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GigaScience

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https://www.readbyqxmd.com/read/29149296/comparative-transcriptomics-of-five-high-altitude-vertebrates-and-their-low-altitude-relatives
#1
Qianzi Tang, Yiren Gu, Xuming Zhou, Long Jin, Jiuqiang Guan, Rui Liu, Jing Li, Kereng Long, Shilin Tian, Tiandong Che, Silu Hu, Yan Liang, Xuemei Yang, Xuan Tao, Zhijun Zhong, Guosong Wang, Xiaohui Chen, Diyan Li, Jideng Ma, Xun Wang, Miaomiao Mai, An'an Jiang, Xiaolin Luo, Xuebin Lv, Vadim N Gladyshev, Xuewei Li, Mingzhou Li
Background: Species living at high altitude are subject to strong selective pressures due to inhospitable environments (e.g., hypoxia, low temperature, high solar radiation, and lack of biological production), making these species valuable models for comparative analyses of local adaptation. Studies that examined high-altitude adaptation identified a vast array of rapidly evolving genes that characterize the dramatic phenotypic changes in high-altitude animals. However, how high-altitude environment shapes gene expression programs remains largely unknown...
November 15, 2017: GigaScience
https://www.readbyqxmd.com/read/29149267/taiwan-biobank-making-cross-database-convergence-possible-in-the-big-data-era
#2
Jui-Chu Lin, Chien-Te Fan, Chia-Cheng Liao, Yao-Sheng Chen
The Taiwan Biobank (TWB) is a biomedical research database of biopsy data from 200,000 participants. Access to this database has been granted to research communities taking part in the development of precision medicines; however, this has raised issues surrounding TWB's access to electronic medical records (EMR). The Personal Data Protection Act of Taiwan restricts access to EMR for purposes not covered by patients' original consent. This commentary explores possible legal solutions to help ensure that the access TWB has to EMR abides with legal obligations, and with governance frameworks associated with ethical, legal and social implications...
November 15, 2017: GigaScience
https://www.readbyqxmd.com/read/29149264/sim3c-simulation-of-hi-c-and-meta3c-proximity-ligation-sequencing-technologies
#3
Matthew Z DeMaere, Aaron E Darling
Background: Chromosome conformation capture (3C) and Hi-C DNA sequencing methods have rapidly advanced our understanding of the spatial organization of genomes and metagenomes. Many variants of these protocols have been developed, each with their own strengths. Currently there is no systematic means for simulating sequence data from this family of sequencing protocols, potentially hindering the advancement of algorithms to exploit this new datatype. Findings: We describe a computational simulator that, given simple parameters and reference genome sequences, will simulate Hi-C sequencing on those sequences...
November 15, 2017: GigaScience
https://www.readbyqxmd.com/read/29136191/genome-sequence-of-the-small-brown-planthopper-laodelphax-striatellus
#4
Junjie Zhu, Feng Jiang, Xianhui Wang, Pengcheng Yang, Yanyuan Bao, Wan Zhao, Wei Wang, Hong Lu, Qianshuo Wang, Na Cui, Jing Li, Xiaofang Chen, Lan Luo, Jinting Yu, Le Kang, Feng Cui
Background: Laodelphax striatellus Fallén (Hemiptera: Delphacidae) is one of the most destructive rice pests. L. striatellus is different from two other rice planthoppers with a released genome sequence, Sogatella furcifera and Nilaparvata lugens, in many biological characteristics, such as host range, dispersal capacity, and vectoring plant viruses. Deciphering the genome of L. striatellus will help to understand the genetic basis of the biological differences among the three rice planthoppers...
