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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.

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  1. Fuzhong buffalo, a native breed of Guangxi Zhuang Autonomous Region, is traditionally used as a draft animal to provide farm power in the rice cultivation. In addition, the Fuzhong buffalo also prepared for th...

    Authors: Ting Sun, Guang-yun Huang, Zi-hao Wang, Shao-hua Teng, Yan-hong Cao, Jun-li Sun, Quratulain Hanif, Ning-bo Chen, Chu-zhao Lei and Yu-ying Liao

    Citation: BMC Genomics 2020 21:674

    Content type: Research article

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  2. Pacu (Piaractus mesopotamicus) is one of the most important Neotropical aquaculture species from South America. Disease outbreaks caused by Aeromonas hydrophila infection have been considered significant contribu...

    Authors: Vito A. Mastrochirico-Filho, Carolina H. S. Borges, Milena V. Freitas, Raquel B. Ariede, Fabiana Pilarski, Ricardo Utsunomia, Roberto Carvalheiro, Alejandro P. Gutierrez, Carolina Peñaloza, José M. Yáñez, Ross D. Houston and Diogo T. Hashimoto

    Citation: BMC Genomics 2020 21:672

    Content type: Research article

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  3. Restrictions to gene flow, genetic drift, and divergent selection associated with different environments are significant drivers of genetic differentiation. The black tiger shrimp (Penaeus monodon), is widely dis...

    Authors: Nga T. T. Vu, Kyall R. Zenger, Jarrod L. Guppy, Melony J. Sellars, Catarina N. S. Silva, Shannon R. Kjeldsen and Dean R. Jerry

    Citation: BMC Genomics 2020 21:669

    Content type: Research article

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  4. Homologous sex chromosomes can differentiate over time because recombination is suppressed in the region of the sex determining locus, leading to the accumulation of repeats, progressive loss of genes that lac...

    Authors: Duminda Sampath Bandara Dissanayake, Clare Ellen Holleley, Laura Kate Hill, Denis O’Meally, Janine Eileen Deakin and Arthur Georges

    Citation: BMC Genomics 2020 21:667

    Content type: Research article

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  5. One of the biggest challenges in chromosome biology is to understand the occurrence and complex genetics of the extra, non-essential karyotype elements, commonly known as supernumerary or B chromosomes (Bs). T...

    Authors: Syed F. Ahmad, Maryam Jehangir, Adauto L. Cardoso, Ivan R. Wolf, Vladimir P. Margarido, Diogo C. Cabral-de-Mello, Rachel O’Neill, Guilherme T. Valente and Cesar Martins

    Citation: BMC Genomics 2020 21:656

    Content type: Research article

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  6. Different morphological structures of hairs having properties like defense and camouflage help animals survive in the wild environment. Horse is one of the rare kinds of animals with complex hair phenotypes in...

    Authors: Ruoyang Zhao, Wu Yihan, Yiping Zhao, Bei Li, Haige Han, Togtokh Mongke, Tugeqin Bao, Wenxing Wang, Manglai Dugarjaviin and Dongyi Bai

    Citation: BMC Genomics 2020 21:651

    Content type: Research article

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  7. Marine medaka (Oryzias melastigma) is considered as an important ecotoxicological indicator to study the biochemical, physiological and molecular responses of marine organisms towards increasing amount of polluta...

    Authors: Pingping Liang, Hafiz Sohaib Ahmed Saqib, Xiaomin Ni and Yingjia Shen

    Citation: BMC Genomics 2020 21:640

    Content type: Research article

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  8. Improving sow fertility is extremely important as it can lead to increased reproductive efficiency and thus profitability for swine producers. There are considerable differences in fertility rates among indivi...

    Authors: Huiyan Hu, Qing Jia, Jianzhong Xi, Bo Zhou and Zhiqiang Li

    Citation: BMC Genomics 2020 21:636

    Content type: Research article

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  9. Goats (Capra hircus), one of the first domesticated species, are economically important for milk and meat production, and their broad geographical distribution reflects their successful adaptation to diverse envi...

    Authors: Francesco Giannico, Serafina Massari, Anna Caputi Jambrenghi, Adriano Soriano, Angela Pala, Giovanna Linguiti, Salvatrice Ciccarese and Rachele Antonacci

    Citation: BMC Genomics 2020 21:623

    Content type: Research article

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  10. Chrysosplenium L. (Saxifragaceae) is a genus of plants widely distributed in Northern Hemisphere and usually found in moist, shaded valleys and mountain slopes. This genus is ideal for studying plant adaptation t...

