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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. 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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  2. 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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  3. 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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  4. 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 Heida, An Zhang, Zhilin Zhou and Qinghe Cao

    Citation: BMC Genomics 2021 22:262

    Content type: Research article

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  5. 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

  6. 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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  7. 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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  8. 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

  9. 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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  10. 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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  11. 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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  12. 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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  13. 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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  14. 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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  15. 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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  16. 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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  17. 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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  18. 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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  19. 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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  20. 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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  21. 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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  22. 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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  23. 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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  24. 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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  25. 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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  26. 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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  27. 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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  28. 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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  29. 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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  30. 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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  31. 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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  32. 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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  33. 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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  34. 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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  35. 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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  36. 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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  37. 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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  38. 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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  39. 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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  40. 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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  41. 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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  42. 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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  43. 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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  44. 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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  45. 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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  46. 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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  47. 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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  48. 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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