November 10, 2017: GigaScience
https://www.readbyqxmd.com/read/29126158/full-genome-survey-and-dynamics-of-gene-expression-in-the-greater-amberjack-seriola-dumerili
#5
E Sarropoulou, A Y M Sundaram, E Kaitetzidou, G Kotoulas, G D Gilfillan, N Papandroulakis, C C Mylonas, A Magoulas
Background: Teleosts of the genus Seriola, commonly known as amberjacks, are of high commercial value in international markets due to their flesh quality and worldwide distribution. The Seriola species of interest to Mediterranean aquaculture is the greater amberjack (Seriola dumerili). This species holds great potential for the aquaculture industry, but in captivity, reproduction has proved to be challenging and observed growth dysfunction hinders their domestication. Insights into molecular mechanisms may contribute to a better understanding of traits like growth and sex, but investigations to unravel the molecular background of amberjacks have begun only recently...
November 8, 2017: GigaScience
https://www.readbyqxmd.com/read/29126115/hominid-a-framework-for-identifying-associations-between-host-genetic-variation-and-microbiome-composition
#6
Joshua Lynch, Karen Tang, Sambhawa Priya, Joanna Sands, Margaret Sands, Evan Tang, Sayan Mukherjee, Dan Knights, Ran Blekhman
Recent studies have uncovered a strong effect of host genetic variation on the composition of host-associated microbiota. Here, we present HOMINID, a computational approach based on Lasso linear regression, that given host genetic variation and microbiome taxonomic composition data, identifies host SNPs that are correlated with microbial taxa abundances. Using simulated data we show that HOMINID has accuracy in identifying associated SNPs, and performs better compared to existing methods. We also show that HOMINID can accurately identify the microbial taxa that are correlated with associated SNPs...
November 8, 2017: GigaScience
https://www.readbyqxmd.com/read/29112761/draft-genome-of-the-marco-polo-sheep-ovis-ammon-polii
#7
Yongzhi Yang, Yutao Wang, Yue Zhao, Xiuying Zhang, Ran Li, Lei Chen, Guojie Zhang, Yu Jiang, Qiang Qiu, Wen Wang, Hongjiang Wei, Kun Wang
Background: The Marco Polo Sheep (Ovis ammon polii), a subspecies of argali (Ovis ammon) which is distributed mainly in the Pamir Mountains, provides a mammalian model to study high-altitude adaptation mechanisms. Due to over-hunting and subsistence poaching, as well as competition with livestock and habitat loss, O. ammon has been categorized as an endangered species on several lists. It can have fertile offspring with sheep. Hence a high quality reference genome of the Marco Polo Sheep will be very helpful in conservation genetics and even in exploiting useful genes in sheep breeding...
November 1, 2017: GigaScience
https://www.readbyqxmd.com/read/29099922/draft-genome-of-the-reindeer-rangifer-tarandus
#8
Zhipeng Li, Zeshan Lin, Hengxing Ba, Lei Chen, Yongzhi Yang, Kun Wang, Qiu Qiang, Wen Wang, Guangyu Li
Background: Reindeer (Rangifer tarandus) is the only fully domesticated species in the Cervidae family, and is the only cervid with a circumpolar distribution. Unlike all other cervids, female reindeer regularly grow cranial appendages (antlers, the defining characteristics of cervids), as well as males. Moreover, reindeer milk contains more protein and less lactose than bovids' milk. A high quality reference genome of this species will assist efforts to elucidate these and other important features in the reindeer...
November 1, 2017: GigaScience
https://www.readbyqxmd.com/read/29077841/filling-reference-gaps-via-assembling-dna-barcodes-using-high-throughput-sequencing-moving-toward-barcoding-the-world
#9
Shanlin Liu, Chentao Yang, Chengran Zhou, Xin Zhou
Over the past decade, biodiversity researchers have dedicated tremendous efforts in constructing DNA reference barcodes for rapid species registration and identification. Although analytical cost for standard DNA barcoding has been significantly reduced since early 2000, further dramatic reduction in barcoding costs is unlikely because the Sanger sequencing is approaching its limits in throughput and chemistry cost. Constraints in barcoding cost not only led to unbalanced barcoding efforts around the globe, but also refrained High-Throughput-Sequencing (HTS) based taxonomic identification from applying binomial species names, which provide crucial linkages to biological knowledge...
