Articles

Genomic epidemiology of SARS-CoV-2 in Esteio, Rio Grande do Sul, Brazil

Brazil is the third country most affected by Coronavirus disease-2019 (COVID-19), but viral evolution in municipality resolution is still poorly understood in Brazil and it is crucial to understand the epidemi...

Authors: Vinícius Bonetti Franceschi, Gabriel Dickin Caldana, Amanda de Menezes Mayer, Gabriela Bettella Cybis, Carla Andretta Moreira Neves, Patrícia Aline Gröhs Ferrareze, Meriane Demoliner, Paula Rodrigues de Almeida, Juliana Schons Gularte, Alana Witt Hansen, Matheus Nunes Weber, Juliane Deise Fleck, Ricardo Ariel Zimerman, Lívia Kmetzsch, Fernando Rosado Spilki and Claudia Elizabeth Thompson

Genomic selection and genetic gain for nut yield in an Australian macadamia breeding population

Improving yield prediction and selection efficiency is critical for tree breeding. This is vital for macadamia trees with the time from crossing to production of new cultivars being almost a quarter of a centu...

Authors: Katie M. O’Connor, Ben J. Hayes, Craig M. Hardner, Mobashwer Alam, Robert J. Henry and Bruce L. Topp

Dynamic transcriptome and histomorphology analysis of developmental traits of hindlimb thigh muscle from Odorrana tormota and its adaptability to different life history stages

Systematic studies on the development and adaptation of hindlimb muscles in anura amphibians are rare. Here, we integrated analysis of transcriptome and histomorphological data for the hindlimb thigh muscle of Od...

Authors: Yilin Shu, Jun He, Huijuan Zhang, Guangxuan Liu, Shikun Li, Shuaitao Deng and Hailong Wu

Prevalence, antibiotic resistance, virulence and genetic diversity of Staphylococcus aureus isolated from bulk tank milk samples of U.S. dairy herds

Colonization of dairy cows by Staphylococcus aureus (S. aureus), especially those which are multi-drug resistant and toxin producing, is a concern for animal health and well-being as well as public health. The ob...

Authors: Kruthika Patel, Sandra M. Godden, Erin E. Royster, Brian A. Crooker, Timothy J. Johnson, Emily A. Smith and Srinand Sreevatsan

Insights into the genome architecture and evolution of Shiga toxin encoding bacteriophages of Escherichia coli

A total of 179 Shiga toxin-producing Escherichia coli (STEC) complete genomes were analyzed in terms of serotypes, prophage coding regions, and stx gene variants and their distribution. We further examined the ge...

Authors: Graça Pinto, Marta Sampaio, Oscar Dias, Carina Almeida, Joana Azeredo and Hugo Oliveira

Correction to: Assessment of the mechanism of drug resistance in Trichophyton mentagrophytes in response to various substances

Authors: Chenwen Xiao, Jiaoyu Wang, Zhenfeng Liao, Yee Huang, Quanan Ji, Yan Liu, Fei Su, Lijun Xu, Qiang Wei, Yao Pan, Ke Li and Guolian Bao

The symbiotic relationship between Caenorhabditis elegans and members of its microbiome contributes to worm fitness and lifespan extension

A healthy microbiome influences host physiology through a mutualistic relationship, which can be important for the host to cope with cellular stress by promoting fitness and survival. The mammalian microbiome ...

Authors: Orçun Haçariz, Charles Viau, Farial Karimian and Jianguo Xia

Investigating the impact of reference assembly choice on genomic analyses in a cattle breed

Reference-guided read alignment and variant genotyping are prone to reference allele bias, particularly for samples that are greatly divergent from the reference genome. A Hereford-based assembly is the widely...

Authors: Audald Lloret-Villas, Meenu Bhati, Naveen Kumar Kadri, Ruedi Fries and Hubert Pausch

Asymmetric expression of homoeologous genes contributes to dietary adaption of an allodiploid hybrid fish derived from Megalobrama amblycephala (♀) × Culter alburnus (♂)

Hybridization, which can quickly merge two or more divergent genomes and form new allopolyploids, is an important technique in fish genetic breeding. However, the merged subgenomes must adjust and coexist with...

