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Non-human and non-rodent vertebrate genomics

Section edited by Shane Burgess and Jacqueline Smith

This section covers all aspects of the genomics of vertebrates, excluding humans, primates and rodents, including livestock species.

Page 5 of 19

  1. The importance of transposable elements (TEs) in the genomic remodeling and chromosomal rearrangements that accompany lineage diversification in vertebrates remains the subject of debate. The major impediment ...

    Authors: J. Auvinet, P. Graça, L. Belkadi, L. Petit, E. Bonnivard, A. Dettaï, W. H Detrich III, C. Ozouf-Costaz and D. Higuet

    Citation: BMC Genomics 2018 19:339

    Content type: Research article

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  2. The level of fat deposition in carcass is a crucial factor influencing meat quality. Guangling Large-Tailed (GLT) and Small-Tailed Han (STH) sheep are important local Chinese fat-tailed breeds that show distin...

    Authors: Baojun Li, Liying Qiao, Lixia An, Weiwei Wang, Jianhua Liu, Youshe Ren, Yangyang Pan, Jiongjie Jing and Wenzhong Liu

    Citation: BMC Genomics 2018 19:338

    Content type: Research article

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  3. Colostrum and milk are essential sources of antibodies and nutrients for the neonate, playing a key role in their survival and growth. Slight abnormalities in the timing of colostrogenesis/lactogenesis potenti...

    Authors: V. Palombo, J. J. Loor, M. D’Andrea, M. Vailati-Riboni, K. Shahzad, U. Krogh and P. K. Theil

    Citation: BMC Genomics 2018 19:322

    Content type: Research article

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  4. Copy number variation (CNV) is an important type of genetic variation contributing to phenotypic differences among mammals and may serve as an alternative molecular marker to single nucleotide polymorphism (SN...

    Authors: Yang Zhou, Erin E. Connor, George R. Wiggans, Yongfang Lu, Robert J. Tempelman, Steven G. Schroeder, Hong Chen and George E. Liu

    Citation: BMC Genomics 2018 19:314

    Content type: Research article

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  5. Divergent selection for meat and egg production in poultry has resulted in strains of birds differing widely in traits related to these products. Modern strains of meat birds can reach live weights of 2 kg in ...

    Authors: Nicky-Lee Willson, Rebecca E. A. Forder, Rick Tearle, John L. Williams, Robert J. Hughes, Greg S. Nattrass and Philip I. Hynd

    Citation: BMC Genomics 2018 19:309

    Content type: Research article

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  6. The understanding of the biological determinism of meat ultimate pH, which is strongly related to muscle glycogen content, is a key point for the control of muscle integrity and meat quality in poultry. In the...

    Authors: Elisabeth Le Bihan-Duval, Christelle Hennequet-Antier, Cécile Berri, Stéphane A. Beauclercq, Marie Christine Bourin, Maryse Boulay, Olivier Demeure and Simon Boitard

    Citation: BMC Genomics 2018 19:294

    Content type: Research article

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  7. In food animal agriculture, there is a need to identify the mechanisms that can improve the efficiency of muscle growth and protein accretion. Callipyge sheep provide excellent machinery since the up-regulatio...

    Authors: Hui Yu, Jolena N. Waddell, Shihuan Kuang, Ross L. Tellam, Noelle E. Cockett and Christopher A. Bidwell

    Citation: BMC Genomics 2018 19:283

    Content type: Research article

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  8. Adipose tissue is a major endocrine organ and is thought to play a central role in the metabolic control of reproductive function in cattle. Plane of nutrition during early life has been shown to influence the...

    Authors: Anne-Marie English, Sineád M. Waters, Paul Cormican, Colin J. Byrne, Seán Fair and David A. Kenny

    Citation: BMC Genomics 2018 19:281

    Content type: Research article

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  9. Prolongation of superstimulatory treatment appears to be associated with a greater superovulatory response and with greater oocyte maturation in cattle. A genome-wide bovine oligo-microarray was used to compar...

    Authors: F. C. F. Dias, M. I. R. Khan, M. A. Sirard, G. P. Adams and J. Singh

    Citation: BMC Genomics 2018 19:258

    Content type: Research article

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  10. It has been suggested that the high phospholipid (PL) requirement in Atlantic salmon (Salmo salar) fry is due to insufficient intestinal de-novo synthesis causing low lipoprotein (LP) production and reduced trans...