October 25, 2017: GigaScience
https://www.readbyqxmd.com/read/29069412/mebs-a-software-platform-to-evaluate-large-meta-genomic-collections-according-to-their-metabolic-machinery-unraveling-the-sulfur-cycle
#10
Valerie De Anda, Icoquih Zapata-Peñasco, Augusto Cesar Poot-Hernandez, Luis E Eguiarte, Bruno Contreras-Moreira, Valeria Souza
BACKGROUND: The increasing number of metagenomic and genomic sequences has dramatically improved our understanding of microbial diversity, yet our ability to infer metabolic capabilities in such datasets remains challenging. FINDINGS: We describe the Multigenomic Entropy Based Score pipeline (MEBS), a software platform designed to evaluate, compare and infer complex metabolic pathways in large "omic" datasets, including entire biogeochemical cycles. MEBS is open source and available through https://github...
October 23, 2017: GigaScience
https://www.readbyqxmd.com/read/29053868/lagos-ne-a-multi-scaled-geospatial-and-temporal-database-of-lake-ecological-context-and-water-quality-for-thousands-of-u-s-lakes
#11
Patricia A Soranno, Linda C Bacon, Michael Beauchene, Karen E Bednar, Edward G Bissell, Claire K Boudreau, Marvin G Boyer, Mary T Bremigan, Stephen R Carpenter, Jamie W Carr, Kendra S Cheruvelil, Samuel T Christel, Matt Claucherty, Sarah M Collins, Joseph D Conroy, John A Downing, Jed Dukett, C Emi Fergus, Christopher T Filstrup, Clara Funk, Maria J Gonzalez, Linda T Green, Corinna Gries, John D Halfman, Stephen K Hamilton, Paul C Hanson, Emily N Henry, Elizabeth M Herron, Celeste Hockings, James R Jackson, Kari Jacobson-Hedin, Lorraine L Janus, William W Jones, John R Jones, Caroline M Keson, Katelyn B S King, Scott A Kishbaugh, Jean-Francois Lapierre, Barbara Lathrop, Jo A Latimore, Yuehlin Lee, Noah R Lottig, Jason A Lynch, Leslie J Matthews, William H McDowell, Karen E B Moore, Brian P Neff, Sarah J Nelson, Samantha K Oliver, Michael L Pace, Donald C Pierson, Autumn C Poisson, Amina I Pollard, David M Post, Paul O Reyes, Donald O Rosenberry, Karen M Roy, Lars G Rudstam, Orlando Sarnelle, Nancy J Schuldt, Caren E Scott, Nicholas K Skaff, Nicole J Smith, Nick R Spinelli, Joseph J Stachelek, Emily H Stanley, John L Stoddard, Scott B Stopyak, Craig A Stow, Jason M Tallant, Pang-Ning Tan, Anthony P Thorpe, Michael J Vanni, Tyler Wagner, Gretchen Watkins, Kathleen C Weathers, Katherine E Webster, Jeffrey D White, Marcy K Wilmes, Shuai Yuan
Background: Understanding the factors that affect water quality and the ecological services provided by freshwater ecosystems is an urgent global environmental issue. Predicting how water quality will respond to global changes not only requires water quality data, but also information about the ecological context of individual water bodies across broad spatial extents. Because lake water quality is usually sampled in limited geographic regions, often for limited time periods, assessing the environmental controls of water quality requires compilation of many datasets across broad regions and across time into an integrated database...
October 19, 2017: GigaScience
https://www.readbyqxmd.com/read/29048533/parallel-sequencing-lives-or-what-makes-large-sequencing-projects-successful
#12
Javier Quilez, Enrique Vidal, François Le Dily, François Serra, Yasmina Cuartero, Ralph Stadhouders, Thomas Graf, Marc A Marti-Renom, Miguel Beato, Guillaume Filion
T47D_rep2 and b1913e6c1_51720e9cf were two Hi-C samples. They were born and processed at the same time, yet their fates were very different. The life of b1913e6c1_51720e9cf was simple and fruitful, while that of T47D_rep2 was full of accidents and sorrow. At the heart of these differences lies the fact that b1913e6c1_51720e9cf was born under a lab culture of Documentation, Automation, Traceability, Autonomy and compliance with the FAIR Principles. Their lives are a lesson for those who wish to embark on the journey of managing high throughput sequencing data...