Authors: Wuhui Li, Shi Wang, Jie Hu, Chenchen Tang, Chang Wu, Junmei Liu, Li Ren, Chengfei Sun, Junjian Dong, Shaojun Liu and Xing Ye

Genome-wide identification and expression analysis of the AT-hook Motif Nuclear Localized gene family in soybean

Soybean is an important legume crop and has significant agricultural and economic value. Previous research has shown that the AT-Hook Motif Nuclear Localized (AHL) gene family is highly conserved in land plants, ...

Authors: Min Wang, Bowei Chen, Wei Zhou, Linan Xie, Lishan Wang, Yonglan Zhang and Qingzhu Zhang

Prunus persica plant endogenous peptides PpPep1 and PpPep2 cause PTI-like transcriptome reprogramming in peach and enhance resistance to Xanthomonas arboricola pv. pruni

Rosaceae species are economically highly relevant crops. Their cultivation systems are constrained by phytopathogens causing severe losses. Plants respond to invading pathogens through signaling mechanisms, a ...

Authors: Laura Foix, Anna Nadal, Maja Zagorščak, Živa Ramšak, Anna Esteve-Codina, Kristina Gruden and Maria Pla

Gene expression and alternative splicing dynamics are perturbed in female head transcriptomes following heterospecific copulation

Despite the growing interest in the female side of copulatory interactions, the roles played by differential expression and alternative splicing mechanisms of pre-RNA on tissues outside of the reproductive tract ...

Authors: Fernando Diaz, Carson W. Allan, Therese Ann Markow, Jeremy M. Bono and Luciano M. Matzkin

Correction to: Comparative genomics and physiological investigation supported safety, cold adaptation, efficient hydrolytic and plant growth-promoting potential of psychrotrophic Glutamicibacter arilaitensis LJH19, isolated from night-soil compost

Authors: Shruti Sinai Borker, Aman Thakur, Sanjeet Kumar, Sareeka Kumari, Rakshak Kumar and Sanjay Kumar

Evaluation of tools for identifying large copy number variations from ultra-low-coverage whole-genome sequencing data

Detection of copy number variations (CNVs) from high-throughput next-generation whole-genome sequencing (WGS) data has become a widely used research method during the recent years. However, only a little is kn...

Authors: Johannes Smolander, Sofia Khan, Kalaimathy Singaravelu, Leni Kauko, Riikka J. Lund, Asta Laiho and Laura L. Elo

Single nucleotide polymorphisms reveal genetic diversity in New Mexican chile peppers (Capsicum spp.)

Chile peppers (Capsicum spp.) are among the most important horticultural crops in the world due to their number of uses. They are considered a major cultural and economic crop in the state of New Mexico in the Un...

Authors: Dennis N. Lozada, Madhav Bhatta, Danise Coon and Paul W. Bosland

ddRAD sequencing: an emerging technology added to the biosecurity toolbox for tracing the origin of brown marmorated stink bug, Halyomorpha halys (Hemiptera: Pentatomidae)

Brown marmorated stink bug (BMSB), Halyomorpha halys (Hemiptera: Pentatomidae) is native to East Asia but has invaded many countries in the world. BMSB is a polyphagous insect pest and causes significant economic...

Authors: Juncong Yan, Gábor Vétek, Chandan Pal, Jinping Zhang, Rania Gmati, Qing-Hai Fan, Disna N. Gunawardana, Allan Burne, Diane Anderson, Rebijith Kayattukandy Balan, Sherly George, Péter Farkas and Dongmei Li

Genome-wide detection of CNVs and their association with performance traits in broilers

Copy number variations (CNVs) are a major type of structural genomic variants that underlie genetic architecture and phenotypic variation of complex traits, not only in humans, but also in livestock animals. W...

