BMC Genomics | Comparative and evolutionary genomics section

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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.	Research article Phage cluster relationships identified through single gene analysis Kyle C Smith, Eduardo Castro-Nallar, Joshua NB Fisher, Donald P Breakwell, Julianne H Grose, Sandra H Burnett BMC Genomics 2013, 14:410 (19 June 2013) Abstract \| Provisional PDF
	2.	Research article The complete mitochondrial genome of Solemya velum (Mollusca: Bivalvia) and its relationships with Conchifera Federico Plazzi, Anisa Ribani, Marco Passamonti BMC Genomics 2013, 14:409 (18 June 2013) Abstract \| Provisional PDF
	3.	Research article Genetic heterogeneity revealed by sequence analysis of Mycobacterium tuberculosis isolates from extra-pulmonary tuberculosis patients Sarbashis Das, Tanmoy Roychowdhury, Parameet Kumar, Anil Kumar, Priya Kalra, Jitendra Singh, Sarman Singh, HK Prasad, Alok Bhattacharya BMC Genomics 2013, 14:404 (17 June 2013) Abstract \| Provisional PDF
	4.	Research article Genome-wide analysis of intraspecific transposon diversity in yeast Claudine Bleykasten-Grosshans, Anne Friedrich, Joseph Schacherer BMC Genomics 2013, 14:399 (14 June 2013) Abstract \| Provisional PDF
	5.	Research article The genesis of an exceptionally lethal venom in the timber rattlesnake (Crotalus horridus) revealed through comparative venom-gland transcriptomics Darin R Rokyta, Kenneth P Wray, Mark J Margres BMC Genomics 2013, 14:394 (12 June 2013) Abstract \| Provisional PDF \| PubMed
	6.	Research article Archaeal nucleosome positioning in vivo and in vitro is directed by primary sequence motifs Narasimharao Nalabothula, Liqun Xi, Sucharita Bhattacharyya, Jonathan Widom, Ji-Ping Wang, John N Reeve, Thomas J Santangelo, Yvonne N Fondufe-Mittendorf BMC Genomics 2013, 14:391 (10 June 2013) Abstract \| Provisional PDF \| PubMed
	7.	Research article Comparative genomic analysis of catfish linkage group 8 reveals two homologous chromosomes in zebrafish and other teleosts with extensive inter-chromosomal rearrangements Yu Zhang, Shikai Liu, Jianguo Lu, Yanliang Jiang, Xiaoyu Gao, Parichart Ninwichian, Chao Li, Geoff Waldbieser, Zhanjiang Liu BMC Genomics 2013, 14:387 (10 June 2013) Abstract \| Provisional PDF \| PubMed
	8.	Research article Evolution of REP diversity: a comparative study Jaroslav Nunvar, Irena Licha, Bohdan Schneider BMC Genomics 2013, 14:385 (10 June 2013) Abstract \| Provisional PDF \| PubMed
	9.	Research article Genomic basis of ecological niche divergence among cryptic sister species of non-biting midges Hanno Schmidt, Bastian Greshake, Barbara Feldmeyer, Thomas Hankeln, Markus Pfenninger BMC Genomics 2013, 14:384 (10 June 2013) Abstract \| Full text \| PDF \| PubMed
	10.	Research article Pan-genome analysis of the emerging foodborne pathogen Cronobacter spp. suggests a species-level bidirectional divergence driven by niche adaptation Christopher J Grim, Michael L Kotewicz, Karen A Power, Gopal Gopinath, Augusto A Franco, Karen G Jarvis, Qiong Q Yan, Scott A Jackson, Venugopal Sathyamoorthy, Lan Hu, Franco Pagotto, Carol Iversen, Angelika Lehner, Roger Stephan, Séamus Fanning, Ben D Tall BMC Genomics 2013, 14:366 (31 May 2013) Abstract \| Full text \| PDF \| ePUB \| PubMed
	11.	Research article The genome sequencing of an albino Western lowland gorilla reveals inbreeding in the wild Javier Prado-Martinez, Irene Hernando-Herraez, Belen Lorente-Galdos, Marc Dabad, Oscar Ramirez, Carlos Baeza-Delgado, Carlos Morcillo-Suarez, Can Alkan, Fereydoun Hormozdiari, Emanuele Raineri, Jordi Estellé, Marcos Fernandez-Callejo, Mònica Valles, Lars Ritscher, Torsten Schöneberg, Elisa de la Calle-Mustienes, Sònia Casillas, Raquel Rubio-Acero, Marta Melé, Johannes Engelken, Mario Caceres, Jose Gomez-Skarmeta, Marta Gut, Jaume Bertranpetit, Ivo G Gut, Teresa Abello, Evan E Eichler, Ismael Mingarro, Carles Lalueza-Fox, Arcadi Navarro, Tomas Marques-Bonet et al. BMC Genomics 2013, 14:363 (31 May 2013) Abstract \| Full text \| PDF \| ePUB \| PubMed \| Editor’s summary A phenotypically unique gorilla carries a private non-synonymous substitution in a transmembrane domain in SLC45A2, one of the candidate genes associated with the OCA4 class of albinism
	12.	Research article The venus kinase receptor (VKR) family: structure and evolution Mathieu Vanderstraete, Nadège Gouignard, Arnaud Ahier, Marion Morel, Jérôme Vicogne, Colette Dissous BMC Genomics 2013, 14:361 (30 May 2013) Abstract \| Provisional PDF \| PubMed