    Authors: Zhihua Wu, Rui Liao, Tiange Yang, Xiang Dong, Deqing Lan, Rui Qin and Hong Liu

    Citation: BMC Genomics 2020 21:621

    Content type: Research article

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  11. According to history, in the pre-Hispanic period, during the conquest and Inka expansion in Ecuador, many Andean families of the Cañar region would have been displaced to several places of Tawantinsuyu, including...

    Authors: José R. Sandoval, Daniela R. Lacerda, Marilza M. S. Jota, Paulo Robles-Ruiz, Pierina Danos, César Paz-y-Miño, Spencer Wells, Fabrício R. Santos and Ricardo Fujita

    Citation: BMC Genomics 2020 21(Suppl 7):413

    Content type: Research

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    This article is part of a Supplement: Volume 21 Supplement 7

  12. Lysin motif-containing proteins (LYP), which act as pattern-recognition receptors, play central roles in growth, node formation, and responses to biotic stresses. The sequence of Chinese white pear genome (cv....

    Authors: Qiming Chen, Qionghou Li, Xin Qiao, Hao Yin and Shaoling Zhang

    Citation: BMC Genomics 2020 21:612

    Content type: Research article

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  13. Sand flies are the vectors of Leishmania parasites. To develop in the sand fly midgut, Leishmania multiplies and undergoes various stage differentiations giving rise to the infective form, the metacyclic promasti...

    Authors: Iliano V. Coutinho-Abreu, Tiago Donatelli Serafim, Claudio Meneses, Shaden Kamhawi, Fabiano Oliveira and Jesus G. Valenzuela

    Citation: BMC Genomics 2020 21:608

    Content type: Research article

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  14. Argeia pugettensis is an isopod species that parasitizes other crustaceans. Its huge native geographic range spans the Pacific from China to California, but molecular data are available only for a handful of spec...

    Authors: Jianmei An, Wanrui Zheng, Jielong Liang, Qianqian Xi, Ruru Chen, Junli Jia, Xia Lu and Ivan Jakovlić

    Citation: BMC Genomics 2020 21:607

    Content type: Research article

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  15. Immune-response (IR) genes have an important role in the defense against highly variable pathogens, and therefore, diversity in these genomic regions is essential for species’ survival and adaptation. Although...

    Authors: Sara Lado, Jean P. Elbers, Mark F. Rogers, José Melo-Ferreira, Adiya Yadamsuren, Jukka Corander, Petr Horin and Pamela A. Burger

    Citation: BMC Genomics 2020 21:606

    Content type: Research article

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  16. Long non-coding RNAs (lncRNAs) are involved in many fundamental biological processes, such as transcription regulation, protein degradation, and cell differentiation. Information on lncRNA in the melon fly, Zeugo...

    Authors: Wei-Jun Li, Yu-Jia Song, Hong-Liang Han, Hui-Qian Xu, Dong Wei, Guy Smagghe and Jin-Jun Wang

    Citation: BMC Genomics 2020 21:600

    Content type: Research article

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  17. Most animals restrict their activity to a specific part of the day, being diurnal, nocturnal or crepuscular. The genetic basis underlying diurnal preference is largely unknown. Under laboratory conditions, Drosop...

    Authors: Mirko Pegoraro, Laura M. M. Flavell, Pamela Menegazzi, Perrine Colombi, Pauline Dao, Charlotte Helfrich-Förster and Eran Tauber

    Citation: BMC Genomics 2020 21:596

    Content type: Research article

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  18. Genomic comparison of Mycoplasma synoviae vaccine strain MS-H and the MS-H parental strain 86,079/7NS established a preliminary profile of genes related to attenuation of MS-H. In this study we aimed to identify ...

    Authors: Somayeh Kordafshari, Pollob Shil, Marc S. Marenda, Olusola M. Olaogun, Barbara Konsak-Ilievski, Jillian Disint and Amir H. Noormohammadi

    Citation: BMC Genomics 2020 21:598

    Content type: Research article

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  19. Duplications of large genomic segments provide genetic diversity in genome evolution. Despite their importance, how these duplications are generated remains uncertain, particularly for distant duplicated genom...

    Authors: Javier U. Chicote, Marcos López-Sánchez, Tomàs Marquès-Bonet, José Callizo, Luis A. Pérez-Jurado and Antonio García-España

    Citation: BMC Genomics 2020 21:593

    Content type: Research article

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  20. More than 2500 species belong to the Meloidae family (Coleoptera: Tenebrionoidea), members of which produce the potent defensive blistering agent cantharidin and are commonly known as blister beetles or Spanishfl...

