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Comparative and evolutionary genomics

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. Influenza viruses are dangerous pathogens. Seventy-Seven genomes of recently emerged genotype 4 reassortant Eurasian avian-like H1N1 virus (G4-EA-H1N1) are currently available. We investigated the presence and va...

    Authors: Václav Brázda, Otília Porubiaková, Alessio Cantara, Natália Bohálová, Jan Coufal, Martin Bartas, Miroslav Fojta and Jean-Louis Mergny

    Citation: BMC Genomics 2021 22:77

    Content type: Research article

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  2. We have previously suggested that some of the mutations defining mitochondrial DNA (mtDNA) haplogroups J and K produce an uncoupling effect on oxidative phosphorylation and thus are detrimental for elite endur...

    Authors: Jukka Kiiskilä, Jari Jokelainen, Laura Kytövuori, Ilona Mikkola, Pirjo Härkönen, Sirkka Keinänen-Kiukaanniemi and Kari Majamaa

    Citation: BMC Genomics 2021 22:75

    Content type: Research article

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  3. Next Generation Sequencing (NGS) is the fundament of various studies, providing insights into questions from biology and medicine. Nevertheless, integrating data from different experimental backgrounds can int...

    Authors: Stephan Weißbach, Stanislav Sys, Charlotte Hewel, Hristo Todorov, Susann Schweiger, Jennifer Winter, Markus Pfenninger, Ali Torkamani, Doug Evans, Joachim Burger, Karin Everschor-Sitte, Helen Louise May-Simera and Susanne Gerber

    Citation: BMC Genomics 2021 22:62

    Content type: Research article

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  4. Loaches of Cobitinae, widely distributed in Eurasian continent, have high economic, ornamental and scientific value. However, the phylogeny of Cobitinae fishes within genera or family level remains complex and...

    Authors: Peng Yu, Li Zhou, Wen-Tao Yang, Li-jun Miao, Zhi Li, Xiao-Juan Zhang, Yang Wang and Jian-Fang Gui

    Citation: BMC Genomics 2021 22:50

    Content type: Research article

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  5. Native cattle breeds are an important source of genetic variation because they might carry alleles that enable them to adapt to local environment and tough feeding conditions. Jiaxian Red, a Chinese native cat...

    Authors: Xiaoting Xia, Shunjin Zhang, Huaju Zhang, Zijing Zhang, Ningbo Chen, Zhigang Li, Hongxia Sun, Xian Liu, Shijie Lyu, Xianwei Wang, Zhiming Li, Peng Yang, Jiawei Xu, Xiaoting Ding, Qiaoting Shi, Eryao Wang…

    Citation: BMC Genomics 2021 22:43

    Content type: Research article

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  6. Streptococcus pneumoniae serotype 1 remains a leading cause of invasive pneumococcal diseases, even in countries with PCV-10/PCV-13 vaccine implementation. The main objective of this study, which is part of the P...

    Authors: Néhémie Nzoyikorera, Idrissa Diawara, Pablo Fresia, Fakhreddine Maaloum, Khalid Katfy, Kaotar Nayme, Mossaab Maaloum, Jennifer Cornick, Chrispin Chaguza, Mohammed Timinouni, Houria Belabess, Khalid Zerouali and Naima Elmdaghri

    Citation: BMC Genomics 2021 22:39

    Content type: Research article

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  7. DNA methylation is likely a key mechanism regulating changes in gene transcription in traits that show temporal fluctuations in response to environmental conditions. To understand the transcriptional role of D...

    Authors: Melanie Lindner, Irene Verhagen, Heidi M. Viitaniemi, Veronika N. Laine, Marcel E. Visser, Arild Husby and Kees van Oers

    Citation: BMC Genomics 2021 22:36

    Content type: Research article

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  8. Olfactory systems take on important tasks to distinguish salient information from a complex olfactory environment, such as locating hosts, mating, aggression, selecting oviposition sites, and avoiding predator...

