Articles

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

Comprehensive analysis of differentially expressed circRNAs and ceRNA regulatory network in porcine skeletal muscle

Circular RNA (circRNA), a novel class of non-coding RNA, has a closed-loop structure with important functions in skeletal muscle growth. The purpose of this study was to investigate the role of differentially ...

Authors: Meng Li, Na Zhang, Wanfeng Zhang, Wei Hei, Chunbo Cai, Yang Yang, Chang Lu, Pengfei Gao, Xiaohong Guo, Guoqing Cao and Bugao Li

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

RNA sequencing-based analysis of the magnum tissues revealed the novel genes and biological pathways involved in the egg-white formation in the laying hen

The mechanism of egg formation in the oviduct of laying hens is tightly controlled; each segment of the oviduct contributes a unique component of the egg. Several genes/proteins are involved in the synthesis o...

Authors: Nirvay Sah, Donna Lee Kuehu, Vedbar Singh Khadka, Youping Deng, Rajesh Jha, Sanjeev Wasti and Birendra Mishra

Identification and characterization of HAK/KUP/KT potassium transporter gene family in barley and their expression under abiotic stress

HAK/KUP/KT (High-affinity K⁺ transporters/K⁺ uptake permeases/K⁺ transporters) is the largest potassium transporter family in plants, and plays pivotal roles in K⁺ uptake and transport, as well as biotic and abio...

Authors: Kangfeng Cai, Fanrong Zeng, Junmei Wang and Guoping Zhang

Basic leucine zipper (bZIP) transcription factor genes and their responses to drought stress in ginseng, Panax ginseng C.A. Meyer

Ginseng is an important medicinal herb in Asia and Northern America. The basic leucine zipper (bZIP) transcription factor genes play important roles in many biological processes and plant responses to abiotic and...

Authors: Hongjie Li, Jing Chen, Qi Zhao, Yilai Han, Li Li, Chunyu Sun, Kangyu Wang, Yanfang Wang, Mingzhu Zhao, Ping Chen, Jun Lei, Yi Wang and Meiping Zhang

Genome-wide analysis of ATP-binding cassette transporter provides insight to genes related to bioactive metabolite transportation in Salvia miltiorrhiza

ATP-binding cassette (ABC) transporters have been found to play important roles in metabolic transport in plant cells, influencing subcellular compartmentalisation and tissue distribution of these metabolic co...

Authors: Li Yan, Jianhong Zhang, Hongyu Chen and Hongmei Luo

Genome-wide identification and analysis of class III peroxidases in Betula pendula

Class III peroxidases (POD) proteins are widely present in the plant kingdom that are involved in a broad range of physiological processes including stress responses and lignin polymerization throughout the pl...

Authors: Kewei Cai, Huixin Liu, Song Chen, Yi Liu, Xiyang Zhao and Su Chen

Comparative genomics of the coconut crab and other decapod crustaceans: exploring the molecular basis of terrestrial adaptation

The complex life cycle of the coconut crab, Birgus latro, begins when an obligate terrestrial adult female visits the intertidal to hatch zoea larvae into the surf. After drifting for several weeks in the ocean, ...

Authors: Werner Pieter Veldsman, Ka Yan Ma, Jerome Ho Lam Hui, Ting Fung Chan, J. Antonio Baeza, Jing Qin and Ka Hou Chu

Decoding first complete chloroplast genome of toothbrush tree (Salvadora persica L.): insight into genome evolution, sequence divergence and phylogenetic relationship within Brassicales

Salvadora persica L. (Toothbrush tree – Miswak; family-Salvadoraceae) grows in the arid-land ecosystem and possesses economic and medicinal importance. The species, genus and the family have no genomic datasets a...

Authors: Abdul Latif Khan, Sajjad Asaf, Lubna, Ahmed Al-Rawahi and Ahmed Al-Harrasi

Genome-wide analyses of the relict gull (Larus relictus): insights and evolutionary implications

The relict gull (Larus relictus), was classified as vulnerable on the IUCN Red List and is a first-class national protected bird in China. Genomic resources for L. relictus are lacking, which limits the study of ...

Authors: Chao Yang, Xuejuan Li, Qingxiong Wang, Hao Yuan, Yuan Huang and Hong Xiao

Genome-wide identification and transcriptional characterization of DNA methyltransferases conferring temperature-sensitive male sterility in wheat

DNA methyltransferase (DMT) genes contribute to plant stress responses and development by de novo establishment and subsequent maintenance of DNA methylation during replication. The photoperiod and/or temperat...

Authors: Dan Li, Bian-E Feng, Yong-Jie Liu, Jie Gong, Yi-Miao Tang, Li-Ping Zhang, Bin-Shuang Pang, Ren-Wei Sun, Feng-Ting Zhang, Zhao-Bo Chen, Yong-Bo Wang, Xian-Chao Chen, Ai-Ping Wang, Chang-Ping Zhao and Shi-Qing Gao

LCM and RNA-seq analyses revealed roles of cell cycle and translational regulation and homoeolog expression bias in cotton fiber cell initiation

Cotton fibers provide a powerful model for studying cell differentiation and elongation. Each cotton fiber is a singular and elongated cell derived from epidermal-layer cells of a cotton seed. Efforts to under...

