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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. In Tunisia a first SARS-CoV-2 confirmed case was reported in March 03, 2020. Since then, an increase of cases number was observed from either imported or local cases. The aim of this preliminary study was to b...

    Authors: Wasfi Fares, Anissa Chouikha, Kais Ghedira, Meriam Gdoura, Dorra Rezig, Sondes Haddad Boubaker, Imen Ben Dhifallah, Henda Touzi, Walid Hammami, Zina Meddeb, Amel Sadraoui, Nahed Hogga, Imen Abouda, Aurélia Kwasiborski, Véronique Hourdel, Guillain Mikaty…

    Citation: BMC Genomics 2021 22:540

    Content type: Research article

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  2. Segmental duplications (SDs) are long DNA sequences that are repeated in a genome and have high sequence identity. In contrast to repetitive elements they are often unique and only sometimes have multiple copi...

    Authors: Eldar T. Abdullaev, Iren R. Umarova and Peter F. Arndt

    Citation: BMC Genomics 2021 22:496

    Content type: Research article

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  3. Global climate oscillation, as a selection dynamic, is an ecologically important element resulting in global biodiversity. During the glacial geological periods, most organisms suffered detrimental selection p...

    Authors: Jia Li, Chao Bian, Yunhai Yi, Hui Yu, Xinxin You and Qiong Shi

    Citation: BMC Genomics 2021 22:490

    Content type: Research article

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  4. Muscle is the predominant portion of any meat product, and growth performance and product quality are the core of modern breeding. The embryonic period is highly critical for muscle development, the number, sh...

    Authors: Lingtong Ren, Anfang Liu, Qigui Wang, Honggan Wang, Deqiang Dong and Lingbin Liu

    Citation: BMC Genomics 2021 22:431

    Content type: Research article

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  5. Whole genome re-sequencing provides powerful data for population genomic studies, allowing robust inferences of population structure, gene flow and evolutionary history. For the major malaria vector in Africa, An...

    Authors: Melina Campos, Luisa D. P. Rona, Katie Willis, George K. Christophides and Robert M. MacCallum

    Citation: BMC Genomics 2021 22:422

    Content type: Research article

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  6. Recent advances in single cell sequencing technologies allow for greater resolution in assessing tumor clonality using chromosome copy number variations (CNVs). While single cell DNA sequencing technologies ar...

    Authors: Stefan Kurtenbach, Anthony M. Cruz, Daniel A. Rodriguez, Michael A. Durante and J. William Harbour

    Citation: BMC Genomics 2021 22:419

    Content type: Software

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  7. The global emergence of community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) has seen the dominance of specific clones in different regions around the world with the PVL-positive ST93-IV as ...

    Authors: Stanley Pang, Denise A Daley, Shafi Sahibzada, Shakeel Mowlaboccus, Marc Stegger and Geoffrey W Coombs

    Citation: BMC Genomics 2021 22:418

    Content type: Research article

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  8. Copper was used for many years in aquaculture operations as an effective algaecide or a parasite treatment of fish. It is an essential nutrient with numerous functions in organisms, but is toxic at high concen...

    Authors: Wenjie Jin, Zixuan Li, Fengxia Ran, Shen Huang, Kefan Huo, Jianjuan Li, Qingshuo Han, Guojie Wang, Zhenji Wang, Shenlong Jian, Kemao Li and Changzhong Li

    Citation: BMC Genomics 2021 22:416

    Content type: Research article

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  9. Nearly 50% of crop yields are lost to pests and disease, with plants and pathogens locked in an amplified co-evolutionary process of disease outbreaks. Coffee wilt disease, caused by Fusarium xylarioides, decimat...

    Authors: Lily D. Peck, Reuben W. Nowell, Julie Flood, Matthew J. Ryan and Timothy G. Barraclough

    Citation: BMC Genomics 2021 22:404

    Content type: Research article

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    The Correction to this article has been published in BMC Genomics 2021 22:514

  10. Duck is an ancient domesticated animal with high economic value, used for its meat, eggs, and feathers. However, the origin of indigenous Chinese ducks remains elusive. To address this question, we performed w...