    Authors: Yang Jin, Rolf Erik Olsen, Mari-Ann Østensen, Gareth Benjamin Gillard, Sven Arild Korsvoll, Nina Santi, Arne Bjørke Gjuvsland, Jon Olav Vik, Jacob Seilø Torgersen, Simen Rød Sandve and Yngvar Olsen

    Citation: BMC Genomics 2018 19:253

    Content type: Research article

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  11. The potential of circulating miRNAs as biomarkers of tissue function, both in health and disease, has been extensively demonstrated in humans. In addition, circulating miRNA biomarkers offer significant potent...

    Authors: Jason Ioannidis and F. Xavier Donadeu

    Citation: BMC Genomics 2018 19:243

    Content type: Research article

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  12. MicroRNAs (miRNAs) are short, non-coding RNAs that regulate gene expression at the post-transcriptional level and play a key role in the control of innate and adaptive immune responses. For a subclinical infec...

    Authors: Anna Monika Lewandowska-Sabat, Silje Furre Hansen, Trygve Roger Solberg, Olav Østerås, Bjørg Heringstad, Preben Boysen and Ingrid Olsaker

    Citation: BMC Genomics 2018 19:241

    Content type: Research article

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  13. Increased availability of genome assemblies for non-model organisms has resulted in invaluable biological and genomic insight into numerous vertebrates, including teleosts. Sequencing of the Atlantic cod (Gadus m...

    Authors: Ole K. Tørresen, Marine S. O. Brieuc, Monica H. Solbakken, Elin Sørhus, Alexander J. Nederbragt, Kjetill S. Jakobsen, Sonnich Meier, Rolf B. Edvardsen and Sissel Jentoft

    Citation: BMC Genomics 2018 19:240

    Content type: Research article

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  14. There are an exceedingly large number of sequence variants discovered through whole genome sequencing in most populations, including cattle. Deciphering which of these affect complex traits is a major challeng...

    Authors: Lambros T. Koufariotis, Yi-Ping Phoebe Chen, Paul Stothard and Ben J. Hayes

    Citation: BMC Genomics 2018 19:237

    Content type: Research article

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  15. Essential oil (EO) dietary supplementation is a new strategy to improve animal health. EO compounds have antiparasitic, antimicrobial, antiviral, antimycotic, antioxidant and anti-inflammatory proprieties. Nut...

    Authors: Marcella Sabino, Victor Adriano Okstoft Carmelo, Gianluca Mazzoni, Katia Cappelli, Stefano Capomaccio, Paolo Ajmone-Marsan, Andrea Verini-Supplizi, Massimo Trabalza-Marinucci and Haja N. Kadarmideen

    Citation: BMC Genomics 2018 19:236

    Content type: Research article

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  16. The ability to imitate the vocalizations of other organisms, a trait known as vocal learning, is shared by only a few organisms, including humans, where it subserves the acquisition of speech and language, and...

    Authors: Peter V. Lovell, Nicole A. Huizinga, Samantha R. Friedrich, Morgan Wirthlin and Claudio V. Mello

    Citation: BMC Genomics 2018 19:231

    Content type: Research article

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  17. A high-density genetic linkage map is essential for QTL fine mapping, comparative genome analysis, identification of candidate genes and marker-assisted selection for economic traits in aquaculture species. Th...

    Authors: Xiu Feng, Xiaomu Yu, Beide Fu, Xinhua Wang, Haiyang Liu, Meixia Pang and Jingou Tong

    Citation: BMC Genomics 2018 19:230

    Content type: Research article

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  18. Ranaviruses (family Iridoviridae, nucleocytoplasmic large DNA viruses) have been reported as promiscuous pathogens of cold-blooded vertebrates. Rana grylio virus (RGV, a ranavirus), from diseased frog Rana grylio

    Authors: Fei Ke, Jian-Fang Gui, Zhong-Yuan Chen, Tao Li, Cun-Ke Lei, Zi-Hao Wang and Qi-Ya Zhang

    Citation: BMC Genomics 2018 19:211

    Content type: Research article

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  19. Measures to improve bird performance have been sought due to the imminent phase out of in-feed antibiotics in poultry and continued demand for higher poultry feeding efficiency. Increasing grain particle size ...

    Authors: Sarbast K. Kheravii, Robert A. Swick, Mingan Choct and Shu-Biao Wu

    Citation: BMC Genomics 2018 19:208

    Content type: Research article

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  20. In monogastric animals, phosphorus (P) homeostasis is maintained by regulating intestinal absorption, bone mobilization, and renal excretion. Since P is a non-renewable resource, a shortage is imminent due to ...

