Chromosome-level genome assembly and annotation of the crested gecko, Correlophus ciliatus, a lizard incapable of tail regeneration
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Editors Assessment:
The crested gecko (Correlophus ciliatus), is a lizard species endemic to New Caledonia, and a potentially interesting model organism due to its unusual (for a gecko) inability to regenerate amputated tails. With that in mind here is presented a new reference genome for the species, assembled using PacBio Sequel II platform and Dovetail Omni-C libraries. Producing a genome with a total size of 1.65 Gb, 152 scaffolds, a L50 of 6, and N50 of 109 Mb. Peer review making sure more detail was added on data acquisition and processing to enhance reproducibility. In the end producing potentially useful data for studying the genetic mechanisms involved in loss of tail regeneration.
This evaluation refers to version 1 of the preprint
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Abstract
The vast majority of gecko species are capable of tail regeneration, but singular geckos of Correlophus, Uroplatus, and Nephrurus genera are unable to regrow lost tails. Of these non-regenerative geckos, the crested gecko (Correlophus ciliatus) is distinguished by ready availability, ease of care, high productivity, and hybridization potential. These features make C. ciliatus particularly suited as a model for studying the genetic, molecular, and cellular mechanisms underlying loss of tail regeneration capabilities. We report a contiguous genome of C. ciliatus with a total size of 1.65 Gb, 152 scaffolds, L50 of 6, and N50 of 109 Mb. Repetitive content consists of 40.41% of the genome, and a total of 30,780 genes were annotated. Our assembly of the crested gecko genome provides a valuable resource for future comparative genomic studies between non-regenerative and regenerative geckos and other squamate reptiles. Findings We report genome sequencing, assembly, and annotation for the crested gecko, Correlophus ciliatus.
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Editors Assessment:
The crested gecko (Correlophus ciliatus), is a lizard species endemic to New Caledonia, and a potentially interesting model organism due to its unusual (for a gecko) inability to regenerate amputated tails. With that in mind here is presented a new reference genome for the species, assembled using PacBio Sequel II platform and Dovetail Omni-C libraries. Producing a genome with a total size of 1.65 Gb, 152 scaffolds, a L50 of 6, and N50 of 109 Mb. Peer review making sure more detail was added on data acquisition and processing to enhance reproducibility. In the end producing potentially useful data for studying the genetic mechanisms involved in loss of tail regeneration.
This evaluation refers to version 1 of the preprint
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AbstractThe vast majority of gecko species are capable of tail regeneration, but singular geckos of Correlophus, Uroplatus, and Nephrurus genera are unable to regrow lost tails. Of these non-regenerative geckos, the crested gecko (Correlophus ciliatus) is distinguished by ready availability, ease of care, high productivity, and hybridization potential. These features make C. ciliatus particularly suited as a model for studying the genetic, molecular, and cellular mechanisms underlying loss of tail regeneration capabilities. We report a contiguous genome of C. ciliatus with a total size of 1.65 Gb, a total of 152 scaffolds, L50 of 6, and N50 of 109 Mb. Repetitive content consists of 40.41% of the genome, and a total of 30,780 genes were annotated. Assembly of the crested gecko genome provides a valuable resource for future comparative …
AbstractThe vast majority of gecko species are capable of tail regeneration, but singular geckos of Correlophus, Uroplatus, and Nephrurus genera are unable to regrow lost tails. Of these non-regenerative geckos, the crested gecko (Correlophus ciliatus) is distinguished by ready availability, ease of care, high productivity, and hybridization potential. These features make C. ciliatus particularly suited as a model for studying the genetic, molecular, and cellular mechanisms underlying loss of tail regeneration capabilities. We report a contiguous genome of C. ciliatus with a total size of 1.65 Gb, a total of 152 scaffolds, L50 of 6, and N50 of 109 Mb. Repetitive content consists of 40.41% of the genome, and a total of 30,780 genes were annotated. Assembly of the crested gecko genome provides a valuable resource for future comparative genomic studies between non-regenerative and regenerative geckos and other squamate reptiles.Findings We report genome sequencing, assembly, and annotation for the crested gecko, Correlophus ciliatus.
This work has been published in GigaByte Journal under a CC-BY 4.0 license (https://doi.org/10.46471/gigabyte.140). These reviews are as follows.
Reviewer 1. Anthony Geneva and Cleo Falvey
In their revised manuscript Gumangan and colleagues have addressed each of the comments we made on the original manuscript via substantial revisions. We appreciate the improvements the authors have made but feel there are a few remaining issues that require attention, detailed below. Those issues notwithstanding, this new assembly and annotation represent a very nice contribution to the field and will certainly be widely used.
Specific comments: Pages 2 and 6: Each time L50 or L90 statistics are reported they are listed with the units “bp”. These values are counts of scaffolds are are typically simply reported as integers without units. Page 3. “Furthermore, C. ciliatus is the only non-regenerative lizard species capable of hybridizing with regenerative relatives, specifically C. sarasinorum, Mniarogekko chahoua, and Rhacodactylus auriculatus.” This statement is very interesting but requires a reference or at least attribution of some kind (eg - personal observation by one of the co-authors). Page 3: “Genomic DNA was sequenced using the Illumina Novaseq 6000 platform. 185.8 gigabase-pairs of PacBio CCS reads were used as inputs to Hifiasm v0.15.4-r347 [8] with default parameters.” The sequencer listed here for generating long reads seems to be an error and should be some PacBio platform (Sequel, Sequel IIe, etc). Page 6: “The contig/scaffold N50 is 109 Mb, and the largest scaffold had a length 1169 Mbp (Table 1)”. 1169 should be 169.
Reviewer 2. Zexian Zhu
Review comments are in the following link: https://gigabyte-review.rivervalleytechnologies.comdownload-api-file?ZmlsZV9wYXRoPXVwbG9hZHMvZ3gvRFIvNTU3L3Jldmlldy5kb2N4
Reviewer 3. Chaochao Yan
Are all data available and do they match the descriptions in the paper? No. In the section "Availability of supporting data," it is stated that "supporting datasets, including annotation, are available at GigaDB." However, I was unable to locate these datasets during my search. Could you please provide a direct link or the accession number to access these resources?
Is the data acquisition clear, complete and methodologically sound? No. The manuscript currently lacks detailed information regarding the samples and data used to assemble and annotate the reference genome. For instance, it does not specify how many samples or libraries were used for RNA-Seq or whole-genome sequencing. I suggest including a table that provides comprehensive information on the samples and sequencing data. Additionally, while the manuscript mentions that "Genomic DNA was sequenced using the Illumina Novaseq 6000 platform," the corresponding Illumina data are not described. I am unclear about how the PacBio CCS reads were produced. Could you please provide more details or clarify the methodology used to generate these reads?
Is there sufficient detail in the methods and data-processing steps to allow reproduction? No. Some methods described in the manuscript lack sufficient detail, particularly for tools such as BLAST, BlobTools, HiRise, and BWA. To ensure reproducibility, I recommend providing the specific parameters used for these analyses.
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