An Effort to Use Human-Based Exome Capture Methods to Analyze Chimpanzee and Macaque Exomes

Jin, Xin; He, Mingze; Ferguson, Betsy; Meng, Yuhuan; Ouyang, Limei; Ren, Jingjing; Mailund, Thomas; Sun, Fei; Sun, Liangdan; Shen, Juan; Zhuo, Min; Song, Li; Wang, Jufang; Ling, Fei; Zhu, Yuqi; Hvilsom, Christina; Siegismund, Hans R.; Liu, Xiaoming; Gong, Zhuolin; Ji, Fang; Wang, Xinzhong; Liu, Boqing; Hou, Jingli; Wang, Jing; Zhao, Hua; Wang, Yanyi; Fang, Xiaodong; Wang, Jian; Zhang, Xuejun; Schierup, Mikkel H.; Du, Hongli; Wang, Jun; Wang, Xiaoning

doi:10.1371/journal.pone.0040637

Cited by 29 publications

(35 citation statements)

References 30 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The data were mapped against cattle genome assembly 22 with overall mapping rate of ~98%. Mapping rate was higher compared to that reported in an earlier study 23 , mainly due to experiment design, wherein we have targeted coding regions which are conserved compared to other parts of the genome, followed by detection of SNPs. Furthermore, unmapped PCR duplicates and multiple mapped reads were removed for downstream analysis to reduce computational time and also to mitigate the effect of PCR amplification bias that might be introduced during library preparation during pre-and post-hybridization amplification steps.…”

Section: Discussioncontrasting

confidence: 56%

Identification of Single Nucleotide Polymorphism from Indian <i>Bubalus bubalis</i> through Targeted Sequence Capture

Patel¹,

Subramanian²,

Padh³

et al. 2017

Current Science

View full text Add to dashboard Cite

Bubalus bubalis (water buffalo) is an agro-economically important livestock species due to its multipurpose use in India and other Asian countries. The aim of this study was to identify single nucleotide polymorphisms (SNPs) from buffalo genome. Genomic DNA was isolated from 24 blood samples of three Indian buffalo breeds and subjected to targeted pyrosequencing, followed by variant calling and annotation. Target probes for enrichment were designed from exome and 5 and 3 untranslated regions of cattle genome. By targeted pyro-sequencing and variant calling from 3.92 Gb data, 923,964 high-quality SNPs were identified. Many SNPs were identified in regulatory regions, leading to conformational changes in factor-binding sites, which play a role in gene expression as in the case of LPL gene from low-milkproducing samples. Gene ontology (GO) enrichment and clustering, resulted in the enrichment of GO terms involved in milk production and transport, and fertility-related categories. Around 75% of SNPs were located on cattle quantitative trait loci, supporting trait-wise sample collection approach. Further, PCA analysis from the identified SNPs also supported sample selection strategy based on contrasting trait performance.

show abstract

Section: Discussioncontrasting

confidence: 56%

Identification of Single Nucleotide Polymorphism from Indian <i>Bubalus bubalis</i> through Targeted Sequence Capture

Patel¹,

Subramanian²,

Padh³

et al. 2017

Current Science

View full text Add to dashboard Cite

show abstract

“…Mean coverage for WES data were 1163 (compared with 143 for WGS data) and 643 (compared with 133 for WGS data), respectively. Human-based exome capture has been shown to be effective in primates as diverged from humans as macaques (Jin et al 2012). Utilizing only exome calls with coverage between 303 and 2003 we found slightly greater concordance between the WGS and WES data for the NLE (99.6%) vs. non-NLE samples (99.4%) (Table S2).…”

mentioning

confidence: 89%

Examining Phylogenetic Relationships Among Gibbon Genera Using Whole Genome Sequence Data Using an Approximate Bayesian Computation Approach

et al. 2015

View full text Add to dashboard Cite

Gibbons are believed to have diverged from the larger great apes 16.8 MYA and today reside in the rainforests of Southeast Asia. Based on their diploid chromosome number, the family Hylobatidae is divided into four genera, Nomascus, Symphalangus, Hoolock, and Hylobates. Genetic studies attempting to elucidate the phylogenetic relationships among gibbons using karyotypes, mitochondrial DNA (mtDNA), the Y chromosome, and short autosomal sequences have been inconclusive . To examine the relationships among gibbon genera in more depth, we performed second-generation whole genome sequencing (WGS) to a mean of 153 coverage in two individuals from each genus. We developed a coalescent-based approximate Bayesian computation (ABC) method incorporating a model of sequencing error generated by high coverage exome validation to infer the branching order, divergence times, and effective population sizes of gibbon taxa. Although Hoolock and Symphalangus are likely sister taxa, we could not confidently resolve a single bifurcating tree despite the large amount of data analyzed. Instead, our results support the hypothesis that all four gibbon genera diverged at approximately the same time. Assuming an autosomal mutation rate of 1 3 10 29 /site/year this speciation process occurred 5 MYA during a period in the Early Pliocene characterized by climatic shifts and fragmentation of the Sunda shelf forests. Whole genome sequencing of additional individuals will be vital for inferring the extent of gene flow among species after the separation of the gibbon genera.KEYWORDS approximate Bayesian computation; gibbon species; rapid radiation; whole genome sequences T HE family Hylobatidae, commonly known as gibbons, is believed to have diverged from the larger great apes 16.8 MYA . Sometimes known as small apes, gibbons demonstrate substantial morphological differentiation from the great apes; their much smaller bodies are highly adapted to an arboreal mode of locomotion in the rainforests of Southeast Asia. They also demonstrate very little sexual dimorphism that may, in part, be related to their generally monogamous mating patterns (Fuentes 2000) (although some gibbon species develop differences in coat color at sexual maturity).Each species demonstrates distinct "call" and "song" types (Geissmann 2002); however, attempts to classify gibbon species and genera based solely on morphological features have been problematic (Mootnick 2006). Primarily on the basis of their karyotypes, gibbons are now divided into four major genera, with Nomascus, Symphalangus, Hylobates, and Hoolock each possessing 52, 50, 44, and 38 diploid chromosomes, respectively. While many genetic studies have been performed, including a number based on karyotypes (Müller et al. 2003), mitochondrial DNA (mtDNA) (Hayashi et al. 1995;Takacs et al. 2005;Monda et al. 2007;Whittaker et al. 2007;Matsudaira and Ishida 2010;Van Ngoc et al. 2010), Y chromosomes (Chan et al. 2012), Arthrobacter luteus (ALU) repeats (Meyer et al. 2012), and short stretches of autosomal seq...

