Chromosome-level genome assembly of the glass catfish (Kryptopterus vitreolus) reveals molecular clues to its transparent phenotype

The 12 representative catfish species diverged from zebrafish approximately 173.5 million years ago, later than the divergence time reported in the blue catfish genome study.

“Based on the maximum-likelihood phylogenetic tree, the 12 representative catfish species diverged from zebrafish approximately 173.5 million years ago (Ma), which is later than the divergence time reported in the blue catfish genome study (Wang et al., 2022).”

• cites Wang et al., 2022 sourceSupported

Both Siluriformes and Cypriniformes may share similar chromosomal rearrangements.

“Some of these rearrangements were similar to those observed in zebrafish (Bian et al., 2016), implying that both Siluriformes and Cypriniformes may share similar chromosomal rearrangements.”

• cites Bian et al., 2016 sourceSupported

The edn3b gene is lost in the glass catfish genome, as identified by synteny comparison with over 30 other fish species.

“a synteny comparison with over 30 other fish species identified the loss of the endothelin-3 (edn3b) gene in the glass catfish genome.”

BUSCO analysis showed 90.3% completeness of the glass catfish genome assembly.

“The BUSCO results showed 90.3% completeness (Supplementary Table S5), demonstrating that the glass catfish genome assembly covered most genetic regions with relatively high completeness.”

The 12 representative catfish species were divided into two main clades.

“These species were divided into two main clades (Figure 2).”

The scaffold N50 of the chromosome-level genome assembly was 22.5 Mb.

“The scaffold N50 value of this chromosome-level genome assembly was 22.5 Mb (Figure 1C).”

Integrated repeat sequences covered approximately 35.2% of the de novo genome assembly, totaling 223.4 Mb.

“For further annotations, the integrated repeat sequences were predicted to cover approximately 35.2% of the de novo genome assembly, totaling 223.4 Mb (Supplementary Table S7).”

The top enriched KEGG pathways in both expanded and contracted gene families were 'Transport and catabolism' and 'Cell growth and death'.

“The top enriched KEGG pathways in both the expanded and contracted gene families were “Transport and catabolism” and “Cell growth and death” (Supplementary Figure S3).”

A chromosome-level haplotypic genome assembly for Kryptopterus vitreolus was constructed, comprising 32 chromosomes and 23,344 protein-coding genes.

“we constructed a chromosome-level haplotypic genome assembly for the glass catfish, encompassing 32 chromosomes and 23344 protein-coding genes, using PacBio and Hi-C sequencing technologies and standard assembly and annotation pipelines.”

The top enriched GO terms in both expanded and contracted gene families included 'cellular process', 'biological regulation', and 'cell'.

“The top enriched GO terms in both expanded and contracted gene families included “cellular process”, “biological regulation”, and “cell” (Supplementary Figure S2).”

edn3b−/− mutant zebrafish exhibited a remarkable reduction in black pigments in body surface stripes compared to wild-type zebrafish.

“we generated edn3b−/− mutant zebrafish, which exhibited a remarkable reduction in black pigments in body surface stripes compared to wild-type zebrafish.”

The glass catfish has a highly transparent body that exposes its internal organs and intermuscular bones.

“this species is distinguished by its highly transparent body, which exposes its internal organs and intermuscular bones (Figure 1A).”

The glass catfish genome was predicted to be 642.7 Mb in size based on 17-mer frequency distribution analysis.

“The glass catfish genome was predicted to be 642.7 Mb in size based on Illumina short reads (from the 500 bp library) and 17-mer frequency distribution analysis (Genome Size=k-mer_num/k-mer_depth; see Supplementary Table S3).”

Seven homolog-based annotation results (16,442-33,943 genes) and transcriptome annotation results (21,375 genes) were merged into a non-redundant set of 23,344 genes.

“For the prediction of gene structures, seven homolog-based annotation results (16 442–33 943 genes) and transcriptome annotation results (21 375 genes; Supplementary Table S8) were merged into a non-redundant set of 23 344 genes.”

277 expanded and 1,034 contracted gene families were identified in the glass catfish genome.

“Furthermore, 277 expanded and 1 034 contracted gene families were identified in the glass catfish genome (Figure 2).”

The tyrp1b gene in the glass catfish genome contains a premature stop codon, rendering it a nonfunctional pseudogene.