    Authors: Franziska Just, Michael Oster, Kirsten Büsing, Luisa Borgelt, Eduard Murani, Siriluck Ponsuksili, Petra Wolf and Klaus Wimmers

    Citation: BMC Genomics 2018 19:207

    Content type: Research article

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  21. White striping (WS) is an emerging muscular defect occurring on breast and thigh muscles of broiler chickens. It is characterized by the presence of white striations parallel to the muscle fibers and has signi...

    Authors: Eva Pampouille, Cécile Berri, Simon Boitard, Christelle Hennequet-Antier, Stéphane A. Beauclercq, Estelle Godet, Christophe Praud, Yves Jégo and Elisabeth Le Bihan-Duval

    Citation: BMC Genomics 2018 19:202

    Content type: Research article

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  22. Understanding variation in genome structure is essential to understand phenotypic differences within populations and the evolutionary history of species. A promising form of this structural variation is copy n...

    Authors: Vinicius H. da Silva, Veronika N. Laine, Mirte Bosse, Kees van Oers, Bert Dibbits, Marcel E. Visser, Richard P. M. A. Crooijmans and Martien A. M. Groenen

    Citation: BMC Genomics 2018 19:195

    Content type: Research article

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  23. Because the cost of cereals is unstable and represents a large part of production charges for meat-type chicken, there is an urge to formulate alternative diets from more cost-effective feedstuff. We have rece...

    Authors: C. Desert, E. Baéza, M. Aite, M. Boutin, A. Le Cam, J. Montfort, M. Houee-Bigot, Y. Blum, P. F. Roux, C. Hennequet-Antier, C. Berri, S. Metayer-Coustard, A. Collin, S. Allais, E. Le Bihan, D. Causeur…

    Citation: BMC Genomics 2018 19:187

    Content type: Research article

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  24. A strain of Leghorn chickens (rd/rd), unable to produce a functional riboflavin-binding protein, lays riboflavin-deficient eggs, in which all embryos suddenly die at mid-incubation (days 13-15). This malady, caus...

    Authors: Larry A. Cogburn, Danielle N. Smarsh, Xiaofei Wang, Nares Trakooljul, Wilfrid Carré and Harold B. White III

    Citation: BMC Genomics 2018 19:177

    Content type: Research article

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  25. Southern flounder, Paralichthys lethostigma, historically support a substantial fishery along the Atlantic and Gulf coasts of the southern United States. Low year-class strengths over the past few years in the we...

    Authors: Shannon J. O’Leary, Christopher M. Hollenbeck, Robert R. Vega, John R. Gold and David S. Portnoy

    Citation: BMC Genomics 2018 19:163

    Content type: Research article

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  26. The annual killifish Austrofundulus limnaeus inhabits ephemeral ponds in northern Venezuela, South America, and is an emerging extremophile model for vertebrate diapause, stress tolerance, and evolution. Embryos ...

    Authors: Josiah T. Wagner, Param Priya Singh, Amie L. Romney, Claire L. Riggs, Patrick Minx, Steven C. Woll, Jake Roush, Wesley C. Warren, Anne Brunet and Jason E. Podrabsky

    Citation: BMC Genomics 2018 19:155

    Content type: Research article

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  27. Improving the efficiency of animal production is a relentless pursuit of ruminant producers. Energy utilization and partition can be affected by dietary composition and nutrient availability. Furthermore, the ...

    Authors: Haitao Shi, Jun Zhang, Shengli Li, Shoukun Ji, Zhijun Cao, Hongtao Zhang and Yajing Wang

    Citation: BMC Genomics 2018 19:148

    Content type: Research article

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  28. RNA is known to play diverse roles in gene regulation. The clues for this regulatory function of RNA are embedded in its ability to fold into intricate secondary and tertiary structure.

    Authors: Kriti Kaushik, Ambily Sivadas, Shamsudheen Karuthedath Vellarikkal, Ankit Verma, Rijith Jayarajan, Satyaprakash Pandey, Tavprithesh Sethi, Souvik Maiti, Vinod Scaria and Sridhar Sivasubbu

    Citation: BMC Genomics 2018 19:147

    Content type: Research article

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  29. The identification of genes differentially expressed in the skeletal muscle of pigs displaying distinct growth and fatness profiles might contribute to identify the genetic factors that influence the phenotypi...

