Chromosome-scale assembly of the Monopterus genome

Zhao, Xueya; Luo, Majing; Li, Zhigang; Pei, Zhong; Cheng, Yang; Lai, Fengling; Wang, Xin; Jiang, Min; Bai, Mingzhou; Yang, Yulan; Cheng, Hanhua; Zhou, Rongjia

doi:10.1093/gigascience/giy046

Cited by 33 publications

(26 citation statements)

References 40 publications

(37 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…It is a major freshwater economic fish in China (Chi et al, 2017). It has the characteristic of undergoing a sex reversal: during the embryonic stage and to the first sexual maturity, it is female; it then enters an intersex state, and then some individuals develop into males (Zhao et al, 2018).…”

Section: Introductionmentioning

confidence: 99%

Analysis of the Intestinal Flora in Male Versus Female Swamp Eels (Monopterus albus)

et al. 2020

View full text Add to dashboard Cite

This study aimed to analyze the intestinal flora of male versus female swamp eels, which have the unique characteristic of sex reversal. Same-aged swamp eels from the same parents, kept under the same conditions in terms of environment, diet, etc., were used as the study materials. After breeding for 1 year, 18 healthy swamp eels (nine males and nine females), weighing 39.4 ± 2.3 g, were selected. The intestinal contents of three swamp eels of the same sex were combined and labeled as follows: FM1-FM3 (n = 3) for females and MM1-MM3 (n = 3) for males. High-throughput sequencing was used to research the v3-v4 region of 16S rDNA in the intestinal flora. The results suggested significant differences in the structure, composition, and diversity of the intestinal flora of male versus female swamp eels. The relative abundances of Actinobacteria and Spirochaetes in female swamp eels were significantly higher (p < 0.05) than in male swamp eels at the phylum level. The relative abundances of Mycobacterium, Bacillus, and Vagococcus in female swamp eels were considerably higher (p < 0.05) than in male swamp eels at the genus level. The Alpha diversity of females was higher than that of males, and the Shannon index of females was also significantly higher (p < 0.05, Tukey's HSD) than that in males. Investigations of Beta diversity, including NMDS ordination, UPGMA cluster analysis, and PLS-DA analysis, showed that female and male swamp eels could be clearly distinguished based on significant differences in intestinal flora between the FM group and the MM group. LEfSe analysis showed that the dominant bacteria were Cetobacterium in male swamp eels and Clostridium_sp_ND2, Mycobacterium, Alphaproteobacteria, and Bacilli in female swamp eels. The results showed dramatic differences in the intestinal flora between the sexes, which indicates the need for a more in-depth study on sex reversal in the future.

show abstract

Section: Introductionmentioning

confidence: 99%

Analysis of the Intestinal Flora in Male Versus Female Swamp Eels (Monopterus albus)

et al. 2020

View full text Add to dashboard Cite

show abstract

“…More than six Gb (gigabase) of clean data of each sample were produced (Table 1), which were submitted to NCBI Sequence Read Archive under the accession number of PRJNA588722. These clean reads were mapped to the published genome of Monopterus albus (Zhao et al., 2018). And the alignment rates were shown in Table 1.…”

Section: Resultsmentioning

confidence: 99%

“…The clean reads were aligned to a Monopterus albus reference genome (Zhao et al., 2018) using HISAT2 software (Daehwan, Ben, & Salzberg, 2015), which were assembled into transcripts using StringTie software (Pertea et al., 2015). Novel transcripts were identified by Cuffcompare, a part of the Cufflinks package (Trapnell et al., 2010).…”

Section: Methodsmentioning

confidence: 99%

Comparative transcriptome analysis of livers from three strains of Chinese swamp eels

et al. 2020

View full text Add to dashboard Cite

Swamp eel or rice field eel (Monopterus albus) is one of the most economically valuable freshwater fishes in China. Based on the body colour patterns, Chinese rice field eels are commonly classified into three strains, including deep‐yellow strain (DY), pale‐yellow strain (PY) and steel‐grey strain (SG). Reports have shown that DY strain is superior to the other two strains at growth rate and fecundity. In the present study, RNA‐Seq technology was employed to profile liver transcriptomes of these three strains, and differentially expressed genes (DEGs) were identified. The hierarchical clustering analysis showed that expression patterns of liver transcripts among the three strains were different. A total of 3,296 DEGs, 3,043 DEGs and 143 DEGs were identified, respectively, from DY versus SG, DY versus PY and PY versus SG. The three comparison groups shared three DEGs, of which one DEG (batf) played a vital role in immune system. Functional enrichment analyses of DEGs in DY versus PY and DY versus SG revealed that significantly enriched Gene Ontology terms and KEGG pathways were mainly involved in innate immune responses and lipid metabolism. Additionally, most of DEGs related to immunity were mainly up‐regulated in DY compared to PY and SG. The above results indicated that the DY strain might have strong adaptability and resistance to disease, which might support their superiority for better growth and reproduction.

show abstract

“…Recently, we sequenced and assembled the whole genome of the teleost Monopterus albus at chromosome level [28]. Given the smallest chromosome number among teleost fishes, it is interesting to see how third whole-genome duplication (the 3R WGD) occurred in the Monopterus albus lineage, because 3R WGD occurred in the other teleost lineages after divergence from the Holostei [4,[29][30][31][32].…”

Section: Introductionmentioning

confidence: 99%

Whole genome-wide chromosome fusion and new gene birth in the Monopterus albus genome

et al. 2020

Self Cite

View full text Add to dashboard Cite

Background: Teleost fishes account for over half of extant vertebrate species. A core question in biology is how genomic changes drive phenotypic diversity that relates to the origin of teleost fishes. Results: Here, we used comparative genomic analyses with chromosome assemblies of diverse lineages of vertebrates and reconstructed an ancestral vertebrate genome, which revealed phylogenomic trajectories in vertebrates. We found that the whole-genome-wide chromosome fission/fusions took place in the Monopterus albus lineage after the 3-round whole-genome duplication. Four times of genomic fission/fusions events resulted in the whole genomewide chromosome fusions in the genomic history of the lineage. In addition, abundant recently evolved new genes for reproduction emerged in the Monopterus albus after separated from medaka. Notably, we described evolutionary trajectories of conserved blocks related to sex determination genes in teleosts. Conclusions: These data pave the way for a better understanding of genomic evolution in extant teleosts.

show abstract

Chromosome-scale assembly of the Monopterus genome

Cited by 33 publications

References 40 publications

Analysis of the Intestinal Flora in Male Versus Female Swamp Eels (Monopterus albus)

Analysis of the Intestinal Flora in Male Versus Female Swamp Eels (Monopterus albus)

Comparative transcriptome analysis of livers from three strains of Chinese swamp eels

Whole genome-wide chromosome fusion and new gene birth in the Monopterus albus genome

Contact Info

Product

Resources

About