Chromosome-level genome assemblies of five Sinocyclocheilus species
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**Editors Assessment: ** Sinocyclocheilus are a genus of freshwater cavefish fish that are endemic to the Karst regions of Southwest China. Having diverse traits in morphology, behavior, and physiology typical of cavefish, that make them interesting models for studying cave adaptation and phylogenetic evolution. The manuscript assembled chromosomal-level genomes of five Sinocyclocheilus species, and conducted allotetraploid origin analysis on these species. Assembling S. grahami (the golden-line barbel), using PacBio and Hi-C sequencing technologies, a final chromosome-level genome assembly was 1.6 Gb in size with a contig N50 of 738.5 kb and a scaffold N50 of 30.7 Mb. With 93.1% of the assembled genome sequences and 93.8% of the predicted genes anchored onto 48 chromosomes. Subsequently the authors conducted a homologous comparison to obtain chromosome-level genome assemblies for four other Sinocyclocheilus species: S. maitianheensis, S. rhinocerous, S. anshuiensis, and S. Anophthalmus. With over 82% of the genome sequences anchored on these constructed chromosomes. Peer review provided clarification on the assembly strategy and provided more benchmarking. This data having the potential to contribute to species conservation and the exploitation of potential economic and ecological values of diverse Sinocyclocheilus members.
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Abstract
Sinocyclocheilus, a genus of tetraploid fishes endemic to Southwest China’s karst regions, are classified as second-class nationally protected species due to their fragile habitat. Limited high-quality genomic resources have hampered studies on their phylogenetic relationships and the origin of their polyploidy. Here, we present a high-quality genome assembly of the most abundant Sinocyclocheilus species, the golden-line barbel (Sinocyclocheilus grahami), by integrating PacBio long-read and Hi-C sequencing. The resulting scaffold-level genome-assembly is 1.6 Gb long, with a scaffold N50 of up to 30.7 Mb. We annotated 42,806 protein-coding genes. Also, 93.1% of the assembled genome sequences (about 1.5 Gb) and 93.8% of the total predicted genes were successfully anchored onto 48 chromosomes. Furthermore, we obtained chromosome-level genome assemblies for four other Sinocyclocheilus species (S. anophthalmus, S. maitianheensis, S. anshuiensis, and S. rhinocerous) based on homologous comparisons. These genomic resources will enable in-depth investigations on cave adaptation, improvement of economic values, and conservation of diverse Sinocyclocheilus fishes.
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**Editors Assessment: ** Sinocyclocheilus are a genus of freshwater cavefish fish that are endemic to the Karst regions of Southwest China. Having diverse traits in morphology, behavior, and physiology typical of cavefish, that make them interesting models for studying cave adaptation and phylogenetic evolution. The manuscript assembled chromosomal-level genomes of five Sinocyclocheilus species, and conducted allotetraploid origin analysis on these species. Assembling S. grahami (the golden-line barbel), using PacBio and Hi-C sequencing technologies, a final chromosome-level genome assembly was 1.6 Gb in size with a contig N50 of 738.5 kb and a scaffold N50 of 30.7 Mb. With 93.1% of the assembled genome sequences and 93.8% of the predicted genes anchored onto 48 chromosomes. Subsequently the authors conducted a homologous comparison to …
**Editors Assessment: ** Sinocyclocheilus are a genus of freshwater cavefish fish that are endemic to the Karst regions of Southwest China. Having diverse traits in morphology, behavior, and physiology typical of cavefish, that make them interesting models for studying cave adaptation and phylogenetic evolution. The manuscript assembled chromosomal-level genomes of five Sinocyclocheilus species, and conducted allotetraploid origin analysis on these species. Assembling S. grahami (the golden-line barbel), using PacBio and Hi-C sequencing technologies, a final chromosome-level genome assembly was 1.6 Gb in size with a contig N50 of 738.5 kb and a scaffold N50 of 30.7 Mb. With 93.1% of the assembled genome sequences and 93.8% of the predicted genes anchored onto 48 chromosomes. Subsequently the authors conducted a homologous comparison to obtain chromosome-level genome assemblies for four other Sinocyclocheilus species: S. maitianheensis, S. rhinocerous, S. anshuiensis, and S. Anophthalmus. With over 82% of the genome sequences anchored on these constructed chromosomes. Peer review provided clarification on the assembly strategy and provided more benchmarking. This data having the potential to contribute to species conservation and the exploitation of potential economic and ecological values of diverse Sinocyclocheilus members.