Authors: Anna Carolina Fernandes, Vinicius Henrique da Silva, Carolina Purcell Goes, Gabriel Costa Monteiro Moreira, Thaís Fernanda Godoy, Adriana Mércia Guaratini Ibelli, Jane de Oliveira Peixoto, Maurício Egídio Cantão, Mônica Corrêa Ledur, Fernanda Marcondes de Rezende and Luiz Lehmann Coutinho

Tissue-specific transcriptome analyses reveal candidate genes for stilbene, flavonoid and anthraquinone biosynthesis in the medicinal plant Polygonum cuspidatum

Polygonum cuspidatum Sieb. et Zucc. is a well-known medicinal plant whose pharmacological effects derive mainly from its stilbenes, anthraquinones, and flavonoids. These compounds accumulate differentially in the...

Authors: Xiaowei Wang, Hongyan Hu, Zhijun Wu, Haili Fan, Guowei Wang, Tuanyao Chai and Hong Wang

Structural landscape of the complete genomes of dengue virus serotypes and other viral hemorrhagic fevers

With more than 300 million potentially infected people every year, and with the expanded habitat of mosquitoes due to climate change, Dengue virus (DENV) cannot be considered anymore only a tropical disease. T...

Authors: Riccardo Delli Ponti and Marek Mutwil

Population genetic considerations for using biobanks as international resources in the pandemic era and beyond

The past years have seen the rise of genomic biobanks and mega-scale meta-analysis of genomic data, which promises to reveal the genetic underpinnings of health and disease. However, the over-representation of...

Authors: Hannah Carress, Daniel John Lawson and Eran Elhaik

Genome-wide analysis of the serine carboxypeptidase-like protein family in Triticum aestivum reveals TaSCPL184-6D is involved in abiotic stress response

The serine carboxypeptidase-like protein (SCPL) family plays a vital role in stress response, growth, development and pathogen defense. However, the identification and functional analysis of SCPL gene family memb...

Authors: Xiaomin Xu, Lili Zhang, Wan Zhao, Liang Fu, Yuxuan Han, Keke Wang, Luyu Yan, Ye Li, Xiao-Hong Zhang and Dong-Hong Min

Transcriptome analysis of ovary tissues from low- and high-yielding Changshun green-shell laying hens

Changshun green-shell laying hens are unique to Guizhou Province, China, and have high egg quality. Improving egg production performance has become an important breeding task, and in recent years, the developm...

Authors: Ren Mu, Yi-yin Yu, Tuya Gegen, Di Wen, Fen Wang, Zhi Chen and Wen-bin Xu

TarDB: an online database for plant miRNA targets and miRNA-triggered phased siRNAs

In plants, microRNAs (miRNAs) are pivotal regulators of plant development and stress responses. Different computational tools and web servers have been developed for plant miRNA target prediction; however, in ...

Authors: Jing Liu, Xiaonan Liu, Siju Zhang, Shanshan Liang, Weijiang Luan and Xuan Ma

De novo transcriptome analysis and comparative expression profiling of genes associated with the taste-modifying protein neoculin in Curculigo latifolia and Curculigo capitulata fruits

Curculigo latifolia is a perennial plant endogenous to Southeast Asia whose fruits contain the taste-modifying protein neoculin, which binds to sweet receptors and makes sour fruits taste sweet. Although similar ...

Authors: Satoshi Okubo, Kaede Terauchi, Shinji Okada, Yoshikazu Saito, Takao Yamaura, Takumi Misaka, Ken-ichiro Nakajima, Keiko Abe and Tomiko Asakura

Species and population specific gene expression in blood transcriptomes of marine turtles

Transcriptomic data has demonstrated utility to advance the study of physiological diversity and organisms’ responses to environmental stressors. However, a lack of genomic resources and challenges associated ...