    Authors: Peishi Feng, Tao Zeng, Hua Yang, Guohong Chen, Jinping Du, Li Chen, Junda Shen, Zhenrong Tao, Ping Wang, Lin Yang and Lizhi Lu

    Citation: BMC Genomics 2021 22:401

    Content type: Research article

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  11. Tsetse flies are the obligate vectors of African trypanosomes, which cause Human and Animal African Trypanosomiasis. Teneral flies (newly eclosed adults) are especially susceptible to parasite establishment an...

    Authors: Miguel Medina Munoz, Caitlyn Brenner, Dylan Richmond, Noah Spencer and Rita V. M. Rio

    Citation: BMC Genomics 2021 22:400

    Content type: Research article

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  12. Elucidating the effects of geography and selection on genetic variation is critical for understanding the relative importance of adaptation in driving differentiation and identifying the environmental factors ...

    Authors: Li Liu, Zhen Wang, Yingjuan Su and Ting Wang

    Citation: BMC Genomics 2021 22:388

    Content type: Research article

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  13. A total of 179 Shiga toxin-producing Escherichia coli (STEC) complete genomes were analyzed in terms of serotypes, prophage coding regions, and stx gene variants and their distribution. We further examined the ge...

    Authors: Graça Pinto, Marta Sampaio, Oscar Dias, Carina Almeida, Joana Azeredo and Hugo Oliveira

    Citation: BMC Genomics 2021 22:366

    Content type: Research article

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  14. The relict gull (Larus relictus), was classified as vulnerable on the IUCN Red List and is a first-class national protected bird in China. Genomic resources for L. relictus are lacking, which limits the study of ...

    Authors: Chao Yang, Xuejuan Li, Qingxiong Wang, Hao Yuan, Yuan Huang and Hong Xiao

    Citation: BMC Genomics 2021 22:311

    Content type: Research article

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  15. Paeonia ostii is a potentially important oilseed crop because its seed yield is high, and the seeds are rich in α-linolenic acid (ALA). However, the molecular mechanisms underlying ALA biosynthesis during seed ke...

    Authors: Shui-Yan Yu, Xiao Zhang, Liang-Bo Huang, Yu-Ping Lyu, Ying Zhang, Zu-Jie Yao, Xiao-Xiao Zhang, Jun-Hui Yuan and Yong-Hong Hu

    Citation: BMC Genomics 2021 22:297

    Content type: Research article

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  16. Histone lysine methylation plays an important role in plant development and stress responses by activating or repressing gene expression. Histone lysine methylation is catalyzed by a class of SET-domain group ...

    Authors: Wenjie Li, Jinjiao Yan, Shicong Wang, Qianying Wang, Caixia Wang, Zhongxing Li, Dehui Zhang, Fengwang Ma, Qingmei Guan and Jidi Xu

    Citation: BMC Genomics 2021 22:283

    Content type: Research article

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  17. Rice, which serves as a staple food for more than half of the world’s population, is grown worldwide. The hybridization of wild and cultivated rice has enabled the incorporation of resistance to varying enviro...

    Authors: Lei Tian, Enze Wang, Xiaolong Lin, Li Ji, Jingjing Chang, Hongping Chen, Jilin Wang, Dazhou Chen, Lam-Son Phan Tran and Chunjie Tian

    Citation: BMC Genomics 2021 22:278

    Content type: Research article

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  18. Polyploid species often originate recurrently. While this is well known, there is little information on the extent to which distinct allotetraploid species formed from the same parent species differ in gene ex...

