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  1. Durum wheat (Triticum turgidum L. ssp. durum Desf. Husn) is the main staple crop used to make pasta products worldwide. Under the current climate change scenarios, genetic variability within a crop plays a crucia...

    Authors: Pablo Federico Roncallo, Adelina Olga Larsen, Ana Laura Achilli, Carolina Saint Pierre, Cristian Andrés Gallo, Susanne Dreisigacker and Viviana Echenique

    Citation: BMC Genomics 2021 22:233

    Content type: Research article

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  2. A body distribution with high intramuscular fat and low abdominal fat is the ideal goal for broiler breeding. Preadipocytes with different origins have differences in terms of metabolism and gene expression. T...

    Authors: Zheng Ma, Na Luo, Lu Liu, Huanxian Cui, Jing Li, Hai Xiang, Huimin Kang, Hua Li and Guiping Zhao

    Citation: BMC Genomics 2021 22:232

    Content type: Research article

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  3. Commelinaceae (Commelinales) comprise 41 genera and are widely distributed in both the Old and New Worlds, except in Europe. The relationships among genera in this family have been suggested in several morphol...

    Authors: Joonhyung Jung, Changkyun Kim and Joo-Hwan Kim

    Citation: BMC Genomics 2021 22:231

    Content type: Research article

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  4. The Chinese giant salamander Andrias davidianus is an important amphibian species in China because of its increasing economic value, protection status and special evolutionary position from aquatic to terrestrial...

    Authors: Qiaomu Hu, Yang Liu, Xiaolin Liao, Haifeng Tian, Xiangshan Ji, Jiajie Zhu and Hanbing Xiao

    Citation: BMC Genomics 2021 22:230

    Content type: Research article

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  5. Olive orchards are threatened by a wide range of pathogens. Of these, Verticillium dahliae has been in the spotlight for its high incidence, the difficulty to control it and the few cultivars that has increased t...

    Authors: Jorge A. Ramírez-Tejero, Jaime Jiménez-Ruiz, Alicia Serrano, Angjelina Belaj, Lorenzo León, Raúl de la Rosa, Jesús Mercado-Blanco and Francisco Luque

    Citation: BMC Genomics 2021 22:229

    Content type: Research article

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  6. The red panda (Ailurus fulgens) is a riddle of morphology, making it hard to tell whether it is an ursid, a procyonid, a mustelid, or a member of its own family. Previous genetic studies have given quite contradi...

    Authors: Matyas Cserhati

    Citation: BMC Genomics 2021 22:228

    Content type: Research article

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  7. Barley is one of the founder crops of Neolithic agriculture and is among the most-grown cereals today. The only trait that universally differentiates the cultivated and wild subspecies is ‘non-brittleness’ of ...

    Authors: Peter Civáň, Konstantina Drosou, David Armisen-Gimenez, Wandrille Duchemin, Jérôme Salse and Terence A. Brown

    Citation: BMC Genomics 2021 22:227

    Content type: Research article

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  8. Short interspersed nuclear elements (SINEs) belong to non-long terminal repeat (non-LTR) retrotransposons, which can mobilize dependent on the help of counterpart long interspersed nuclear elements (LINEs). Al...

    Authors: Guangjie Han, Nan Zhang, Heng Jiang, Xiangkun Meng, Kun Qian, Yang Zheng, Jian Xu and Jianjun Wang

    Citation: BMC Genomics 2021 22:226

    Content type: Research article

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  9. Cattle are ideally suited to investigate the genetics of male fertility. Semen from individual bulls is used for thousands of artificial inseminations for which the fertilization success is monitored. Results ...

    Authors: Maya Hiltpold, Naveen Kumar Kadri, Fredi Janett, Ulrich Witschi, Fritz Schmitz-Hsu and Hubert Pausch

    Citation: BMC Genomics 2021 22:225

    Content type: Research article

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  10. Understanding viral infection of the olfactory epithelium is essential because the olfactory nerve is an important route of entry for viruses to the central nervous system. Specialized chemosensory epithelial ...

    Authors: B. Dnate’ Baxter, Eric D. Larson, Laetitia Merle, Paul Feinstein, Arianna Gentile Polese, Andrew N. Bubak, Christy S. Niemeyer, James Hassell Jr, Doug Shepherd, Vijay R. Ramakrishnan, Maria A. Nagel and Diego Restrepo

    Citation: BMC Genomics 2021 22:224

    Content type: Research article

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  11. The larvacean Oikopleura dioica is an abundant tunicate plankton with the smallest (65–70 Mbp) non-parasitic, non-extremophile animal genome identified to date. Currently, there are two genomes available for the ...