    Authors: Li Xu, Kai-Yue Tang, Xiao-Feng Chen, Yong Tao, Hong-Bo Jiang and Jin-Jun Wang

    Citation: BMC Genomics 2021 22:25

    Content type: Research article

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  9. Cadmium (Cd) is a nonessential heavy metal with potentially deleterious effects on different organisms. The organisms have evolved sophisticated defense system to alleviate heavy metal toxicity. Hydrogen sulfi...

    Authors: Hongrui Lv, Jing Xu, Tao Bo and Wei Wang

    Citation: BMC Genomics 2021 22:21

    Content type: Research article

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  10. Walnut anthracnose caused by Colletotrichum gloeosporioides (Penz.) Penz. and Sacc. is an important walnut production problem in China. Although the long non-coding RNAs (lncRNAs) are important for plant disease ...

    Authors: Shan Feng, Hongcheng Fang, Xia Liu, Yuhui Dong, Qingpeng Wang and Ke Qiang Yang

    Citation: BMC Genomics 2021 22:15

    Content type: Research article

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  11. Actinidia eriantha is a precious material to study the metabolism and regulation of ascorbic acid (AsA) because of its high AsA content. Although the pathway of AsA biosynthesis in kiwifruit has been identified, ...

    Authors: Guanglian Liao, Lu Chen, Yanqun He, Xishi Li, Zhengxin Lv, Shuyao Yi, Min Zhong, Chunhui Huang, Dongfeng Jia, Xueyan Qu and Xiaobiao Xu

    Citation: BMC Genomics 2021 22:13

    Content type: Research article

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  12. Population history, production system and within-breed selection pressure impacts the genome architecture resulting in reduced genetic diversity and increased frequency of runs of homozygosity islands. This st...

    Authors: E. F. Dzomba, M. Chimonyo, R. Pierneef and F. C. Muchadeyi

    Citation: BMC Genomics 2021 22:7

    Content type: Research article

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  13. The degradation of cellulose and hemicellulose molecules into simpler sugars such as glucose is part of the second generation biofuel production process. Hydrolysis of lignocellulosic substrates is usually per...

    Authors: Aurélie Pirayre, Laurent Duval, Corinne Blugeon, Cyril Firmo, Sandrine Perrin, Etienne Jourdier, Antoine Margeot and Frédérique Bidard

    Citation: BMC Genomics 2020 21:885

    Content type: Research article

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  14. Women account for 60% of all stroke deaths and are more often permanently disabled than men, despite their higher observed stroke incidence. Considering the clinical population affected by stroke, an obvious d...

    Authors: Mimmi Rehnström, Simona Denise Frederiksen, Saema Ansar and Lars Edvinsson

    Citation: BMC Genomics 2020 21:883

    Content type: Research article

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  15. Whole mitogenomes or short fragments (i.e., 300–700 bp of the cox1 gene) are the markers of choice for revealing within- and among-species genealogies. Protocols for sequencing and assembling mitogenomes include ...

    Authors: J. Antonio Baeza

    Citation: BMC Genomics 2020 21:882

    Content type: Methodology article

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  16. Bird mitogenomes differ from other vertebrates in gene rearrangement. The most common avian gene order, identified first in Gallus gallus, is considered ancestral for all Aves. However, other rearrangements inclu...

    Authors: Adam Dawid Urantówka, Aleksandra Kroczak and Paweł Mackiewicz

    Citation: BMC Genomics 2020 21:874

    Content type: Research article

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  17. Orang-utans comprise three critically endangered species endemic to the islands of Borneo and Sumatra. Though whole-genome sequencing has recently accelerated our understanding of their evolutionary history, t...

    Authors: Graham L. Banes, Emily D. Fountain, Alyssa Karklus, Hao-Ming Huang, Nian-Hong Jang-Liaw, Daniel L. Burgess, Jennifer Wendt, Cynthia Moehlenkamp and George F. Mayhew

    Citation: BMC Genomics 2020 21:873

    Content type: Research article

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  18. NITRATE TRANSPORTER 1/PEPTIDE TRANSPORTER (NRT1/PTR) family (NPF) members are essential transporters for many substrates in plants, including nitrate, hormones, peptides, and secondary metabolites. Here, we re...