    Authors: Tainã Figueiredo Cardoso, Raquel Quintanilla, Anna Castelló, Rayner González-Prendes, Marcel Amills and Ángela Cánovas

    Citation: BMC Genomics 2018 19:145

    Content type: Research article

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  30. Bovine leukemia virus (BLV) infection is omnipresent in dairy herds causing direct economic losses due to trade restrictions and lymphosarcoma-related deaths. Milk production drops and increase in the culling ...

    Authors: Hugo A. Carignano, Dana L. Roldan, María J. Beribe, María A. Raschia, Ariel Amadio, Juan P. Nani, Gerónimo Gutierrez, Irene Alvarez, Karina Trono, Mario A. Poli and Marcos M. Miretti

    Citation: BMC Genomics 2018 19:142

    Content type: Research article

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  31. Repetitive elements make up significant proportions of genomes. However, their roles in evolution remain largely unknown. To provide insights into the roles of repetitive elements in fish genomes, we conducted...

    Authors: Zihao Yuan, Shikai Liu, Tao Zhou, Changxu Tian, Lisui Bao, Rex Dunham and Zhanjiang Liu

    Citation: BMC Genomics 2018 19:141

    Content type: Research article

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  32. Infertility is a longstanding limitation in livestock production with important economic impact for the cattle industry. Female reproductive traits are polygenic and lowly heritable in nature, thus selection f...

    Authors: Sarah E. Dickinson, Brock A. Griffin, Michelle F. Elmore, Lisa Kriese-Anderson, Joshua B. Elmore, Paul W. Dyce, Soren P. Rodning and Fernando H. Biase

    Citation: BMC Genomics 2018 19:129

    Content type: Research article

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  33. The purpose of this study was to identify transcripts of retinal rod photoreceptors of the zebrafish. The zebrafish is an important animal model for vision science due to rapid and tractable development, persi...

    Authors: Chi Sun, Carlos Galicia and Deborah L. Stenkamp

    Citation: BMC Genomics 2018 19:127

    Content type: Research article

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  34. The amount of intramuscular fat can influence the sensory characteristics and nutritional value of beef, thus the selection of animals with adequate fat deposition is important to the consumer. There is growin...

    Authors: Gabriella B. Oliveira, Luciana C. A. Regitano, Aline S. M. Cesar, James M. Reecy, Karina Y. Degaki, Mirele D. Poleti, Andrezza M. Felício, James E. Koltes and Luiz L. Coutinho

    Citation: BMC Genomics 2018 19:126

    Content type: Research article

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  35. Numerous studies have established a link between maternal diet and the physiological and metabolic phenotypes of their offspring. In previous studies in sheep, we demonstrated that different maternal diets alt...

    Authors: Hadjer Namous, Francisco Peñagaricano, Marcello Del Corvo, Emanuele Capra, David L. Thomas, Alessandra Stella, John L. Williams, Paolo Ajmone Marsan and Hasan Khatib

    Citation: BMC Genomics 2018 19:123

    Content type: Research article

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  36. Skeletal muscle in livestock develops into meat, an important source of protein and other nutrients for human consumption. The muscle is largely composed of a fixed number of multinucleated myofibers determine...

    Authors: Tomasz Sadkowski, Anna Ciecierska, Jolanta Oprządek and Edyta Balcerek

    Citation: BMC Genomics 2018 19:109

    Content type: Research article

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  37. Genomic prediction using Diversity Arrays Technology (DArT) genotype by sequencing platform has not been reported in yellowtail kingfish (Seriola lalandi). The principal aim of this study was to address this know...

    Authors: Nguyen H. Nguyen, H. K. A. Premachandra, Andrzej Kilian and Wayne Knibb

    Citation: BMC Genomics 2018 19:107

    Content type: Research article

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  38. The highly prolific breeds of domestic sheep (Ovis aries) are globally valuable genetic resources for sheep industry. Genetic, nutritional and other environmental factors affect prolificacy traits in sheep. To im...

    Authors: Kisun Pokharel, Jaana Peippo, Mervi Honkatukia, Arja Seppälä, Johanna Rautiainen, Nasser Ghanem, Tuula-Marjatta Hamama, Mark A. Crowe, Magnus Andersson, Meng-Hua Li and Juha Kantanen

    Citation: BMC Genomics 2018 19:104

    Content type: Research article

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  39. While autozygosity as a consequence of selection is well understood, there is limited information on the ability of different methods to measure true inbreeding. In the present study, a gene dropping simulatio...