    Authors: Aleksandra Bliznina, Aki Masunaga, Michael J. Mansfield, Yongkai Tan, Andrew W. Liu, Charlotte West, Tanmay Rustagi, Hsiao-Chiao Chien, Saurabh Kumar, Julien Pichon, Charles Plessy and Nicholas M. Luscombe

    Citation: BMC Genomics 2021 22:222

    Content type: Research article

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  12. B-box (BBX) zinc-finger transcription factors play important roles in plant growth, development, and stress response. Although these proteins have been studied in model plants such as Arabidopsis thaliana or Oryz...

    Authors: Xiuming Zhang, Li Zhang, Miaomiao Ji, Yifei Wu, Songlin Zhang, Yanxun Zhu, Jin Yao, Zhi Li, Hua Gao and Xiping Wang

    Citation: BMC Genomics 2021 22:221

    Content type: Research article

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  13. Many recent studies have shown that miRNAs play important roles in the regulation of animal reproduction, including seasonal reproduction. The pineal gland is a crucial hub in the regulation of seasonal reprod...

    Authors: Ran Di, Qiu-Yue Liu, Shu-Hui Song, Dong-Mei Tian, Jian-Ning He, Ying Ge, Xiang-Yu Wang, Wen-Ping Hu, Joram-Mwashigadi Mwacharo, Zhang-Yuan Pan, Jian-Dong Wang, Qing Ma, Gui-Ling Cao, Hui-Hui Jin, Xiao-Jun Liang and Ming-Xing Chu

    Citation: BMC Genomics 2021 22:217

    Content type: Research article

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  14. While leeches in the genus Hirudo have long been models for neurobiology, the molecular underpinnings of nervous system structure and function in this group remain largely unknown. To begin to bridge this gap, we...

    Authors: Elizabeth Heath-Heckman, Shinja Yoo, Christopher Winchell, Maurizio Pellegrino, James Angstadt, Veronica B. Lammardo, Diana Bautista, Francisco F. De-Miguel and David Weisblat

    Citation: BMC Genomics 2021 22:215

    Content type: Research article

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  15. In addition to their well characterized role in cellular energy production, new evidence has revealed the involvement of mitochondria in diverse signaling pathways that regulate a broad array of cellular funct...

    Authors: John C. Santiago, Joan M. Boylan, Faye A. Lemieux, Philip A. Gruppuso, Jennifer A. Sanders and David M. Rand

    Citation: BMC Genomics 2021 22:213

    Content type: Research article

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  16. While nuclear transcription and RNA processing and localization are well established for protein coding genes (PCGs), these processes are poorly understood for long non-coding (lnc)RNAs. Here, we characterize ...

    Authors: Christine N. Goldfarb and David J. Waxman

    Citation: BMC Genomics 2021 22:212

    Content type: Research article

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  17. Early-onset familial Alzheimer’s disease (EOfAD) is promoted by dominant mutations, enabling the study of Alzheimer’s disease (AD) pathogenic mechanisms through generation of EOfAD-like mutations in animal mod...

    Authors: Yang Dong, Morgan Newman, Stephen M. Pederson, Karissa Barthelson, Nhi Hin and Michael Lardelli

    Citation: BMC Genomics 2021 22:211

    Content type: Research article

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  18. Safety issues of probiotic products have been reported frequently in recent years. Ten bacterial strains isolated from seven commercial probiotic products on market were evaluated for their safety, by whole-ge...

    Authors: Ying Wang, Qian Liang, Bian Lu, Hong Shen, Shuyan Liu, Ya Shi, Sebastian Leptihn, Hong Li, Jin Wei, Chengzhi Liu, Hailong Xiao, Xiaoling Zheng, Chao Liu and Huan Chen

    Citation: BMC Genomics 2021 22:210

    Content type: Research article

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  19. There is a dearth of sequenced and closed microbial genomes from environments that exceed > 500 m below level terrestrial surface. Coupled with even fewer cultured isolates, study and understanding of how life...

    Authors: Trevor R. Murphy, Rui Xiao and Scott D. Hamilton-Brehm

    Citation: BMC Genomics 2021 22:209

    Content type: Research article

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  20. CRISPR/Cas9-mediated transcriptional interference (CRISPRi) enables programmable gene knock-down, yielding loss-of-function phenotypes for nearly any gene. Effective, inducible CRISPRi has been demonstrated in...

    Authors: Nicholas J. McGlincy, Zuriah A. Meacham, Kendra K. Reynaud, Ryan Muller, Rachel Baum and Nicholas T. Ingolia

    Citation: BMC Genomics 2021 22:205

    Content type: Methodology article

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  21. Variation in locomotor capacity among animals often reflects adaptations to different environments. Despite evidence that physical performance is heritable, the molecular basis of locomotor performance and per...

