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https://www.readbyqxmd.com/read/28327996/genome-sequencing-of-the-sweetpotato-whitefly-bemsia-tabaci-med-q
#1
Wen Xie, Chunhai Chen, Zezhong Yang, Litao Guo, Xin Yang, Dan Wang, Ming Chen, Jinqun Huang, Yanan Wen, Yang Zeng, Yating Liu, Jixing Xia, Lixia Tian, Hongying Cui, Qingjun Wu, Shaoli Wang, Baoyun Xu, Xianchun Li, Xinqiu Tan, Murad Ghanim, Baoli Qiu, Huipeng Pan, Dong Chu, Helene Delatte, M N Maruthi, Feng Ge, Xueping Zhou, Xiaowei Wang, Fanghao Wan, Yuzhou Du, Chen Luo, Fengming Yan, Evan L Preisser, Xiaoguo Jiao, Brad S Coates, Jinyang Zhao, Qiang Gao, Jinquan Xia, Ye Yin, Yong Liu, Judith K Brown, Xuguo Joe Zhou, Youjun Zhang
Background: The sweetpotato whitefly Bemisia tabaci is a highly destructive agricultural and ornamental crop pest. It damages host plants through both phloem feeding and vectoring plant pathogens. Introductions of B. tabaci are difficult to quarantine and eradicate because of its high reproductive rates, broad host plant range, and insecticide resistance. Findings: A total of 791 Gb of raw DNA sequence from whole genome shotgun sequencing, and 13 BAC pooling libraries were generated by Illumina sequencing using different combinations of mate-pair and pair-end libraries...
March 15, 2017: GigaScience
https://www.readbyqxmd.com/read/28327967/genome-sequence-of-pacific-abalone-haliotis-discus-hannai-the-first-draft-genome-in-family-haliotidae
#2
Bo-Hye Nam, Woori Kwak, Young-Ok Kim, Dong-Gyun Kim, Hee Jeong Kong, Woo-Jin Kim, Jeong-Ha Kang, Jung Youn Park, Cheul Min An, Ji-Young Moon, Choul Ji Park, Jae Woong Yu, Joon Yoon, Minseok Seo, Kwondo Kim, Duk Kyung Kim, SaetByeol Lee, Samsun Sung, Chul Lee, Younhee Shin, Myunghee Jung, Byeong-Chul Kang, Shin Ga-Hee, Sojeong Ka, Kelsey Caetano-Anolles, Seoae Cho, Heebal Kim
Background: Abalones are large marine snails in the family Haliotidae and the genus Haliotis belonging to the class Gastropoda of the phylum Mollusca. The family Haliotidae contains only one genus, Haliotis, and this single genus is known to contain several species of abalone. With 18 additional subspecies, the most comprehensive treatment of Haliotidae considers 56 species valid [1]. Abalone is an economically important fishery and aquaculture animal which is considered a highly-prized seafood delicacy...
March 7, 2017: GigaScience
https://www.readbyqxmd.com/read/28327954/genome-sequencing-of-the-winged-midge-parochlus-steinenii-from-the-antarctic-peninsula
#3
Sanghee Kim, Mijin Oh, Woongsic Jung, Joonho Park, Han-Gu Choi, Seung Chul Shin
Background: In the Antarctic, only two species of Chironomidae occur naturally-the wingless midge, Belgica antarctica , and the winged midge, Parochlus steinenii . B. antarctica is an extremophile with unusual adaptations. The larvae of B. antarctica are desiccation- and freeze-tolerant and the adults are wingless. Recently, the compact genome of B. antarctica was reported and it is the first Antarctic eukaryote to be sequenced. Although P. steinenii occurs naturally in the Antarctic with B...
February 24, 2017: GigaScience
https://www.readbyqxmd.com/read/28327911/the-genome-sequence-of-the-wisent-bison-bonasus
#4
Kun Wang, Lizhong Wang, Johannes A Lenstra, Jianbo Jian, Yongzhi Yang, Quanjun Hu, Deyong Lai, Qiang Qiu, Tao Ma, Zheng Du, Richard Abbott, Jianquan Liu
Background: The wisent, also known as the European bison, was rescued from extinction approximately 80 years ago through the conservation of 12 individuals. Here, we present the draft genome sequence of a male wisent individual descended from this founding stock. Findings: A total of 366 billion base pairs (Gb) of raw reads from whole-genome sequencing of this wisent were generated using the Illumina HiSeq2000 platform. The final genome assembly (2.58 Gb) is composed of 29,074 scaffolds with an N50 of 4...