    Authors: Yuan-Ming Wu, Yang-Yang Liu and Xiang-Sheng Chen

    Citation: BMC Genomics 2020 21:589

    Content type: Research article

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  21. Antagonistic co-evolution can drive rapid adaptation in pathogens and shape genome architecture. Comparative genome analyses of several fungal pathogens revealed highly variable genomes, for many species chara...

    Authors: Alice Feurtey, Cécile Lorrain, Daniel Croll, Christoph Eschenbrenner, Michael Freitag, Michael Habig, Janine Haueisen, Mareike Möller, Klaas Schotanus and Eva H. Stukenbrock

    Citation: BMC Genomics 2020 21:588

    Content type: Research article

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  22. Cotton (Gossypium spp.) is the most important world-wide fiber crop but salt stress limits cotton production in coastal and other areas. Growth regulation factors (GRFs) play regulatory roles in response to salt ...

    Authors: Jun-Feng Cao, Jin-Quan Huang, Xia Liu, Chao-Chen Huang, Zi-Shou Zheng, Xiu-Fang Zhang, Xiao-Xia Shangguan, Ling-Jian Wang, Yu-Gao Zhang, Jonathan F. Wendel, Corrinne E. Grover and Zhi-Wen Chen

    Citation: BMC Genomics 2020 21:575

    Content type: Research article

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  23. The only licensed live Bacille Calmette-Guérin (BCG) vaccine used to prevent severe childhood tuberculosis comprises genetically divergent strains with variable protective efficacy and rates of BCG-induced adv...

    Authors: Olga Narvskaya, Daria Starkova, Diana Levi, Natalia Alexandrova, Vladimir Molchanov, Ekaterina Chernyaeva, Anna Vyazovaya, Alexander Mushkin, Viacheslav Zhuravlev, Natalia Solovieva, Boris Vishnevskiy and Igor Mokrousov

    Citation: BMC Genomics 2020 21:567

    Content type: Research article

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  25. The ubiquitous presence of short tandem repeats (STRs) in virtually all genomes implicates their functional relevance, while a widely-accepted definition of STR is yet to be established. Previous studies major...

    Authors: Hongxi Zhang, Douyue Li, Xiangyan Zhao, Saichao Pan, Xiaolong Wu, Shan Peng, Hanrou Huang, Ruixue Shi and Zhongyang Tan

    Citation: BMC Genomics 2020 21:563

    Content type: Research article

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  26. Advances in next-generation sequencing technologies have provided an opportunity to perform population-level comparative genomic analysis to discover unique genomic characteristics of domesticated animals. Duc...

    Authors: Daehwan Lee, Jongin Lee, Kang-Neung Heo, Kisang Kwon, Youngbeen Moon, Dajeong Lim, Kyung-Tai Lee and Jaebum Kim

    Citation: BMC Genomics 2020 21:554

    Content type: Research article

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  27. Polar bears are uniquely adapted to an Arctic existence. Since their relatively recent divergence from their closest living relative, brown bears, less than 500,000 years ago, the species has evolved an array ...

    Authors: Jose Alfredo Samaniego Castruita, Michael V. Westbury and Eline D. Lorenzen

    Citation: BMC Genomics 2020 21:543

    Content type: Research article

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  29. Aquaporins (AQPs), as members of the major intrinsic protein (MIP) superfamily, facilitated the permeation of water and other solutes and are involved in multiple biological processes. AQP family exists in alm...

    Authors: Yanglei Jia and Xiao Liu

    Citation: BMC Genomics 2020 21:525

    Content type: Research article

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  30. Alcohol dehydrogenases (ADHs) in plants are encoded by a multigene family. ADHs participate in growth, development, and adaptation in many plant species, but the evolution and function of the ADH gene family in s...

    Authors: Weihua Su, Yongjuan Ren, Dongjiao Wang, Yachun Su, Jingfang Feng, Chang Zhang, Hanchen Tang, Liping Xu, Khushi Muhammad and Youxiong Que

    Citation: BMC Genomics 2020 21:521

    Content type: Research article

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  31. Chaka sheep, named after Chaka Salt Lake, are adapted to a harsh, highly saline environment. They are known for their high-grade meat quality and are a valuable genetic resource in China. Furthermore, the Chak...