    Authors: Valérie Ducret, Adam J. Richards, Mathieu Videlier, Thibault Scalvenzi, Karen A. Moore, Konrad Paszkiewicz, Camille Bonneaud, Nicolas Pollet and Anthony Herrel

    Citation: BMC Genomics 2021 22:204

    Content type: Research article

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  22. Persimmon (Diospyros kaki Thunb.) has various labile sex types, and studying its sex differentiation can improve breeding efficiency. However, studies on sexual regulation patterns in persimmon have focused mainl...

    Authors: Huawei Li, Liyuan Wang, Yini Mai, Weijuan Han, Yujing Suo, Songfeng Diao, Peng Sun and Jianmin Fu

    Citation: BMC Genomics 2021 22:203

    Content type: Research article

    Published on:

  23. Cotton fiber is a model system for studying plant cell development. At present, the functions of many transcription factors in cotton fiber development have been elucidated, however, the roles of auxin respons...

    Authors: Xiufang Zhang, Junfeng Cao, Chaochen Huang, Zishou Zheng, Xia Liu, Xiaoxia Shangguan, Lingjian Wang, Yugao Zhang and Zhiwen Chen

    Citation: BMC Genomics 2021 22:202

    Content type: Research article

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  24. Datura stramonium (Jimsonweed) is a medicinally and pharmaceutically important plant in the nightshade family (Solanaceae) known for its production of various toxic, hallucinogenic, and therapeutic tropane alkalo...

    Authors: Alex Rajewski, Derreck Carter-House, Jason Stajich and Amy Litt

    Citation: BMC Genomics 2021 22:201

    Content type: Research article

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  25. Tilapia (Oreochromis niloticus) cultures are frequently infected by Vibrio vulnificus, causing major economic losses to production units. Previously, tilapia expressing recombinant delta-5 desaturase and delta-6 ...

    Authors: Pin-Yang Tu, Shin-Jie Huang, Venugopal Rajanbabu, Jen-Leih Wu and Jyh-Yih Chen

    Citation: BMC Genomics 2021 22:200

    Content type: Research article

    Published on:

  26. The red swamp crayfish Procambarus clarkii is a freshwater species that possesses high adaptability, environmental tolerance, and fecundity. P. clarkii is artificially farmed on a large scale in China. However, t...

    Authors: Yizhi Zhong, Wenbin Zhao, Zhangsheng Tang, Liming Huang, Xiangxing Zhu, Xiang Liang, Aifen Yan, Zhifa Lu, Yanling Yu, Dongsheng Tang, Dapeng Wang and Zhuanling Lu

    Citation: BMC Genomics 2021 22:199

    Content type: Research article

    Published on:

  27. Lineage-specific gene expansions represent one of the driving forces in the evolutionary dynamics of unique phylum traits. Myxozoa, a cnidarian subphylum of obligate parasites, are evolutionarily altered and h...

    Authors: Jiří Kyslík, Anush Kosakyan, Serafim Nenarokov, Astrid S. Holzer and Ivan Fiala

    Citation: BMC Genomics 2021 22:198

    Content type: Research article

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  28. Low pass sequencing has been proposed as a cost-effective alternative to genotyping arrays to identify genetic variants that influence multifactorial traits in humans. For common diseases this typically has re...

    Authors: Kaja Wasik, Tomaz Berisa, Joseph K. Pickrell, Jeremiah H. Li, Dana J. Fraser, Karen King and Charles Cox

    Citation: BMC Genomics 2021 22:197

    Content type: Research article

    Published on:

  29. MicroRNAs play an important role in many fundamental biological and pathological processes. Defining the microRNAs profile underlying the processes by beneficial and detrimental lifestyles, including caloric r...

    Authors: Huan Gong, Ming Zhang, Yiwen Han, Ying Zhang, Jing Pang, Yanyang Zhao, Beidong Chen, Wei Wu, Ruomei Qi and Tiemei Zhang

    Citation: BMC Genomics 2021 22:196

    Content type: Research article

    Published on:

  30. The technology of single cell RNA sequencing (scRNA-seq) has gained massively in popularity as it allows unprecedented insights into cellular heterogeneity as well as identification and characterization of (su...

    Authors: Andreas Hoek, Katharina Maibach, Ebru Özmen, Ana Ivonne Vazquez-Armendariz, Jan Philipp Mengel, Torsten Hain, Susanne Herold and Alexander Goesmann

    Citation: BMC Genomics 2021 22:195

    Content type: Software

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  31. Lima bean (Phaseolus lunatus L.) is a member of subfamily Phaseolinae belonging to the family Leguminosae and an important source of plant proteins for the human diet. As we all know, lima beans have important ec...