Authors: Shreya M. Banerjee, Jamie Adkins Stoll, Camryn D. Allen, Jennifer M. Lynch, Heather S. Harris, Lauren Kenyon, Richard E. Connon, Eleanor J. Sterling, Eugenia Naro-Maciel, Kathryn McFadden, Margaret M. Lamont, James Benge, Nadia B. Fernandez, Jeffrey A. Seminoff, Scott R. Benson, Rebecca L. Lewison…

Exploring genetic resistance to infectious salmon anaemia virus in Atlantic salmon by genome-wide association and RNA sequencing

Infectious Salmonid Anaemia Virus (ISAV) causes a notifiable disease that poses a large threat for Atlantic salmon (Salmo salar) aquaculture worldwide. There is no fully effective treatment or vaccine, and theref...

Authors: O. Gervais, A. Barria, A. Papadopoulou, R. L. Gratacap, B. Hillestad, A. E. Tinch, S. A. M. Martin, D. Robledo and R. D. Houston

Differential expression of miRNAs in the presence of B chromosome in the cichlid fish Astatotilapia latifasciata

B chromosomes (Bs) are extra elements observed in diverse eukaryotes, including animals, plants and fungi. Although Bs were first identified a century ago and have been studied in hundreds of species, their bi...

Authors: Jordana Inácio Nascimento-Oliveira, Bruno Evaristo Almeida Fantinatti, Ivan Rodrigo Wolf, Adauto Lima Cardoso, Erica Ramos, Nathalie Rieder, Rogerio de Oliveira and Cesar Martins

Integrative genomics of the mammalian alveolar macrophage response to intracellular mycobacteria

Bovine TB (bTB), caused by infection with Mycobacterium bovis, is a major endemic disease affecting global cattle production. The key innate immune cell that first encounters the pathogen is the alveolar macropha...

Authors: Thomas J. Hall, Michael P. Mullen, Gillian P. McHugo, Kate E. Killick, Siobhán C. Ring, Donagh P. Berry, Carolina N. Correia, John A. Browne, Stephen V. Gordon and David E. MacHugh

A comprehensive RNA-Seq-based gene expression atlas of the summer squash (Cucurbita pepo) provides insights into fruit morphology and ripening mechanisms

Summer squash (Cucurbita pepo: Cucurbitaceae) are a popular horticultural crop for which there is insufficient genomic and transcriptomic information. Gene expression atlases are crucial for the identification of...

Authors: Aliki Xanthopoulou, Javier Montero-Pau, Belén Picó, Panagiotis Boumpas, Eleni Tsaliki, Harry S. Paris, Athanasios Tsaftaris, Apostolos Kalivas, Ifigeneia Mellidou and Ioannis Ganopoulos

How imputation can mitigate SNP ascertainment Bias

Population genetic studies based on genotyped single nucleotide polymorphisms (SNPs) are influenced by a non-random selection of the SNPs included in the used genotyping arrays. The resulting bias in the estim...

Authors: Johannes Geibel, Christian Reimer, Torsten Pook, Steffen Weigend, Annett Weigend and Henner Simianer

Disentangling the aging gene expression network of termite queens

Most insects are relatively short-lived, with a maximum lifespan of a few weeks, like the aging model organism, the fruit-fly Drosophila melanogaster. By contrast, the queens of many social insects (termites, ant...

Authors: José Manuel Monroy Kuhn, Karen Meusemann and Judith Korb

Transcriptomics analysis of differentially expressed genes in subcutaneous and perirenal adipose tissue of sheep as affected by their pre- and early postnatal malnutrition histories

Early life malnutrition is known to target adipose tissue with varying impact depending on timing of the insult. This study aimed to identify differentially expressed genes in subcutaneous (SUB) and perirenal ...

Authors: Sharmila Ahmad, Markus Hodal Drag, Suraya Mohamad Salleh, Zexi Cai and Mette Olaf Nielsen

Transcriptomic analysis reveals pronounced changes in gene expression due to sub-lethal pyrethroid exposure and ageing in insecticide resistance Anopheles coluzzii

Malaria control is heavily reliant on the use of insecticides that target and kill the adult female Anopheline vector. The intensive use of insecticides of the pyrethroid class has led to widespread resistance...

