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Journal BMC Genomics

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Functional insights from the GC-poor genomes of two aphid parasitoids, Aphidius ervi and Lysiphlebus fabarum.

Alice B Dennis, Gabriel I Ballesteros, Stéphanie Robin, Lukas Schrader, Jens Bast, Jan Berghöfer, Leo W Beukeboom, Maya Belghazi, Anthony Bretaudeau, Jan Buellesbach, Elizabeth Cash, Dominique Colinet, Zoé Dumas, Mohammed Errbii, Patrizia Falabella, Jean-Luc Gatti, Elzemiek Geuverink, Joshua D Gibson, Corinne Hertaeg, Stefanie Hartmann, Emmanuelle Jacquin-Joly, Mark Lammers, Blas I Lavandero, Ina Lindenbaum, Lauriane Massardier-Galata, Camille Meslin, Nicolas Montagné, Nina Pak, Marylène Poirié, Rosanna Salvia, Chris R Smith, Denis Tagu, Sophie Tares, Heiko Vogel, Tanja Schwander, Jean-Christophe Simon, Christian C Figueroa, Christoph Vorburger, Fabrice Legeai, Jürgen Gadau,

BACKGROUND:Parasitoid wasps have fascinating life cycles and play an important role in trophic networks, yet little is known about their genome content and function. Parasitoids that infect aphids are an important group with the potential for biological control. Their success depends on adapting to develop inside aphids and overcoming both ... Read more >>

BMC Genomics (BMC genomics)
[2020, 21(1):376]

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Similar yet different: phylogenomic analysis to delineate Salmonella and Citrobacter species boundaries.

Ana Victoria C Pilar, Nicholas Petronella, Forest M Dussault, Adrian J Verster, Sadjia Bekal, Roger C Levesque, Lawrence Goodridge, Sandeep Tamber,

BACKGROUND:Salmonella enterica is a leading cause of foodborne illness worldwide resulting in considerable public health and economic costs. Testing for the presence of this pathogen in food is often hampered by the presence of background microflora that may present as Salmonella (false positives). False positive isolates belonging to the genus ... Read more >>

BMC Genomics (BMC genomics)
[2020, 21(1):377]

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MethGET: web-based bioinformatics software for correlating genome-wide DNA methylation and gene expression.

Chin-Sheng Teng, Bing-Heng Wu, Ming-Ren Yen, Pao-Yang Chen,

BACKGROUND:DNA methylation is a major epigenetic modification involved in regulating gene expression. The effects of DNA methylation on gene expression differ by genomic location and vary across kingdoms, species and environmental conditions. To identify the functional regulatory roles of DNA methylation, the correlation between DNA methylation changes and alterations in ... Read more >>

BMC Genomics (BMC genomics)
[2020, 21(1):375]

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Comparative genomic analysis of 142 bacteriophages infecting Salmonella enterica subsp. enterica.

Ruimin Gao, Sohail Naushad, Sylvain Moineau, Roger Levesque, Lawrence Goodridge, Dele Ogunremi,

BACKGROUND:Bacteriophages are bacterial parasites and are considered the most abundant and diverse biological entities on the planet. Previously we identified 154 prophages from 151 serovars of Salmonella enterica subsp. enterica. A detailed analysis of Salmonella prophage genomics is required given the influence of phages on their bacterial hosts and should ... Read more >>

BMC Genomics (BMC genomics)
[2020, 21(1):374]

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Multipathway synergy promotes testicular transition from growth to spermatogenesis in early-puberty goats.

Dongdong Bo, Xunping Jiang, Guiqiong Liu, Feng Xu, Ruixue Hu, Teketay Wassie, Yuqing Chong, Sohail Ahmed, Chenhui Liu, Shishay Girmay,

BACKGROUND:The microscopic process of postnatal testicular development in early-puberty animals is poorly understood. Therefore, in this study, 21 male Yiling goats with average ages of 0, 30, 60, 90, 120, 150 and 180 days old (each age group comprised three goats) were used to study the changes in organs, tissues and ... Read more >>

BMC Genomics (BMC genomics)
[2020, 21(1):372]

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Correction to: Genome analysis of Salmonella enterica subsp. diarizonae isolates from invasive human infections reveals enrichment of virulence-related functions in lineage ST1256.

