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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. 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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  2. 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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  3. 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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  4. 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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  5. 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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  6. 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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  7. 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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  8. 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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  9. 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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  10. 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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  11. 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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  12. 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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  14. The plastome of medicinal and endangered species in Kingdom of Saudi Arabia, Barleria prionitis was sequenced. The plastome was compared with that of seven Acanthoideae species in order to describe the plastome, ...

    Authors: Dhafer A. Alzahrani, Samaila S. Yaradua, Enas J. Albokhari and Abidina Abba

    Citation: BMC Genomics 2020 21:393

    Content type: Research article

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  15. Nitrogen is an indispensable nutrient for plant growth. It is used and transported in the form of amino acids in living organisms. Transporting amino acids to various parts of plants requires relevant transpor...

    Authors: Chao Zhang, Nana Kong, Minxuan Cao, Dongdong Wang, Yue Chen and Qin Chen

    Citation: BMC Genomics 2020 21:391

    Content type: Research article

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  16. Fructose-1,6-bisphosphatase (FBP) is a key enzyme in the plant sucrose synthesis pathway, in the Calvin cycle, and plays an important role in photosynthesis regulation in green plants. However, no systemic ana...

    Authors: Qún Gě, Yànli Cūi, Jùnwén Lǐ, Jǔwǔ Gōng, Quánwěi Lú, Péngtāo Lǐ, Yùzhēn Shí, Hǎihóng Shāng, Àiyīng Liú, Xiǎoyīng Dèng, Jìngtāo Pān, Qúanjiā Chén, Yǒulù Yuán and Wànkuí Gǒng

    Citation: BMC Genomics 2020 21:379

    Content type: Research article

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  17. Parasitoid wasps have fascinating life cycles and play an important role in trophic networks, yet little is known about their genome content and function. Parasitoids that infect aphids are an important group ...

    Authors: Alice B. Dennis, Gabriel I. Ballesteros, Stéphanie Robin, Lukas Schrader, Jens Bast, Jan Berghöfer, Leo W. Beukeboom, Maya Belghazi, Anthony Bretaudeau, Jan Buellesbach, Elizabeth Cash, Dominique Colinet, Zoé Dumas, Mohammed Errbii, Patrizia Falabella, Jean-Luc Gatti…

    Citation: BMC Genomics 2020 21:376

    Content type: Research article

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  18. The nuclear genomes of eukaryotes vary enormously in size, with much of this variability attributable to differential accumulation of transposable elements (TEs). To date, the precise evolutionary and ecologic...

    Authors: Stefan C. Kremer, Stefan Linquist, Brent Saylor, Tyler A. Elliott, T. Ryan Gregory and Karl Cottenie

    Citation: BMC Genomics 2020 21:367

    Content type: Research article

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  19. The taxonomic history of Ceratocystis, a genus in the Ceratocystidaceae, has been beset with questions and debate. This is due to many of the commonly used species recognition concepts (e.g., morphological and bi...

    Authors: Aquillah M. Kanzi, Conrad Trollip, Michael J. Wingfield, Irene Barnes, Magriet A. Van der Nest and Brenda D. Wingfield

    Citation: BMC Genomics 2020 21:362

    Content type: Research article

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  21. Adaptive changes in cis-regulatory elements are an essential component of evolution by natural selection. Identifying adaptive and functional noncoding DNA elements throughout the genome is therefore crucial for ...

    Authors: Alejandro Berrio, Ralph Haygood and Gregory A. Wray

    Citation: BMC Genomics 2020 21:359

    Content type: Methodology article

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  22. Histone post-translational modifications play crucial roles in epigenetic regulation of gene expression and are known to be associated with the phenotypic differences of different cell types. Therefore, it is ...

    Authors: Jing Tang, Zefeng Wu, Yuhan Tian and Ruolin Yang

    Citation: BMC Genomics 2020 21:356

    Content type: Methodology article

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  23. The hybridization of female D. raddei and male D. valentini gave rise to the parthenogenetic Caucasian rock lizard Darevskia unisexualis. A previously identified genetic polymorphism in the species consisted of o...

    Authors: Andrey A. Vergun, Anastasiya E. Girnyk, Vitaly I. Korchagin, Seraphima K. Semyenova, Marine S. Arakelyan, Felix D. Danielyan, Robert W. Murphy and Alexey P. Ryskov

    Citation: BMC Genomics 2020 21:351

    Content type: Research article

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  24. Despite high vaccination coverage using acellular (ACV) and whole-cell pertussis (WCV) vaccines, the resurgence of pertussis is observed globally. Genetic divergence in circulating strains of Bordetella pertussis

    Authors: Shweta Alai, Vikas C. Ghattargi, Manish Gautam, Krunal Patel, Shrikant P. Pawar, Dhiraj P. Dhotre, Umesh Shaligram and Sunil Gairola

    Citation: BMC Genomics 2020 21:345

    Content type: Research article

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  26. Allopolyploidy is widespread in angiosperms, and they can coordinate two or more different genomes through genetic and epigenetic modifications to exhibit stronger vigor and adaptability. To explore the change...

