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Journal BMC Genomics

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SCReadCounts: estimation of cell-level SNVs expression from scRNA-seq data.

N M Prashant, Nawaf Alomran, Yu Chen, Hongyu Liu, Pavlos Bousounis, Mercedeh Movassagh, Nathan Edwards, Anelia Horvath,

<h4>Background</h4>Recent studies have demonstrated the utility of scRNA-seq SNVs to distinguish tumor from normal cells, characterize intra-tumoral heterogeneity, and define mutation-associated expression signatures. In addition to cancer studies, SNVs from single cells have been useful in studies of transcriptional burst kinetics, allelic expression, chromosome X inactivation, ploidy estimations, and haplotype ... Read more >>

BMC Genomics (BMC genomics)
[2021, 22(1):689]

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Culture and genome-based analysis of four soil Clostridium isolates reveal their potential for antimicrobial production.

Amila S N W Pahalagedara, Ruy Jauregui, Paul Maclean, Eric Altermann, Steve Flint, Jon Palmer, Gale Brightwell, Tanushree Barua Gupta,

<h4>Background</h4>Soil bacteria are a major source of specialized metabolites including antimicrobial compounds. Yet, one of the most diverse genera of bacteria ubiquitously present in soil, Clostridium, has been largely overlooked in bioactive compound discovery. As Clostridium spp. thrive in extreme environments with their metabolic mechanisms adapted to the harsh conditions, ... Read more >>

BMC Genomics (BMC genomics)
[2021, 22(1):686]

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Genome sequencing of the neotype strain CBS 554.65 reveals the MAT1-2 locus of Aspergillus niger.

Valeria Ellena, Sjoerd J Seekles, Gabriel A Vignolle, Arthur F J Ram, Matthias G Steiger,

<h4>Background</h4>Aspergillus niger is a ubiquitous filamentous fungus widely employed as a cell factory thanks to its abilities to produce a wide range of organic acids and enzymes. Its genome was one of the first Aspergillus genomes to be sequenced in 2007, due to its economic importance and its role as ... Read more >>

BMC Genomics (BMC genomics)
[2021, 22(1):679]

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Genome-wide identification and characterization of the BES/BZR gene family in wheat and foxtail millet.

Dan Liu, Yanjiao Cui, Zilong Zhao, Suying Li, Dan Liang, Conglei Wang, Gang Feng, Jianhe Wang, Zhengli Liu,

<h4>Background</h4>BES/BZR family genes have vital roles in plant growth, development, and adaptation to environmental stimuli. However, they have not yet been characterized and systematically analyzed in wheat and foxtail millet.<h4>Results</h4>In the current study, five common and two unique BES/BZR genes were identified by genome-wide analysis in wheat and foxtail millet, ... Read more >>

BMC Genomics (BMC genomics)
[2021, 22(1):682]

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Unveiling the transcriptomic complexity of Miscanthus sinensis using a combination of PacBio long read- and Illumina short read sequencing platforms.

Yongli Wang, Xia Li, Congsheng Wang, Lu Gao, Yanfang Wu, Xingnan Ni, Jianzhong Sun, Jianxiong Jiang,

<h4>Background</h4>Miscanthus sinensis Andersson is a perennial grass that exhibits remarkable lignocellulose characteristics suitable for sustainable bioenergy production. However, knowledge of the genetic resources of this species is relatively limited, which considerably hampers further work on its biology and genetic improvement.<h4>Results</h4>In this study, through analyzing the transcriptome of mixed samples of ... Read more >>

BMC Genomics (BMC genomics)
[2021, 22(1):690]

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A single chromosome strain of S. cerevisiae exhibits diminished ethanol metabolism and tolerance.

Tyler W Doughty, Rosemary Yu, Lucy Fang-I Chao, Zhongjun Qin, Verena Siewers, Jens Nielsen,

<h4>Background</h4>Eukaryotic organisms, like the model yeast S. cerevisiae, have linear chromosomes that facilitate organization and protection of nuclear DNA. A recent work described a stepwise break/repair method that enabled fusion of the 16 chromosomes of S. cerevisiae into a single large chromosome. Construction of this strain resulted in the removal ... Read more >>

BMC Genomics (BMC genomics)
[2021, 22(1):688]

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Transcriptome and metabolome analysis reveals anthocyanin biosynthesis pathway associated with ramie (Boehmeria nivea (L.) Gaud.) leaf color formation.

