http://www.biomedcentral.com/bmcgenomics/ The editor's pick of recent articles published by BMC Genomics 2013-05-31T00:00:00Z Background: The only known albino gorilla, named Snowflake, was a male wild born individual from Equatorial Guinea who lived at the Barcelona Zoo for almost 40 years. He was diagnosed with non-syndromic oculocutaneous albinism, i.e. white hair, light eyes, pink skin, photophobia and reduced visual acuity. Despite previous efforts to explain the genetic cause, this is still unknown. Here, we study the genetic cause of his albinism and making use of whole genome sequencing data we find a higher inbreeding coefficient compared to other gorillas. Results: We successfully identified the causal genetic variant for Snowflake’s albinism, a non-synonymous single nucleotide variant located in a transmembrane region of SLC45A2. This transporter is known to be involved in oculocutaneous albinism type 4 (OCA4) in humans. We provide experimental evidence that shows that this amino acid replacement alters the membrane spanning capability of this transmembrane region. Finally, we provide a comprehensive study of genome-wide patterns of autozygogosity revealing that Snowflake’s parents were related, being this the first report of inbreeding in a wild born Western lowland gorilla. Conclusions: In this study we demonstrate how the use of whole genome sequencing can be extended to link genotype and phenotype in non-model organisms and it can be a powerful tool in conservation genetics (e.g., inbreeding and genetic diversity) with the expected decrease in sequencing cost. http://www.biomedcentral.com/1471-2164/14/363 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 BMC Genomics 2013, 14:363 2013-05-31T00:00:00Z 10.1186/1471-2164-14-363 Wild albino gorilla Snowflake is inbred <p>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</p> /content/figures/1471-2164-14-363-toc.gif BMC Genomics 1471-2164 14 363 2013-05-31T00:00:00Z XML Background: MicroRNAs have been suggested to play important roles in the regulation of gene expression in various biological processes. To investigate the function of miRNAs in chicken ovarian development and folliculogenesis, two small RNA libraries constructed from sexually mature (162-day old) and immature (42-day old) ovary tissues of Single Comb White Leghorn chicken were sequenced using Illumina small RNA deep sequencing. Results: In the present study, 14,545,100 and 14,774,864 clean reads were obtained from sexually mature (162-d) and sexually immature (42-d) ovaries, respectively. In total, 202 known miRNAs were identified, and 93 of them were found to be significantly differentially expressed: 42 miRNAs were up-regulated and 51 miRNAs were down-regulated in the mature ovary compared to the immature ovary. Among the up-regulated miRNAs, gga-miR-1a has the largest fold-change (6.405-fold), while gga-miR-375 has the largest fold-change (11.345-fold) among the down-regulated miRNAs. The three most abundant miRNAs in the chicken ovary are gga-miR-10a, gga-let-7 and gga-miR-21. Five differentially expressed miRNAs (gga-miR-1a, 21, 26a, 137 and 375) were validated by real-time quantitative RT-PCR (qRT-PCR). Furthermore, the expression patterns of the five miRNAs were analyzed in different developmental stages of chicken ovary and follicles of various sizes. Conclusion: The present study provides the first miRNA profile in sexually immature and mature chicken ovaries. Some miRNAs such as gga-miR-1a and gga-miR-21are expressed differentially in immature and mature chicken ovaries as well as among different sized follicles, suggesting an important role in the follicular growth or ovulation mechanism in the chicken. http://www.biomedcentral.com/1471-2164/14/352 Li Kang Xinxing Cui Yujie Zhang Chunhong Yang Yunliang Jiang BMC Genomics 2013, 14:352 2013-05-26T00:00:00Z 10.1186/1471-2164-14-352 Chicken ovary miRNA profiles <p>Using a small RNA deep sequencing method on sexually immature and mature chicken ovaries differentially expressed miRNAs were identified and validated, including gga-miR-1a and gga-miR-21 thereby indicating a role in the follicular growth or ovulation mechanism.