    Authors: Mengdi Li, Ruihua Wang, Xiaoming Wu and Jianbo Wang

    Citation: BMC Genomics 2020 21:330

    Content type: Research article

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  27. Yellow-feathered chickens (YFCs) have a long history in China. They are well-known for the nutritional and commercial importance attributable to their yellow color phenotype. Currently, there is a huge paucity...

    Authors: Xunhe Huang, Newton O. Otecko, Minsheng Peng, Zhuoxian Weng, Weina Li, Jiebo Chen, Ming Zhong, Fusheng Zhong, Sihua Jin, Zhaoyu Geng, Wei Luo, Danlin He, Cheng Ma, Jianlin Han, Sheila C. Ommeh, Yaping Zhang…

    Citation: BMC Genomics 2020 21:316

    Content type: Research article

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  28. In gene expression studies, RNA sample pooling is sometimes considered because of budget constraints or lack of sufficient input material. Using microarray technology, RNA sample pooling strategies have been r...

    Authors: Alemu Takele Assefa, Jo Vandesompele and Olivier Thas

    Citation: BMC Genomics 2020 21:312

    Content type: Research Article

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    The Correction to this article has been published in BMC Genomics 2020 21:384

  29. Hypothyroidism is a common complex endocrinopathy that typically has an autoimmune etiology, and it affects both humans and dogs. Genetic and environmental factors are both known to play important roles in the...

    Authors: Matteo Bianchi, Nima Rafati, Åsa Karlsson, Eva Murén, Carl-Johan Rubin, Katarina Sundberg, Göran Andersson, Olle Kämpe, Åke Hedhammar, Kerstin Lindblad-Toh and Gerli Rosengren Pielberg

    Citation: BMC Genomics 2020 21:307

    Content type: Research article

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  30. The sea cucumber Holothuria leucospilota belongs to echinoderm, which is evolutionally the most primitive group of deuterostomes. Sea cucumber has a cavity between its digestive tract and the body wall that is fi...

    Authors: Xiaofen Wu, Ting Chen, Da Huo, Zonghe Yu, Yao Ruan, Chuhang Cheng, Xiao Jiang and Chunhua Ren

    Citation: BMC Genomics 2020 21:306

    Content type: Research article

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  32. The Weddell Seal (Leptonychotes weddelli) represents a remarkable example of adaptation to diving among marine mammals. This species is capable of diving > 900 m deep and remaining underwater for more than 60 min...

    Authors: Luca Penso-Dolfin, Wilfried Haerty, Allyson Hindle and Federica Di Palma

    Citation: BMC Genomics 2020 21:303

    Content type: Research article

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  33. Opportunistic pathogens are important for clinical practice as they often cause antibiotic-resistant infections. However, little is documented for many emerging opportunistic pathogens and their biological cha...

    Authors: Zhao Zhang, Daixi Li, Xing Shi, Yao Zhai, Yatao Guo, Yali Zheng, Lili Zhao, Yukun He, Yusheng Chen, Zhanwei Wang, Jianrong Su, Yu Kang and Zhancheng Gao

    Citation: BMC Genomics 2020 21:297

    Content type: Research article

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  34. The draft genome assemblies produced by new sequencing technologies present important challenges for automatic gene prediction pipelines, leading to less accurate gene models. New benchmark methods are needed ...

    Authors: Nicolas Scalzitti, Anne Jeannin-Girardon, Pierre Collet, Olivier Poch and Julie D. Thompson

    Citation: BMC Genomics 2020 21:293

    Content type: Research article

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  36. Spermatogenesis is the process by which germ cells develop into spermatozoa in the testis. Sperm protamines are small, arginine-rich nuclear proteins which replace somatic histones during spermatogenesis, allo...

    Authors: Christian D. Powell, Daniel C. Kirchoff, Jason E. DeRouchey and Hunter N. B. Moseley

    Citation: BMC Genomics 2020 21:277

    Content type: Research Article

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  37. DNA binding with one finger (Dof) transcription factors play important roles in plant growth and abiotic stress responses. Although genome-wide identification and analysis of the DOF transcription factor famil...

    Authors: Yue Liu, Nannan Liu, Xiong Deng, Dongmiao Liu, Mengfei Li, Dada Cui, Yingkao Hu and Yueming Yan

    Citation: BMC Genomics 2020 21:276

    Content type: Research article

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  38. The nucleoli, including their proteomes, of higher eukaryotes have been extensively studied, while few studies about the nucleoli of the lower eukaryotes – protists were reported. Giardia lamblia, a protist with ...

