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Comparative and evolutionary genomics

Section edited by Igor Rogozin and Alexei Fedorov

This section covers comparative genomic studies and novel methods, including phylogenetic analyses, evolutionary genomics and all studies with a cross-taxonomic focus.

Page 5 of 18

  1. Content type: Research article

    A gene regulatory network (GRN) comprises many weak links that are often regulated by microRNAs. Since miRNAs rarely repress their target genes by more than 30%, doubts have been expressed about the biological...

    Authors: Fuqiang Ma, Pei Lin, Qingjian Chen, Xuemei Lu, Yong E. Zhang and Chung-I Wu

    Citation: BMC Genomics 2018 19:362

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  2. Content type: Methodology article

    Acoustic or hydrodynamic shearing, sonication and enzymatic digestion are used to fragment DNA. However, these methods have several disadvantages, such as DNA damage, difficulties in fragmentation control, irr...

    Authors: Daria Krefft, Aliaksei Papkov, Maciej Prusinowski, Agnieszka Zylicz-Stachula and Piotr M. Skowron

    Citation: BMC Genomics 2018 19:361

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  3. Content type: Research article

    Cryptosporidium baileyi is the most common Cryptosporidium species in birds. However, effective prevention measures and treatment for C. baileyi infection were still not available. Long non-coding RNAs (lncRNAs) ...

    Authors: Guan-Jing Ren, Xian-Cheng Fan, Ting-Li Liu, Sha-Sha Wang and Guang-Hui Zhao

    Citation: BMC Genomics 2018 19:356

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  4. Content type: Research article

    Evolution occurred exclusively under the full spectrum of sunlight. Conscription of narrow regions of the solar spectrum by specific photoreceptors suggests a common strategy for regulation of genetic pathways...

    Authors: Ronald B. Walter, Mikki Boswell, Jordan Chang, William T. Boswell, Yuan Lu, Kaela Navarro, Sean M. Walter, Dylan J. Walter, Raquel Salinas and Markita Savage

    Citation: BMC Genomics 2018 19:355

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  5. Content type: Research article

    Mitochondrial DNA sequences have long been used in phylogenetic studies. However, little attention has been paid to the changes in gene arrangement patterns in the snake’s mitogenome. Here, we analyzed the com...

    Authors: Lifu Qian, Hui Wang, Jie Yan, Tao Pan, Shanqun Jiang, Dingqi Rao and Baowei Zhang

    Citation: BMC Genomics 2018 19:354

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  6. Content type: Research article

    Brucellosis is a bacterial zoonotic disease. Annually in the world more than 500,000 new cases of brucellosis in humans are registered. In this study, we propose an evolutionary model of the historical distrib...

    Authors: Sergey V. Pisarenko, Dmitry A. Kovalev, Anna S. Volynkina, Dmitry G. Ponomarenko, Diana V. Rusanova, Nina V. Zharinova, Anna A. Khachaturova, Lyudmila E. Tokareva, Irina G. Khvoynova and Alexander N. Kulichenko

    Citation: BMC Genomics 2018 19:353

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  7. Content type: Research article

    Most genetic analyses of ancient and modern dogs have focused on variation in the autosomes or on the mitochondria. Mitochondrial DNA is more easily obtained from ancient samples than nuclear DNA and mitochond...

    Authors: Matthew T. Oetjens, Axel Martin, Krishna R. Veeramah and Jeffrey M. Kidd

    Citation: BMC Genomics 2018 19:350

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  8. Content type: Research article

    Genomic tools are increasingly being used on non-model organisms to provide insights into population structure and variability, including signals of selection. However, most studies are carried out in regions ...

    Authors: Erica S. Nielsen, Romina Henriques, Robert J. Toonen, Ingrid S. S. Knapp, Baocheng Guo and Sophie von der Heyden

    Citation: BMC Genomics 2018 19:347

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  9. Content type: Research article

    The BES1 gene family, an important class of plant-specific transcription factors, play key roles in the BR signal pathway in plants, regulating various development processes. Until now, there has been no comprehe...

    Authors: Xiaoming Song, Xiao Ma, Chunjin Li, Jingjing Hu, Qihang Yang, Tong Wang, Li Wang, Jinpeng Wang, Di Guo, Weina Ge, Zhenyi Wang, Miaomiao Li, Qiumei Wang, Tianzeng Ren, Shuyan Feng, Lixia Wang…

    Citation: BMC Genomics 2018 19:346

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  10. Content type: Methodology article

    Identification of mutations from next-generation sequencing data typically requires a balance between sensitivity and accuracy. This is particularly true of DNA insertions and deletions (indels), that can impa...

