Bioproject ID: PRJNA684636

bioproject id PRJNA684636      to NCBI
key word baseline;GENETIC DIVERSITY;PROVIDES INSIGHTS;MODEL SELECTION;GENOME SEQUENCE;READ ALIGNMENT;POLYPLOIDY;ORIGIN;ANNOTATION;RECONSTRUCTION;FRACTIONATION
experiment type baseline
publication Jiong-Tang, L. , et al. "Parallel subgenome structure and divergent expression evolution of allo-tetraploid common carp and goldfish." Nature Genetics.
description We performed the genome sequencing of Puntius tetrazona using Nanopore, Illumina and HiC technologies and generate a chromosome-level assembly. Using transcriptome sequencing from multiple tissues, we predicted protein-coding genes of this species.
abstract Genomic analysis of allo-tetraploid common carp and goldfish identifies parallel subgenome structure and divergent expression processes. How two subgenomes in allo-tetraploids adapt to coexistence and coordinate through structure and expression evolution requires extensive studies. In the present study, we report an improved genome assembly of allo-tetraploid common carp, an updated genome annotation of allo-tetraploid goldfish and the chromosome-scale assemblies of a progenitor-like diploid Puntius tetrazona and an outgroup diploid Paracanthobrama guichenoti. Parallel subgenome structure evolution in the allo-tetraploids was featured with equivalent chromosome components, higher protein identities, similar transposon divergence and contents, homoeologous exchanges, better synteny level, strong sequence compensation and symmetric purifying selection. Furthermore, we observed subgenome expression divergence processes in the allo-tetraploids, including inter-/intrasubgenome trans-splicing events, expression dominance, decreased expression levels, dosage compensation, stronger expression correlation, dynamic functionalization and balancing of differential expression. The potential disorders introduced by different progenitors in the allo-tetraploids were hypothesized to be alleviated by increasing structural homogeneity and performing versatile expression processes. Resequencing three common carp strains revealed two major ecotypes and uncovered candidate genes relevant to growth and survival rate.

Sample Information

sample id sample name tissue strain treatment description
1. SRR13356954 liver liver nan untreatment liver RNA-seq replicate 1
2. SRR13356955 muscle muscle nan untreatment muscle RNA-seq replicate 3
3. SRR13356956 muscle muscle nan untreatment muscle RNA-seq replicate 2
4. SRR13356959 muscle muscle nan untreatment muscle RNA-seq replicate 1
5. SRR13356960 skin skin nan untreatment skin RNA-seq replicate 3
6. SRR13356961 skin skin nan untreatment skin RNA-seq replicate 2
7. SRR13356962 skin skin nan untreatment skin RNA-seq replicate 1
8. SRR13356963 spleen spleen nan untreatment spleen RNA-seq replicate 3
9. SRR13356964 spleen spleen nan untreatment spleen RNA-seq replicate 2
10. SRR13356965 spleen spleen nan untreatment spleen RNA-seq replicate 1
11. SRR13356966 brain brain nan untreatment brain RNA-seq replicate 3
12. SRR13356967 brain brain nan untreatment brain RNA-seq replicate 2
13. SRR13356968 brain brain nan untreatment brain RNA-seq replicate 1
14. SRR13356969 gill gill nan untreatment gill RNA-seq replicate 3
15. SRR13356970 gill gill nan untreatment gill RNA-seq replicate 2
16. SRR13356971 gill gill nan untreatment gill RNA-seq replicate 1
17. SRR13356972 heart heart nan untreatment Heart RNA-seq replicate 3
18. SRR13356973 heart heart nan untreatment Heart RNA-seq replicate 2
19. SRR13356974 heart heart nan untreatment Heart RNA-seq replicate 1
20. SRR13356975 intestine intestine nan untreatment intestine RNA-seq replicate 3
21. SRR13356977 intestine intestine nan untreatment intestine RNA-seq replicate 2
22. SRR13356978 intestine intestine nan untreatment intestine RNA-seq replicate 1
23. SRR13356979 kidney kidney nan untreatment kidney RNA-seq replicate 3
24. SRR13356980 kidney kidney nan untreatment kidney RNA-seq replicate 2
25. SRR13356981 kidney kidney nan untreatment kidney RNA-seq replicate 1
26. SRR13356982 liver liver nan untreatment liver RNA-seq replicate 3
27. SRR13356983 liver liver nan untreatment liver RNA-seq replicate 2