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  1. The hard clam Mercenaria mercenaria is a major marine resource along the Atlantic coasts of North America and has been introduced to other continents for resource restoration or aquaculture activities. Significan...

    Authors: Sarah Farhat, Eric Bonnivard, Emmanuelle Pales Espinosa, Arnaud Tanguy, Isabelle Boutet, Nadège Guiglielmoni, Jean-François Flot and Bassem Allam
    Citation: BMC Genomics 2022 23:192
  2. Tibetan cashmere goats are served as a valuable model for high altitude adaptation and hypoxia complications related studies, while the cashmere produced by these goats is an important source of income for the...

    Authors: Bingru Zhao, Cuiling Wu, Abdul Sammad, Zhen Ma, Langda Suo, Yujiang Wu and Xuefeng Fu
    Citation: BMC Genomics 2022 23:191
  3. Walnuts (Juglans regia L.) are known for their nutrient-rich nuts and are one of the important economic tree species in the world. However, due to global warming and soil salinization, walnuts suffer from various...

    Authors: Xuejiao Liu, Feiyan Yu, Guiyan Yang, Xiaoqiang Liu and Shaobing Peng
    Citation: BMC Genomics 2022 23:190
  4. Subclinical mastitis, the inflammation of the mammary gland lacking clinical symptoms, is one of the most prevalent and costly diseases in dairy farming worldwide. Milk microRNAs (miRNAs) encapsulated in extra...

    Authors: Mara D. Saenz-de-Juano, Giulia Silvestrelli, Stefan Bauersachs and Susanne E. Ulbrich
    Citation: BMC Genomics 2022 23:189
  5. The repulsive guidance molecule a (RGMa) is a GPI-anchor axon guidance molecule first found to play important roles during neuronal development. RGMa expression patterns and signaling pathways via Neogenin and...

    Authors: Aline Gonçalves Lio Copola, Íria Gabriela Dias dos Santos, Luiz Lehmann Coutinho, Luiz Eduardo Vieira Del-Bem, Paulo Henrique de Almeida Campos-Junior, Izabela Mamede Costa Andrade da Conceição, Júlia Meireles Nogueira, Alinne do Carmo Costa, Gerluza Aparecida Borges Silva and Erika Cristina Jorge
    Citation: BMC Genomics 2022 23:188
  6. A variety of protocols exist for producing whole genome run-on transcription datasets. However, little is known about how differences between these protocols affect the signal within the resulting libraries.

    Authors: Samuel Hunter, Rutendo F. Sigauke, Jacob T. Stanley, Mary A. Allen and Robin D. Dowell
    Citation: BMC Genomics 2022 23:187
  7. MicroRNAs (miRNAs) are a family of short non-coding RNA molecules and play important roles in various biological processes. However, knowledge of the expression profiles and function of miRNAs on the regulatio...

    Authors: Xin Liu, Yuehua Zhu, Siyuan Zhan, Tao Zhong, Jiazhong Guo, Jiaxue Cao, Li Li, Hongping Zhang and Linjie Wang
    Citation: BMC Genomics 2022 23:186
  8. Citrus is one of the most important fresh fruit crops worldwide. Juice sac granulation is a physiological disorder, which leads to a reduction in soluble solid concentration, total sugar, and titratable acidit...

    Authors: Zixuan Li, Liming Wu, Ce Wang, Yue Wang, Ligang He, Zhijing Wang, Xiaofang Ma, Fuxi Bai, Guizhi Feng, Jihong Liu, Yingchun Jiang and Fang Song
    Citation: BMC Genomics 2022 23:185
  9. Maize is one of the most important food crops worldwide. Roots play important role in maize productivity through water and nutrient uptake from the soil. Improving maize root traits for efficient water uptake ...

    Authors: Junqiao Song, Daowen Lu, Yongfeng Niu, Haichao Sun, Pan Zhang, Wenheng Dong, Yongjiang Li, Yingying Zhang, Lianyong Lu, Qi Men, Xiaohui Zhang, Pengxun Ren and Chuankui Chen
    Citation: BMC Genomics 2022 23:184
  10. Meiotic recombination is one of the important phenomena contributing to gamete genome diversity. However, except for human and a few model organisms, it is not well studied in livestock, including cattle.

