Near-chromosomal de novo assembly of Bengal tiger genome reveals genetic hallmarks of apex predation
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Abstract
The tiger, a poster child for conservation, remains an endangered apex predator. Continued survival and recovery will require a comprehensive understanding of genetic diversity and the use of such information for population management. A high-quality tiger genome assembly will be an important tool for conservation genetics, especially for the Indian tiger, the most abundant subspecies in the wild. Here, we present high-quality near-chromosomal genome assemblies of a female and a male wild Indian tiger (Panthera tigris tigris). Our assemblies had a scaffold N50 of >140 Mb, with 19 scaffolds corresponding to the 19 numbered chromosomes, containing 95% of the genome. Our assemblies also enabled detection of longer stretches of runs of homozygosity compared to previous assemblies, which will help improve estimates of genomic inbreeding. Comprehensive genome annotation identified 26,068 protein-coding genes, including several gene families involved in key morphological features such as the teeth, claws, vision, olfaction, taste, and body stripes. We also identified 301 microRNAs, 365 small nucleolar RNAs, 632 transfer RNAs, and other noncoding RNA elements, several of which are predicted to regulate key biological pathways that likely contribute to the tiger's apex predatory traits. We identify signatures of positive selection in the tiger genome that are consistent with the Panthera lineage. Our high-quality genome will enable use of noninvasive samples for comprehensive assessment of genetic diversity, thus supporting effective conservation and management of wild tiger populations.
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The tiger
This work has been peer reviewed in GigaScience (see https://doi.org/10.1093/gigascience/giac112), which carries out open, named peer-review. These reviews are published under a CC-BY 4.0 license and were as follows:
Reviewer 1: Jong Hwa Bhak
This manuscript is about assemblies of Bengal tigers. It is a great improvement over past two tiger genome assemblies. The assemblies quality is unprecedented (exceeding perhaps any feline genome in terms of contiguity).
This represented a ~50x improvement in genome contiguity (see materials and methods). PanTigT.MC.v2
What was the most important factor in this big jump of improvement in length?
the overall contiguity was better than the domestic cat reference genome
The quality comparison section is informative.
We identified the "repetitive elements" in the genome by combining both
The tiger
This work has been peer reviewed in GigaScience (see https://doi.org/10.1093/gigascience/giac112), which carries out open, named peer-review. These reviews are published under a CC-BY 4.0 license and were as follows:
Reviewer 1: Jong Hwa Bhak
This manuscript is about assemblies of Bengal tigers. It is a great improvement over past two tiger genome assemblies. The assemblies quality is unprecedented (exceeding perhaps any feline genome in terms of contiguity).
This represented a ~50x improvement in genome contiguity (see materials and methods). PanTigT.MC.v2
What was the most important factor in this big jump of improvement in length?
the overall contiguity was better than the domestic cat reference genome
The quality comparison section is informative.
We identified the "repetitive elements" in the genome by combining both
==> repeat elements is better.
How close are the two genomes (MC & SI)?
This reviewer finds it a great contribution to existing feline genome assemblies. The authors have done all the usual QC and constructed really high quality assemblies.
Reviewer 2: Gang Li
The submitted manuscript 'Near-chromosomal de novo assembly of Bengal tiger genome reveals genetic hallmarks of apex-predation' assemble the high-quality near-chromosomal leveled reference genomes of Bengal tiger, which will be of great significance for the conservation and rejuvenation of tigers, even other endangered felids. I have some comments on this manuscript:
- Considering this the assembled genome used the Hic technology to figure out the chromosome structure, the figure of Hic results need to be presented. While, the assemble of sex chromosome always attract attentions, especially Y chromosome of tiger. More detailed information need to be specified, such as the conserved Y chromosome genes compared to other mammals, or whether there are tiger-specific Y linked gene has been observed or not.
- In this work, authors used four zoo-bred individuals with known pedigree to test the inbreeding index of ROH and intend to evaluate the assembly quality. But I don't find any information about these four individuals and I guess they should be Bengal tigers. If it is the case, the question is that the quantity of ROH will not be only decided by the reference quality, but also the divergence between the target resequencing date and the used reference genome. That is to say, if the resequencing data and the reference genome are all from the same tiger sub-species, Bengal tiger, the quantity of ROH supposed to be more than that of the different sub-species comparison, which may not be an appropriate method used to evaluate the assembly quality.
- I have some advice about the evolutionary divergence calibrations. Using some other species which have closer phylogenetic relationship might be better, according to their shared similar substitution rate and generation time, for instance, other species of Panthera .
- The format of references part need to be rechecked.
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