    Authors: Mehrnush Forutan, Saeid Ansari Mahyari, Christine Baes, Nina Melzer, Flavio Schramm Schenkel and Mehdi Sargolzaei

    Citation: BMC Genomics 2018 19:98

    Content type: Research article

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  40. Meat and egg-type chickens have been selected for several generations for different traits. Artificial and natural selection for different phenotypes can change frequency of genetic variants, leaving particula...

    Authors: Clarissa Boschiero, Gabriel Costa Monteiro Moreira, Almas Ara Gheyas, Thaís Fernanda Godoy, Gustavo Gasparin, Pilar Drummond Sampaio Corrêa Mariani, Marcela Paduan, Aline Silva Mello Cesar, Mônica Corrêa Ledur and Luiz Lehmann Coutinho

    Citation: BMC Genomics 2018 19:83

    Content type: Research article

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  41. The genetics underlying body mass and growth are key to understanding a wide range of topics in biology, both evolutionary and developmental. Body mass and growth traits are affected by many genetic variants o...

    Authors: Martin Johnsson, Rie Henriksen, Andrey Höglund, Jesper Fogelholm, Per Jensen and Dominic Wright

    Citation: BMC Genomics 2018 19:72

    Content type: Research article

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  42. One of the approaches to detect genetics variants affecting fitness traits is to identify their surrounding genomic signatures of past selection. With established methods for detecting selection signatures and...

    Authors: Christina Marie Rochus, Flavie Tortereau, Florence Plisson-Petit, Gwendal Restoux, Carole Moreno-Romieux, Gwenola Tosser-Klopp and Bertrand Servin

    Citation: BMC Genomics 2018 19:71

    Content type: Research article

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  43. Infectious disease is the single greatest threat to taxa such as amphibians (chytrid fungus), bats (white nose syndrome), Tasmanian devils (devil facial tumor disease), and black-footed ferrets (canine distemp...

    Authors: Jean P. Elbers, Mary B. Brown and Sabrina S. Taylor

    Citation: BMC Genomics 2018 19:64

    Content type: Research article

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  44. The neural crest (NC) is a class of transitory stem cell-like cells unique to vertebrate embryos. NC cells arise within the dorsal neural tube where they undergo an epithelial to mesenchymal transition in orde...

    Authors: Nicole J. Ward, Darrell Green, Janet Higgins, Tamas Dalmay, Andrea Münsterberg, Simon Moxon and Grant N. Wheeler

    Citation: BMC Genomics 2018 19:59

    Content type: Research article

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  45. Intramuscular fat (IMF) is one of the important factors influencing meat quality, however, for chickens, the molecular regulatory mechanisms underlying this trait have not yet been clear. In this study, a syst...

    Authors: Huanxian Cui, Maiqing Zheng, Guiping Zhao, Ranran Liu and Jie Wen

    Citation: BMC Genomics 2018 19:55

    Content type: Research article

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  46. Runs of homozygosity (ROH) are continuous homozygous segments of the DNA sequence. They have been applied to quantify individual autozygosity and used as a potential inbreeding measure in livestock species. Th...

    Authors: Elisa Peripolli, Nedenia Bonvino Stafuzza, Danísio Prado Munari, André Luís Ferreira Lima, Renato Irgang, Marco Antonio Machado, João Cláudio do Carmo Panetto, Ricardo Vieira Ventura, Fernando Baldi and Marcos Vinícius Gualberto Barbosa da Silva

    Citation: BMC Genomics 2018 19:34

    Content type: Research article

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  47. Salmonid fishes exhibit high levels of phenotypic and ecological variation and are thus ideal model systems for studying evolutionary processes of adaptive divergence and speciation. Furthermore, salmonids are...

    Authors: Madeleine Carruthers, Andrey A. Yurchenko, Julian J. Augley, Colin E. Adams, Pawel Herzyk and Kathryn R. Elmer

    Citation: BMC Genomics 2018 19:32

    Content type: Research article

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    The Correction to this article has been published in BMC Genomics 2018 19:448

  48. The assembly and annotation of a genome is a valuable resource for a species, with applications ranging from conservation genomics to gene discovery. Genomic resource development is especially important for sp...

    Authors: Catherine M. Purcell, Arun S. Seetharam, Owyn Snodgrass, Sofia Ortega-García, John R. Hyde and Andrew J. Severin

    Citation: BMC Genomics 2018 19:31

    Content type: Research article

    Published on:

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