Joaquín Giner-Lamia, Pablo Vinuesa, Laura Betancor, Claudia Silva, Julieta Bisio, Lorena Soleto, José A Chabalgoity, José Luis Puente, , Francisco García-Del Portillo,

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

BMC Genomics (BMC genomics)
[2020, 21(1):373]

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Gene expression of functionally-related genes coevolves across fungal species: detecting coevolution of gene expression using phylogenetic comparative methods.

Alexander L Cope, Brian C O'Meara, Michael A Gilchrist,

BACKGROUND:Researchers often measure changes in gene expression across conditions to better understand the shared functional roles and regulatory mechanisms of different genes. Analogous to this is comparing gene expression across species, which can improve our understanding of the evolutionary processes shaping the evolution of both individual genes and functional pathways. ... Read more >>

BMC Genomics (BMC genomics)
[2020, 21(1):370]

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Genome-wide characterization of the SPL gene family involved in the age development of Jatropha curcas.

Niu Yu, Jin-Chang Yang, Guang-Tian Yin, Rong-Sheng Li, Wen-Tao Zou,

BACKGROUND:SPL (SQUAMOSA-promoter binding protein-like) proteins form a large family of plant-specific transcription factors that play essential roles in various aspects of plant growth and development. They are potentially important candidates for genetic improvement of agronomic traits. However, there were limited information about the SPL genes in Jatropha curcas, an important ... Read more >>

BMC Genomics (BMC genomics)
[2020, 21(1):368]

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Impacts of local population history and ecology on the evolution of a globally dispersed pathogen.

Andreina I Castillo, Carlos Chacón-Díaz, Neysa Rodríguez-Murillo, Helvecio D Coletta-Filho, Rodrigo P P Almeida,

BACKGROUND:Pathogens with a global distribution face diverse biotic and abiotic conditions across populations. Moreover, the ecological and evolutionary history of each population is unique. Xylella fastidiosa is a xylem-dwelling bacterium infecting multiple plant hosts, often with detrimental effects. As a group, X. fastidiosa is divided into distinct subspecies with allopatric ... Read more >>

BMC Genomics (BMC genomics)
[2020, 21(1):369]

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Correction to: Sex-specific changes in gene expression in response to estrogen pollution around the onset of sex differentiation in grayling (Salmonidae).

Oliver M Selmoni, Diane Maitre, Julien Roux, Laetitia G E Wilkins, Lucas Marques da Cunha, Etienne L M Vermeirssen, Susanne Knörr, Marc Robinson-Rechavi, Claus Wedekind,

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

BMC Genomics (BMC genomics)
[2020, 21(1):371]

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Transposable element persistence via potential genome-level ecosystem engineering.

Stefan C Kremer, Stefan Linquist, Brent Saylor, Tyler A Elliott, T Ryan Gregory, Karl Cottenie,

BACKGROUND:The nuclear genomes of eukaryotes vary enormously in size, with much of this variability attributable to differential accumulation of transposable elements (TEs). To date, the precise evolutionary and ecological conditions influencing TE accumulation remain poorly understood. Most previous attempts to identify these conditions have focused on evolutionary processes occurring at ... Read more >>

BMC Genomics (BMC genomics)
[2020, 21(1):367]

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PretiMeth: precise prediction models for DNA methylation based on single methylation mark.

Jianxiong Tang, Jianxiao Zou, Xiaoran Zhang, Mei Fan, Qi Tian, Shuyao Fu, Shihong Gao, Shicai Fan,

BACKGROUND:The computational prediction of methylation levels at single CpG resolution is promising to explore the methylation levels of CpGs uncovered by existing array techniques, especially for the 450 K beadchip array data with huge reserves. General prediction models concentrate on improving the overall prediction accuracy for the bulk of CpG loci ... Read more >>

BMC Genomics (BMC genomics)
[2020, 21(1):364]

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Intron and gene size expansion during nervous system evolution.

Matthew J McCoy, Andrew Z Fire,

BACKGROUND:The evolutionary radiation of animals was accompanied by extensive expansion of gene and genome sizes, increased isoform diversity, and complexity of regulation. RESULTS:Here we show that the longest genes are enriched for expression in neuronal tissues of diverse vertebrates and of invertebrates. Additionally, we show that neuronal gene size expansion ... Read more >>

BMC Genomics (BMC genomics)
[2020, 21(1):360]

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Phylogenomic incongruence in Ceratocystis: a clue to speciation?