Xinkang Feng, Gang Gao, Chunming Yu, Aiguo Zhu, Jikang Chen, Kunmei Chen, Xiaofei Wang, Aminu Shehu Abubakar, Ping Chen,

<h4>Background</h4>The bast fiber crop ramie can be used as high-quality forage resources, especially in tropical or subtropical region where there is lack of high-quality protein feed. Hongxuan No.1 (HX_1) is a unique ramie variety with a light reddish brown leaf color, which is obviously different from elite cultivar, Zhongzhu No.1 ... Read more >>

BMC Genomics (BMC genomics)
[2021, 22(1):684]

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Genome-wide identification and expression profile under abiotic stress of the barley non-specific lipid transfer protein gene family and its Qingke Orthologues.

Jiecuo Duo, Huiyan Xiong, Xiongxiong Wu, Yuan Li, Jianping Si, Chao Zhang, Ruijun Duan,

<h4>Background</h4>Plant non-specific lipid transfer proteins (nsLTPs), a group of small, basic ubiquitous proteins to participate in lipid transfer, cuticle formation and stress response, are involved in the regulation of plant growth and development. To date, although the nsLTP gene family of barley (Hordeum vulgare L.) has been preliminarily identified, it ... Read more >>

BMC Genomics (BMC genomics)
[2021, 22(1):674]

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Elevated transcription of transposable elements is accompanied by het-siRNA-driven de novo DNA methylation in grapevine embryogenic callus.

Darrell Lizamore, Ross Bicknell, Chris Winefield,

<h4>Background</h4>Somatic variation is a valuable source of trait diversity in clonally propagated crops. In grapevine, which has been clonally propagated worldwide for centuries, important phenotypes such as white berry colour are the result of genetic changes caused by transposable elements. Additionally, epiallele formation may play a role in determining geo-specific ... Read more >>

BMC Genomics (BMC genomics)
[2021, 22(1):676]

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Characterization of the chicken T cell receptor γ repertoire by high-throughput sequencing.

Tongtong Zhang, Qian Li, Xiaoqing Li, Li Kang, Yunliang Jiang, Yi Sun,

<h4>Background</h4>As one of "γδ-high" species, chicken is an excellent model for the study of γδ T cells in non-mammalian animals. However, a comprehensive characterization of the TCRγδ repertoire is still missing in chicken. The objective of this study was to characterize the expressed TCRγ repertoire in chicken thymus using high-throughput ... Read more >>

BMC Genomics (BMC genomics)
[2021, 22(1):683]

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Transcriptional profiling reveals changes in gene regulation and signaling transduction pathways during temperature stress in wucai (Brassica campestris L.).

Lingyun Yuan, Yushan Zheng, Libing Nie, Liting Zhang, Ying Wu, Shidong Zhu, Jinfeng Hou, Guo Lei Shan, Tong Kun Liu, Guohu Chen, Xiaoyan Tang, Chenggang Wang,

<h4>Background</h4>Wucai (Brassica campestris L. ssp. chinensis var. rosularis Tsen) is a cold-tolerant plant that is vulnerable to high temperature. This study explored the response mechanism of wucai to low temperature. In this study, wucai seedlings were treated with different temperatures, including low temperature (LT), high temperature (HT), and a control.<h4>Results</h4>According ... Read more >>

BMC Genomics (BMC genomics)
[2021, 22(1):687]

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Revelation of candidate genes and molecular mechanism of reproductive seasonality in female rohu (Labeo rohita Ham.) by RNA sequencing.

Sarika Jaiswal, Samiran Nandi, Mir Asif Iquebal, Rahul Singh Jasrotia, Sunita Patra, Gayatri Mishra, Uday Kumar Udit, Dinesh Kumar Sahu, U B Angadi, Prem Kumar Meher, Padmanav Routray, Jitendra Kumar Sundaray, Dhananjay Kumar Verma, Paramananda Das, Pallipuram Jayasankar, Anil Rai, Dinesh Kumar,

<h4>Background</h4>Carp fish, rohu (Labeo rohita Ham.) is important freshwater aquaculture species of South-East Asia having seasonal reproductive rhythm. There is no holistic study at transcriptome level revealing key candidate genes involved in such circannual rhythm regulated by biological clock genes (BCGs). Seasonality manifestation has two contrasting phases of reproduction, i.e., ... Read more >>

BMC Genomics (BMC genomics)
[2021, 22(1):685]

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Characterization and genomic analysis of the first Oceanospirillum phage, vB_OliS_GJ44, representing a novel siphoviral cluster.