    Authors: Duo Chen, Peng-Cheng Yan and Yan-Ping Guo

    Citation: BMC Genomics 2021 22:264

    Content type: Research article

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  19. Sweetpotato (Ipomoea batatas [L.] Lam.) is an important food crop. However, the genetic information of the nuclear genome of this species is difficult to determine accurately because of its large genome and compl...

    Authors: Shizhuo Xiao, Pan Xu, Yitong Deng, Xibin Dai, Lukuan Zhao, Bettina Heider, An Zhang, Zhilin Zhou and Qinghe Cao

    Citation: BMC Genomics 2021 22:262

    Content type: Research article

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    The Correction to this article has been published in BMC Genomics 2021 22:368

  20. This correspondence responds to the critique by Butler et al. (BMC Genomics 22:241, 2021) of our recent paper on transposable element (TE) persistence. We address the three main objections raised by Butler et ...

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

    Citation: BMC Genomics 2021 22:260

    Content type: Correspondence

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    The original article was published in BMC Genomics 2021 22:241

  21. Plant transitions to land require robust cell walls for regulatory adaptations and to resist changing environments. Cell walls provide essential plasticity for plant cell division and defense, which are often ...

    Authors: Wenjun Sun, Haomiao Yu, Moyang Liu, Zhaotang Ma and Hui Chen

    Citation: BMC Genomics 2021 22:252

    Content type: Research article

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  22. Altica (Coleoptera: Chrysomelidae) is a highly diverse and taxonomically challenging flea beetle genus that has been used to address questions related to host plant specialization, reproductive isolation, and eco...

    Authors: Huai-Jun Xue, Yi-Wei Niu, Kari A. Segraves, Rui-E Nie, Ya-Jing Hao, Li-Li Zhang, Xin-Chao Cheng, Xue-Wen Zhang, Wen-Zhu Li, Run-Sheng Chen and Xing-Ke Yang

    Citation: BMC Genomics 2021 22:243

    Content type: Research article

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  23. Transposable elements are significant components of most organism’s genomes, yet the reasons why their abundances vary significantly among species is poorly understood. A recent study has suggested that even i...

    Authors: Christopher L. Butler, Ellen A. Bell and Martin I. Taylor

    Citation: BMC Genomics 2021 22:241

    Content type: Correspondence

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    The original article was published in BMC Genomics 2020 21:367

    The Correspondence to this article has been published in BMC Genomics 2021 22:260

  24. Colossoma macropomum (tambaqui) and Piaractus mesopotamicus (pacu) are good fish species for aquaculture. The tambacu, individuals originating from the induced hybridization of the female tambaqui with the male p...

    Authors: Bruno E. A. Fantinatti, Erika S. Perez, Bruna T. T. Zanella, Jéssica S. Valente, Tassiana G. de Paula, Edson A. Mareco, Robson F. Carvalho, Silvano Piazza, Michela A. Denti and Maeli Dal-Pai-Silva

    Citation: BMC Genomics 2021 22:237

    Content type: Research article

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  25. A body distribution with high intramuscular fat and low abdominal fat is the ideal goal for broiler breeding. Preadipocytes with different origins have differences in terms of metabolism and gene expression. T...

    Authors: Zheng Ma, Na Luo, Lu Liu, Huanxian Cui, Jing Li, Hai Xiang, Huimin Kang, Hua Li and Guiping Zhao

    Citation: BMC Genomics 2021 22:232

    Content type: Research article

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  26. The Chinese giant salamander Andrias davidianus is an important amphibian species in China because of its increasing economic value, protection status and special evolutionary position from aquatic to terrestrial...

    Authors: Qiaomu Hu, Yang Liu, Xiaolin Liao, Haifeng Tian, Xiangshan Ji, Jiajie Zhu and Hanbing Xiao

    Citation: BMC Genomics 2021 22:230

    Content type: Research article

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  27. Short interspersed nuclear elements (SINEs) belong to non-long terminal repeat (non-LTR) retrotransposons, which can mobilize dependent on the help of counterpart long interspersed nuclear elements (LINEs). Al...