    Authors: Adam B. Burkholder, Scott A. Lujan, Christopher A. Lavender, Sara A. Grimm, Thomas A. Kunkel and David C. Fargo

    Citation: BMC Genomics 2018 19:345

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  11. Content type: Research article

    Valine-glutamine (VQ) motif containing proteins play important roles in abiotic and biotic stress responses in plants. However, little is known about the origin and evolution as well as comprehensive expressio...

    Authors: Shu-Ye Jiang, Mayalagu Sevugan and Srinivasan Ramachandran

    Citation: BMC Genomics 2018 19:342

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  12. Content type: Research article

    Recent large-scale whole genome sequencing efforts in birds have elucidated broad patterns of avian phylogeny and genome evolution. However, despite the great interest in economically important phasianids like Ga...

    Authors: G. P. Tiley, R. T. Kimball, E. L. Braun and J. G. Burleigh

    Citation: BMC Genomics 2018 19:336

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  13. Content type: Research article

    Xylella fastidiosa (Xf) is a gram negative bacterium inhabiting the plant vascular system. In most species this bacterium lives as a benign symbiote, but in several agriculturally important plants (e.g. coffee, c...

    Authors: Gregory A. Gambetta, Mark A. Matthews and Michael Syvanen

    Citation: BMC Genomics 2018 19:329

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  14. Content type: Software

    Genomic islands (GIs) are inserts of foreign DNA that have potentially arisen through horizontal gene transfer (HGT). There are evidences that GIs can contribute significantly to the evolution of prokaryotes. ...

    Authors: Frederick Johannes Clasen, Rian Ewald Pierneef, Bernard Slippers and Oleg Reva

    Citation: BMC Genomics 2018 19:323

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  15. Content type: Research article

    The renewed interest in epigenetics has led to the understanding that both the environment and individual lifestyle can directly interact with the epigenome to influence its dynamics. Epigenetic phenomena are ...

    Authors: Loris Pratx, Corinne Rancurel, Martine Da Rocha, Etienne G. J. Danchin, Philippe Castagnone-Sereno, Pierre Abad and Laetitia Perfus-Barbeoch

    Citation: BMC Genomics 2018 19:321

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  16. Content type: Research article

    Temperature adaptation of biological molecules is fundamental in evolutionary studies but remains unsolved. Fishes living in cold water are adapted to low temperatures through adaptive modification of their bi...

    Authors: Dongsheng Zhang, Peng Hu, Taigang Liu, Jian Wang, Shouwen Jiang, Qianghua Xu and Liangbiao Chen

    Citation: BMC Genomics 2018 19:315

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  17. Content type: Methodology article

    Plasmodium falciparum is the most virulent malaria parasite capable of parasitizing human erythrocytes. The identification of genes related to this capability can enhance our understanding of the molecular mechan...

    Authors: Xuewu Liu, Yuanyuan Wang, Jiao Liang, Luojun Wang, Na Qin, Ya Zhao and Gang Zhao

    Citation: BMC Genomics 2018 19:312

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  18. Content type: Research article

    Both calcium signals and protein phosphorylation responses are universal signals in eukaryotic cell signaling. Currently three pathways have been characterized in different eukaryotes converting the Ca2+ signals ...

    Authors: Fei Chen, Liangsheng Zhang, Zhenguo Lin and Zong-Ming Max Cheng

    Citation: BMC Genomics 2018 19:306

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  19. Content type: Research article

    At the end of the Pliocene and the beginning of Pleistocene glaciation and deglaciation cycles Ginkgo biloba went extinct all over the world, and only few populations remained in China in relict areas serving as ...

    Authors: Nora Hohmann, Eva M. Wolf, Philippe Rigault, Wenbin Zhou, Markus Kiefer, Yunpeng Zhao, Cheng-Xin Fu and Marcus A. Koch

    Citation: BMC Genomics 2018 19:299

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  20. Content type: Research article

    Theileria orientalis (Apicomplexa: Piroplasmida) has caused clinical disease in cattle of Eastern Asia for many years and its recent rapid spread throughout Australian and New Zealand herds has caused substantial...