Wenjing Zhang, Yantao Liang, Kaiyang Zheng, Chengxiang Gu, Yundan Liu, Ziyue Wang, Xinran Zhang, Hongbing Shao, Yong Jiang, Cui Guo, Hui He, Hualong Wang, Yeong Yik Sung, Wen Jye Mok, Yuzhong Zhang, Andrew McMinn, Min Wang,

<h4>Background</h4>Marine bacteriophages play key roles in the community structure of microorganisms, biogeochemical cycles, and the mediation of genetic diversity through horizontal gene transfer. Recently, traditional isolation methods, complemented by high-throughput sequencing metagenomics technology, have greatly increased our understanding of the diversity of bacteriophages. Oceanospirillum, within the order Oceanospirillales, are important ... Read more >>

BMC Genomics (BMC genomics)
[2021, 22(1):675]

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A complete mitochondrial genome for fragrant Chinese rosewood (Dalbergia odorifera, Fabaceae) with comparative analyses of genome structure and intergenomic sequence transfers.

Zhou Hong, Xuezhu Liao, Yuanjun Ye, Ningnan Zhang, Zengjiang Yang, Weidong Zhu, Wei Gao, Joel Sharbrough, Luke R Tembrock, Daping Xu, Zhiqiang Wu,

<h4>Background</h4>Dalbergia odorifera is an economically and culturally important species in the Fabaceae because of the high-quality lumber and traditional Chinese medicines made from this plant, however, overexploitation has increased the scarcity of D. odorifera. Given the rarity and the multiple uses of this species, it is important to expand the ... Read more >>

BMC Genomics (BMC genomics)
[2021, 22(1):672]

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The molecular interplay of the establishment of an infection - gene expression of Diaphorina citri gut and Candidatus Liberibacter asiaticus.

Flavia Moura Manoel Bento, Josiane Cecília Darolt, Bruna Laís Merlin, Leandro Penã, Nelson Arno Wulff, Fernando Luis Cônsoli,

<h4>Background</h4>Candidatus Liberibacter asiaticus (CLas) is one the causative agents of greening disease in citrus, an unccurable, devastating disease of citrus worldwide. CLas is vectored by Diaphorina citri, and the understanding of the molecular interplay between vector and pathogen will provide additional basis for the development and implementation of successful management ... Read more >>

BMC Genomics (BMC genomics)
[2021, 22(1):677]

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DNA damage repair system in C57BL/6 J mice is evolutionarily stable.

Xiaoyu Wang, San Ming Wang,

<h4>Background</h4>DNA damage repair (DDR) system is vital in maintaining genome stability and survival. DDR consists of over 160 genes in 7 different pathways to repair specific type of DNA damage caused by external and internal damaging factors. The functional importance of DDR system implies that evolution could play important roles ... Read more >>

BMC Genomics (BMC genomics)
[2021, 22(1):669]

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Altered expression of microRNAs in the rat diaphragm in a model of ventilator-induced diaphragm dysfunction after controlled mechanical ventilation.

Pengcheng Wang, Xianlong Zhou, Gang Li, Haoli Ma, Ruining Liu, Yan Zhao,

<h4>Background</h4>Ventilator-induced diaphragm dysfunction (VIDD) is a common complication of life support by mechanical ventilation observed in critical patients in clinical practice and may predispose patients to severe complications such as ventilator-associated pneumonia or ventilator discontinuation failure. To date, the alterations in microRNA (miRNA) expression in the rat diaphragm in a ... Read more >>

BMC Genomics (BMC genomics)
[2021, 22(1):671]

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Recombination mapping of the Brazilian stingless bee Frieseomelitta varia confirms high recombination rates in social hymenoptera.

Prashant Waiker, Fabiano Carlos Pinto de Abreu, Danielle Luna-Lucena, Flávia Cristina Paula Freitas, Zilá Luz Paulino Simões, Olav Rueppell,

<h4>Background</h4>Meiotic recombination is a fundamental genetic process that shuffles allele combinations and promotes accurate segregation of chromosomes. Analyses of the ubiquitous variation of recombination rates within and across species suggest that recombination is evolving adaptively. All studied insects with advanced eusociality have shown exceptionally high recombination rates, which may represent ... Read more >>

BMC Genomics (BMC genomics)
[2021, 22(1):673]

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Runs of homozygosity analysis reveals consensus homozygous regions affecting production traits in Chinese Simmental beef cattle.

