Detection of internal exon deletion with exon Del

Background

Exome sequencing allows researchers to study the human genome in unprecedented detail. Among the many types of variants detectable through exome sequencing, one of the most over looked types of mutation is internal deletion of exons. Internal exon deletions are the absence of consecutive exons in a gene. Such deletions have potentially significant biological meaning, and they are often too short to be considered copy number variation. Therefore, to the need for efficient detection of such deletions using exome sequencing data exists.

Results

We present ExonDel, a tool specially designed to detect homozygous exon deletions efficiently. We tested ExonDel on exome sequencing data generated from 16 breast cancer cell lines and identified both novel and known IEDs. Subsequently, we verified our findings using RNAseq and PCR technologies. Further comparisons with multiple sequencing-based CNV tools showed that ExonDel is capable of detecting unique IEDs not found by other CNV tools.

Conclusions

ExonDel is an efficient way to screen for novel and known IEDs using exome sequencing data. ExonDel and its source code can be downloaded freely at https://github.com/slzhao/ExonDel.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2105-15-332) contains supplementary material, which is available to authorized users.     

Genetic Variations of 13 Indigenous Chinese Goat Breeds Based on Cytochrome b Gene Sequences

Phylogenetic relationships among and genetic variability within 13 Chinese indigenous goat breeds and Boer goat were analyzed using cytochrome b gene sequences. There were 44 variable sites found in a 642 bp sequence, and 46 Cyt b haplotypes were subsequently defined. The phylogeny analysis of haplotypes in combination with goat Cyt b sequences from GenBank shows that Chinese goats are obviously separated from wild goats and might come from Capra aegagrus. Further analysis indicated that indigenous Chinese goats might descend from at least two lineages; most of the individuals analyzed could be classified into lineage A as defined by Luikart, but five other goats were of uncertain lineage. The Tibet plateau is a possible place of origin for Chinese goats. The neighbor-joining tree based on pairwise differences among populations shows that most Tibetan goats, except the Middle Tibet type, cluster closely with North China goats, and then with South China goats. This result confirms that differences in genetic structure exist among goats in different geographic locations. Nucleotide diversity varied among populations. Tibet and North China goats had higher genetic diversity than South China goats. The fixation index (F _st=87.72%) suggested that most of the total genetic variation was due to variation within populations. In addition, the results indicate that Cyt b gene sequence information alone might not be enough for phylogeny analysis among breeds within species, as shown by fewer polymorphic sites and lower bootstrap values on the neighbor-joining tree.     

Polymerase chain reaction primers for polymorphic microsatellite loci from the Korean sandfish,Arctoscopus japonicus

We developed 12 polymorphic microsatellite markers from Arctoscopus japonicus by screening an enriched genomic library using polymerase chain reaction (PCR) techniques. The average of alleles size was 16.2, and the average observed and expected heterozygosities were 0.59 and 0.78, respectively. The observed genotypic frequencies in five loci were significantly deviated from Hardy–Weinberg expectations. The high variability revealed in this study suggested that these microsatellite loci should provide useful markers for population genetics of A. japonicus.     

Association of the OCA2 Polymorphism His615Arg with Melanin Content in East Asian Populations: Further Evidence of Convergent Evolution of Skin Pigmentation

The last decade has witnessed important advances in our understanding of the genetics of pigmentation in European populations, but very little is known about the genes involved in skin pigmentation variation in East Asian populations. Here, we present the results of a study evaluating the association of 10 Single Nucleotide Polymorphisms (SNPs) located within 5 pigmentation candidate genes (OCA2, DCT, ADAM17, ADAMTS20, and TYRP1) with skin pigmentation measured quantitatively in a sample of individuals of East Asian ancestry living in Canada. We show that the non-synonymous polymorphism rs1800414 (His615Arg) located within the OCA2 gene is significantly associated with skin pigmentation in this sample. We replicated this result in an independent sample of Chinese individuals of Han ancestry. This polymorphism is characterized by a derived allele that is present at a high frequency in East Asian populations, but is absent in other population groups. In both samples, individuals with the derived G allele, which codes for the amino acid arginine, show lower melanin levels than those with the ancestral A allele, which codes for the amino acid histidine. An analysis of this non-synonymous polymorphism using several programs to predict potential functional effects provides additional support for the role of this SNP in skin pigmentation variation in East Asian populations. Our results are consistent with previous research indicating that evolution to lightly-pigmented skin occurred, at least in part, independently in Europe and East Asia.     

Use of ITS2 Region as the Universal DNA Barcode for Plants and Animals

Background

The internal transcribed spacer 2 (ITS2) region of nuclear ribosomal DNA is regarded as one of the candidate DNA barcodes because it possesses a number of valuable characteristics, such as the availability of conserved regions for designing universal primers, the ease of its amplification, and sufficient variability to distinguish even closely related species. However, a general analysis of its ability to discriminate species in a comprehensive sample set is lacking.