    Authors: Daniel R. Bogema, Melinda L. Micallef, Michael Liu, Matthew P. Padula, Steven P. Djordjevic, Aaron E. Darling and Cheryl Jenkins

    Citation: BMC Genomics 2018 19:298

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  21. Content type: Research article

    Chagas disease is a parasitic infection caused by Trypanosoma cruzi. It is an important public health problem affecting around seven to eight million people in the Americas. A large number of hematophagous triato...

    Authors: Jesús Martínez-Barnetche, Andrés Lavore, Melina Beliera, Juan Téllez-Sosa, Federico A. Zumaya-Estrada, Victorio Palacio, Ernestina Godoy-Lozano, Rolando Rivera-Pomar and Mario Henry Rodríguez

    Citation: BMC Genomics 2018 19:296

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  22. Content type: Research article

    The mammalian adipose tissue plays a central role in energy-balance control, whereas the avian visceral fat hardly expresses leptin, the key adipokine in mammals. Therefore, to assess the endocrine role of adi...

    Authors: Susanne Bornelöv, Eyal Seroussi, Sara Yosefi, Sharon Benjamini, Shoval Miyara, Mark Ruzal, Manfred Grabherr, Nima Rafati, Anna-Maja Molin, Ken Pendavis, Shane C. Burgess, Leif Andersson and Miriam Friedman-Einat

    Citation: BMC Genomics 2018 19:295

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  23. Content type: Research article

    The common deletion of the glutathione S-transferase Mu 1 (GSTM1) gene in humans has been shown to be involved in xenobiotic metabolism and associated with bladder cancer. However, the evolution of this deletion ...

    Authors: M. Saitou, Y. Satta, O. Gokcumen and T. Ishida

    Citation: BMC Genomics 2018 19:293

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  24. Content type: Research article

    Pyrenophora tritici-repentis (Ptr) is a necrotrophic fungal pathogen that causes the major wheat disease, tan spot. We set out to provide essential genomics-based resources in order to better understand the patho...

    Authors: Paula Moolhuijzen, Pao Theen See, James K. Hane, Gongjun Shi, Zhaohui Liu, Richard P. Oliver and Caroline S. Moffat

    Citation: BMC Genomics 2018 19:279

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    The Correction to this article has been published in BMC Genomics 2018 19:673

  25. Content type: Research article

    Malaria mosquitoes have had a remarkable stability in the number of chromosomes in their karyotype (2n = 6) during 100 million years of evolution. Moreover, autosomal arms were assumed to maintain their integr...

    Authors: Gleb N. Artemov, Semen M. Bondarenko, Anastasia N. Naumenko, Vladimir N. Stegniy, Maria V. Sharakhova and Igor V. Sharakhov

    Citation: BMC Genomics 2018 19:278

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  26. Content type: Methodology article

    The characterization of genomic or epigenomic variation in human and animal models could provide important insight into pathophysiological mechanisms of various diseases, and lead to new developments in diseas...

    Authors: Ja-Rang Lee, Dong-Sung Ryu, Sang-Je Park, Se-Hee Choe, Hyeon-Mu Cho, Sang-Rae Lee, Sun-Uk Kim, Young-Hyun Kim and Jae-Won Huh

    Citation: BMC Genomics 2018 19:267

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  27. Content type: Research article

    GC-Biased Gene Conversion (gBGC) is one of the important theories put forward to explain profound long-range non-randomness in nucleotide compositions along mammalian chromosomes. Nucleotide changes due to gBG...

    Authors: Rajib Dutta, Arnab Saha-Mandal, Xi Cheng, Shuhao Qiu, Jasmine Serpen, Larisa Fedorova and Alexei Fedorov

    Citation: BMC Genomics 2018 19:256

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  28. Content type: Research article

    The intracerebroventricular injection of visfatin increases feed intake. However, little is known about the molecular mechanism in chicks. This study was conducted to assess the effect of visfatin on the feedi...

    Authors: Zhuanjian Li, Xuelian Liu, Panpan Zhang, Ruili Han, Guirong Sun, Ruirui Jiang, Yanbin Wang, Xiaojun Liu, Wenya Li, Xiangtao Kang and Yadong Tian

    Citation: BMC Genomics 2018 19:249

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  29. Content type: Research article

    Glucose plays a key role as an energy source in most mammals, but its importance in fish appears to be limited that so far seemed to belong to diabetic humans only. Several laboratories worldwide have made imp...