    Authors: Guangjie Han, Nan Zhang, Heng Jiang, Xiangkun Meng, Kun Qian, Yang Zheng, Jian Xu and Jianjun Wang

    Citation: BMC Genomics 2021 22:226

    Content type: Research article

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  28. Cotton fiber is a model system for studying plant cell development. At present, the functions of many transcription factors in cotton fiber development have been elucidated, however, the roles of auxin respons...

    Authors: Xiufang Zhang, Junfeng Cao, Chaochen Huang, Zishou Zheng, Xia Liu, Xiaoxia Shangguan, Lingjian Wang, Yugao Zhang and Zhiwen Chen

    Citation: BMC Genomics 2021 22:202

    Content type: Research article

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  29. Lineage-specific gene expansions represent one of the driving forces in the evolutionary dynamics of unique phylum traits. Myxozoa, a cnidarian subphylum of obligate parasites, are evolutionarily altered and h...

    Authors: Jiří Kyslík, Anush Kosakyan, Serafim Nenarokov, Astrid S. Holzer and Ivan Fiala

    Citation: BMC Genomics 2021 22:198

    Content type: Research article

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  30. Basenjis are considered an ancient dog breed of central African origins that still live and hunt with tribesmen in the African Congo. Nicknamed the barkless dog, Basenjis possess unique phylogeny, geographical...

    Authors: Richard J. Edwards, Matt A. Field, James M. Ferguson, Olga Dudchenko, Jens Keilwagen, Benjamin D. Rosen, Gary S. Johnson, Edward S. Rice, La Deanna Hillier, Jillian M. Hammond, Samuel G. Towarnicki, Arina Omer, Ruqayya Khan, Ksenia Skvortsova, Ozren Bogdanovic, Robert A. Zammit…

    Citation: BMC Genomics 2021 22:188

    Content type: Research article

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  31. K-mer-based methods have greatly advanced in recent years, largely driven by the realization of their biological significance and by the advent of next-generation sequencing. Their speed and their independence...

    Authors: Ariane Bize, Cédric Midoux, Mahendra Mariadassou, Sophie Schbath, Patrick Forterre and Violette Da Cunha

    Citation: BMC Genomics 2021 22:186

    Content type: Research article

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  32. Only 1.5% of the human genome encodes proteins, while large part of the remaining encodes noncoding RNAs (ncRNA). Many ncRNAs form structures and perform many important functions. Accurately identifying struct...

    Authors: Lijuan Hou, Jin Xie, Yaoyao Wu, Jiaojiao Wang, Anqi Duan, Yaqi Ao, Xuejiao Liu, Xinmei Yu, Hui Yan, Jonathan Perreault and Sanshu Li

    Citation: BMC Genomics 2021 22:164

    Content type: Research article

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  33. Drought is the main stress factor for the cultivation of Pterocarya stenoptera in urban areas, and this factor will cause its dehydration and affect its growth. Identifying drought-related genes will be useful fo...

    Authors: Yong Li, Yu-Tao Si, Yan-Xia He and Jia-Xin Li

    Citation: BMC Genomics 2021 22:155

    Content type: Research article

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  34. During vertebrate evolution, the heart has undergone remarkable changes that lead to morphophysiological differences in the fully formed heart of these species, such as chamber septation, heart rate frequency,...

    Authors: Pedro G. Nachtigall, Luiz A. Bovolenta, James G. Patton, Bastian Fromm, Ney Lemke and Danillo Pinhal

    Citation: BMC Genomics 2021 22:153

    Content type: Research article

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  35. The irruption of Next-generation sequencing (NGS) and restriction site-associated DNA sequencing (RAD-seq) in the last decade has led to the identification of thousands of molecular markers and their genotypin...