</p> /content/figures/1471-2164-14-352-toc.gif BMC Genomics 1471-2164 14 352 2013-05-26T00:00:00Z PDF Background: A classical example of repeated speciation coupled with ecological diversification is the evolution of 14 closely related species of Darwin’s (Galápagos) finches (Thraupidae, Passeriformes). Their adaptive radiation in the Galápagos archipelago took place in the last 2–3 million years and some of the molecular mechanisms that led to their diversification are now being elucidated. Here we report evolutionary analyses of genome of the large ground finch, Geospiza magnirostris. Results: 13,291 protein-coding genes were predicted from a 991.0 Mb G. magnirostris genome assembly. We then defined gene orthology relationships and constructed whole genome alignments between the G. magnirostris and other vertebrate genomes. We estimate that 15% of genomic sequence is functionally constrained between G. magnirostris and zebra finch. Genic evolutionary rate comparisons indicate that similar selective pressures acted along the G. magnirostris and zebra finch lineages suggesting that historical effective population size values have been similar in both lineages. 21 otherwise highly conserved genes were identified that each show evidence for positive selection on amino acid changes in the Darwin's finch lineage. Two of these genes (Igf2r and Pou1f1) have been implicated in beak morphology changes in Darwin’s finches. Five of 47 genes showing evidence of positive selection in early passerine evolution have cilia related functions, and may be examples of adaptively evolving reproductive proteins. Conclusions: These results provide insights into past evolutionary processes that have shaped G. magnirostris genes and its genome, and provide the necessary foundation upon which to build population genomics resources that will shed light on more contemporaneous adaptive and non-adaptive processes that have contributed to the evolution of the Darwin’s finches. http://www.biomedcentral.com/1471-2164/14/95 Chris M Rands Aaron Darling Matthew Fujita Lesheng Kong Matthew T Webster Céline Clabaut Richard D Emes Andreas Heger Stephen Meader Michael Brent Hawkins Michael B Eisen Clotilde Teiling Jason Affourtit Benjamin Boese Peter R Grant Barbara Rosemary Grant Jonathan A Eisen Arhat Abzhanov Chris P Ponting BMC Genomics 2013, 14:95 2013-02-12T00:00:00Z 10.1186/1471-2164-14-95 Genomic insights into Geospiza <p>204 years after Charles Darwin&rsquo;s birth, sequencing of the genome of the Darwin&rsquo;s Finch <em>Geospiza magnirostris</em> reveals over 13,000 predicted genes, of which two under positive selection may have contributed to beak morphology evolution, which so interested Darwin.</p> /content/figures/1471-2164-14-95-toc.gif BMC Genomics 1471-2164 14 95 2013-02-12T00:00:00Z XML Background: Hevea brasiliensis, a member of the Euphorbiaceae family, is the major commercial source of natural rubber (NR). NR is a latex polymer with high elasticity, flexibility, and resilience that has played a critical role in the world economy since 1876. Results: Here, we report the draft genome sequence of H. brasiliensis. The assembly spans ~1.1 Gb of the estimated 2.15 Gb haploid genome. Overall, ~78% of the genome was identified as repetitive DNA. Gene prediction shows 68,955 gene models, of which 12.7% are unique to Hevea. Most of the key genes associated with rubber biosynthesis, rubberwood formation, disease resistance, and allergenicity have been identified. Conclusions: The knowledge gained from this genome sequence will aid in the future development of high-yielding clones to keep up with the ever increasing need for natural rubber. http://www.biomedcentral.com/1471-2164/14/75 Ahmad Yamin Abdul Rahman Abhilash O Usharraj Biswapriya B Misra Gincy P Thottathil Kandakumar Jayasekaran Yun Feng Shaobin Hou Su Yean Ong Fui Ling Ng Ling Sze Lee Hock Siew Tan Muhd Khairul Luqman Muhd Sakaff Beng Soon Teh Bee Khoo Siti Suriawati Badai Nurohaida Ab Aziz Anton Yuryev Bjarne Knudsen Alexandre Dionne-Laporte Nokuthula P Mchunu Qingyi Yu Brennick J Langston Tracey Allen K Freitas Aaron G Young Rui Chen Lei Wang Nazalan Najimudin Jennifer A Saito Maqsudul Alam BMC Genomics 2013, 14:75 2013-02-02T00:00:00Z 10.1186/1471-2164-14-75 Rubber tree draft genome reported <p>The draft genome of the rubber tree <em>Hevea brasiliensis</em> is almost 80% repetitive DNA with 12.7% of genes models identified being unique to this species, including key rubber biosynthesis and disease resistance genes</p> /content/figures/1471-2164-14-75-toc.gif BMC Genomics 1471-2164 14 75 2013-02-02T00:00:00Z XML