March 10, 2017: GigaScience
https://www.readbyqxmd.com/read/28327671/candidate-loci-involved-in-domestication-and-improvement-detected-by-a-published-90k-wheat-snp-array
#5
Lifeng Gao, Guangyao Zhao, Dawei Huang, Jizeng Jia
Selection is one of the most important forces in crop evolution. Common wheat is a major world food crop and a typical allopolyploid with a huge and complex genome. We applied four approaches to detect loci selected in wheat during domestication and improvement. A total of 7,984 candidate loci were detected, accounting for 23.3% of all 34,317 SNPs analysed, a much higher proportion than estimated in previous reports. We constructed a first generation wheat selection map which revealed the following new insights on genome-wide selection: (1) diversifying selection acted by increasing, decreasing or not affecting gene frequencies; (2) the number of loci under selection during domestication was much higher than that during improvement; (3) the contribution to wheat improvement by the D sub-genome was relatively small due to the bottleneck of hexaploidisation and diversity can be expanded by using synthetic wheat and introgression lines; and (4) clustered selection regions occur throughout the wheat genome, including the centromere regions...
March 22, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28327641/sequential-displacement-of-type-vi-secretion-system-effector-genes-leads-to-evolution-of-diverse-immunity-gene-arrays-in-vibrio-cholerae
#6
Paul C Kirchberger, Daniel Unterweger, Daniele Provenzano, Stefan Pukatzki, Yan Boucher
Type VI secretion systems (T6SS) enable bacteria to engage neighboring cells in contact-dependent competition. In Vibrio cholerae, three chromosomal clusters each encode a pair of effector and immunity genes downstream of those encoding the T6SS structural machinery for effector delivery. Different combinations of effector-immunity proteins lead to competition between strains of V. cholerae, which are thought to be protected only from the toxicity of their own effectors. Screening of all publically available V...
March 22, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28326096/tagw2-a-good-reflection-of-wheat-polyploidization-and-evolution
#7
Lin Qin, Junjie Zhao, Tian Li, Jian Hou, Xueyong Zhang, Chenyang Hao
Hexaploid wheat consists of three subgenomes, namely, A, B, and D. These well-characterized ancestral genomes also exist at the diploid and tetraploid levels, thereby rendering wheat as a good model species for studying polyploidization. Here, we performed intra- and inter-species comparative analyses of wheat and its relatives to dissect polymorphism and differentiation of the TaGW2 genes. Our results showed that genetic diversity of TaGW2 decreased with progression from the diploids to tetraploids and hexaploids...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28326078/inside-out-archaeal-ectosymbionts-suggest-a-second-model-of-reduced-genome-evolution
#8
REVIEW
Trevor Nicks, Lilah Rahn-Lee
Reduced-genome symbionts and their organelle counterparts, which have even smaller genomes, are essential to the lives of many organisms. But how and why have these genomes become so small? Endosymbiotic genome reduction is a product of isolation within the host, followed by massive pseudogenization and gene loss often including DNA repair mechanisms. This phenomenon can be observed in insect endosymbionts such as the bacteria Carsonella ruddii and Buchnera aphidicola. Yet endosymbionts are not the only organisms with reduced genomes...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28326016/early-origin-and-evolution-of-the-angelman-syndrome-ubiquitin-ligase-gene-ube3a
#9
REVIEW
Masaaki Sato
The human Ube3a gene encodes an E3 ubiquitin ligase and exhibits brain-specific genomic imprinting. Genetic abnormalities that affect the maternal copy of this gene cause the neurodevelopmental disorder Angelman syndrome (AS), which is characterized by severe mental retardation, speech impairment, seizure, ataxia and some unique behavioral phenotypes. In this review article, I highlight the evolution of the Ube3a gene and its imprinting to provide evolutionary insights into AS. Recent comparative genomic studies have revealed that Ube3a is most phylogenetically similar to HECTD2 among the human HECT (homologous to the E6AP carboxyl terminus) family of E3 ubiquitin ligases, and its distant evolutionary origin can be traced to common ancestors of fungi and animals...