    Authors: Jing Wen, Peng-Feng Li, Feng Ran, Peng-Cheng Guo, Jia-Tian Zhu, Jin Yang, Lan-Lan Zhang, Ping Chen, Jia-Na Li and Hai Du

    Citation: BMC Genomics 2020 21:871

    Content type: Research article

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  19. Unlike mammals, zebrafish have a remarkable capacity to regenerate a variety of tissues, including central nervous system tissue. The function of macrophages in tissue regeneration is of great interest, as mac...

    Authors: Ousseini Issaka Salia and Diana M. Mitchell

    Citation: BMC Genomics 2020 21:870

    Content type: Research article

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  20. Humpless Bos taurus cattle are one of the earliest domestic cattle in Africa, followed by the arrival of humped Bos indicus cattle. The diverse indigenous cattle breeds of Africa are derived from these migrations...

    Authors: N. Z. Gebrehiwot, E. M. Strucken, H. Aliloo, K. Marshall and J. P. Gibson

    Citation: BMC Genomics 2020 21:869

    Content type: Research article

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  21. Numerous megafauna species from northern latitudes went extinct during the Pleistocene/Holocene transition as a result of climate-induced habitat changes. However, several ungulate species managed to successfu...

    Authors: Nicolas Dussex, Federica Alberti, Matti T. Heino, Remi-Andre Olsen, Tom van der Valk, Nils Ryman, Linda Laikre, Hans Ahlgren, Igor V. Askeyev, Oleg V. Askeyev, Dilyara N. Shaymuratova, Arthur O. Askeyev, Doris Döppes, Ronny Friedrich, Susanne Lindauer, Wilfried Rosendahl…

    Citation: BMC Genomics 2020 21:854

    Content type: Research article

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  22. Anaerobic ammonium oxidizing bacteria (anammox bacteria) are contributing significantly to the nitrogen cycle and are successfully used in wastewater treatment. Due to the lack of complete genomes in the datab...

    Authors: Chang Ding and Lorenz Adrian

    Citation: BMC Genomics 2020 21:851

    Content type: Research article

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  23. After over a decade of developments in field collection, laboratory methods and advances in high-throughput sequencing, contamination remains a key issue in ancient DNA research. Currently, human and microbial...

    Authors: Tatiana R. Feuerborn, Eleftheria Palkopoulou, Tom van der Valk, Johanna von Seth, Arielle R. Munters, Patrícia Pečnerová, Marianne Dehasque, Irene Ureña, Erik Ersmark, Vendela Kempe Lagerholm, Maja Krzewińska, Ricardo Rodríguez-Varela, Anders Götherström, Love Dalén and David Díez-del-Molino

    Citation: BMC Genomics 2020 21:844

    Content type: Methodology article

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  24. Diversity of the CRISPR locus of Mycobacterium tuberculosis complex has been studied since 1997 for molecular epidemiology purposes. By targeting solely the 43 spacers present in the two first sequenced genomes (...

    Authors: Guislaine Refrégier, Christophe Sola and Christophe Guyeux

    Citation: BMC Genomics 2020 21:841

    Content type: Research article

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  26. Insect-killing fungal species, Beauveria bassiana, is as an environment-friendly pest management tool, and many isolates are on the track of industrialization. However, some of B. bassiana isolates show similar m...

    Authors: Sihyeon Kim, Jong Cheol Kim, Se Jin Lee, Mi Rong Lee, So Eun Park, Dongwei Li, Sehyeon Baek, Tae Young Shin and Jae Su Kim

    Citation: BMC Genomics 2020 21:836

    Content type: Research article

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  27. The evolution of bacteria is shaped by different mechanisms such as mutation, gene deletion, duplication, or insertion of foreign DNA among others. These genetic changes can accumulate in the descendants as a ...

    Authors: Juan F. Guerra Maldonado, Antony T. Vincent, Martin Chenal and Frederic J. Veyrier

    Citation: BMC Genomics 2020 21:832

    Content type: Software

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  30. Large genotyping datasets have become commonplace due to efficient, cheap methods for SNP identification. Typical genotyping datasets may have thousands to millions of data points per accession, across tens to...