Methodology/Principal Findings

In the current study, 50,790 plant and 12,221 animal ITS2 sequences downloaded from GenBank were evaluated according to sequence length, GC content, intra- and inter-specific divergence, and efficiency of identification. The results show that the inter-specific divergence of congeneric species in plants and animals was greater than its corresponding intra-specific variations. The success rates for using the ITS2 region to identify dicotyledons, monocotyledons, gymnosperms, ferns, mosses, and animals were 76.1%, 74.2%, 67.1%, 88.1%, 77.4%, and 91.7% at the species level, respectively. The ITS2 region unveiled a different ability to identify closely related species within different families and genera. The secondary structure of the ITS2 region could provide useful information for species identification and could be considered as a molecular morphological characteristic.

Conclusions/Significance

As one of the most popular phylogenetic markers for eukaryota, we propose that the ITS2 locus should be used as a universal DNA barcode for identifying plant species and as a complementary locus for CO1 to identify animal species. We have also developed a web application to facilitate ITS2-based cross-kingdom species identification (http://its2-plantidit.dnsalias.org).     

Effects of warming on soil respiration during the non-growing seasons in a semiarid temperate steppe

尽管许多研究认为增温对陆地生态系统非生长季土壤呼吸的影响非常重要,但是关于这一问题仍缺乏充分的理解。本论文研究了非生长季增温对温带半干旱草原土壤呼吸的影响,并探讨了其影响机制。本实验位于温带半干旱典型草原,包括10对样地,每对样地包括一个对照和模拟增温处理。模拟增温样地自2014年10月开始,采用开顶箱(OTC)进行。2014年10月到2015年4月,2015年10月到2016年4月期间每月测定几次土壤呼吸、土壤温度与土壤湿度;并测定0-20 cm微生物量碳(MBC)、微生物量氮(MBN)和土壤速效氮。采用重复测量方差和成对t检验方法分析增温、时间及其交互作用对土壤呼吸的影响。采用简单回归确定各指标之间的因果关系。结果表明,对照样地非生长季平均土壤呼吸速率为0.24 µmol m^-2 s^-1,约占当地生长季碳通量的14.4%。模拟增温在两个非生长季使土壤温度和土壤呼吸分别比对照样地提高了1.48°C (P < 0.001)和42.1% (P < 0.01)。2015-2016年非生长季模拟增温降低了0.66%的土壤湿度,降低幅度不显著。模拟增温处理下2015-2016年非生长季MBC和MBN分别显著提高了19.72%和20.99% (P < 0.05)。此外,研究结果还表明,土壤温度、MBC和MBN的变化调控了土壤呼吸对模拟增温的响应。本结果揭示非生长季土壤呼吸变化能影响碳循环的其它组分,并可以有效促进气候变化背景下陆地生态系统碳循环的模型预测。     

火烧迹地柽柳灌丛资源岛特征及植被的自然恢复

干旱半干旱地区灌丛资源岛特征及形成机制多有报道,但资源岛土壤对群落稳定性与火烧迹地植被的自然恢复作用尚不明确。以酒泉盐碱地柽柳灌丛地火烧3年后,自然恢复的柽柳(Tamarix ramosissima)及其冠下草本群落为研究对象,构建柽柳枯立株体量指数(SSI,Shrub Size Index)和恢复力综合指数,探讨了资源岛特征与植被恢复、冠下草本群落多样性的关系,量化不同大小柽柳灌丛的恢复力稳定性。结果表明:(1)在不同SSI的柽柳枯立株下土壤有机质和含水率明均显高于灌丛间地,形成了明显的资源岛特征。土壤有机质最大值出现在0—10 cm土层,中灌丛的肥力积聚效果最明显。(2)土壤主要以中性盐为主,在0—40 cm土层,灌丛区域土壤可溶性盐低于冠外,呈明显的盐谷特征,中灌丛的盐谷分布最为明显。(3)随着枯立株SSI的增大,柽柳新生枝条的数量及其高度均有所增大,冠下植物的高度、盖度、密度和地上植物量也明显高于灌丛间地,且灌丛越大恢复效果越明显。(4)灌下植物Simpson指数、Shannon⁃Wiener指数、Margalef指数和Pielou指数随着枯立株SSI的增大均先降后升,多样性指数低,群落结构简单。(5)恢复力综合指数随着枯立株SSI的增大呈先升后降的趋势,当SSI=52.17时灌丛群落的稳定性最强。柽柳较小时主要是冠下草本植物的恢复维持群落稳定性,随着灌丛的增大逐渐以柽柳灌木的恢复来维持群落稳定性。柽柳灌丛形成的高养低盐的土壤环境对植物群落稳定性的维持和植被的恢复有促进作用,对荒漠生态系统火烧迹地植被恢复和生态保护具有重要意义。     

miR-30b-5p inhibits cancer progression and enhances cisplatin sensitivity in lung cancer through targeting LRP8

Apoptosis - Accumulated evidence has demonstrated that miRNAs are closely implicated in lung carcinogenesis. Herein, we explored the expression pattern of miR-30b-5p in lung cancer, and aimed to...