    Authors: Liu Yang, Yahui Gao, Mingxun Li, Ki-Eun Park, Shuli Liu, Xiaolong Kang, Mei Liu, Adam Oswalt, Lingzhao Fang, Bhanu P. Telugu, Charles G. Sattler, Cong-jun Li, John B. Cole, Eyal Seroussi, Lingyang Xu, Lv Yang…
    Citation: BMC Genomics 2022 23:181
  11. The cyclical nature of gene expression in the intraerythrocytic development cycle (IDC) of the malaria parasite, Plasmodium falciparum, confounds the accurate detection of specific transcriptional differences, e....

    Authors: Gabriel J. Foster, Mackenzie A. C. Sievert, Katrina Button-Simons, Katelyn M. Vendrely, Jeanne Romero-Severson and Michael T. Ferdig
    Citation: BMC Genomics 2022 23:180
  12. The TIFY gene family is a group of plant-specific transcription factors involved in regulation of plant growth and development and a variety of stress responses. However, the TIFY family has not yet been well cha...

    Authors: Junjie Tao, Huimin Jia, Mengting Wu, Wenqi Zhong, Dongfeng Jia, Zupeng Wang and Chunhui Huang
    Citation: BMC Genomics 2022 23:179
  13. High temperature shock is becoming increasingly common in our climate, affecting plant growth and productivity. The ability of a plant to survive stress is a complex phenomenon. One of the essential tissues fo...

    Authors: Krzysztof Mikołajczak, Anetta Kuczyńska, Piotr Ogrodowicz, Agnieszka Kiełbowicz-Matuk, Hanna Ćwiek-Kupczyńska, Agata Daszkowska-Golec, Iwona Szarejko, Maria Surma and Paweł Krajewski
    Citation: BMC Genomics 2022 23:177
  14. Long noncoding RNAs (lncRNAs) are now proven as essential regulatory elements, playing diverse roles in many biological processes including mammary gland development. However, little is known about their roles...

    Authors: Peerzada Tajamul Mumtaz, Basharat Bhat, Eveline M. Ibeagha-Awemu, Qamar Taban, Mengqi Wang, Mashooq Ahmad Dar, Shakil Ahmad Bhat, Nadeem Shabir, Riaz Ahmad Shah, Nazir A. Ganie, Dinesh Velayutham, Zulfqar ul Haq and Syed Mudasir Ahmad
    Citation: BMC Genomics 2022 23:176
  15. Diaporthe caulivora is a fungal pathogen causing stem canker in soybean worldwide. The generation of genomic and transcriptomic information of this ascomycete, together with a comparative genomic approach with o...

    Authors: Eilyn Mena, Silvia Garaycochea, Silvina Stewart, Marcos Montesano and Inés Ponce De León
    Citation: BMC Genomics 2022 23:175
  16. Melanin is an important antioxidant in food and has been used in medicine and cosmetology. Chicken meat with high melanin content from black-boned chickens have been considered a high nutritious food with pote...

    Authors: Tengfei Dou, Shixiong Yan, Lixian Liu, Kun Wang, Zonghui Jian, Zhiqiang Xu, Jingying Zhao, Qiuting Wang, Shuai Sun, Mir Zulqarnain Talpur, Xiaohua Duan, Dahai Gu, Yang He, Yanli Du, Alsoufi Mohammed Abdulwahid, Qihua Li…
    Citation: BMC Genomics 2022 23:173
  17. Recent discovery of the gene editing system - CRISPR (Clustered Regularly Interspersed Short Palindromic Repeats) associated proteins (Cas), has resulted in its widespread use for improved understanding of a v...

    Authors: Alexander Krohannon, Mansi Srivastava, Simone Rauch, Rajneesh Srivastava, Bryan C. Dickinson and Sarath Chandra Janga
    Citation: BMC Genomics 2022 23:172
  18. Soybean mosaic virus (SMV) is one of the most devastating pathogens of soybean. MicroRNAs (miRNAs) are a class of non-coding RNAs (21–24 nucleotides) which are endogenously produced by the plant host as part o...