    Authors: Yuru Zhang, Chaobin Qin, Liping Yang, Ronghua Lu, Xiaoyan Zhao and Guoxing Nie

    Citation: BMC Genomics 2018 19:246

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  30. Content type: Research article

    Striped bass (Morone saxatilis) spermatozoa are used to fertilize in vitro the eggs of white bass (M. chrysops) to produce the preferred hybrid for the striped bass aquaculture industry. Currently, only one sourc...

    Authors: L. Curry Woods III, Yaokun Li, Yi Ding, Jianan Liu, Benjamin J. Reading, S. Adam Fuller and Jiuzhou Song

    Citation: BMC Genomics 2018 19:244

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  31. Content type: Software

    A strong focus of the post-genomic era is mining of the non-coding regulatory genome in order to unravel the function of regulatory elements that coordinate gene expression (Nat 489:57–74, 2012; Nat 507:462–70...

    Authors: Louis T. Dang, Markus Tondl, Man Ho H. Chiu, Jerico Revote, Benedict Paten, Vincent Tano, Alex Tokolyi, Florence Besse, Greg Quaife-Ryan, Helen Cumming, Mark J. Drvodelic, Michael P. Eichenlaub, Jeannette C. Hallab, Julian S. Stolper, Fernando J. Rossello, Marie A. Bogoyevitch…

    Citation: BMC Genomics 2018 19:238

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  32. Content type: Research article

    Epilithic sister genera Oresitrophe and Mukdenia (Saxifragaceae) have an epilithic habitat (rocky slopes) and a parapatric distribution in East Asia, which makes them an ideal model for a more comprehensive under...

    Authors: Luxian Liu, Yuewen Wang, Peizi He, Pan Li, Joongku Lee, Douglas E. Soltis and Chengxin Fu

    Citation: BMC Genomics 2018 19:235

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  33. Content type: Research article

    Management requires a robust understanding of between- and within-species genetic variability, however such data are still lacking in many species. For example, although multiple population genetics studies of...

    Authors: Jacqueline M. Doyle, Douglas A. Bell, Peter H. Bloom, Gavin Emmons, Amy Fesnock, Todd E. Katzner, Larry LaPré, Kolbe Leonard, Phillip SanMiguel, Rick Westerman and J. Andrew DeWoody

    Citation: BMC Genomics 2018 19:233

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  34. Content type: Research article

    In recent years, epigenetics has gained a central role in the understanding of the process of natural selection. It is now clear how environmental impacts on the methylome could promote methylation variability...

    Authors: Domenico Palumbo, Ornella Affinito, Antonella Monticelli and Sergio Cocozza

    Citation: BMC Genomics 2018 19:229

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  35. Content type: Research article

    Cashmere is a keratinized product derived from the secondary hair follicles (SHFs) of cashmere goat skins. The cashmere fiber stops growing following the transition from the actively proliferating anagen stage...

    Authors: Guangxian Zhou, Danju Kang, Sen Ma, Xingtao Wang, Ye Gao, Yuxin Yang, Xiaolong Wang and Yulin Chen

    Citation: BMC Genomics 2018 19:222

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  36. Content type: Research article

    Heterobasidion parviporum is an economically most important fungal forest pathogen in northern Europe, causing root and butt rot disease of Norway spruce (Picea abies (L.) Karst.). The mechanisms underlying the p...

    Authors: Zhen Zeng, Hui Sun, Eeva J. Vainio, Tommaso Raffaello, Andriy Kovalchuk, Emmanuelle Morin, Sébastien Duplessis and Fred O. Asiegbu

    Citation: BMC Genomics 2018 19:220

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  37. Content type: Methodology article

    Although high-throughput sequencers (HTS) have largely displaced their Sanger counterparts, the short read lengths and high error rates of most platforms constrain their utility for amplicon sequencing. The pr...

    Authors: Paul D. N. Hebert, Thomas W. A. Braukmann, Sean W. J. Prosser, Sujeevan Ratnasingham, Jeremy R. deWaard, Natalia V. Ivanova, Daniel H. Janzen, Winnie Hallwachs, Suresh Naik, Jayme E. Sones and Evgeny V. Zakharov

    Citation: BMC Genomics 2018 19:219

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  38. Content type: Research article

    With approximately one-third of their genomes consisting of linear and circular plasmids, the Lyme disease agent cluster of species has the most complex genomes among known bacteria. We report here a comparati...

    Authors: Sherwood R. Casjens, Lia Di, Saymon Akther, Emmanuel F. Mongodin, Benjamin J. Luft, Steven E. Schutzer, Claire M. Fraser and Wei-Gang Qiu

    Citation: BMC Genomics 2018 19:218

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  39. Content type: Research article

    Adaptive genomics may help predicting how a species will respond to future environmental changes. Genomic signatures of local adaptation in marine organisms are often driven by environmental selective agents i...