    Authors: Jie Cheng, Huangqing Zhao, Ningbo Chen, Xiukai Cao, Quratulain Hanif, Li Pi, Linyong Hu, Buren Chaogetu, Yongzhen Huang, Xianyong Lan, Chuzhao Lei and Hong Chen

    Citation: BMC Genomics 2020 21:520

    Content type: Research article

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  32. Large difference in cerebrum size exist between avian species and populations of the same species and is believed to reflect differences in processing power, i.e. in the speed and efficiency of processing info...

    Authors: Andrey Höglund, Katharina Strempfl, Jesper Fogelholm, Dominic Wright and Rie Henriksen

    Citation: BMC Genomics 2020 21:518

    Content type: Research article

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  33. Gene expression profiles can provide insights into the molecular machinery behind tissue functions and, in turn, can further our understanding of environmental responses, and developmental and evolutionary pro...

    Authors: María Torres-Sánchez, Mark Wilkinson, David J. Gower, Christopher J. Creevey and Diego San Mauro

    Citation: BMC Genomics 2020 21:515

    Content type: Research article

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  34. Domesticated chickens have a wide variety of phenotypes, in contrast with their wild progenitors. Unlike other chicken breeds, Xichuan black-bone chickens have blue-shelled eggs, and black meat, beaks, skin, b...

    Authors: Donghua Li, Guirong Sun, Meng Zhang, Yanfang Cao, Chenxi Zhang, Yawei Fu, Fang Li, Guoxi Li, Ruirui Jiang, Ruili Han, Zhuanjian Li, Yanbin Wang, Yadong Tian, Xiaojun Liu, Wenting Li and Xiangtao Kang

    Citation: BMC Genomics 2020 21:511

    Content type: Research article

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  35. Sphingolipids are structural components and signaling molecules in eukaryotic membranes, and many organisms produce compounds that inhibit sphingolipid metabolism. Some of the inhibitors are structurally simil...

    Authors: Hye-Seon Kim, Jessica M. Lohmar, Mark Busman, Daren W. Brown, Todd A. Naumann, Hege H. Divon, Silvio Uhlig and Robert H. Proctor

    Citation: BMC Genomics 2020 21:510

    Content type: Research article

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  36. Body size is considered as one of the most fundamental properties of an organism. Due to intensive breeding and artificial selection throughout the domestication history, horses exhibit striking variations for...

    Authors: Hojjat Asadollahpour Nanaei, Ali Esmailizadeh, Ahmad Ayatollahi Mehrgardi, Jianlin Han, Dong-Dong Wu, Yan Li and Ya-Ping Zhang

    Citation: BMC Genomics 2020 21:496

    Content type: Research article

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  37. In the present study, we used long-PCR amplification coupled with Next-Generation Sequencing (NGS) to obtain complete mitochondrial (mt) genomes of individual ticks and unprecedently performed precise annotati...

    Authors: Ze Chen, Yibo Xuan, Guangcai Liang, Xiaolong Yang, Zhijun Yu, Stephen C. Barker, Samuel Kelava, Wenjun Bu, Jingze Liu and Shan Gao

    Citation: BMC Genomics 2020 21:488

    Content type: Research article

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  38. Zebrafish is a popular model organism, which is widely used in developmental biology research. Despite its general use, the direct comparison of the zebrafish and human oocyte transcriptomes has not been well ...

    Authors: Handan Can, Sree K. Chanumolu, Elena Gonzalez-Muñoz, Sukumal Prukudom, Hasan H. Otu and Jose B. Cibelli

    Citation: BMC Genomics 2020 21:471

    Content type: Research article

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  39. We performed an in-depth analysis of the ABC gene family in Aedes aegypti (Diptera: Culicidae), which is an important vector species of arthropod-borne viral infections such as chikungunya, dengue, and Zika. Desp...

    Authors: Janaina Figueira-Mansur, Carlos G. Schrago, Tiago S. Salles, Evelyn S. L. Alvarenga, Brenda M. Vasconcellos, Ana Claudia A. Melo and Monica F. Moreira

    Citation: BMC Genomics 2020 21:463

    Content type: Research article

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  40. The genus Macrostomum consists of small free-living flatworms and contains Macrostomum lignano, which has been used in investigations of ageing, stem cell biology, bioadhesion, karyology, and sexual selection in ...

    Authors: Jeremias N. Brand, R. Axel W. Wiberg, Robert Pjeta, Philip Bertemes, Christian Beisel, Peter Ladurner and Lukas Schärer

    Citation: BMC Genomics 2020 21:462

    Content type: Research article

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  41. Maternal effects contribute to adaptive significance for shaping various phenotypes of many traits. Potential implications of maternal effects are the cause of expression diversity, but these effects on mRNA e...