    Authors: Andrew P. Wilkey, Anne V. Brown, Steven B. Cannon and Ethalinda K. S. Cannon

    Citation: BMC Genomics 2020 21:822

    Content type: Software

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  31. Annelids are one the most speciose and ecologically diverse groups of metazoans. Although a significant effort has been recently invested in sequencing genomes of a wide array of metazoans, many orders and fam...

    Authors: Astrid Tempestini, Gloria Massamba-N’Siala, Fanny Vermandele, Nicholas Beaudreau, Mathieu Mortz, France Dufresne and Piero Calosi

    Citation: BMC Genomics 2020 21:815

    Content type: Research article

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  33. With declining wild fish populations, farmed salmon has gained popularity as a source for healthy long-chain highly unsaturated fatty acids (LC-HUFA). However, the introduction of plant oil in farmed salmon fe...

    Authors: Yang Jin, Alex K. Datsomor, Rolf E. Olsen, Jon Olav Vik, Jacob S. Torgersen, Rolf B. Edvardsen, Anna Wargelius, Per Winge and Fabian Grammes

    Citation: BMC Genomics 2020 21:805

    Content type: Research article

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  34. Fat tail is a unique trait in sheep acquired during domestication. Several genomic analyses have been conducted in sheep breeds from limited geographic origins to identify the genetic factors underlying this t...

    Authors: Kunzhe Dong, Min Yang, Jiangang Han, Qing Ma, Jilong Han, Ziyi Song, Cuicheng Luosang, Neena Amatya Gorkhali, Bohui Yang, Xiaohong He, Yuehui Ma and Lin Jiang

    Citation: BMC Genomics 2020 21:800

    Content type: Research article

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  35. RNA interference (RNAi) is a highly conserved, sequence-specific gene silencing mechanism present in Eukaryotes. Three RNAi pathways are known, namely micro-RNA (miRNA), piwi-interacting RNA (piRNA) and short ...

    Authors: Beatrice T. Nganso, Noa Sela and Victoria Soroker

    Citation: BMC Genomics 2020 21:791

    Content type: Research article

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  36. Studying functional divergences between paralogs that originated from genome duplication is a significant topic in investigating molecular evolution. Genes that exhibit basal level cyclic expression patterns i...

    Authors: Yuan Lu, Mikki Boswell, William Boswell, Raquel Ybanez Salinas, Markita Savage, Jose Reyes, Sean Walter, Rebecca Marks, Trevor Gonzalez, Geraldo Medrano, Wesley C. Warren, Manfred Schartl and Ronald B. Walter

    Citation: BMC Genomics 2020 21:787

    Content type: Research article

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  37. WRKY transcription factors are a superfamily of regulators involved in diverse biological processes and stress responses in plants. However, there is limited knowledge about the WRKY family in camelina (Camelina ...

    Authors: Yanan Song, Hongli Cui, Ying Shi, Jinai Xue, Chunli Ji, Chunhui Zhang, Lixia Yuan and Runzhi Li

    Citation: BMC Genomics 2020 21:786

    Content type: Research article

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  38. Specific adaptive features including disease resistance and growth abilities in harsh environments are attributed to indigenous cattle breeds of Benin, but these breeds are endangered due to crossbreeding. So ...

    Authors: Sèyi Fridaïus Ulrich Vanvanhossou, Carsten Scheper, Luc Hippolyte Dossa, Tong Yin, Kerstin Brügemann and Sven König

    Citation: BMC Genomics 2020 21:783

    Content type: Research article

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  39. Development and application of DNA-based methods to distinguish highly virulent isolates of Fusarium oxysporum f. sp. koae [Fo koae; cause of koa wilt disease on Acacia koa (koa)] will help disease management thr...

    Authors: John T. Dobbs, Mee-Sook Kim, Nicklos S. Dudley, Ned B. Klopfenstein, Aileen Yeh, Robert D. Hauff, Tyler C. Jones, R. Kasten Dumroese, Philip G. Cannon and Jane E. Stewart

    Citation: BMC Genomics 2020 21:764

    Content type: Research article

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  40. Azadirachtin A is a triterpenoid from neem tree exhibiting excellent activities against over 600 insect species in agriculture. The production of azadirachtin A depends on extraction from neem tissues, which i...