	13.	Software Unsupervised genome-wide recognition of local relationship patterns Neda Zamani, Pamela Russell, Henrik Lantz, Marc P Hoeppner, Jennifer RS Meadows, Nagarjun Vijay, Evan Mauceli, Federica di Palma, Kerstin Lindblad-Toh, Patric Jern, Manfred G Grabherr BMC Genomics 2013, 14:347 (24 May 2013) Abstract \| Full text \| PDF \| ePUB \| PubMed
	14.	Research article Frequent loss of lineages and deficient duplications accounted for low copy number of disease resistance genes in Cucurbitaceae Xiao Lin, Yu Zhang, Hanhui Kuang, Jiongjiong Chen BMC Genomics 2013, 14:335 (17 May 2013) Abstract \| Full text \| PDF \| ePUB \| PubMed
	15.	Research article Short and long-term genome stability analysis of prokaryotic genomes Matteo Brilli, Pietro Liò, Vincent Lacroix, Marie-France Sagot BMC Genomics 2013, 14:309 (8 May 2013) Abstract \| Full text \| PDF \| PubMed
	16.	Research article Origins of amyloid-β William G Tharp, Indra Sarkar BMC Genomics 2013, 14:290 (30 April 2013) Abstract \| Full text \| PDF \| ePUB \| PubMed
	17.	Research article The Nocardia cyriacigeorgica GUH-2 genome shows ongoing adaptation of an environmental Actinobacteria to a pathogen's lifestyle Anthony Zoropogui, Petar Pujic, Philippe Normand, Valérie Barbe, Patrick Belli, Arnault Graindorge, David Roche, David Vallenet, Sophie Mangenot, Patrick Boiron, Véronica Rodriguez-Nava, Sebastien Ribun, Yves Richard, Benoit Cournoyer, Didier Blaha BMC Genomics 2013, 14:286 (27 April 2013) Abstract \| Provisional PDF \| PubMed
	18.	Research article Unscrambling butterfly oogenesis Jean-Michel Carter, Simon C Baker, Ryan Pink, David RF Carter, Aiden Collins, Jeremie Tomlin, Melanie Gibbs, Casper J Breuker BMC Genomics 2013, 14:283 (26 April 2013) Abstract \| Full text \| PDF \| ePUB \| PubMed
	19.	Research article Comparative analysis of fungal genomes reveals different plant cell wall degrading capacity in fungi Zhongtao Zhao, Huiquan Liu, Chenfang Wang, Jin-Rong Xu BMC Genomics 2013, 14:274 (23 April 2013) Abstract \| Full text \| PDF \| ePUB \| PubMed
	20.	Research article Genome analyses of the wheat yellow (stripe) rust pathogen Puccinia striiformis f. sp. tritici reveal polymorphic and haustorial expressed secreted proteins as candidate effectors Dario Cantu, Vanesa Segovia, Daniel MacLean, Rosemary Bayles, Xianming Chen, Sophien Kamoun, Jorge Dubcovsky, Diane GO Saunders, Cristobal Uauy BMC Genomics 2013, 14:270 (22 April 2013) Abstract \| Full text \| PDF \| ePUB \| PubMed
	21.	Research article Novel genomes and genome constitutions identified by GISH and 5S rDNA and knotted1 genomic sequences in the genus Setaria Meicheng Zhao, Hui Zhi, Andrew N Doust, Wei Li, Yongfang Wang, Haiquan Li, Guanqing Jia, Yongqiang Wang, Ning Zhang, Xianmin Diao BMC Genomics 2013, 14:244 (11 April 2013) Abstract \| Full text \| PDF \| ePUB \| PubMed
	22.	Research article Reevaluation of the evolutionary events within recA/RAD51 phylogeny Sree V Chintapalli, Gaurav Bhardwaj, Jagadish Babu, Loukia Hadjiyianni, Yoojin Hong, George K Todd, Casey A Boosalis, Zhenhai Zhang, Xiaofan Zhou, Hong Ma, Andriy Anishkin, Damian B van Rossum, Randen L Patterson BMC Genomics 2013, 14:240 (10 April 2013) Abstract \| Full text \| PDF \| ePUB \| PubMed
	23.	Research article Molecular cloning of doublesex genes of four cladocera (water flea) species Kenji Toyota, Yasuhiko Kato, Masaru Sato, Naomi Sugiura, Shinichi Miyagawa, Hitoshi Miyakawa, Hajime Watanabe, Shigeto Oda, Yukiko Ogino, Chizue Hiruta, Takeshi Mizutani, Norihisa Tatarazako, Susanne Paland, Craig Jackson, John K Colbourne, Taisen Iguchi BMC Genomics 2013, 14:239 (10 April 2013) Abstract \| Full text \| PDF \| ePUB \| PubMed
	24.	Database RegTransBase – a database of regulatory sequences and interactions based on literature: a resource for investigating transcriptional regulation in prokaryotes Michael J Cipriano, Pavel N Novichkov, Alexey E Kazakov, Dmitry A Rodionov, Adam P Arkin, Mikhail S Gelfand, Inna Dubchak BMC Genomics 2013, 14:213 (2 April 2013) Abstract \| Full text \| PDF \| ePUB \| PubMed
	25.	Research article Construction of a plant-transformation-competent BIBAC library and genome sequence analysis of polyploid Upland cotton (Gossypium hirsutum L.) Mi-Kyung Lee, Yang Zhang, Meiping Zhang, Mark Goebel, Hee Kim, Barbara A Triplett, David M Stelly, Hong-Bin Zhang BMC Genomics 2013, 14:208 (28 March 2013) Abstract \| Full text \| PDF \| ePUB \| PubMed