    Authors: Bowen Li, Adhimoolam Karthikeyan, Liqun Wang, Jinlong Yin, Tongtong Jin, Hui Liu, Kai Li, Junyi Gai and Haijian Zhi
    Citation: BMC Genomics 2022 23:171
  19. Jasmonate-ZIM domain (JAZ) repressors negatively regulate signal transduction of jasmonates, which regulate plant development and immunity. However, no comprehensive analysis of the JAZ gene family members has be...

    Authors: Miaoyu Song, Haomiao Wang, Huiqin Ma and Chuanlin Zheng
    Citation: BMC Genomics 2022 23:170
  20. Flavonoid glycosides extracted from roots of Scutellaria baicalensis exhibit strong pharmaceutical antitumor, antioxidative, anti-inflammatory, and antiviral activities. UDP glycosyltransferase (UGT) family membe...

    Authors: Tianlin Pei, Mengxiao Yan, Tian Li, Xiaoqiang Li, Yijia Yin, Mengying Cui, Yumin Fang, Jie Liu, Yu Kong, Ping Xu and Qing Zhao
    Citation: BMC Genomics 2022 23:169
  21. Head of fish species, an exquisitely complex anatomical system, is important not only for studying fish evolution and development, but also for economic values. Currently, although some studies have been made ...

    Authors: Weiwei Luo, Junru Wang, Ying Zhou, Meixia Pang, Xiaomu Yu and Jingou Tong
    Citation: BMC Genomics 2022 23:168
  22. Ticks are obligate haematophagous ectoparasites considered second to mosquitos as vectors and reservoirs of multiple pathogens of global concern. Individual variation in tick infestation has been reported in i...

    Authors: Abulgasim M. Ahbara, Médiha Khamassi Khbou, Rihab Rhomdhane, Limam Sassi, Mohamed Gharbi, Aynalem Haile, Mourad Rekik, Barbara Rischkowsky and Joram M. Mwacharo
    Citation: BMC Genomics 2022 23:167
  23. Aeromonas veronii is a Gram-negative rod-shaped motile bacterium that inhabits mainly freshwater environments. A. veronii is a pathogen of aquatic animals, causing diseases in fish. A. veronii is also an emerging...

    Authors: Fang Liu, Christopher Yuwono, Alfred Chin Yen Tay, Michael C. Wehrhahn, Stephen M. Riordan and Li Zhang
    Citation: BMC Genomics 2022 23:166
  24. Several studies have been performed to study transcriptome profiles after dengue virus infections with partly different results. Due to slightly different settings of the individual studies, different genes an...

    Authors: Christine Winter, António A. R. Camarão, Imke Steffen and Klaus Jung
    Citation: BMC Genomics 2022 23:165
  25. The ability of plants to withstand and thrive in an adverse environment is crucial to ensure their survivability and yield performance. The WRKY transcription factors (TFs) have crucial roles in plant growth, ...

    Authors: Fong Chin Lee, Wan Chin Yeap, David Ross Appleton, Chai-Ling Ho and Harikrishna Kulaveerasingam
    Citation: BMC Genomics 2022 23:164
  26. Technological advancements in the era of massive parallel sequencing have enabled the functional dissection of the human transcriptome. However, 5′ ends of mRNAs are significantly underrepresented in these dat...

    Authors: Panagiotis G. Adamopoulos, Panagiotis Tsiakanikas, Irene Stolidi and Andreas Scorilas
    Citation: BMC Genomics 2022 23:163
  27. Blunt snout bream (Megalobrama amblycephala) is sensitive to hypoxia. A new blunt snout bream strain, “Pujiang No.2”, was developed to overcome this shortcoming. As a proteasome inhibitor, bortezomib (PS-341) has...

    Authors: Shan-Shan Zhao, Xiao-Lei Su, Rong-Jia Pan, Li-Qun Lu, Guo-Dong Zheng and Shu-Ming Zou
    Citation: BMC Genomics 2022 23:162
  28. Paris polyphylla is a herb widely used in traditional Chinese medicine to treat various diseases. Stem rot diseases seriously affected the yield of P. polyphylla in subtropical areas of China. Therefore, cost-eff...

