RNA-Seq analysis and annotation of a draft blueberry genome assembly identifies candidate genes involved in fruit ripening, biosynthesis of bioactive compounds, and stage-specific alternative splicing

RNA-Seq analysis and annotation of a draft blueberry genome assembly identifies candidate genes involved in fruit ripening, biosynthesis of bioactive compounds, and stage-specific alternative splicing

Vikas Gupta, April Dawn Estrada, Ivory Clabaugh Blakley, Rob Reid, Ketan Patel, Mason D. Meyer, Stig Uggerhoj Andersen, Allan F. Brown, Mary Ann Lila, Ann Loraine
doi: http://dx.doi.org/10.1101/010116

Background: Blueberries are a rich source of antioxidants and other beneficial compounds that can protect against disease. Identifying genes involved in synthesis of bioactive compounds could enable breeding berry varieties with enhanced health benefits. Results: Toward this end, we annotated a draft blueberry genome assembly using RNA-Seq data from five stages of berry fruit development and ripening. Genome-guided assembly of RNA-Seq read alignments combined with output from ab initio gene finders produced around 60,000 gene models, of which more than half were similar to proteins from other species, typically the grape Vitis vinifera. Comparison of gene models to the PlantCyc database of metabolic pathway enzymes identified candidate genes involved in synthesis of bioactive compounds, including bixin, an apocarotenoid with potential disease-fighting properties, and defense-related cyanogenic glycosides, which are toxic. Cyanogenic glycoside (CG) biosynthetic enzymes were highly expressed in green fruit, and a candidate CG detoxification enzyme was up regulated during fruit ripening. Candidate genes for ethylene, anthocyanin, and 400 other biosynthetic pathways were also identified. RNA-Seq expression profiling showed that blueberry growth, maturation, and ripening involve dynamic gene expression changes, including coordinated up and down regulation of metabolic pathway enzymes, cell growth-related genes, and putative transcriptional regulators. Analysis of RNA-seq alignments also identified developmentally regulated alternative splicing, promoter use, and 3′ end formation. Conclusions: We report genome sequence, gene models, functional annotations, and RNA-Seq expression data which provide an important new resource enabling high throughput studies in blueberry. RNA-Seq data are freely available for visualization in Integrated Genome Browser, and analysis code is available from the git repository at http://bitbucket.org/lorainelab/blueberrygenome.

Origins and impacts of new exons

Origins and impacts of new exons
Jason Merkin*, Ping Chen*, Sampsa Hautaniemi, Christopher Burge
doi: http://dx.doi.org/10.1101/009282

Mammalian genes are typically broken into several protein-coding and non-coding exons, but the evolutionary origins and functions of new exons are not well understood. Here, we analyzed patterns of exon gain using deep cDNA sequencing data from several mammals and one bird, identifying thousands of species- and lineage-specific exons. While exons conserved across mammals are mostly protein-coding and constitutively spliced, species-specific exons were mostly located in 5′ untranslated regions and alternatively spliced. New exons most often derived from unique intronic sequence rather than repetitive elements, and were associated with upstream intronic deletions, increased nucleosome occupancy and RNA polymerase II pausing. Surprisingly, exon gain was associated with increased gene expression, but only in tissues where the exon was included, suggesting that splicing enhances steady-state mRNA levels and that changes in splicing represent a major contributor to the evolution of gene expression.

Genome-wide Comparative Analysis Reveals Possible Common Ancestors of NBS Domain Containing Genes in Hybrid Citrus sinensis Genome and Original Citrus clementina Genome

Genome-wide Comparative Analysis Reveals Possible Common Ancestors of NBS Domain Containing Genes in Hybrid Citrus sinensis Genome and Original Citrus clementina Genome

Yunsheng Wang, Lijuan Zhou, Dazhi Li, Amy Lawton-Rauh, Pradip K. Srimani, Liangying Dai, Yongping Duan, Feng Luo
doi: http://dx.doi.org/10.1101/008219