“Analysis revealed a premature stop codon in the putative albinism-related tyrp1b gene, encoding tyrosinase-related protein 1, rendering it a nonfunctional pseudogene.”

22,537 genes (96.5%) in the final gene set exhibited annotated functions with at least one hit from InterPro, KEGG, SwissProt, or TrEMBL.

“Within the final gene set of the glass catfish, 22 537 genes (96.5%, Supplementary Table S9) exhibited annotated functions with at least one hit from the searched databases, including InterPro, KEGG, SwissProt, and TrEMBL.”

A common fission and a similar translocation were also observed in the glass catfish, Chinese large-mouth catfish, and two Pangasiidae catfish species.

“Additionally, a common fission and a similar translocation were also observed in the glass catfish, Chinese large-mouth catfish, and two Pangasiidae catfish species (Figure 3G–J).”

The tyrp1b gene in the glass catfish contained a premature stop codon in its first exon.

“However, the tyrp1b gene (encoding tyrosinase-related protein 1b) in the glass catfish contained a premature stop codon in its first exon (Figure 4), likely resulting in the gene becoming a nonfunctional pseudogene.”

• Also stated in: § DISCUSSION · plain

  “However, the critical tyrp1b gene in the glass catfish harbors a nonsense mutation in its first exon (Figure 4B), resulting in a loss-of-function pseudogene.”

Genomic synteny comparisons demonstrated the loss of edn3b in glass catfish.

“Genomic synteny comparisons demonstrated the loss of edn3b in glass catfish (top in Figure 5).”

• Also stated in: § DISCUSSION · plain

  “Additionally, genomic comparisons with over 30 other fish species confirmed the loss of the edn3b gene in the glass catfish.”

Chromosome numbers of the 10 representative catfish species with chromosome-level genomes ranged from 26 to 32.

“Chromosome numbers of the 10 representative catfish species with chromosome-level genomes ranged from 26 to 32 (see Supplementary Table S12).”

The edn3b−/− mutant exhibited a remarkable reduction of melanin and silver pigment in its stripes compared to wild-type zebrafish.

“The edn3b−/− mutant exhibited a remarkable reduction of melanin and silver pigment in its stripes (Figure 6A) compared to wild-type zebrafish (Figure 6B).”

• Also stated in: § DISCUSSION · plain

  “The generated edn3b knockout zebrafish mutant exhibited a marked reduction in black pigment in skin stripes, further supporting the role of edn3b in pigmentation.”

The stripe patterns in the edn3b−/− mutants were notably different, breaking into circular spots or disappearing entirely.

“The stripe patterns in the mutants were notably different, breaking into circular spots or disappearing entirely (Figure 6A).”

• Also stated in: § DISCUSSION · plain

  “Our edn3b−/− knockout mutant exhibited melanophore deficiencies, presenting with a spotted pattern rather than the wild-type stripes (Figure 6A).”

Some lineage-specific small-scale translocations were identified in the catfish ancestor.

“Additionally, some lineage-specific small-scale translocations were identified in the catfish ancestor.”

Two Bagridae catfish species (yellow and North African catfish) with fewer chromosomes (26 and 28, respectively) were observed to have undergone one or three fusions.

“Two Bagridae catfish species (yellow and North African catfish) with fewer chromosomes (26 and 28, respectively) were observed to have undergone one or three fusions (Figure 3C, E).”

Detailed comparisons of the melanin synthesis pathway revealed that the overall gene copy numbers in the glass catfish were similar to those in zebrafish and medaka.

“Detailed comparisons of the melanin synthesis pathway revealed that the overall gene copy numbers in the glass catfish were similar to those in zebrafish and medaka (Supplementary Tables S14, 15).”

The glass catfish genome contains the majority of known black pigment-related genes.

“Interestingly, genomic comparisons and gene identification revealed that the glass catfish genome contains the majority of known black pigment-related genes.”

Over 10,000 best-hit gene pairs were identified between each catfish and the teleost ancestor protein set.

“Over 10 000 best-hit gene pairs were identified between each catfish and the teleost ancestor protein set (Supplementary Table S11).”

tyrp1a exhibits significantly lower transcription levels in transparent muscle compared to colored muscle.

“In addition, tyrp1a exhibits significantly lower transcription levels in transparent muscle compared to colored muscle.”