Aquillah M Kanzi, Conrad Trollip, Michael J Wingfield, Irene Barnes, Magriet A Van der Nest, Brenda D Wingfield,

BACKGROUND:The taxonomic history of Ceratocystis, a genus in the Ceratocystidaceae, has been beset with questions and debate. This is due to many of the commonly used species recognition concepts (e.g., morphological and biological species concepts) providing different bases for interpretation of taxonomic boundaries. Species delineation in Ceratocystis primarily relied on ... Read more >>

BMC Genomics (BMC genomics)
[2020, 21(1):362]

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Identification of QTL for resistance to root rot in sweetpotato (Ipomoea batatas (L.) Lam) with SSR linkage maps.

Zhimin Ma, Wenchuan Gao, Lanfu Liu, Minghui Liu, Ning Zhao, Meikun Han, Zhao Wang, Weijing Jiao, Zhiyuan Gao, Yaya Hu, Qingchang Liu,

BACKGROUND:Sweetpotato root rot is a devastating disease caused by Fusarium solani that seriously endangers the yield of sweetpotato in China. Although there is currently no effective method to control the disease, breeding of resistant varieties is the most effective and economic option. Moreover, quantitative trait locus (QTL) associated with resistance ... Read more >>

BMC Genomics (BMC genomics)
[2020, 21(1):366]

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Identifying branch-specific positive selection throughout the regulatory genome using an appropriate proxy neutral.

Alejandro Berrio, Ralph Haygood, Gregory A Wray,

BACKGROUND:Adaptive changes in cis-regulatory elements are an essential component of evolution by natural selection. Identifying adaptive and functional noncoding DNA elements throughout the genome is therefore crucial for understanding the relationship between phenotype and genotype. RESULTS:We used ENCODE annotations to identify appropriate proxy neutral sequences and demonstrate that the conservativeness ... Read more >>

BMC Genomics (BMC genomics)
[2020, 21(1):359]

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Metabolic and transcriptomic analysis of two Cucurbita moschata germplasms throughout fruit development.

Hafiz Muhammad Khalid Abbas, He-Xun Huang, An-Jun Wang, Ting-Quan Wu, Shu-Dan Xue, Aqeel Ahmad, Da-Sen Xie, Jun-Xing Li, Yu-Juan Zhong,

BACKGROUND:Pumpkins (Cucurbita moschata; Cucurbitaceae) are valued for their fruits and seeds and are rich in nutrients. Carotenoids and sugar contents, as main feature of pumpkin pulp, are used to determine the fruit quality. RESULTS:Two pumpkin germplasms, CMO-X and CMO-E, were analyzed regarding the essential quality traits such as dry weight, ... Read more >>

BMC Genomics (BMC genomics)
[2020, 21(1):365]

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Linkage mapping and genome-wide association study reveals conservative QTL and candidate genes for Fusarium rot resistance in maize.

Yabin Wu, Zijian Zhou, Chaopei Dong, Jiafa Chen, Junqiang Ding, Xuecai Zhang, Cong Mu, Yuna Chen, Xiaopeng Li, Huimin Li, Yanan Han, Ruixia Wang, Xiaodong Sun, Jingjing Li, Xiaodong Dai, Weibin Song, Wei Chen, Jianyu Wu,

BACKGROUND:Fusarium ear rot (FER) caused by Fusarium verticillioides is a major disease of maize that reduces grain yield and quality globally. However, there have been few reports of major loci for FER were verified and cloned. RESULT:To gain a comprehensive understanding of the genetic basis of natural variation in FER ... Read more >>

BMC Genomics (BMC genomics)
[2020, 21(1):357]

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ICGEC: a comparative method for measuring epigenetic conservation of genes via the integrated signal from multiple histone modifications between cell types.