show abstract

“…A final approach is to design target probes based on a divergent reference genome (Cosart et al 2011; George et al 2011; Saintenac et al 2011; Jin et al 2012; Nadeau et al 2012; Good et al 2013; Hancock-Hanser et al 2013; Hedtke et al 2013; Li et al 2013; Ilves & Lopez-Fernandez 2014) or a multisequence alignment (e.g., ultraconserved element capture; Faircloth et al 2012; Lemmon et al 2012; McCormack et al 2012; Faircloth et al 2013; McCormack et al 2013a; Crawford et al 2015; Leaché et al 2015). The principle behind this strategy is straightforward: orthologous regions of the genome between divergent species can be captured if their sequences are sufficiently conserved.…”

Section: Targeted Capture Without a Reference Genomementioning

confidence: 99%

“…Several studies have examined the ability of probes designed from a single reference genome to capture DNA from a range of species (Vallender 2011; Jin et al 2012; Lemmon et al 2012; Good et al 2013; Hancock-Hanser et al 2013; Hedtke et al 2013). For instance, commercially available human exome kits perform equivalently in humans and chimpanzees (~90–91% capture sensitivity) yet decline in sensitivity and depth of coverage when applied to species with >5% sequence divergence, such as macaques (Vallender 2011; Jin et al 2012).…”

Section: Targeted Capture Without a Reference Genomementioning

confidence: 99%

“…For instance, commercially available human exome kits perform equivalently in humans and chimpanzees (~90–91% capture sensitivity) yet decline in sensitivity and depth of coverage when applied to species with >5% sequence divergence, such as macaques (Vallender 2011; Jin et al 2012). A capture based on de novo transcriptomes from the alpine chipmunk ( Tamias alpinus ) was used to capture T. alpinus and three other species of chipmunks ranging up to 1.5% sequence divergence (Bi et al 2012; 2013; Good et al 2015).…”

Section: Targeted Capture Without a Reference Genomementioning

confidence: 99%

See 1 more Smart Citation

Targeted capture in evolutionary and ecological genomics

2015

View full text Add to dashboard Cite

The rapid expansion of next-generation sequencing has yielded a powerful array of tools to address fundamental biological questions at a scale that was inconceivable just a few years ago. Various genome partitioning strategies to sequence select subsets of the genome have emerged as powerful alternatives to whole genome sequencing in ecological and evolutionary genomic studies. High throughput targeted capture is one such strategy that involves the parallel enrichment of pre-selected genomic regions of interest. The growing use of targeted capture demonstrates its potential power to address a range of research questions, yet these approaches have yet to expand broadly across labs focused on evolutionary and ecological genomics. In part, the use of targeted capture has been hindered by the logistics of capture design and implementation in species without established reference genomes. Here we aim to 1) increase the accessibility of targeted capture to researchers working in non-model taxa by discussing capture methods that circumvent the need of a reference genome, 2) highlight the evolutionary and ecological applications where this approach is emerging as a powerful sequencing strategy, and 3) discuss the future of targeted capture and other genome partitioning approaches in light of the increasing accessibility of whole genome sequencing. Given the practical advantages and increasing feasibility of high-throughput targeted capture, we anticipate an ongoing expansion of capture-based approaches in evolutionary and ecological research, synergistic with an expansion of whole genome sequencing.

show abstract

An Effort to Use Human-Based Exome Capture Methods to Analyze Chimpanzee and Macaque Exomes

Cited by 29 publications

References 30 publications

Identification of Single Nucleotide Polymorphism from Indian <i>Bubalus bubalis</i> through Targeted Sequence Capture

Identification of Single Nucleotide Polymorphism from Indian <i>Bubalus bubalis</i> through Targeted Sequence Capture

Examining Phylogenetic Relationships Among Gibbon Genera Using Whole Genome Sequence Data Using an Approximate Bayesian Computation Approach

Targeted capture in evolutionary and ecological genomics

Contact Info

Product

Resources

About