This evaluation refers to version 1 of the preprint
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ABSTRACTSinocyclocheilus, a genus of tetraploid fishes, is endemic to the karst regions of Southwest China. All species within this genus are classified as second-class national protected species due to their unique and fragile habitat. However, absence of high-quality genomic resources has hindered various research efforts to elucidate their phylogenetic relationships and the origin of polyploidy. To address these academic challenges, we at first constructed a high-quality genome assembly for the most abundant representative, golden-line barbel (Sinocyclocheilus grahami), by integration of PacBio long-read and Hi-C sequencing technologies. The final scaffold-level genome assembly of S. grahami is 1.6 Gb in length, with a scaffold N50 up to 30.7 Mb. A total of 42,205 protein-coding genes were annotated. Subsequently, 93.1% of the …
ABSTRACTSinocyclocheilus, a genus of tetraploid fishes, is endemic to the karst regions of Southwest China. All species within this genus are classified as second-class national protected species due to their unique and fragile habitat. However, absence of high-quality genomic resources has hindered various research efforts to elucidate their phylogenetic relationships and the origin of polyploidy. To address these academic challenges, we at first constructed a high-quality genome assembly for the most abundant representative, golden-line barbel (Sinocyclocheilus grahami), by integration of PacBio long-read and Hi-C sequencing technologies. The final scaffold-level genome assembly of S. grahami is 1.6 Gb in length, with a scaffold N50 up to 30.7 Mb. A total of 42,205 protein-coding genes were annotated. Subsequently, 93.1% of the assembled genome sequences (about 1.5 Gb) and 93.8% of the total predicted genes were successfully anchored onto 48 chromosomes. Furthermore, we obtained chromosome-level genome assemblies for four other Sinocyclocheilus species (including S. anophthalmus, S. maitianheensis, S. anshuiensis, and S. rhinocerous) based on homologous comparison. These genomic data we present in this study provide valuable genetic resources for in-depth investigation on cave adaptation and improvement of economic values and conservation of diverse Sinocyclocheilus fishes.
Reviewer 1. Jun Wang
The manuscript assembled chromosomal-level genomes of five Sinocyclocheilus species, and conducted allotetraploid origin analysis on these species. The manuscript was meaningful and provided valuable genome resources in Sinocyclocheilus genus, which will further help with the evolution and functional genomics of these species. The analysis was accurate, and the results were solid. My comments are as follows
- Please detail the method how you assembled four other species on homologous comparison? You just map the assembled scaffold to the reference genome?
- In the manuscript, the author only provide the sequencing info of S. grahami but not the other four species. What are the sequencing information of other four species, like how many reads have been sequenced with Illumina?
- There was no results description for figure 2 and why there are there only repeat annotation results for S. grahami and not the other four species?
Reviewer 2. Fei Li and Shili Li
This paper entitled “Chromosome-level genome assemblies of five Sinocyclocheilus species” reported a chromosome-level golden-line barbel genome by using combination of Pacbio and Hi-C data. Using this chromosome-level assembly as reference, the author also constructed other four psedo chromosome-level assemblies of S. anophthalmus, S. maitianheensis, S. anshuiensis, and S. rhinocerous. These data are really important resource for conservation of these endangered species. However, some important results have not shown:
- Protein BUSCO result has not been shown.
- Raw reads were not uploaded to NCBI.
- What’s the detailed number for functional annotation.
Some minor suggestions: Add “,” before “and conservation”. What’s the meaning of “R & D”? Line 58, “a good model” should be “good models”. Line 64, remove “at first”. Line 84, change “a” to “the”. Line 90, change ‘muscle’ to “muscle tissue”. Line 105, remove ‘which was’. Line 112, remove ‘this study’. Line 122, change “Repeat annotation, gene prediction, and function prediction” to “Annotation of repeat, gene and function”. Line 137, ‘with’ should be ‘by using’. Line 127, remove ‘(TEs)’. Line 134, What’s meaning of NCBI GenBank? Remove GenBank. Line 140, ‘was’ should be ‘were’. Line 178, ‘Species’ should be ‘species’.
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