    Authors: Jin-Mei Feng, Chun-Lin Yang, Hai-Feng Tian, Jiang-Xin Wang and Jian-Fan Wen

    Citation: BMC Genomics 2020 21:269

    Content type: Research article

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  39. Brassica is a very important genus of Brassicaceae, including many important oils, vegetables, forage crops, and ornamental horticultural plants. TLP family genes play important regulatory roles in the growth and...

    Authors: Tong Wang, Jingjing Hu, Xiao Ma, Chunjin Li, Qihang Yang, Shuyan Feng, Miaomiao Li, Nan Li and Xiaoming Song

    Citation: BMC Genomics 2020 21:264

    Content type: Research article

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  40. Upstream open reading frames (uORFs) in the 5′-untranslated regions (5′-UTRs) of certain eukaryotic mRNAs encode evolutionarily conserved functional peptides, such as cis-acting regulatory peptides that contro...

    Authors: Hiro Takahashi, Noriya Hayashi, Yuta Hiragori, Shun Sasaki, Taichiro Motomura, Yui Yamashita, Satoshi Naito, Anna Takahashi, Kazuyuki Fuse, Kenji Satou, Toshinori Endo, Shoko Kojima and Hitoshi Onouchi

    Citation: BMC Genomics 2020 21:260

    Content type: Research article

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  41. Ribosomally synthesized and post-translationally modified peptides (RiPPs) are a highly diverse group of secondary metabolites (SM) of bacterial and fungal origin. While RiPPs have been intensively studied in ...

    Authors: Gabriel A. Vignolle, Robert L. Mach, Astrid R. Mach-Aigner and Christian Derntl

    Citation: BMC Genomics 2020 21:258

    Content type: Methodology article

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  43. The Fusarium oxysporum species complex (FOSC) is a ubiquitous group of fungal species readily isolated from agroecosystem and natural ecosystem soils which includes important plant and human pathogens. Genetic re...

    Authors: Saidi R. Achari, Jatinder Kaur, Quang Dinh, Ross Mann, Tim Sawbridge, Brett A. Summerell and Jacqueline Edwards

    Citation: BMC Genomics 2020 21:248

    Content type: Research article

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  44. Triticum and Aegilops diploid species have morphological and genetic diversity and are crucial genetic resources for wheat breeding. According to the chromosomal pairing-affinity of these species, their genome no...

    Authors: Sayaka Tanaka, Kentaro Yoshida, Kazuhiro Sato and Shigeo Takumi

    Citation: BMC Genomics 2020 21:246

    Content type: Research article

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  45. Mice of the genus Apodemus are one the most common mammals in the Palaearctic region. Despite their broad range and long history of ecological observations, there are no whole-genome data available for Apodemus, ...

    Authors: Maria Luisa Martin Cerezo, Marek Kucka, Karol Zub, Yingguang Frank Chan and Jarosław Bryk

    Citation: BMC Genomics 2020 21:241

    Content type: Research Article

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  46. Barnacles are specialized marine organisms that differ from other crustaceans in possession of a calcareous shell, which is attached to submerged surfaces. Barnacles have a wide distribution, mostly in the int...

    Authors: Zhibin Gan, Jianbo Yuan, Xinming Liu, Dong Dong, Fuhua Li and Xinzheng Li

    Citation: BMC Genomics 2020 21:240

    Content type: Research article

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  48. Based on an initial collecting of database sequences from the gap junction protein gene family (also called connexin genes) in a few teleosts, the naming of these sequences appeared variable. The reasons could...

    Authors: Svein-Ole Mikalsen, Marni Tausen and Sunnvør í Kongsstovu

    Citation: BMC Genomics 2020 21:223

    Content type: Research article

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  49. Cyanobacteria are of special concern because they proliferate in eutrophic water bodies worldwide and affect water quality. As an ancient photosynthetic microorganism, cyanobacteria can survive in ecologically...

    Authors: Meng Chen, Chun-Yang Xu, Xu Wang, Chong-Yang Ren, Jiao Ding and Li Li

    Citation: BMC Genomics 2020 21:217

    Content type: Research article

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  50. PhasiRNAs (phased secondary siRNAs) play important regulatory roles in the development processes and biotic or abiotic stresses in plants. Some of phasiRNAs involve in the reproductive development in grasses, ...

    Authors: Rongzhi Zhang, Siyuan Huang, Shiming Li, Guoqi Song, Yulian Li, Wei Li, Jihu Li, Jie Gao, Tiantian Gu, Dandan Li, Shujuan Zhang and Genying Li

    Citation: BMC Genomics 2020 21:200

    Content type: Research article

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