Authors: V. A. Ingham, F. Brown and H. Ranson

Identification of the conserved long non-coding RNAs in myogenesis

Our understanding of genome regulation is ever-evolving with the continuous discovery of new modes of gene regulation, and transcriptomic studies of mammalian genomes have revealed the presence of a considerab...

Authors: Anupam Bhattacharya, Simang Champramary, Tanya Tripathi, Debajit Thakur, Ilya Ioshikhes, Satyendra Kumar Singh and Soumyadeep Nandi

Structural variations in papaya genomes

Structural variations (SVs) are a type of mutations that have not been widely detected in plant genomes and studies in animals have shown their role in the process of domestication. An in-depth study of SVs wi...

Authors: Zhenyang Liao, Xunxiao Zhang, Shengcheng Zhang, Zhicong Lin, Xingtan Zhang and Ray Ming

Genome-wide association study reveals novel loci associated with feeding behavior in Pekin ducks

Feeding behavior traits are an essential part of livestock production. However, the genetic base of feeding behavior traits remains unclear in Pekin ducks. This study aimed to determine novel loci related to f...

Authors: Guang-Sheng Li, Feng Zhu, Fan Zhang, Fang-Xi Yang, Jin-Ping Hao and Zhuo-Cheng Hou

Analysis of differentially expressed Sclerotinia sclerotiorum genes during the interaction with moderately resistant and highly susceptible chickpea lines

Sclerotinia sclerotiorum, the cause of Sclerotinia stem rot (SSR), is a host generalist necrotrophic fungus that can cause major yield losses in chickpea (Cicer arietinum) production. This study used RNA sequenci...

Authors: Virginia W. Mwape, Fredrick M. Mobegi, Roshan Regmi, Toby E. Newman, Lars G. Kamphuis and Mark C. Derbyshire

Genome-wide detection of CNV regions and their potential association with growth and fatness traits in Duroc pigs

In the process of pig breeding, the average daily gain (ADG), days to 100 kg (AGE), and backfat thickness (BFT) are directly related to growth rate and fatness. However, the genetic mechanisms involved are not...

Authors: Yibin Qiu, Rongrong Ding, Zhanwei Zhuang, Jie Wu, Ming Yang, Shenping Zhou, Yong Ye, Qian Geng, Zheng Xu, Sixiu Huang, Gengyuan Cai, Zhenfang Wu and Jie Yang

Metabolome and transcriptome profiling reveals anthocyanin contents and anthocyanin-related genes of chimeric leaves in Ananas comosus var. bracteatus

Ananas comosus var. bracteatus is a colorful plant used as a cut flower or landscape ornamental. The unique foliage color of this plant includes both green and red leaves and, as a trait of interest, deserves inv...

Authors: Xuzixin Zhou, Yanbin Xue, Meiqin Mao, Yehua He, Mark Owusu Adjei, Wei Yang, Hao Hu, Jiawen Liu, Lijun Feng, Huiling Zhang, Jiaheng Luo, Xi Li, Lingxia Sun, Zhuo Huang and Jun Ma

Long-read metagenomics retrieves complete single-contig bacterial genomes from canine feces

Long-read sequencing in metagenomics facilitates the assembly of complete genomes out of complex microbial communities. These genomes include essential biologic information such as the ribosomal genes or the m...

Authors: Anna Cuscó, Daniel Pérez, Joaquim Viñes, Norma Fàbregas and Olga Francino

Whole-genome resequencing using next-generation and Nanopore sequencing for molecular characterization of T-DNA integration in transgenic poplar 741

The molecular characterization information of T-DNA integration is not only required by public risk assessors and regulators, but is also closely related to the expression of exogenous and endogenous genes. At...

Authors: Xinghao Chen, Yan Dong, Yali Huang, Jianmin Fan, Minsheng Yang and Jun Zhang

Comparative transcriptomic analysis reveals an association of gibel carp fatty liver with ferroptosis pathway

Fatty liver has become a main problem that causes huge economic losses in many aquaculture modes. It is a common physiological or pathological phenomenon in aquaculture, but the causes and occurring mechanism ...