    Authors: Shoubo Tian, Panling Lu, Zhaohui Zhang, Jian Qiang Wu, Hui Zhang and Haibin Shen

    Citation: BMC Genomics 2021 22:194

    Content type: Research article

    Published on:

  32. The effect of heat stress on livestock production is a worldwide issue. Animal performance is influenced by exposure to harsh environmental conditions potentially causing genotype-by-environment interactions (...

    Authors: Rui Shi, Luiz Fernando Brito, Aoxing Liu, Hanpeng Luo, Ziwei Chen, Lin Liu, Gang Guo, Herman Mulder, Bart Ducro, Aart van der Linden and Yachun Wang

    Citation: BMC Genomics 2021 22:193

    Content type: Research article

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  33. Entomopathogenic nematodes (EPNs) emerge as compatible alternatives to conventional insecticides in controlling Holotrichia parallela larvae (Coleoptera: Scarabaeidae). However, the immune responses of H. paralle...

    Authors: Ertao Li, Jianhui Qin, Honglin Feng, Jinqiao Li, Xiaofeng Li, Innocent Nyamwasa, Yazhong Cao, Weibin Ruan, Kebin Li and Jiao Yin

    Citation: BMC Genomics 2021 22:192

    Content type: Research article

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  34. Enrichment or over-representation analysis is a common method used in bioinformatics studies of transcriptomics, metabolomics, and microbiome datasets. The key idea behind enrichment analysis is: given a set o...

    Authors: Peter D. Karp, Peter E. Midford, Ron Caspi and Arkady Khodursky

    Citation: BMC Genomics 2021 22:191

    Content type: Research article

    Published on:

  35. The preferred choice for molecular marker development is identifying existing variation in populations through DNA sequencing. With the genome resources currently available for bitter gourd (Momordica charantia),...

    Authors: Junjie Cui, Jiazhu Peng, Jiaowen Cheng and Kailin Hu

    Citation: BMC Genomics 2021 22:190

    Content type: Research article

    Published on:

  36. In many insect species, the larvae/nymphs are unable to disperse far from the oviposition site selected by adults. The Sakhalin pine sawyer Monochamus saltuarius (Gebler) is the newly discovered insect vector of ...

    Authors: Zehai Hou, Fengming Shi, Sixun Ge, Jing Tao, Lili Ren, Hao Wu and Shixiang Zong

    Citation: BMC Genomics 2021 22:189

    Content type: Research article

    Published on:

  37. Basenjis are considered an ancient dog breed of central African origins that still live and hunt with tribesmen in the African Congo. Nicknamed the barkless dog, Basenjis possess unique phylogeny, geographical...

    Authors: Richard J. Edwards, Matt A. Field, James M. Ferguson, Olga Dudchenko, Jens Keilwagen, Benjamin D. Rosen, Gary S. Johnson, Edward S. Rice, La Deanna Hillier, Jillian M. Hammond, Samuel G. Towarnicki, Arina Omer, Ruqayya Khan, Ksenia Skvortsova, Ozren Bogdanovic, Robert A. Zammit…

    Citation: BMC Genomics 2021 22:188

    Content type: Research article

    Published on:

  38. Environmental adaptation and expanding harvest seasons are primary goals of most peach [Prunus persica (L.) Batsch] breeding programs. Breeding perennial crops is a challenging task due to their long breeding cyc...

    Authors: Zena J. Rawandoozi, Timothy P. Hartmann, Silvia Carpenedo, Ksenija Gasic, Cassia da Silva Linge, Lichun Cai, Eric Van de Weg and David H. Byrne

    Citation: BMC Genomics 2021 22:187

    Content type: Research article

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  39. K-mer-based methods have greatly advanced in recent years, largely driven by the realization of their biological significance and by the advent of next-generation sequencing. Their speed and their independence...

    Authors: Ariane Bize, Cédric Midoux, Mahendra Mariadassou, Sophie Schbath, Patrick Forterre and Violette Da Cunha

    Citation: BMC Genomics 2021 22:186

    Content type: Research article

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  40. Apomixis, an asexual mode of plant reproduction, is a genetically heritable trait evolutionarily related to sexuality, which enables the fixation of heterozygous genetic combinations through the development of...

    Authors: Maricel Podio, Carolina Colono, Lorena Siena, Juan Pablo A. Ortiz and Silvina Claudia Pessino

    Citation: BMC Genomics 2021 22:185

    Content type: Research article

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  41. Aging is a multifactorial process that affects multiple tissues and is characterized by changes in homeostasis over time, leading to increased morbidity. Whole blood gene expression signatures have been associ...

    Authors: Damiano Pellegrino-Coppola, Annique Claringbould, Maartje Stutvoet, Dorret I. Boomsma, M. Arfan Ikram, P. Eline Slagboom, Harm-Jan Westra and Lude Franke

    Citation: BMC Genomics 2021 22:184

    Content type: Research article

    Published on:

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