Authors: Atsumi Ando, Ryan C. Kirkbride, Don C. Jones, Jane Grimwood and Z. Jeffrey Chen

Knock out of specific maternal vitellogenins in zebrafish (Danio rerio) evokes vital changes in egg proteomic profiles that resemble the phenotype of poor quality eggs

We previously reported the results of CRISPR/Cas9 knock-out (KO) of type-I and type-III vitellogenins (Vtgs) in zebrafish, which provided the first experimental evidence on essentiality and disparate functioni...

Authors: Ozlem Yilmaz, Amelie Patinote, Emmanuelle Com, Charles Pineau and Julien Bobe

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

Night-soil compost (NSC) has traditionally been conserving water and a source of organic manure in northwestern Himalaya. Lately, this traditional method is declining due to modernization, its unhygienic condi...

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

Correction to: Comparative genome analyses of four rice-infecting Rhizoctonia solani isolates reveal extensive enrichment of homogalacturonan modification genes

Authors: Da-Young Lee, Jongbum Jeon, Ki-Tae Kim, Kyeongchae Cheong, Hyeunjeong Song, Gobong Choi, Jaeho Ko, Stephen O. Opiyo, James C. Correll, Shimin Zuo, Sheshu Madhav, Guo-Liang Wang and Yong-Hwan Lee

A genome-wide scan of copy number variants in three Iranian indigenous river buffaloes

In Iran, river buffalo is of great importance. It plays an important role in the economy of the Country, because its adaptation to harsh climate conditions and long productive lifespan permitting its farming a...

Authors: Maria G. Strillacci, Hossein Moradi-Shahrbabak, Pourya Davoudi, Seyed Mohammad Ghoreishifar, Mahdi Mokhber, Anoar Jamai Masroure and Alessandro Bagnato

Dense time-course gene expression profiling of the Drosophila melanogaster innate immune response

Immune responses need to be initiated rapidly, and maintained as needed, to prevent establishment and growth of infections. At the same time, resources need to be balanced with other physiological processes. O...

Authors: Florencia Schlamp, Sofie Y. N. Delbare, Angela M. Early, Martin T. Wells, Sumanta Basu and Andrew G. Clark

Genome sequence, transcriptome, and annotation of rodent malaria parasite Plasmodium yoelii nigeriensis N67

Rodent malaria parasites are important models for studying host-malaria parasite interactions such as host immune response, mechanisms of parasite evasion of host killing, and vaccine development. One of the r...

Authors: Cui Zhang, Cihan Oguz, Sue Huse, Lu Xia, Jian Wu, Yu-Chih Peng, Margaret Smith, Jack Chen, Carole A. Long, Justin Lack and Xin-zhuan Su

Genome of the destructive oomycete Phytophthora cinnamomi provides insights into its pathogenicity and adaptive potential

Phytophthora cinnamomi is an oomycete pathogen of global relevance. It is considered as one of the most invasive species, which has caused irreversible damage to natural ecosystems and horticultural crops. There ...

Authors: Juanita Engelbrecht, Tuan A. Duong, S. Ashok Prabhu, Mohamed Seedat and Noëlani van den Berg

Draft genome of a biparental beetle species, Lethrus apterus

The lack of an understanding about the genomic architecture underpinning parental behaviour in subsocial insects displaying simple parental behaviours prevents the development of a full understanding about the...

Authors: Nikoletta A. Nagy, Rita Rácz, Oliver Rimington, Szilárd Póliska, Pablo Orozco-terWengel, Michael W. Bruford and Zoltán Barta

Genome-wide identification of sucrose nonfermenting-1-related protein kinase (SnRK) genes in barley and RNA-seq analyses of their expression in response to abscisic acid treatment

Sucrose nonfermenting-1 (SNF1)-related protein kinases (SnRKs) play important roles in regulating metabolism and stress responses in plants, providing a conduit for crosstalk between metabolic and stress signa...

Authors: Zhiwei Chen, Longhua Zhou, Panpan Jiang, Ruiju Lu, Nigel G. Halford and Chenghong Liu

Transcriptome analysis reveals gene responses to herbicide, tribenuron methyl, in Brassica napus L. during seed germination

Tribenuron methyl (TBM) is an herbicide that inhibits sulfonylurea acetolactate synthase (ALS) and is one of the most widely used broad-leaved herbicides for crop production. However, soil residues or drifting...

Authors: Liuyan Wang, Ruili Wang, Wei Lei, Jiayi Wu, Chenyang Li, Hongsong Shi, Lijiao Meng, Fang Yuan, Qingyuan Zhou and Cui Cui

Transcriptomic analysis of α-linolenic acid content and biosynthesis in Paeonia ostii fruits and seeds

Paeonia ostii is a potentially important oilseed crop because its seed yield is high, and the seeds are rich in α-linolenic acid (ALA). However, the molecular mechanisms underlying ALA biosynthesis during seed ke...

Authors: Shui-Yan Yu, Xiao Zhang, Liang-Bo Huang, Yu-Ping Lyu, Ying Zhang, Zu-Jie Yao, Xiao-Xiao Zhang, Jun-Hui Yuan and Yong-Hong Hu