Background Recently available whole genome sequences of three citrus species: one Citrus clementina and two Citrus sinensis genomes have made it possible to understand the features of candidate disease resistance genes with nucleotide-binding sites (NBS) domain in Citrus and how NBS genes differ between hybrid and original Citrus species. Result We identified and re-annotated NBS genes from three citrus genomes and found similar numbers of NBS genes in those citrus genomes. Phylogenetic analysis of all citrus NBS genes across three genomes showed that there are three approximately evenly numbered groups: one group contains the Toll-Interleukin receptor (TIR) domain and two different groups that contain the Coiled Coil (CC) domain. Motif analysis confirmed that the two groups of CC-containing NBS genes are from different evolutionary origins. We partitioned NBS genes into clades using NBS domain sequence distances and found most clades include NBS genes from all three citrus genomes. This suggests that NBS genes in three citrus genomes may come from shared ancestral origins. We also mapped the re-sequenced reads of three pomelo and three Mandarin orange genomes onto the Citrus sinensis genome. We found that most NBS genes of the hybrid C. sinensis genome have corresponding homologous genes in both pomelo and mandarin genome. The homologous NBS genes in pomelo and mandarin may explain why the NBS genes in their hybrid Citrus sinensis are similar to those in Citrus clementina in this study. Furthermore, sequence variation amongst citrus NBS genes were shaped by multiple independent and shared accelerated mutation accumulation events among different groups of NBS genes and in different citrus genomes. Conclusion Our comparative analyses yield valuable insight into the understanding of the structure, evolution and organization of NBS genes in Citrus genomes. There are significantly more NBS genes in Citrus genomes compared to other plant species. NBS genes in hybrid C. sinensis genomes are very similar to those in progenitor C. clementina genome and they may be derived from possible common ancestral gene copies. Furthermore, our comprehensive analysis showed that there are three groups of plant NBS genes while CC-containing NBS genes can be divided into two groups.

Genome sequencing of the perciform fish Larimichthys crocea provides insights into stress adaptation

Genome sequencing of the perciform fish Larimichthys crocea provides insights into stress adaptation

Jingqun Ao, Yinnan Mu, Li-Xin Xiang, DingDing Fan, MingJi Feng, Shicui Zhang, Qiong Shi, Lv-Yun Zhu, Ting Li, Yang Ding, Li Nie, Qiuhua Li, Wei-ren Dong, Liang Jiang, Bing Sun, XinHui Zhang, Mingyu Li, Hai-Qi Zhang, ShangBo Xie, YaBing Zhu, XuanTing Jiang, Xianhui Wang, Pengfei Mu, Wei Chen, Zhen Yue, Zhuo Wang, Jun Wang, Jian-Zhong Shao, Xinhua Chen
doi: http://dx.doi.org/10.1101/008136

The large yellow croaker Larimichthys crocea (L. crocea) is one of the most economically important marine fish in China and East Asian countries. It also exhibits peculiar behavioral and physiological characteristics, especially sensitive to various environmental stresses, such as hypoxia and air exposure. These traits may render L. crocea a good model for investigating the response mechanisms to environmental stress. To understand the molecular and genetic mechanisms underlying the adaptation and response of L. crocea to environmental stress, we sequenced and assembled the genome of L. crocea using a bacterial artificial chromosome and whole-genome shotgun hierarchical strategy. The final genome assembly was 679 Mb, with a contig N50 of 63.11 kb and a scaffold N50 of 1.03 Mb, containing 25,401 protein-coding genes. Gene families underlying adaptive behaviours, such as vision-related crystallins, olfactory receptors, and auditory sense-related genes, were significantly expanded in the genome of L. crocea relative to those of other vertebrates. Transcriptome analyses of the hypoxia-exposed L. crocea brain revealed new aspects of neuro-endocrine-immune/metabolism regulatory networks that may help the fish to avoid cerebral inflammatory injury and maintain energy balance under hypoxia. Proteomics data demonstrate that skin mucus of the air-exposed L. crocea had a complex composition, with an unexpectedly high number of proteins (3,209), suggesting its multiple protective mechanisms involved in antioxidant functions, oxygen transport, immune defence, and osmotic and ionic regulation. Our results provide novel insights into the mechanisms of fish adaptation and response to hypoxia and air exposure.