    Authors: Huiyan Wang, Ning Wang and Yixin Huo

    Citation: BMC Genomics 2020 21:749

    Content type: Research article

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  41. Temperature is known to affect living organisms and alter the expression of responsive genes, which affects a series of life processes, such as development, reproduction and metabolism. Several genes and gene ...

    Authors: Qian Wang, Xiancai Hao, Kaiqiang Liu, Bo Feng, Shuo Li, Zhihua Zhang, Lili Tang, Shahid Mahboob and Changwei Shao

    Citation: BMC Genomics 2020 21:745

    Content type: Research article

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  42. Finding orthologs remains an important bottleneck in comparative genomics analyses. While the authors of software for the quick comparison of protein sequences evaluate the speed of their software and compare ...

    Authors: Julie E. Hernández-Salmerón and Gabriel Moreno-Hagelsieb

    Citation: BMC Genomics 2020 21:741

    Content type: Methodology article

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  43. Understanding the genetic basis of phenotype variations during domestication and breeding is of great interest. Epigenetics and epigenetic modification enzymes (EMEs) may play a role in phenotypic variations; ...

    Authors: Rui Gao, Chun-Lin Li, Xiao-Ling Tong, Min-Jin Han, Kun-Peng Lu, Shu-Bo Liang, Hai Hu, Yue Luan, Bi-Li Zhang, Yan-Yu Liu and Fang-Yin Dai

    Citation: BMC Genomics 2020 21:740

    Content type: Research article

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  44. TIFY is a plant-specific protein family with a diversity of functions in plant development and responses to stress and hormones, which contains JASMONATE ZIM-domain (JAZ), TIFY, PPD and ZML subfamilies. Despit...

    Authors: Xin He, Yu Kang, Wenqian Li, Wei Liu, Pan Xie, Li Liao, Luyao Huang, Min Yao, Lunwen Qian, Zhongsong Liu, Chunyun Guan, Mei Guan and Wei Hua

    Citation: BMC Genomics 2020 21:736

    Content type: Research article

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  45. Sexual reproduction of scleractinians has captured the attention of researchers and the general public for decades. Although extensive ecological data has been acquired, underlying molecular and cellular mecha...

    Authors: Yi-Ling Chiu, Shinya Shikina, Yuki Yoshioka, Chuya Shinzato and Ching-Fong Chang

    Citation: BMC Genomics 2020 21:732

    Content type: Research article

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  47. Teleost fish play important roles in aquatic ecosystems and aquaculture. Threadfins (Perciformes: Polynemidae) show a range of interesting biology, and are of considerable importance for both wild fisheries an...

    Authors: Zhe Qu, Wenyan Nong, Yifei Yu, Tobias Baril, Ho Yin Yip, Alexander Hayward and Jerome H. L. Hui

    Citation: BMC Genomics 2020 21:726

    Content type: Research article

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  48. Belonging to lineage I of Brassicaceae, Camelina sativa is formed by two hybridizations of three species (three sub-genomes). The three sub-genomes were diverged from a common ancestor, likely derived from lineag...

    Authors: Zhikang Zhang, Fanbo Meng, Pengchuan Sun, Jiaqing Yuan, Ke Gong, Chao Liu, Weijie Wang and Xiyin Wang

    Citation: BMC Genomics 2020 21:705

    Content type: Research article

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  49. Selenium is an essential trace element, and selenocysteine (Sec, U) is its predominant form in vivo. Proteins that contain Sec are selenoproteins, whose special structural features include not only the TGA cod...

    Authors: Liang Jiang, Yiqian Lu, Lin Zheng, Gaopeng Li, Lianchang Chen, Maona Zhang, Jiazuan Ni, Qiong Liu and Yan Zhang

    Citation: BMC Genomics 2020 21:699

    Content type: Research article

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  50. Species of the genus Monascus are considered to be economically important and have been widely used in the production of yellow and red food colorants. In particular, three Monascus species, namely, M. pilosus, M...

    Authors: Yuki Higa, Young-Soo Kim, Md. Altaf-Ul-Amin, Ming Huang, Naoaki Ono and Shigehiko Kanaya

    Citation: BMC Genomics 2020 21:679

    Content type: Research article

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