Guoyao Zhao, Yuqiang Liu, Qunhao Niu, Xu Zheng, Tianliu Zhang, Zezhao Wang, Lei Xu, Bo Zhu, Xue Gao, Lupei Zhang, Huijiang Gao, Junya Li, Lingyang Xu,

<h4>Background</h4>Genomic regions with a high frequency of runs of homozygosity (ROH) are related to important traits in farm animals. We carried out a comprehensive analysis of ROH and evaluated their association with production traits using the BovineHD (770 K) SNP array in Chinese Simmental beef cattle.<h4>Results</h4>We detected a total of 116,953 homozygous ... Read more >>

BMC Genomics (BMC genomics)
[2021, 22(1):678]

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Transcriptome profiling of Malus sieversii under freezing stress after being cold-acclimated.

Ping Zhou, Xiaoshuang Li, Xiaojie Liu, Xuejing Wen, Yan Zhang, Daoyuan Zhang,

<h4>Background</h4>Freezing temperatures are an abiotic stress that has a serious impact on plant growth and development in temperate regions and even threatens plant survival. The wild apple tree (Malus sieversii) needs to undergo a cold acclimation process to enhance its freezing tolerance in winter. Changes that occur at the molecular ... Read more >>

BMC Genomics (BMC genomics)
[2021, 22(1):681]

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Integrative analyses of targeted metabolome and transcriptome of Isatidis Radix autotetraploids highlighted key polyploidization-responsive regulators.

Zixuan Zhang, Mingpu Tan, Yingying Zhang, Yue Jia, Shuxian Zhu, Jiang Wang, Jiajing Zhao, Yueyue Liao, Zengxu Xiang,

<h4>Background</h4>Isatidis Radix, the root of Isatis indigotica Fort. (Chinese woad) can produce a variety of efficacious compound with medicinal properties. The tetraploid I. indigotica plants exhibit superior phenotypic traits, such as greater yield, higher bioactive compounds accumulation and enhanced stress tolerance. In this study, a comparative transcriptomic and metabolomic study ... Read more >>

BMC Genomics (BMC genomics)
[2021, 22(1):670]

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Microbial trend analysis for common dynamic trend, group comparison, and classification in longitudinal microbiome study.

Chan Wang, Jiyuan Hu, Martin J Blaser, Huilin Li,

<h4>Background</h4>The human microbiome is inherently dynamic and its dynamic nature plays a critical role in maintaining health and driving disease. With an increasing number of longitudinal microbiome studies, scientists are eager to learn the comprehensive characterization of microbial dynamics and their implications to the health and disease-related phenotypes. However, due ... Read more >>

BMC Genomics (BMC genomics)
[2021, 22(1):667]

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PathFams: statistical detection of pathogen-associated protein domains.

Briallen Lobb, Benjamin Jean-Marie Tremblay, Gabriel Moreno-Hagelsieb, Andrew C Doxey,

<h4>Background</h4>A substantial fraction of genes identified within bacterial genomes encode proteins of unknown function. Identifying which of these proteins represent potential virulence factors, and mapping their key virulence determinants, is a challenging but important goal.<h4>Results</h4>To facilitate virulence factor discovery, we performed a comprehensive analysis of 17,929 protein domain families within ... Read more >>

BMC Genomics (BMC genomics)
[2021, 22(1):663]

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Dual RNA-seq transcriptome analysis of caecal tissue during primary Eimeria tenella infection in chickens.

Arnar K S Sandholt, Eva Wattrang, Tobias Lilja, Harri Ahola, Anna Lundén, Karin Troell, Staffan G Svärd, Robert Söderlund,

<h4>Background</h4>Coccidiosis is an infectious disease with large negative impact on the poultry industry worldwide. It is an enteric infection caused by unicellular Apicomplexan parasites of the genus Eimeria. The present study aimed to gain more knowledge about interactions between parasites and the host immune system during the early asexual replication ... Read more >>

BMC Genomics (BMC genomics)
[2021, 22(1):660]

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Correction to: Post-diapause transcriptomic restarts: insight from a high-latitude copepod.

Vittoria Roncalli, Matthew C Cieslak, Ann M Castelfranco, Russell R Hopcroft, Daniel K Hartline, Petra H Lenz,

BMC Genomics (BMC genomics)
[2021, 22(1):659]

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