No evidence that sex and transposable elements drive genome size variation in evening primroses

No evidence that sex and transposable elements drive genome size variation in evening primroses
J Arvid Agren, Stephan Greiner, Marc TJ Johnson, Stephen I Wright

Genome size varies dramatically across species, but despite an abundance of attention there is little agreement on the relative contributions of selective and neutral processes in governing this variation. The rate of sexual reproduction can potentially play an important role in genome size evolution because of its effect on the efficacy of selection and transmission of transposable elements. Here, we used a phylogenetic comparative approach and whole genome sequencing to investigate the contribution of sex and transposable element content to genome size variation in the evening primrose (Oenothera) genus. We determined genome size using flow cytometry from 30 Oenothera species of varying reproductive system and find that variation in sexual/asexual reproduction cannot explain the almost two-fold variation in genome size. Moreover, using whole genome sequences of three species of varying genome sizes and reproductive system, we found that genome size was not associated with transposable element abundance; instead the larger genomes had a higher abundance of simple sequence repeats. Although it has long been clear that sexual reproduction may affect various aspects of genome evolution in general and transposable element evolution in particular, it does not appear to have played a major role in the evening primroses.

Mitochondrial Genomes of Domestic Animals Need Scrutiny

Mitochondrial Genomes of Domestic Animals Need Scrutiny

Ni-Ni Shi, Long Fan, Yong-Gang Yao, Min-Sheng Peng, Ya-Ping Zhang
(Submitted on 16 Jul 2014)

More than 1000 complete or near-complete mitochondrial DNA (mtDNA) sequences have been deposited in GenBank for eight common domestic animals (i.e. cattle, dog, goat, horse, pig, sheep, yak and chicken) and their close wild ancestors or relatives. Nevertheless, few efforts have been performed to evaluate the sequence data quality, which heavily impact the original conclusion. Herein, we conducted a phylogenetic survey of these complete or near-complete mtDNA sequences based on mtDNA haplogroup trees for the eight animals. We show that, errors due to artificial recombination, surplus of mutations, and phantom mutations, do exist in 14.5% (194/1342) of mtDNA sequences and shall be treated with wide caution. We propose some caveats for mtDNA studies of domestic animals in the future.

Chromosomal distribution of cyto-nuclear genes in a dioecious plant with sex chromosomes

Chromosomal distribution of cyto-nuclear genes in a dioecious plant with sex chromosomes
Josh Hough, J Arvid Agren, Spencer CH Barrett, Stephen I Wright

The coordination between nuclear and organellar genes is essential to many aspects of eukaryotic life, including basic metabolism, energy production, and ultimately, organismal fitness. Whereas nuclear genes are bi-parentally inherited, mitochondrial and chloroplast genes are almost exclusively maternally inherited, and this asymmetry may lead to a bias in the chromosomal distribution of nuclear genes whose products act in the mitochondria or chloroplasts. In particular, because X-linked genes have a higher probability of co-transmission with organellar genes (2/3) compared to autosomal genes (1/2), selection for co-adaptation has been predicted to lead to an over-representation of nuclear-mitochondrial (N-mt) or nuclear-chloroplast (N-cp) genes on the X chromosome relative to autosomes. In contrast, the occurrence of sexually antagonistic organellar mutations might lead to selection for movement of cyto-nuclear genes from the X chromosome to autosomes to reduce male mutation load. Recent broad-scale comparative studies of N-mt distributions in animals have found evidence for these hypotheses in some species, but not others. Here, we use transcriptome sequences to conduct the first study of the chromosomal distribution of cyto-nuclear interacting genes in a plant species with sex chromosomes (Rumex hastatulus; Polygonaceae). We found no evidence of under- or over-representation of either N-mt or N-cp genes on the X chromosome, and thus no support for either the co-adaptation or the sexual-conflict hypothesis. We discuss how our results from a species with recently evolved sex chromosomes fit into an emerging picture of the evolutionary forces governing the chromosomal distribution of N-mt and N-cp genes.