October 18, 2017: GigaScience
https://www.readbyqxmd.com/read/29048483/draft-genome-of-the-gayal-bos-frontalis
#13
Ming-Shan Wang, Yan Zeng, Xiao Wang, Wen-Hui Nie, Jin-Huan Wang, Wei-Ting Su, Newton O Otecko, Zi-Jun Xiong, Sheng Wang, Kai-Xing Qu, Shou-Qing Yan, Min-Min Yang, Wen Wang, Yang Dong, Dong-Dong Wu, Ya-Ping Zhang
Background: Gayal (Bos frontalis), also known as mithan or mithun, is a large endangered semi-domesticated bovine that has a limited geographical distribution in the hill-forests of China, Northeast India, Bangladesh, Myanmar, and Bhutan. Many questions about the gayal such as its origin, population history as well as genetic basis of local adaptation remain largely unresolved. De novo sequencing and assembly of the whole gayal genome provides an opportunity to address these issues. Findings: We report a high-depth sequencing, de novo assembly, and annotation of a female Chinese gayal genome...
October 5, 2017: GigaScience
https://www.readbyqxmd.com/read/29048480/panax-ginseng-genome-examination-for-ginsenoside-biosynthesis
#14
Xu Jiang, Chu Yang, Liao Baosheng, Xiao Shuiming, Yin Qinggang, Bai Rui, Su He, Dong Linlin, Li Xiwen, Qian Jun, Zhang Jingjing, Zhang Yujun, Zhang Xiaoyan, Wu Mingli, Zhang Jie, Li Guozheng, Zhang Lei, Chang Zhenzhan, Zhang Yuebin, Jia Zhengwei, Liu Zhixiang, Daniel Afreh, Ruth Nahurira, Zhang Lianjuan, Cheng Ruiyang, Zhu Yingjie, Zhu Guangwei, Rao Wei, Zhou Chao, Qiao Lirui, Huang Zhihai, Cheng Yung-Chi, Chen Shilin
Background: Ginseng, which contain ginsenosides as bioactive compounds, has been regarded as an important traditional medicine for several millennia. However, the genetic background of ginseng remains poorly understood partly because of the plant's large and complex genome composition. Results: We report the entire genome sequence of Panax ginseng using next-generation sequencing. The 3.5Gb nucleotide sequence contained more than 60% repeats and encoded 42,006 predicted genes...
October 5, 2017: GigaScience
https://www.readbyqxmd.com/read/29048559/plant-phenomics-an-overview-of-image-acquisition-technologies-and-image-data-analysis-algorithms
#15
Fernando Perez-Sanz, Pedro J Navarro, Marcos Egea-Cortines
The study of phenomes or phenomics has been a central part of biology. The field of automatic phenotype acquisition technologies based on images has seen an important advance in the last years. As other high throughput technologies, it bears from a common set of problems, including data acquisition and analysis. In this review, we give an overview of the main systems developed to acquire images. We give an in-depth analysis of image processing with its major issues, and the algorithms that are being used or emerging as useful to obtain data out of images in an automatic fashion...
October 3, 2017: GigaScience
https://www.readbyqxmd.com/read/29048539/indexcov-fast-coverage-quality-control-for-whole-genome-sequencing
#16
Brent S Pedersen, Ryan L Collins, Michael E Talkowski, Aaron R Quinlan
The BAM1 and CRAM2 formats provide a supplementary linear index that facilitates rapid access to sequence alignments in arbitrary genomic regions. Comparing consecutive entries in a BAM or CRAM index allows one to infer the number of alignment records per genomic region for use as an effective proxy of sequence depth in each genomic region. Based on these properties, we have developed indexcov, an efficient estimator of whole-genome sequencing coverage to rapidly identify samples with aberrant coverage profiles, reveal large scale chromosomal anomalies, recognize potential batch effects, and infer the sex of a sample...