Authors: Xiao-Juan Zhang, Li Zhou, Wei-Jia Lu, Wen-Xuan Du, Xiang-Yuan Mi, Zhi Li, Xi-Yin Li, Zhong-Wei Wang, Yang Wang, Ming Duan and Jian-Fang Gui

Correction to: A prototypical non-malignant epithelial model to study genome dynamics and concurrently monitor micro-RNAs and proteins in situ during oncogene-induced senescence

An amendment to this paper has been published and can be accessed via the original article.

Authors: Eirini-Stavroula Komseli, Ioannis S. Pateras, Thorbjørn Krejsgaard, Konrad Stawiski, Sophia V. Rizou, Alexander Polyzos, Fani-Marlen Roumelioti, Maria Chiourea, Ioanna Mourkioti, Eleni Paparouna, Christos P. Zampetidis, Sentiljana Gumeni, Ioannis P. Trougakos, Dafni-Eleftheria Pefani, Eric O’Neill, Sarantis Gagos…

Transcriptional profile of oil palm pathogen, Ganoderma boninense, reveals activation of lignin degradation machinery and possible evasion of host immune response

The white-rot fungi in the genus Ganoderma interact with both living and dead angiosperm tree hosts. Two Ganoderma species, a North American taxon, G. zonatum and an Asian taxon, G. boninense, have primarily been...

Authors: Braham Dhillon, Richard C. Hamelin and Jeffrey A. Rollins

Mitogenomic diversity and phylogeny analysis of yak (Bos grunniens)

Mitochondrial genome has aseries of characteristics such as simple structure, no recombination, maternalinheritance, stable structure, fast evolution rate, and high copy number. Moreover, it is easy to be sequ...

Authors: Xingdong Wang, Jie Pei, Pengjia Bao, Mengli Cao, Shaoke Guo, Rende Song, Weiru Song, Chunnian Liang, Ping Yan and Xian Guo

Transcriptome of different fruiting stages in the cultivated mushroom Cyclocybe aegerita suggests a complex regulation of fruiting and reveals enzymes putatively involved in fungal oxylipin biosynthesis

Cyclocybe aegerita (syn. Agrocybe aegerita) is a commercially cultivated mushroom. Its archetypal agaric morphology and its ability to undergo its whole life cycle under laboratory conditions makes this fungus a ...

Authors: Axel Orban, Annsophie Weber, Robert Herzog, Florian Hennicke and Martin Rühl

Genomic analysis of novel Yarrowia-like yeast symbionts associated with the carrion-feeding burying beetle Nicrophorus vespilloides

Mutualistic interactions with microbes can help insects adapt to extreme environments and unusual diets. An intriguing example is the burying beetle Nicrophorus vespilloides, which feeds and reproduces on small v...

Authors: Karina Brinkrolf, Shantanu P. Shukla, Sven Griep, Oliver Rupp, Philipp Heise, Alexander Goesmann, David G. Heckel, Heiko Vogel and Andreas Vilcinskas

Strategies for detecting and identifying biological signals amidst the variation commonly found in RNA sequencing data

RNA sequencing analysis focus on the detection of differential gene expression changes that meet a two-fold minimum change between groups. The variability present in RNA sequencing data may obscure the detecti...

Authors: William W. Wilfinger, Robert Miller, Hamid R. Eghbalnia, Karol Mackey and Piotr Chomczynski

A fast wavelet-based functional association analysis replicates several susceptibility loci for birth weight in a Norwegian population

Birth weight (BW) is one of the most widely studied anthropometric traits in humans because of its role in various adult-onset diseases. The number of loci associated with BW has increased dramatically since t...

Authors: William R. P. Denault, Julia Romanowska, Øyvind Helgeland, Bo Jacobsson, Håkon K. Gjessing and Astanand Jugessur

Hierarchicell: an R-package for estimating power for tests of differential expression with single-cell data

Study design is a critical aspect of any experiment, and sample size calculations for statistical power that are consistent with that study design are central to robust and reproducible results. However, the e...

Authors: Kip D. Zimmerman and Carl D. Langefeld