    Authors: Li Ren, Xiaojing Yan, Xin Gao, Jialin Cui, Pengcheng Yan, Chang Wu, Wuhui Li and Shaojun Liu

    Citation: BMC Genomics 2020 21:457

    Content type: Research article

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  42. Although horizontal gene transfer (HGT) is a widely accepted force in the evolution of prokaryotic genomes, its role in the evolution of eukaryotic genomes remains hotly debated. Some bdelloid rotifers that ar...

    Authors: Xixi Li, Cheng Fang, Jun-Peng Zhao, Xiao-Yu Zhou, Zhihua Ni and Deng-Ke Niu

    Citation: BMC Genomics 2020 21:452

    Content type: Research article

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  43. The rice leaf folder Cnaphalocrocis medinalis Güenée is a serious insect pest of rice in Asia. This pest occurs in summer, and it is sensitive to high temperature. However, the larvae exhibit heat acclimation/ada...

    Authors: Peng-Qi Quan, Ming-Zhu Li, Gao-Rong Wang, Ling-Ling Gu and Xiang-Dong Liu

    Citation: BMC Genomics 2020 21:450

    Content type: Research article

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  44. Dickeya solani is an important plant pathogenic bacterium causing severe losses in European potato production. This species draws a lot of attention due to its remarkable virulence, great devastating potential an...

    Authors: Agata Motyka-Pomagruk, Sabina Zoledowska, Agnieszka Emilia Misztak, Wojciech Sledz, Alessio Mengoni and Ewa Lojkowska

    Citation: BMC Genomics 2020 21:449

    Content type: Research article

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  45. The identification of bona fide microbial taxa in microbiomes derived from ancient and historical samples is complicated by the unavoidable mixture between DNA from ante- and post-mortem microbial colonizers. ...

    Authors: Clemens L. Weiß, Marie-Theres Gansauge, Ayinuer Aximu-Petri, Matthias Meyer and Hernán A. Burbano

    Citation: BMC Genomics 2020 21:432

    Content type: Research article

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  46. The brown alga, Cladosiphon okamuranus (Okinawa mozuku), is one of the most important edible seaweeds, and it is cultivated for market primarily in Okinawa, Japan. Four strains, denominated S, K, O, and C, with d...

    Authors: Koki Nishitsuji, Asuka Arimoto, Yoshitaka Yonashiro, Kanako Hisata, Manabu Fujie, Mayumi Kawamitsu, Eiichi Shoguchi and Noriyuki Satoh

    Citation: BMC Genomics 2020 21:422

    Content type: Research article

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  47. The circadian clock drives endogenous 24-h rhythms that allow organisms to adapt and prepare for predictable and repeated changes in their environment throughout the day-night (diurnal) cycle. Many components ...

    Authors: Xianjun Lai, Claire Bendix, Lang Yan, Yang Zhang, James C. Schnable and Frank G. Harmon

    Citation: BMC Genomics 2020 21:428

    Content type: Research article

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  48. Mitochondrial genomic sequences are known to be variable. Comparative analyses of mitochondrial genomes can reveal the nature and extent of their variation.

    Authors: Youjin Deng, Xunxiao Zhang, Baogui Xie, Longji Lin, Tom Hsiang, Xiangzhi Lin, Yiying Lin, Xingtan Zhang, Yanhong Ma, Wenjing Miao and Ray Ming

    Citation: BMC Genomics 2020 21:426

    Content type: Research article

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  49. The metabolic capacity, stress response and evolution of uncultured environmental Tenericutes have remained elusive, since previous studies have been largely focused on pathogenic species. In this study, we ex...

    Authors: Yong Wang, Jiao-Mei Huang, Ying-Li Zhou, Alexandre Almeida, Robert D. Finn, Antoine Danchin and Li-Sheng He

    Citation: BMC Genomics 2020 21:408

    Content type: Research article

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  50. Recent advances in the next-generation sequencing (NGS) allowed the metagenomic analyses of DNA from many different environments and sources, including thousands of years old skeletal remains. It has been show...

    Authors: Anna Philips, Ireneusz Stolarek, Luiza Handschuh, Katarzyna Nowis, Anna Juras, Dawid Trzciński, Wioletta Nowaczewska, Anna Wrzesińska, Jan Potempa and Marek Figlerowicz

    Citation: BMC Genomics 2020 21:402

    Content type: Research article

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