diversity of functions during plant development. In this study, we identify 33 HD-Zip transcription factors in grape and detect their expressions in ovules and somatic embryos, as well as in various vegetative organs. RESULTS: A genome-wide survey for HD-Zip transcription factors in Vitis was conducted based on the 12 X grape genome (V. vinifera L.). A total of 33 members were identified and classified into four subfamilies (I-IV) based on phylogeny analysis with Arabidopsis, rice and maize...
September 21, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28934627/in-it-for-the-long-haul-evolutionary-consequences-of-persistent-endosymbiosis
#11
REVIEW
Jennifer J Wernegreen
Phylogenetically independent bacterial lineages have undergone a profound lifestyle shift: from a free-living to obligately host-associated existence. Among these lineages, intracellular bacterial mutualists of insects are among the most intimate, constrained symbioses known. These obligate endosymbionts exhibit severe gene loss and apparent genome deterioration. Evolutionary theory provides a basis to link their unusual genomic features with shifts in fundamental mechanisms - selection, genetic drift, mutation, and recombination...
September 18, 2017: Current Opinion in Genetics & Development
https://www.readbyqxmd.com/read/28934592/getting-nervous-an-evolutionary-overhaul-for-communication
#12
Frederique Varoqueaux, Dirk Fasshauer
The evolution of a nervous system as a control system of the body's functions is a key innovation of animals. Its fundamental units are neurons, highly specialized cells dedicated to fast cell-cell communication. Neurons pass signals to other neurons, muscle cells, or gland cells at specialized junctions, the synapses, where transmitters are released from vesicles in a Ca(2+)-dependent fashion to activate receptors in the membrane of the target cell. Reconstructing the origins of neuronal communication out of a more simple process remains a central challenge in biology...
September 20, 2017: Annual Review of Genetics
https://www.readbyqxmd.com/read/28934485/detecting-gene-subnetworks-under-selection-in-biological-pathways
#13
Alexandre Gouy, Joséphine T Daub, Laurent Excoffier
Advances in high throughput sequencing technologies have created a gap between data production and functional data analysis. Indeed, phenotypes result from interactions between numerous genes, but traditional methods treat loci independently, missing important knowledge brought by network-level emerging properties. Therefore, detecting selection acting on multiple genes affecting the evolution of complex traits remains challenging. In this context, gene network analysis provides a powerful framework to study the evolution of adaptive traits and facilitates the interpretation of genome-wide data...
September 19, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28934377/the-environmental-acinetobacter-baumannii-isolate-dsm30011-reveals-clues-into-the-preantibiotic-era-genome-diversity-virulence-potential-and-niche-range-of-a-predominant-nosocomial-pathogen
#14
Guillermo D Repizo, Alejandro M Viale, Vítor Borges, María M Cameranesi, Najwa Taib, Martín Espariz, Céline Brochier-Armanet, João Paulo Gomes, Suzana P Salcedo
Acinetobacter baumannii represents nowadays an important nosocomial opportunistic pathogen whose reservoirs outside the clinical setting are obscure. Here, we traced the origins of the collection strain A. baumannii DSM30011 to an isolate first reported in 1944, obtained from the enriched microbiota responsible of the aerobic decomposition of the resinous desert shrub guayule. Whole-genome sequencing and phylogenetic analysis based on core genes confirmed DSM30011 affiliation to A. baumannii. Comparative studies with 32 complete A...
September 1, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28934256/transcriptome-analysis-of-sex-related-genes-in-the-blood-clam-tegillarca-granosa
#15
Heng Chen, Guoqiang Xiao, Xueliang Chai, Xingguan Lin, Jun Fang, Shuangshuang Teng
BACKGROUND: Blood clams (Tegillarca granosa) are one of the most commercial shellfish in China and South Asia with wide distribution in Indo-Pacific tropical to temperate estuaries. However, recent data indicate a decline in the germplasm of this species. Furthermore, the molecular mechanisms underpinning reproductive regulation remain unclear and information regarding genetic diversity is limited. Understanding the reproductive biology of shellfish is important in interpreting their embryology development, reproduction and population structure...