    Authors: Adrián Casanova, Francesco Maroso, Andrés Blanco, Miguel Hermida, Néstor Ríos, Graciela García, Alice Manuzzi, Lorenzo Zane, Ana Verissimo, José-Luís García-Marín, Carmen Bouza, Manuel Vera and Paulino Martínez

    Citation: BMC Genomics 2021 22:150

    Content type: Research article

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  36. Hepatitis C (HCV) and many other RNA viruses exist as rapidly mutating quasi-species populations in a single infected host. High throughput characterization of full genome, within-host variants is still not po...

    Authors: Nasir Riaz, Preston Leung, Kirston Barton, Martin A. Smith, Shaun Carswell, Rowena Bull, Andrew R. Lloyd and Chaturaka Rodrigo

    Citation: BMC Genomics 2021 22:148

    Content type: Research article

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  37. Chloroplast genome resources can provide useful information for the evolution of plant species. Tea plant (Camellia sinensis) is among the most economically valuable member of Camellia. Here, we determined the ch...

    Authors: Li Li, Yunfei Hu, Min He, Bo Zhang, Wei Wu, Pumo Cai, Da Huo and Yongcong Hong

    Citation: BMC Genomics 2021 22:138

    Content type: Research article

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  38. Pregnancy-specific glycoprotein (PSG) genes belong to the carcinoembryonic antigen (CEA) gene family, within the immunoglobulin gene superfamily. In humans, 10 PSG genes encode closely related secreted glycoprote...

    Authors: Wolfgang Zimmermann and Robert Kammerer

    Citation: BMC Genomics 2021 22:128

    Content type: Research article

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  39. Micrococcus luteus is a group of actinobacteria that is widely used in biotechnology and is being thought as an emerging nosocomial pathogen. With one of the smallest genomes of free-living actinobacteria, it is ...

    Authors: Yisong Li, Zhong-Zhi Sun, Jin-Cheng Rong and Bin-Bin Xie

    Citation: BMC Genomics 2021 22:124

    Content type: Research article

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  40. Insect body coloration often functions as camouflage to survive from predators or mate selection. Transportation of pigment precursors or related metabolites from cytoplasm to subcellular pigment granules is o...

    Authors: Guichun Liu, Wei Liu, Ruoping Zhao, Jinwu He, Zhiwei Dong, Lei Chen, Wenting Wan, Zhou Chang, Wen Wang and Xueyan Li

    Citation: BMC Genomics 2021 22:120

    Content type: Research article

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  41. In evolutionary theory, divergence and speciation can arise from long periods of reproductive isolation, genetic mutation, selection and environmental adaptation. After divergence, alleles can either persist i...

    Authors: Maulana M. Naji, Yuri T. Utsunomiya, Johann Sölkner, Benjamin D. Rosen and Gábor Mészáros

    Citation: BMC Genomics 2021 22:108

    Content type: Research article

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  42. Staphylococcus and Streptococcus species can cause many different diseases, ranging from mild skin infections to life-threatening necrotizing fasciitis. Both genera consist of commensal species that colonize the ...

    Authors: Niels A. Zondervan, Vitor A. P. Martins dos Santos, Maria Suarez-Diez and Edoardo Saccenti

    Citation: BMC Genomics 2021 22:102

    Content type: Research article

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    The Correction to this article has been published in BMC Genomics 2021 22:384

  43. With numerous endemic subspecies representing four of its five evolutionary lineages, Europe holds a large fraction of Apis mellifera genetic diversity. This diversity and the natural distribution range have been...

    Authors: Jamal Momeni, Melanie Parejo, Rasmus O. Nielsen, Jorge Langa, Iratxe Montes, Laetitia Papoutsis, Leila Farajzadeh, Christian Bendixen, Eliza Căuia, Jean-Daniel Charrière, Mary F. Coffey, Cecilia Costa, Raffaele Dall’Olio, Pilar De la Rúa, M. Maja Drazic, Janja Filipi…

    Citation: BMC Genomics 2021 22:101

    Content type: Methodology article

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