The glass catfish genome contained most of the iridophore development-related genes, similar to zebrafish and medaka, except for edn3b.

“Interestingly, the glass catfish genome contained most of these important genes, similar to zebrafish and medaka, except for edn3b.”

Compared to other closely related species, the glass catfish has undergone specific chromosomal rearrangements, including three fissions, one fusion, and five translocations.

“Notably, compared to other closely related species, the glass catfish has undergone specific chromosomal rearrangements, including three fissions, one fusion, and five translocations (Figure 3G).”

The glass catfish contained the highest haplotypic chromosome number (32) among the representative catfish species.

“The glass catfish contained the highest haplotypic chromosome number (32) among the representative catfish species.”

Loss of edn3b contributes to the transparent phenotype of the glass catfish.

“These findings indicate that edn3b loss contributes to the transparent phenotype of the glass catfish.”

• AssumptionRests on an assumption: The role of edn3b in pigmentation is conserved between zebrafish and glass catfish.

Compared to other catfish species, molecular cellular process genes have undergone significant changes in the glass catfish during evolution.

“Compared to other catfish species, molecular cellular process genes have undergone significant changes in the glass catfish during evolution.”

The glass catfish retains minimal pigmentation, with small amounts of black, silver, and yellow pigments concentrated in a narrow zone along the dorsal midline and head.

“The fish retains minimal pigmentation, with small amounts of black, silver, and yellow pigments concentrated in a narrow zone along the dorsal midline and head.”

• cites Ng & Kottelat, 2013 sourceNot checked — no full text of the source

The tyrp1b gene, expressed in melanophores, plays a crucial role in melanocyte maintenance and proliferation.

“The tyrp1b gene, expressed in melanophores, plays a crucial role in melanocyte maintenance and proliferation (Braasch et al., 2009; Krauss et al., 2014b).”

• cites Braasch et al., 2009 sourceNot checked — no full text of the source
• cites Krauss et al., 2014bNot matched

  Couldn’t be matched to a paper in Crossref, so it can’t be checked.

Species from the orders Siluriformes and Pangasiidae appear to have originated with an ancestral haplotypic chromosome number of 29.

“Species from the orders Siluriformes and Pangasiidae appear to have originated with an ancestral haplotypic chromosome number of 29.”

The catfish ancestor may have experienced relatively complex inter-chromosome rearrangements after diverging from the teleost ancestor.

“These observations suggest that the catfish ancestor may have experienced relatively complex inter-chromosome rearrangements after diverging from the teleost ancestor.”

These large-scale chromosomal arrangements contribute to the high diversity in chromosome karyotypes observed among various catfish species.

“These large-scale chromosomal arrangements contribute to the high diversity in chromosome karyotypes observed among various catfish species.”

Loss of edn3b likely contributes to the transparent phenotype observed in glass catfish.

“Thus, loss of edn3b likely contributes to the transparent phenotype observed in glass catfish.”

• AssumptionRests on an assumption: The function of edn3b in iridophore development and pigmentation is conserved between zebrafish and glass catfish.

The edn3b gene, identified as a ligand for the endothelin receptor signaling in larval iridophores, significantly reduces iridophore number when knocked down in zebrafish.

“The edn3b gene, identified as a ligand for the endothelin receptor signaling in larval iridophores, significantly reduces iridophore number when knocked down in zebrafish (Krauss et al., 2014a).”

• cites Krauss et al., 2014aNot matched

  Couldn’t be matched to a paper in Crossref, so it can’t be checked.

These species then underwent extensive chromosomal rearrangements during evolution.

“These species then underwent extensive chromosomal rearrangements during evolution.”

The premature stop codon in tyrp1b likely results in the gene becoming a nonfunctional pseudogene.

“likely resulting in the gene becoming a nonfunctional pseudogene.”

• Also stated in: § DISCUSSION · plain

  “resulting in a loss-of-function pseudogene.”

The edn3b gene plays a role in altering cellular coloration and stripe formation.

“These findings confirmed that the edn3b gene plays a role in altering cellular coloration and stripe formation.”

The loss-of-function mutation in tyrp1b may be a significant factor contributing to the melanin loss phenotype in glass catfish.

“Therefore, the loss-of-function mutation in tyrp1b may be a significant factor contributing to the melanin loss phenotype in glass catfish.”