2017: Frontiers in Cellular Neuroscience
https://www.readbyqxmd.com/read/28325942/comparative-genomics-reveals-contraction-in-olfactory-receptor-genes-in-bats
#10
Georgia Tsagkogeorga, Steven Müller, Christophe Dessimoz, Stephen J Rossiter
Gene loss and gain during genome evolution are thought to play important roles in adaptive phenotypic diversification. Among mammals, bats possess the smallest genomes and have evolved the unique abilities of powered flight and laryngeal echolocation. To investigate whether gene family evolution has contributed to the genome downsizing and phenotypic diversification in this group, we performed comparative evolutionary analyses of complete proteome data for eight bat species, including echolocating and non-echolocating forms, together with the proteomes of 12 other laurasiatherian mammals...
March 21, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28325903/whole-genome-analysis-of-human-papillomavirus-types-16-18-and-58-isolated-from-cervical-precancer-and-cancer-samples-in-chinese-women
#11
Ying Liu, Yaqi Pan, Weijiao Gao, Yang Ke, Zheming Lu
Human papillomavirus (HPV) types 16, 18 and 58 are ranked the top three high-risk HPV types for cervical intraepithelial neoplasia (CIN) and invasive carcinoma. We aimed to evaluate the diversity of HPV16, HPV18, and HPV58 genetic variants by HPV capture technology combined with next generation sequencing. 295, 73, and 148 variations were observed in 51 HPV16, 7 HPV18, and 11 HPV58 genomes, respectively. HPV16 isolates were predominantly of the A variant lineage, and sublineage A4 (Asian) was the most common...
March 21, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28325850/phenotypic-diversity-and-genotypic-flexibility-of-burkholderia-cenocepacia-during-long-term-chronic-infection-of-cystic-fibrosis-lungs
#12
Amy Huei-Yi Lee, Stephane Flibotte, Sunita Sinha, Adrianna Paiero, Rachel L Ehrlich, Sergey Balashov, Garth D Ehrlich, James E A Zlosnik, Joshua Chang Mell, Corey Nislow
Chronic bacterial infections of the lung are the leading cause of morbidity and mortality in cystic fibrosis patients. Tracking bacterial evolution during chronic infections can provide insights into how host selection pressures-including immune responses and therapeutic interventions-shape bacterial genomes. We carried out genomic and phenotypic analyses of 215 serially collected Burkholderia cenocepacia isolates from 16 cystic fibrosis patients, spanning a period of 2-20 yr and a broad range of epidemic lineages...
March 21, 2017: Genome Research
https://www.readbyqxmd.com/read/28325210/breast-cancer-immunology-and-immunotherapy-current-status-and-future-perspectives
#13
L de la Cruz-Merino, M Chiesa, R Caballero, F Rojo, N Palazón, F H Carrasco, V Sánchez-Margalet
Cancer immunology has gained renewed interest in the past few years due to emerging findings on mechanisms involved in tumoral immune evasion. Indisputably, immune edition is currently considered a critical hallmark of cancer. Basic research has revealed new targets which can be modulated in the clinical setting with new compounds and strategies. As recent evidence confirms, breast cancer (BC) is a complex and heterogeneous disease in which host immune responses play a substantial role. T-infiltrating lymphocytes measurement is suggested as a powerful new tool necessary to predict early BC evolution, especially in HER2-positive and triple negative subtypes...
2017: International Review of Cell and Molecular Biology
https://www.readbyqxmd.com/read/28323658/changing-face-of-metastatic-prostate-cancer-the-law-of-diminishing-returns-holds-true
#14
Ulka N Vaishampayan
PURPOSE OF REVIEW: Prostate cancer presents with a multitude of faces. It ranges from localized cancers staying quiescent for many years during active surveillance to the raging diffuse liver metastases causing terminal disease. The incidence of metastatic disease is increasing. This review will highlight some of the recent developments as well as ongoing challenges of managing advanced prostate cancer. RECENT FINDINGS: Significant strides are being made in managing metastatic prostate cancer...
March 18, 2017: Current Opinion in Oncology
https://www.readbyqxmd.com/read/28323281/chance-and-necessity-in-the-genome-evolution-of-endosymbiotic-bacteria-of-insects
#15
Beatriz Sabater-Muñoz, Christina Toft, David Alvarez-Ponce, Mario A Fares
An open question in evolutionary biology is how does the selection-drift balance determine the fates of biological interactions. We searched for signatures of selection and drift in genomes of five endosymbiotic bacterial groups known to evolve under strong genetic drift. Although most genes in endosymbiotic bacteria showed evidence of relaxed purifying selection, many genes in these bacteria exhibited stronger selective constraints than their orthologs in free-living bacterial relatives. Remarkably, most of these highly constrained genes had no role in the host-symbiont interactions but were involved in either buffering the deleterious consequences of drift or other host-unrelated functions, suggesting that they have either acquired new roles or their role became more central in endosymbiotic bacteria...