2017: PloS One
https://www.readbyqxmd.com/read/28934148/tomato-leaf-curl-new-delhi-virus-an-emerging-virus-complex-threatening-vegetable-and-fiber-crops
#16
REVIEW
Enrique Moriones, Shelly Praveen, Supriya Chakraborty
The tomato leaf curl New Delhi virus (ToLCNDV) (genus Begomovirus, family Geminiviridae) represents an important constraint to tomato production, as it causes the most predominant and economically important disease affecting tomato in the Indian sub-continent. However, in recent years, ToLCNDV has been fast extending its host range and spreading to new geographical regions, including the Middle East and the western Mediterranean Basin. Extensive research on the genome structure, protein functions, molecular biology, and plant-virus interactions of ToLCNDV has been conducted in the last decade...
September 21, 2017: Viruses
https://www.readbyqxmd.com/read/28932623/proteomics-technique-opens-new-frontiers-in-mobilome-research
#17
COMMENT
Andrew D Davidson, David A Matthews, Kevin Maringer
A large proportion of the genome of most eukaryotic organisms consists of highly repetitive mobile genetic elements. The sum of these elements is called the "mobilome," which in eukaryotes is made up mostly of transposons. Transposable elements contribute to disease, evolution, and normal physiology by mediating genetic rearrangement, and through the "domestication" of transposon proteins for cellular functions. Although 'omics studies of mobilome genomes and transcriptomes are common, technical challenges have hampered high-throughput global proteomics analyses of transposons...
2017: Mobile Genetic Elements
https://www.readbyqxmd.com/read/28932414/hox-gene-cluster-of-the-ascidian-halocynthia-roretzi-reveals-multiple-ancient-steps-of-cluster-disintegration-during-ascidian-evolution
#18
Yuka Sekigami, Takuya Kobayashi, Ai Omi, Koki Nishitsuji, Tetsuro Ikuta, Asao Fujiyama, Noriyuki Satoh, Hidetoshi Saiga
BACKGROUND: Hox gene clusters with at least 13 paralog group (PG) members are common in vertebrate genomes and in that of amphioxus. Ascidians, which belong to the subphylum Tunicata (Urochordata), are phylogenetically positioned between vertebrates and amphioxus, and traditionally divided into two groups: the Pleurogona and the Enterogona. An enterogonan ascidian, Ciona intestinalis (Ci), possesses nine Hox genes localized on two chromosomes; thus, the Hox gene cluster is disintegrated...
2017: Zoological Letters
https://www.readbyqxmd.com/read/28932346/insights-from-the-draft-genome-into-the-pathogenicity-of-a-clinical-isolate-of-elizabethkingia-meningoseptica-em3
#19
Shicheng Chen, Marty Soehnlen, Frances P Downes, Edward D Walker
Elizabethkingia meningoseptica is an emerging, healthcare-associated pathogen causing a high mortality rate in immunocompromised patients. We report the draft genome sequence of E. meningoseptica Em3, isolated from sputum from a patient with multiple underlying diseases. The genome has a length of 4,037,922 bp, a GC-content 36.4%, and 3673 predicted protein-coding sequences. Average nucleotide identity analysis (>95%) assigned the bacterium to the species E. meningoseptica. Genome analysis showed presence of the curli formation and assembly operon and a gene encoding hemagglutinins, indicating ability to form biofilm...
2017: Standards in Genomic Sciences
https://www.readbyqxmd.com/read/28932232/re-analyses-of-algal-genes-suggest-a-complex-evolutionary-history-of-oomycetes
#20
Qia Wang, Hang Sun, Jinling Huang
The spread of photosynthesis is one of the most important but constantly debated topics in eukaryotic evolution. Various hypotheses have been proposed to explain the plastid distribution in extant eukaryotes. Notably, the chromalveolate hypothesis suggested that multiple eukaryotic lineages were derived from a photosynthetic ancestor that had a red algal endosymbiont. As such, genes of plastid/algal origin in aplastidic chromalveolates, such as oomycetes, were considered to be important supporting evidence...
2017: Frontiers in Plant Science
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