Dataset Information

Centromere localization for Bighead Carp (Aristichthys nobilis) through half-tetrad analysis in diploid gynogenetic families.

ABSTRACT: Gene-centromere (G-C) mapping provides insights into structural and behavioural properties of chromosomes. In this study, G-C mapping using microsatellite markers and meiogynogenetic (meiotic gynogenetic) families were performed in bighead carp (Aristichthys nobilis, 2N?=?48), which belongs to Cyprinidae. A total of 218 microsatellites were selected across 24 linkage groups (LGs) of a recently well-defined genetic linkage map for bighead carp, with 151 being heterozygous in at least one of six dams in diploid meiogynogenetic families. After tests for Mendelian segregation in two diploid control families, 103 microsatellites were used for G-C distance calculation in 383 gynogens. The second division segregation frequency (y) was computed through half-tetrad analyses, and the values ranged from 0 to 0.97 (mean 0.40). High G-C recombination frequencies (over 0.667) were observed in 18 (17.5%) of the loci examined, which revealed a low level of chiasma interferences compared with other fishes studied previously. Distribution of G-C distances across LGs ranged from 0 cM to 48.5 cM (mean 20 cM) under the assumption of complete interference. All 24 centromeres were localized according to their closest-related microsatellites at 95% confident intervals. The average distance between centromeres and their closest-linked markers was 6.1 cM with 15 out of 24 LGs having a distance below 5 cM. Based on the centromere positions in this study, we proposed a formula of 24 m/sm+24 t/st chromosomes with 92 arms for bighead carp, which was mostly in accordance with a previously reported karyotype for bighead carp (24 m/sm+24 st). These results of centromere localization provide a basic framework and important resources for genetics and comparative genomics studies in bighead carp and its closely-related cyprinid species.

SUBMITTER: Zhu C

PROVIDER: S-EPMC3869750 | biostudies-literature | 2013

REPOSITORIES: biostudies-literature

ACCESS DATA

Similar Datasets

Project description:BackgroundEarly development is a key process of the life history of fish. However, the relationship between the transcriptome and the dynamic regulation of early development is still uncharacterized in the bighead carp (Hypophthalmichthys nobilis). In the present study, we performed transcriptome analysis of six development stages in H. nobilis, aiming to understand the dynamic molecular regulation of early development in this fish.ResultsA total of 76,573 unigenes were assembled from clean sequence reads, with an average length of 1768 base. Among which, 41,742 (54.54%) unigenes were annotated to public protein databases, and an additional 59,014 simple sequence repeat (SSR) loci were identified among the unigenes. Furthermore, 30,199 differentially expressed transcripts (DETs) (fold change > 4 or < 0.25, and the false discovery rate FDR < 0.01) were observed in comparisons between the adjacent developmental stages, and nine expression patterns (profiles) were simulated using series-cluster analysis across six developmental stages. The unigenes expression level markedly increased after the DS1 stage (early blastula), and the numbers of DETs gradually decreased during subsequent development. The largest transcriptomic change (up- or down-regulated) was detected during the period from DS1 to DS2 (6-somite stage), which was enriched for many biological processes and metabolic pathways related to maternal to zygotic transition (MZT). Distinctly protein-protein interaction (PPI) networks were plotted for DETs during the period from DS1 to DS2. The genes (or proteins) from the same pathways were integrated together, and showed with obvious co-regulation patterns. In the series-cluster analysis, a remarkable profile of gene expression (profile_48) was identified that is probably related to the hatching during H. nobilis development, and the strict co-expression of a hatching enzyme gene (hce1) with 33 other annotated genes was identified from this profile.ConclusionsThe results indicated that strict dynamic regulation occurs during the early development in H. nobilis, especially in embryogenesis before hatching. This study provides valuable new information and transcriptomic resources related to H. nobilis early development, and for certain events such as MZT and hatching.

Dataset Information

Centromere localization for Bighead Carp (Aristichthys nobilis) through half-tetrad analysis in diploid gynogenetic families.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets