Genome assembly and annotation at the chromosomal level of first Pleuronectidae: Verasper variegatus provides a basis for phylogenetic study of Pleuronectiformes

Zhao, Na; Guo, Hao; Lu, Jia; Guo, Biao; Zheng, Donghai; Liu, Shanshan; Zhang, Bo

doi:10.1016/j.ygeno.2021.01.024

Cited by 11 publications

(11 citation statements)

References 56 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The Chromonomer program anchored and oriented a total of 51 scaffolds to the consensus map (Table S7) and only one contig was split into two fragments assigned to LG6 and LG9 (Figure 2). This resulted in 99.02% of the 613 Mb placed into the 21 chromosomes of the Senegalese sole karyotype, improving upon the 90.0% reported by Guerrero-Cózar et al (2021) and similar to other flatfish species recently assembled following a similar methodology (Einfeldt et al, 2021; Zhao et al, 2021; Ferchaud et al, 2022) (Table S8). The new assembly showed a high one-to-one correspondence at the chromosome level with the previous version of Guerrero-Cózar et al (2021) (Fig.…”

Section: Resultssupporting

confidence: 74%

A chromosome-level genome assembly enables the identification of the follicle stimulating hormone receptor as the master sex determining gene in Solea senegalensis

Herrán

Hermida

Rubiolo

et al. 2022

Preprint

View full text Add to dashboard Cite

Sex determination (SD) mechanisms are exceptionally diverse and show high evolutionary rates in fish. Pleuronectiformes is an emblematic fish group characterized by its adaptation to demersal life and its compact genomes. Here, we present a chromosome-level genome assembly of Senegalese sole, a promising European aquaculture species. We combined long- and short-read sequencing and a highly dense genetic map to obtain a contiguous assembly of 613 Mb (N50 = 29.0 Mb, 99% of the assembly in the n = 21 chromosomes of its karyotype). The correspondence between this new assembly and the Senegalese sole chromosomes was established by fluorescence in situ hybridization with BAC probes. Orthology within Pleuronectiformes was assessed by using the chromosome-level genomes of six important commercial flatfishes covering a broad phylogenetic spectrum of the order. A total of 7936 single-gene orthologues, shared by the six species, were used to identify syntenies in Pleuronectiformes and to explore chromosome evolutionary patterns in the order. Whole genome resequencing of six males and six females enabled the identification of 41 fixed allelic variants in the follicle stimulating hormone receptor (fshr) gene, homozygous in females and heterozygous in males, consistent with an XX / XY chromosome system. The observed association between fshr SNPs and sex was confirmed at the species level in a broad sample, which allowed tuning up a molecular sexing tool. Fshr demonstrated differential gene expression between male and female gonads since 86 days post-fertilization, when the gonad was still an undifferentiated primordium, concomitant with the activation of other testis and ovary marker genes, such as amh and cyp19a1a genes, respectively. Interestingly, the Y-linked fshr allele, which included 24 non-synonymous variants, expressed to a higher level than the X-linked allele at all stages. We hypothesize a molecular mechanism hampering the action of the follicle stimulating hormone that would drive the undifferentiated gonad toward testis.

show abstract

Section: Resultssupporting

confidence: 74%

A chromosome-level genome assembly enables the identification of the follicle stimulating hormone receptor as the master sex determining gene in Solea senegalensis

Herrán

Hermida

Rubiolo

et al. 2022

Preprint

View full text Add to dashboard Cite

show abstract

“…This is slightly more than the 21,787 protein-coding genes discovered in Japanese flounder (Shao et al, 2017). The estimated genome size of black flounder is ~538 Mbp, similar to the genome size of other flatfish species: Japanese flounder (534 Mb) (Shao et al, 2017), Turbot (568 Mb) (Figueras et al, 2016), Spotted halibut (556 Mb) (Zhao et al, 2021), ~15% bigger than the tongue sole genome (477 Mb) (Chen et al, 2014), and ~11% smaller compared to the Senegalese sole genome (~612 Mb) (Manchado et al, 2016). It is recommended to use multiple complementary methods to assess the genome quality (Gurevich et al, 2013).…”

Section: Discussionmentioning

confidence: 84%

“…According to the Ensembl Genome Browser (https://www.ensembl.org), hundreds of fish species with whole genome sequences (WGS) are available to date, and the number of species whose genomes have been sequenced continuous increasing. Among Pleuronectiformes, for example, thirteen species have their genome sequenced: tongue sole ( Cynoglossus semilaevis ) (Chen et al, 2014), Turbot ( Scophthalmus maximus ) (Maroso et al, 2018), Senegalese sole ( Solea senegalensis ) (Guerrero-Cózar, et al, 2021), Japanese flounder ( Paralichthys olivaceus ) (Shao et al, 2017), Spotted halibut ( Verasper variegatus ) (Zhao et al, 2021), Hogchoker ( Trinectes maculatus) , Pelican flounder ( Chascanopsetta lugubris) , Oriental sole ( Brachirus orientalis) , Bloch’s tonguesole ( Paraplagusia blochii) , New Zealand turbot ( Colistium nudipinnis) , Ocellated flounder ( Pseudorhombus dupliocellatus) , Starry flounder ( Platichthys stellatus) , and Indian halibut Psettodes erumei ) (Lü et al, 2021). In addition, recent studies have compiled the genomes at the chromosome level of turbot (Martínez et al, 2021) and spotted halibut (Zhao et al, 2021).…”

