Limitations of the rhesus macaque draft genome assembly and annotation

Zhang, Xiongfei; Goodsell, Joel; Norgren, Robert B.

doi:10.1186/1471-2164-13-206

Cited by 58 publications

(76 citation statements)

References 16 publications

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“…Breakpoints generated by rearrangements of these smaller SFs are either the footprint of bona fide structural rearrangements, or they may be artifacts produced by misassembled sequences. For example, previous studies revealed problems in the rheMac2 assembly version of the rhesus genome (31)(32)(33), which is one of the species showing a large discrepancy of the number and the rate of breakpoints at the two resolutions. Even though we used a more recent version of the rhesus genome (rheMac3), it is not clear whether all of the assembly problems in the previous version were completely fixed.…”

Section: Discussionmentioning

confidence: 99%

Reconstruction and evolutionary history of eutherian chromosomes

Kim

Farré

Auvil

et al. 2017

Proc. Natl. Acad. Sci. U.S.A.

126

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Whole-genome assemblies of 19 placental mammals and two outgroup species were used to reconstruct the order and orientation of syntenic fragments in chromosomes of the eutherian ancestor and six other descendant ancestors leading to human. For ancestral chromosome reconstructions, we developed an algorithm (DESCHRAMBLER) that probabilistically determines the adjacencies of syntenic fragments using chromosome-scale and fragmented genome assemblies. The reconstructed chromosomes of the eutherian, boreoeutherian, and euarchontoglires ancestor each included >80% of the entire length of the human genome, whereas reconstructed chromosomes of the most recent common ancestor of simians, catarrhini, great apes, and humans and chimpanzees included >90% of human genome sequence. These high-coverage reconstructions permitted reliable identification of chromosomal rearrangements over ∼105 My of eutherian evolution. Orangutan was found to have eight chromosomes that were completely conserved in homologous sequence order and orientation with the eutherian ancestor, the largest number for any species. Ruminant artiodactyls had the highest frequency of intrachromosomal rearrangements, and interchromosomal rearrangements dominated in murid rodents. A total of 162 chromosomal breakpoints in evolution of the eutherian ancestral genome to the human genome were identified; however, the rate of rearrangements was significantly lower (0.80/My) during the first ∼60 My of eutherian evolution, then increased to greater than 2.0/My along the five primate lineages studied. Our results significantly expand knowledge of eutherian genome evolution and will facilitate greater understanding of the role of chromosome rearrangements in adaptation, speciation, and the etiology of inherited and spontaneously occurring diseases. chromosome evolution | ancestral genome reconstruction | genome rearrangements C hromosome rearrangements are a hallmark of genome evolution and essential for understanding the mechanisms of speciation and adaptation (1). Determining chromosome rearrangements over evolutionary time scales has been a difficult problem, primarily because of the lack of high-quality, chromosome-scale genome assemblies that are necessary for reliable reconstruction of ancestral genomes. For closely related species with good map-anchored assemblies, such as human, chimpanzee, and rhesus, it is possible to infer most inversions, translocations, fusions, and fissions that occurred during evolution by simple observational comparisons (2). However, for sequence-based genome-wide comparisons that require resolving large numbers of rearrangements of varying scale, determining ancestral chromosomal states is challenging both methodologically and computationally because of the complexity of genomic events that have led to extant genome organizations, including duplications, deletions, and reuse of evolutionary breakpoint regions (EBRs) flanking regions of homologous synteny (3, 4).A variety of methods have been used for resolving the evolutionary historie...

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Section: Discussionmentioning

confidence: 99%

Reconstruction and evolutionary history of eutherian chromosomes

Kim

Farré

Auvil

et al. 2017

Proc. Natl. Acad. Sci. U.S.A.

126

View full text Add to dashboard Cite

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“…One can compare gene lists from different assemblies, but gaps and other issues in assemblies create ambiguity 21, 22 . Available evidence suggests that humans and chimpanzees experienced more rapid changes in gene copy number than did orangutans or rhesus macaques 13 .…”

Section: Genomic Differences Among Primatesmentioning

confidence: 99%

“…The initial draft assemblies for nonhuman primates all provide much useful information, but are not complete or reliable enough to support all current scientific goals 21, 22 . One limitation of draft genomes is the presence of gaps in chromosomal sequences, resulting in missing exons or genes.…”

Section: Future Directionsmentioning

confidence: 99%

Comparative primate genomics: emerging patterns of genome content and dynamics

2014

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Preface Advances in genome sequencing technologies have created new opportunities for comparative primate genomics. Genome assemblies have been published for several primates, with analyses of several others underway. Whole genome assemblies for the great apes provide remarkable new information about the evolutionary origins of the human genome and the processes involved. Genomic data for macaques and other nonhuman primates provide valuable insight into genetic similarities and differences among species used as models for disease-related research. This review summarizes current knowledge regarding primate genome content and dynamics and offers a series of goals for the near future.

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“…Interestingly, we observed 72-78% aligned reads for NHP #2 independent of region or sequencing depth. Overall 72-84% aligned read results are less than anticipated as compared to alignment with well annotated human, mouse or rat reference genome builds and is suggested to be a result of missing gene models annotated in the draft MMUL 1.0 reference genome build (Zhang et al, 2012). However, despite non-optimal alignment efficiency using the draft Rhesus macaque genome build, the sample data yielded accurately detectable transcript abundance counts from 7845 to 9937 transcripts for brain regions of NHP #1 and from 6331 to 8826 transcripts for brain regions of NHP #2.…”

Section: 7mentioning

confidence: 83%

A novel analytical brain block tool to enable functional annotation of discriminatory transcript biomarkers among discrete regions of the fronto-limbic circuit in primate brain

et al. 2015

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Fronto-limbic circuits in the primate brain are responsible for executive function, learning and memory, and emotions, including fear. Consequently, changes in gene expression in cortical and subcortical brain regions housing these circuits are associated with many important psychiatric and neurological disorders. While high quality gene expression profiles can be identified in brains from model organisms, primate brains have unique features such as Brodmann Area 25, which is absent in rodents, yet profoundly important in primates, including humans. The potential insights to be gained from studying the human brain are complicated by the fact that the post-mortem interval (PMI) is variable, and most repositories keep solid tissue in the deep frozen state. Consequently, sampling the important medial and internal regions of these brains is difficult. Here we describe a novel method for obtaining discrete regions from the fronto-limbic circuits of a 4 year old and a 5 year old, male, intact, frozen non-human primate (NHP) brain, for which the PMI is exactly known. The method also preserves high quality RNA, from which we use transcriptional profiling and a new algorithm to identify region-exclusive RNA signatures for Area 25 (NFκB and dopamine receptor signaling), the anterior cingulate cortex (LXR/RXR signaling), the amygdala (semaphorin signaling), and the hippocampus (Ca(++) and retinoic acid signaling). The RNA signatures not only reflect function of the different regions, but also include highly expressed RNAs for which function is either poorly understood, or which generate proteins presently lacking annotated functions. We suggest that this new approach will provide a useful strategy for identifying changes in fronto-limbic system biology underlying normal development, aging and disease in the human brain.

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Limitations of the rhesus macaque draft genome assembly and annotation

Cited by 58 publications

References 16 publications

Reconstruction and evolutionary history of eutherian chromosomes

Reconstruction and evolutionary history of eutherian chromosomes

Comparative primate genomics: emerging patterns of genome content and dynamics

A novel analytical brain block tool to enable functional annotation of discriminatory transcript biomarkers among discrete regions of the fronto-limbic circuit in primate brain

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