    Authors: Aiming Jiang, Chengwu Zou, Xiang Xu, Zunwei Ke, Jiangan Hou, Guihe Jiang, Chunli Fan, Jianhua Gong and Jiguang Wei
    Citation: BMC Genomics 2022 23:161
  29. Whole genomes are commonly assembled into a collection of scaffolds and often lack annotations of autosomes, sex chromosomes, and organelle genomes (i.e., mitochondrial and chloroplast). As these chromosome ty...

    Authors: Charles Christian Riis Hansen, Kristen M. Westfall and Snæbjörn Pálsson
    Citation: BMC Genomics 2022 23:160
  30. ‘Nebbiolo’ is a grapevine cultivar typical of north-western Italy, appreciated for producing high-quality red wines. Grapevine cultivars are characterized by possessing highly heterozygous genomes, including a...

    Authors: Simone Maestri, Giorgio Gambino, Giulia Lopatriello, Andrea Minio, Irene Perrone, Emanuela Cosentino, Barbara Giovannone, Luca Marcolungo, Massimiliano Alfano, Stephane Rombauts, Dario Cantu, Marzia Rossato, Massimo Delledonne and Luciano Calderón
    Citation: BMC Genomics 2022 23:159
  31. Fusarium langsethiae is a T-2 and HT-2 mycotoxins producing species firstly characterised in 2004. It is commonly isolated from oats in Northern Europe. T-2 and HT-2 mycotoxins exhibit immunological and haemotolo...

    Authors: Ya Zuo, Carol Verheecke-Vaessen, Corentin Molitor, Angel Medina, Naresh Magan and Fady Mohareb
    Citation: BMC Genomics 2022 23:158
  32. Pacific Biosciences HiFi read technology is currently the industry standard for high accuracy long-read sequencing that has been widely adopted by large sequencing and assembly initiatives for generation of de...

    Authors: Sheina B. Sim, Renee L. Corpuz, Tyler J. Simmonds and Scott M. Geib
    Citation: BMC Genomics 2022 23:157
  33. Patient-derived xenografts (PDX) mice models play an important role in preclinical trials and personalized medicine. Sharing data on the models is highly valuable for numerous reasons – ethical, economical, re...

    Authors: Zdenka Dudová, Nathalie Conte, Jeremy Mason, Dalibor Stuchlík, Radim Peša, Csaba Halmagyi, Zinaida Perova, Abayomi Mosaku, Ross Thorne, Alex Follette, Ľuboslav Pivarč, Radim Šašinka, Muhammad Usman, Steven Neuhauser, Dale A. Begley, Debra M. Krupke…
    Citation: BMC Genomics 2022 23:156
  34. Accurate variant detection in the coding regions of the human genome is a key requirement for molecular diagnostics of Mendelian disorders. Efficiency of variant discovery from next-generation sequencing (NGS)...

    Authors: Yury A. Barbitoff, Ruslan Abasov, Varvara E. Tvorogova, Andrey S. Glotov and Alexander V. Predeus
    Citation: BMC Genomics 2022 23:155
  35. Plant miRNAs are a class of small non-coding RNAs that can repress gene expression at the post-transcriptional level by targeting RNA degradation or promoting translational repression. There is increasing evid...

    Authors: Juan M. Crescente, Diego Zavallo, Mariana del Vas, Sebastián Asurmendi, Marcelo Helguera, Elmer Fernandez and Leonardo S. Vanzetti
    Citation: BMC Genomics 2022 23:154
  36. global trade in living plants and plant material has significantly increased the geographic distribution of many plant pathogens. As a consequence, several pathogens have been first found and described in thei...

    Authors: Tetyana Tsykun, Simone Prospero, Corine N. Schoebel, Alexander Rea and Treena I. Burgess
    Citation: BMC Genomics 2022 23:153
  37. Biocontrol agents are sustainable eco-friendly alternatives for chemical pesticides that cause adverse effects in the environment and toxicity in animals including humans. An improved understanding of the phyl...