Section: Introductionmentioning

confidence: 99%

“…Among Pleuronectiformes, for example, thirteen species have their genome sequenced: tongue sole ( Cynoglossus semilaevis ) (Chen et al, 2014), Turbot ( Scophthalmus maximus ) (Maroso et al, 2018), Senegalese sole ( Solea senegalensis ) (Guerrero-Cózar, et al, 2021), Japanese flounder ( Paralichthys olivaceus ) (Shao et al, 2017), Spotted halibut ( Verasper variegatus ) (Zhao et al, 2021), Hogchoker ( Trinectes maculatus) , Pelican flounder ( Chascanopsetta lugubris) , Oriental sole ( Brachirus orientalis) , Bloch’s tonguesole ( Paraplagusia blochii) , New Zealand turbot ( Colistium nudipinnis) , Ocellated flounder ( Pseudorhombus dupliocellatus) , Starry flounder ( Platichthys stellatus) , and Indian halibut Psettodes erumei ) (Lü et al, 2021). In addition, recent studies have compiled the genomes at the chromosome level of turbot (Martínez et al, 2021) and spotted halibut (Zhao et al, 2021). A recent study also analyzed the origin of the specialized body structure of flatfishes, the genomes of 11 flatfish species representing 9 of the 14 pleuronectiform families of this order were sequenced (Lü et al, 2021).…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

De novoassembly of the black flounder genome. Why do pleuronectiformes have such a small genome size?

Villarreal

Burguener

Sosa

et al. 2023

Preprint

View full text Add to dashboard Cite

Black flounder (Paralichthys orbignyanus) is an economically important marine fish with aquaculture potential in Argentina due to its market value. In this study, we sequenced the whole genome using an Illumina sequencing technology. We started with two independent libraries (from one female and one pool of females; each with 150 bp paired-end reads, a mean insert length of 350 bp, and >35 X-fold coverage). Each library was assembled separately using SOAPdenovo2 and the resulting contigs were scaffolded with SSPACE3 before gaps were filled with GapCloser. In vertebrates, including teleosts, the number of transposable elements (TEs) is related to genome size, but it remains unclear whether the size of introns and exons also plays a role. Therefore, the main objective of the present study was to test whether the small genome size of Pleuronectiformes is related to the size of their introns and exons. The assemblies resulted in a genome size of ~538 Mbp (41.35% GC content, 0.11% undetermined bases). Analysis of the assemblies at the core genes level (subset of the 458 universally expressed KOG families) revealed that more than 98% of core genes are present, with more than 78% of them having more than 50% coverage. This indicates a fairly complete and accurate genome at the coding sequence level. Prediction of genes based on statistical predictors (geneid) and sequence-based predictors (Exonerate, using a closely related species, Paralichthys olivaceus, as a reference) was performed. This revealed 25,231 protein-coding genes, 445 tRNAs, 3 rRNAs, and more than 1,500 non-coding RNAs of other types (including a complete set of spliceosomes and several types of snoRNA and miRNA). As a result, this study concluded that the reduced genome size of flounders is related to a reduction in transcript size, mainly through a reduction in exon number, but also through a reduction in large introns. Thus, both components seem to be involved in the strategy of genome reduction in Pleuronectiformes.

show abstract

“…In addition, RepeatMasker v4.06 (Chen, 2004) and RepeatProteinMask v4.06 (Chen, 2004) were applied for homology prediction after identification of transposable elements based on RepBase (Jurka et al, 2005). Moreover, Tandem Repeat Finder v4.09 (Benson, 1999) was separately used to predict comprehensive tandem repeats in our pipeline as previously reported (Liu et al, 2019;Zhao et al, 2021). Finally, these results from the aforementioned three methods are integrated by our in-house perl scripts (https://github.com/liruihanguo/Repeats_integration).…”

Section: Repeat Annotationmentioning

confidence: 99%

Whole-Genome Sequencing of Sinocyclocheilus maitianheensis Reveals Phylogenetic Evolution and Immunological Variances in Various Sinocyclocheilus Fishes

Wang

Bian

et al. 2021

Front. Genet.

View full text Add to dashboard Cite

An adult Sinocyclocheilus maitianheensis, a surface-dwelling golden-line barbel fish, was collected from Maitian river (Kunming City, Yunnan Province, China) for whole-genome sequencing, assembly, and annotation. We obtained a genome assembly of 1.7 Gb with a scaffold N50 of 1.4 Mb and a contig N50 of 24.7 kb. A total of 39,977 protein-coding genes were annotated. Based on a comparative phylogenetic analysis of five Sinocyclocheilus species and other five representative vertebrates with published genome sequences, we found that S. maitianheensis is close to Sinocyclocheilus anophthalmus (a cave-restricted species with similar locality). Moreover, the assembled genomes of S. maitianheensis and other four Sinocyclocheilus counterparts were used for a fourfold degenerative third-codon transversion (4dTv) analysis. The recent whole-genome duplication (WGD) event was therefore estimated to occur about 18.1 million years ago. Our results also revealed a decreased tendency of copy number in many important genes related to immunity and apoptosis in cave-restricted Sinocyclocheilus species. In summary, we report the first genome assembly of S. maitianheensis, which provides a valuable genetic resource for comparative studies on cavefish biology, species protection, and practical aquaculture of this potentially economical fish.

show abstract

Genome assembly and annotation at the chromosomal level of first Pleuronectidae: Verasper variegatus provides a basis for phylogenetic study of Pleuronectiformes

Cited by 11 publications

References 56 publications

A chromosome-level genome assembly enables the identification of the follicle stimulating hormone receptor as the master sex determining gene in Solea senegalensis

A chromosome-level genome assembly enables the identification of the follicle stimulating hormone receptor as the master sex determining gene in Solea senegalensis

De novoassembly of the black flounder genome. Why do pleuronectiformes have such a small genome size?

Whole-Genome Sequencing of Sinocyclocheilus maitianheensis Reveals Phylogenetic Evolution and Immunological Variances in Various Sinocyclocheilus Fishes

Contact Info

Product

Resources

About