March 21, 2017: ISME Journal
https://www.readbyqxmd.com/read/28323279/spontaneous-mutations-of-a-model-heterotrophic-marine-bacterium
#16
Ying Sun, Kate E Powell, Way Sung, Michael Lynch, Mary Ann Moran, Haiwei Luo
Heterotrophic marine bacterioplankton populations display substantive genomic diversity that is commonly explained to be the result of selective forces imposed by resource limitation or interactions with phage and predators. Here we use a mutation-accumulation experiment followed by whole-genome sequencing of mutation lines to determine an unbiased rate and molecular spectrum of spontaneous mutations for a model heterotrophic marine bacterium in the globally important Roseobacter clade, Ruegeria pomeroyi DSS-3...
March 21, 2017: ISME Journal
https://www.readbyqxmd.com/read/28323123/circumventing-intratumoral-heterogeneity-to-identify-potential-therapeutic-targets-in-hepatocellular-carcinoma
#17
Ao Huang, Xin Zhao, Xin-Rong Yang, Fu-Qiang Li, Xin-Lan Zhou, Kui Wu, Xin Zhang, Qi-Man Sun, Ya Cao, Hong-Mei Zhu, Xiang-Dong Wang, Huan-Ming Yang, Jian Wang, Zhao-You Tang, Yong Hou, Jia Fan, Jian Zhou
BACKGROUND AND AIMS: Intratumoral heterogeneity (ITH) challenges identifying mutations with target therapy potential whereas circulating cell-free DNAs (cfDNAs) in blood could possibly reflect the entire mutation spectrum in certain tumors. We investigated how to minimize the limit of ITH for profiling hepatocellular carcinoma (HCC). METHODS: Thirty-two multi-regional tumor samples from five patients were subjected to whole exome sequencing (WES) and targeted deep sequencing (TDS); matched preoperative cfDNAs were sequenced accordingly...
March 17, 2017: Journal of Hepatology
https://www.readbyqxmd.com/read/28323122/exome-analysis-of-the-evolutionary-path-of-hepatocellular-adenoma-carcinoma-transition-vascular-invasion-and-brain-dissemination
#18
Sílvia Vilarinho, Zeynep Erson-Omay, Kisha Mitchell-Richards, Charles Cha, Carol Nelson-Williams, Akdes Serin Harmancı, Katsuhito Yasuno, Murat Günel, Tamar H Taddei
Hepatocellular adenoma (HCA) is a rare benign liver tumor, predominantly seen in young women. Its major complications are malignant transformation, spontaneous hemorrhage, and rupture. We describe a case of a young female with no underlying liver disease who presented with acute abdominal pain and was found to have a 17 cm heterogeneous mass in the left lobe of the liver. She underwent left hepatectomy and pathology revealed a 14 cm moderately differentiated hepatocellular carcinoma (HCC) arising in a shell of a HCA...
March 17, 2017: Journal of Hepatology
https://www.readbyqxmd.com/read/28322934/comparative-immunogenomics-of-molluscs
#19
Jonathan H Schultz, Coen M Adema
Comparative immunology, studying both vertebrates and invertebrates, provided the earliest descriptions of phagocytosis as a general immune mechanism. However, the large scale of animal diversity challenges all-inclusive investigations and the field of immunology has developed by mostly emphasizing study of a few vertebrate species. In addressing the lack of comprehensive understanding of animal immunity, especially that of invertebrates, comparative immunology helps toward management of invertebrates that are food sources, agricultural pests, pathogens, or transmit diseases, and helps interpret the evolution of animal immunity...
March 18, 2017: Developmental and Comparative Immunology
https://www.readbyqxmd.com/read/28322435/genomic-changes-following-the-reversal-of-a-y-chromosome-to-an-autosome-in-drosophila-pseudoobscura
#20
Ching-Ho Chang, Amanda M Larracuente
Robertsonian translocations resulting in fusions between sex chromosomes and autosomes shape karyotype evolution by creating new sex chromosomes from autosomes. These translocations can also reverse sex chromosomes back into autosomes, which is especially intriguing given the dramatic differences between autosomes and sex chromosomes. To study the genomic events following a Y chromosome reversal, we investigated an autosome-Y translocation in Drosophila pseudoobscura. The ancestral Y chromosome fused to a small autosome (the dot chromosome) approximately 10-15 Mya...
March 21, 2017: Evolution; International Journal of Organic Evolution
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