Jing Tang, Zefeng Wu, Yuhan Tian, Ruolin Yang,

BACKGROUND:Histone post-translational modifications play crucial roles in epigenetic regulation of gene expression and are known to be associated with the phenotypic differences of different cell types. Therefore, it is of fundamental importance to dissect the genes and pathways involved in such a phenotypic variation at the level of epigenetics. However, ... Read more >>

BMC Genomics (BMC genomics)
[2020, 21(1):356]

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Evolution of Fusarium tricinctum and Fusarium avenaceum mitochondrial genomes is driven by mobility of introns and of a new type of palindromic microsatellite repeats.

Nadia Ponts, Charlotte Gautier, Jérôme Gouzy, Laetitia Pinson-Gadais, Marie Foulongne-Oriol, Christine Ducos, Florence Richard-Forget, Jean-Michel Savoie, Chen Zhao, Gérard Barroso,

BACKGROUND:Increased contamination of European and Asian wheat and barley crops with "emerging" mycotoxins such as enniatins or beauvericin, produced by Fusarium avenaceum and Fusarium tricinctum, suggest that these phylogenetically close species could be involved in future food-safety crises. RESULTS:The mitochondrial genomes of F. tricinctum strain INRA104 and F. avenaceum strain ... Read more >>

BMC Genomics (BMC genomics)
[2020, 21(1):358]

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Origin, clonal diversity, and evolution of the parthenogenetic lizard Darevskia unisexualis.

Andrey A Vergun, Anastasiya E Girnyk, Vitaly I Korchagin, Seraphima K Semyenova, Marine S Arakelyan, Felix D Danielyan, Robert W Murphy, Alexey P Ryskov,

BACKGROUND:The hybridization of female D. raddei and male D. valentini gave rise to the parthenogenetic Caucasian rock lizard Darevskia unisexualis. A previously identified genetic polymorphism in the species consisted of one common and two allozyme clones. Analysis of microsatellites and single nucleotide polymorphisms (SNPs) from the three species yields estimates ... Read more >>

BMC Genomics (BMC genomics)
[2020, 21(1):351]

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Genomic variation among closely related Vibrio alginolyticus strains is located on mobile genetic elements.

Cynthia Maria Chibani, Olivia Roth, Heiko Liesegang, Carolin Charlotte Wendling,

BACKGROUND:Species of the genus Vibrio, one of the most diverse bacteria genera, have undergone niche adaptation followed by clonal expansion. Niche adaptation and ultimately the formation of ecotypes and speciation in this genus has been suggested to be mainly driven by horizontal gene transfer (HGT) through mobile genetic elements (MGEs). ... Read more >>

BMC Genomics (BMC genomics)
[2020, 21(1):354]

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Decoupling behavioral and transcriptional responses to color in an eyeless cnidarian.

Whitney B Leach, Adam M Reitzel,

BACKGROUND:Animals have specific molecular, physiological, and behavioral responses to light that are influenced by wavelength and intensity. Predictable environmental changes - predominantly solar and lunar cycles - drive endogenous daily oscillations by setting internal pacemakers, otherwise known as the circadian clock. Cnidarians have been a focal group to discern the ... Read more >>

BMC Genomics (BMC genomics)
[2020, 21(1):361]

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Transcriptome profiling of human thymic CD4+ and CD8+ T cells compared to primary peripheral T cells.

Hanna Helgeland, Ingvild Gabrielsen, Helle Akselsen, Arvind Y M Sundaram, Siri Tennebø Flåm, Benedicte Alexandra Lie,

BACKGROUND:The thymus is a highly specialized organ of the immune system where T cell precursors develop and differentiate into self-tolerant CD4+ or CD8+ T cells. No studies to date have investigated how the human transcriptome profiles differ, between T cells still residing in the thymus and T cells in the ... Read more >>

BMC Genomics (BMC genomics)
[2020, 21(1):350]

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Optimized breeding strategies to harness genetic resources with different performance levels.

Antoine Allier, Simon Teyssèdre, Christina Lehermeier, Laurence Moreau, Alain Charcosset,

BACKGROUND:The narrow genetic base of elite germplasm compromises long-term genetic gain and increases the vulnerability to biotic and abiotic stresses in unpredictable environmental conditions. Therefore, an efficient strategy is required to broaden the genetic base of commercial breeding programs while not compromising short-term variety release. Optimal cross selection aims at ... Read more >>

BMC Genomics (BMC genomics)
[2020, 21(1):349]

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