    Authors: Alicia Dalongeville, Laura Benestan, David Mouillot, Stephane Lobreaux and Stéphanie Manel

    Citation: BMC Genomics 2018 19:217

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  40. Content type: Research article

    Human herpesvirus-6A and -6B (HHV-6) are betaherpesviruses that reach > 90% seroprevalence in the adult population. Unique among human herpesviruses, HHV-6 can integrate into the subtelomeric regions of human ...

    Authors: Alexander L. Greninger, Giselle M. Knudsen, Pavitra Roychoudhury, Derek J. Hanson, Ruth Hall Sedlak, Hong Xie, Jon Guan, Thuy Nguyen, Vikas Peddu, Michael Boeckh, Meei-Li Huang, Linda Cook, Daniel P. Depledge, Danielle M. Zerr, David M. Koelle, Soren Gantt…

    Citation: BMC Genomics 2018 19:204

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  41. Content type: Research article

    The ballan wrasse (Labrus bergylta) belongs to a large teleost family containing more than 600 species showing several unique evolutionary traits such as lack of stomach and hermaphroditism. Agastric fish are fou...

    Authors: Kai K. Lie, Ole K. Tørresen, Monica Hongrø Solbakken, Ivar Rønnestad, Ave Tooming-Klunderud, Alexander J. Nederbragt, Sissel Jentoft and Øystein Sæle

    Citation: BMC Genomics 2018 19:186

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  42. Content type: Research article

    Animals living at high altitude must adapt to environments with hypoxia and low temperatures, but relatively little is known about underlying genetic changes. Toad-headed lizards of the genus Phrynocephalus cover...

    Authors: Yuanting Jin, Yubin Wo, Haojie Tong, Sen Song, Lixun Zhang and Richard P. Brown

    Citation: BMC Genomics 2018 19:185

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  43. Content type: Database

    Gastropoda, with approximately 80,000 living species, is the largest class of Mollusca. Among gastropods, apple snails (family Ampullariidae) are globally distributed in tropical and subtropical freshwater eco...

    Authors: Jack C. H. Ip, Huawei Mu, Qian Chen, Jin Sun, Santiago Ituarte, Horacio Heras, Bert Van Bocxlaer, Monthon Ganmanee, Xin Huang and Jian-Wen Qiu

    Citation: BMC Genomics 2018 19:179

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  44. Content type: Research article

    Increased reports of Neisseria meningitidis urethritis in multiple U.S. cities during 2015 have been attributed to the emergence of a novel clade of nongroupable N. meningitidis within the ST-11 clonal complex, t...

    Authors: Adam C. Retchless, Cécilia B. Kretz, How-Yi Chang, Jose A. Bazan, A. Jeanine Abrams, Abigail Norris Turner, Laurel T. Jenkins, David L. Trees, Yih-Ling Tzeng, David S. Stephens, Jessica R. MacNeil and Xin Wang

    Citation: BMC Genomics 2018 19:176

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  45. Content type: Research article

    Polyploidy is considered a major driving force in genome expansion, yielding duplicated genes whose expression may be conserved or divergence as a consequence of polyploidization.

    Authors: Bingliang Liu, Xueying Guan, Wenhua Liang, Jiedan Chen, Lei Fang, Yan Hu, Wangzhen Guo, Junkang Rong, Guohua Xu and Tianzhen Zhang

    Citation: BMC Genomics 2018 19:162

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  46. Content type: Research article

    The rise and fall of the Y chromosome was demonstrated in animals but plants often possess the large evolutionarily young Y chromosome that is thought has expanded recently. Break-even points dividing expansio...

    Authors: Janka Puterova, Zdenek Kubat, Eduard Kejnovsky, Wojciech Jesionek, Jana Cizkova, Boris Vyskot and Roman Hobza

    Citation: BMC Genomics 2018 19:153

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  47. Content type: Research article

    Peptidases (EC 3.4) consist of a large group of hydrolytic enzymes that catalyze the hydrolysis of proteins accounting for approximately 65% of the total worldwide enzyme production. Peptidases from thermophil...

    Authors: Tássio Brito de Oliveira, Cene Gostinčar, Nina Gunde-Cimerman and Andre Rodrigues

    Citation: BMC Genomics 2018 19:152

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