September 18, 2017: GigaScience
https://www.readbyqxmd.com/read/29048540/long-read-sequencing-of-the-coffee-bean-transcriptome-reveals-the-diversity-of-full-length-transcripts
#17
Bing Cheng, Agnelo Furtado, Robert J Henry
Background: Polyploidization contributes to the complexity of gene expression resulting in numerous related but different transcripts. This study explored the transcriptome diversity and complexity of tetraploid Arabica coffee ( Coffea arabica ) bean. Long-read sequencing (LRS) by Pacbio Isoform sequencing (Iso-seq) was used to obtain full-length transcripts without the difficulty and uncertainty of assembly required for reads from short read technologies. The tetraploid transcriptome was annotated and compared with data from the sub-genome progenitors...
August 30, 2017: GigaScience
https://www.readbyqxmd.com/read/29092041/a-3-way-hybrid-approach-to-generate-a-new-high-quality-chimpanzee-reference-genome-pan_tro_3-0
#18
Lukas F K Kuderna, Chad Tomlinson, LaDeana W Hillier, Annabel Tran, Ian T Fiddes, Joel Armstrong, Hafid Laayouni, David Gordon, John Huddleston, Raquel Garcia Perez, Inna Povolotskaya, Aitor Serres Armero, Jèssica Gómez Garrido, Daniel Ho, Paolo Ribeca, Tyler Alioto, Richard E Green, Benedict Paten, Arcadi Navarro, Jaume Betranpetit, Javier Herrero, Evan E Eichler, Andrew J Sharp, Lars Feuk, Wesley C Warren, Tomas Marques-Bonet
The chimpanzee is arguably the most important species for the study of human origins. A key resource for these studies is a high-quality reference genome assembly; however, as with most mammalian genomes, the current iteration of the chimpanzee reference genome assembly is highly fragmented. In the current iteration of the chimpanzee reference genome assembly (Pan_tro_2.1.4), the sequence is scattered across more then 183 000 contigs, incorporating more than 159 000 gaps, with a genome-wide contig N50 of 51 Kbp...
November 1, 2017: GigaScience
https://www.readbyqxmd.com/read/29069494/the-first-near-complete-assembly-of-the-hexaploid-bread-wheat-genome-triticum-aestivum
#19
Aleksey V Zimin, Daniela Puiu, Richard Hall, Sarah Kingan, Bernardo J Clavijo, Steven L Salzberg
Common bread wheat, Triticum aestivum, has one of the most complex genomes known to science, with 6 copies of each chromosome, enormous numbers of near-identical sequences scattered throughout, and an overall haploid size of more than 15 billion bases. Multiple past attempts to assemble the genome have produced assemblies that were well short of the estimated genome size. Here we report the first near-complete assembly of T. aestivum, using deep sequencing coverage from a combination of short Illumina reads and very long Pacific Biosciences reads...
November 1, 2017: GigaScience
https://www.readbyqxmd.com/read/29048555/an-architecture-for-genomics-analysis-in-a-clinical-setting-using-galaxy-and-docker
#20
W Digan, H Countouris, M Barritault, D Baudoin, P Laurent-Puig, H Blons, A Burgun, B Rance
Next-generation sequencing is used on a daily basis to perform molecular analysis to determine subtypes of disease (e.g., in cancer) and to assist in the selection of the optimal treatment. Clinical bioinformatics handles the manipulation of the data generated by the sequencer, from the generation to the analysis and interpretation. Reproducibility and traceability are crucial issues in a clinical setting. We have designed an approach based on Docker container technology and Galaxy, the popular bioinformatics analysis support open-source software...
November 1, 2017: GigaScience
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