    Authors: Claudia Y. Muñoz, Lu Zhou, Yunhai Yi and Oscar P. Kuipers
    Citation: BMC Genomics 2022 23:152
  38. The oocyte development ability of prepubertal animals is significantly lower than that of adult animals. Granulosa cells (GCs) have an important function on regulation of follicular and oocyte development. The...

    Authors: Hao Tian, Panyu Ren, Kailing Liu, Chunjuan Qiu, Lihong Fan, Junlong Li and Jian Hou
    Citation: BMC Genomics 2022 23:151
  39. Zinc finger homeodomain (ZHD) protein is a plant-specific transcription factor and a potential regulator of phosphoenolpyruvate carboxylase (PEPCase)-coding genes, and it also participates in plant growth regu...

    Authors: Kai He, Chunxin Li, Zhenyue Zhang, Lifeng Zhan, Chunlong Cong, Depeng Zhang and Hua Cai
    Citation: BMC Genomics 2022 23:150
  40. Transgenic animal models are crucial for the study of gene function and disease, and are widely utilized in basic biological research, agriculture and pharma industries. Since the current methods for generatin...

    Authors: Vanja Börjesson, Angela Martinez-Monleon, Susanne Fransson, Per Kogner, John Inge Johnsen, Jelena Milosevic and Marcela Dávila López
    Citation: BMC Genomics 2022 23:149
  41. While large genome-wide association studies have identified nearly one thousand loci associated with variation in blood pressure, rare variant identification is still a challenge. In family-based cohorts, geno...

    Authors: Karen Y. He, Tanika N. Kelly, Heming Wang, Jingjing Liang, Luke Zhu, Brian E. Cade, Themistocles L. Assimes, Lewis C. Becker, Amber L. Beitelshees, Lawrence F. Bielak, Adam P. Bress, Jennifer A. Brody, Yen-Pei Christy Chang, Yi-Cheng Chang, Paul S. de Vries, Ravindranath Duggirala…
    Citation: BMC Genomics 2022 23:148
  42. Among the Mangifera species, mango (Mangifera indica) is an important commercial fruit crop. However, very few studies have been conducted on the Mangifera mitochondrial genome. This study reports and compares th...

    Authors: Yingfeng Niu, Chengwen Gao and Jin Liu
    Citation: BMC Genomics 2022 23:147
  43. Deciphering the hereditary mechanism of seed iron (Fe) and zinc (Zn) content in soybean is important and sustainable to address the “hidden hunger” that presently affects approximately 2 billion people worldwi...

    Authors: Huan Wang, Jia Jia, Zhandong Cai, Mingming Duan, Ze Jiang, Qiuju Xia, Qibin Ma, Tengxiang Lian and Hai Nian
    Citation: BMC Genomics 2022 23:146
  44. Lysine 2-hydroxyisobutyrylation (Khib) is a newly discovered posttranslational modification (PTM) and has been identified in several prokaryotic and eukaryotic organisms. Fusarium graminearum, a major pathogen of...

    Authors: Yanxiang Zhao, Limin Zhang, Chao Ju, Xiaoyan Zhang and Jinguang Huang
    Citation: BMC Genomics 2022 23:145
  45. DNA methylation is thought to influence the expression of genes, especially in response to changing environmental conditions and developmental changes. Sugar beet (Beta vulgaris ssp. vulgaris), and other biennial...

    Authors: Sindy Gutschker, José María Corral, Alfred Schmiedl, Frank Ludewig, Wolfgang Koch, Karin Fiedler-Wiechers, Olaf Czarnecki, Karsten Harms, Isabel Keller, Cristina Martins Rodrigues, Benjamin Pommerrenig, H. Ekkehard Neuhaus, Wolfgang Zierer, Uwe Sonnewald and Christina Müdsam
    Citation: BMC Genomics 2022 23:144
  46. Animal genomes are strikingly conserved in terms of local gene order (microsynteny). While some of these microsyntenies have been shown to be coregulated or to form gene regulatory blocks, the diversity of the...

    Authors: Nicolas S. M. Robert, Fatih Sarigol, Bob Zimmermann, Axel Meyer, Christian R. Voolstra and Oleg Simakov
    Citation: BMC Genomics 2022 23:143

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