Table 1.
Summary statistics of the transcriptome assembly for Crassostrea hongkongensis.
Fig 1.
Gene Ontology(GO) analysis of the Crassostrea hongkongensis transcriptome on level 2.
The percentage and distribution of top-level GO-terms were portrayed in the three categories: (A) Cellular component; (B) Molecular function and (C) Biological process.
Fig 2.
KEGG biochemical mappings for C. hongkongensis transcriptome.
Table 2.
Reproduction-related pathways identified in the C. hongkongensis transcriptome.
Table 3.
Selection of some novel germline development genes identified in the C.hongkongensis transcriptome.
Fig 3.
Vasa gene identified in the Crassostrea hongkongensis transcriptome and its expression profile.
(A) Domain structure of the C.hongkongensis vasa ortholog. (B) Molecular phylogenetic tree of Vasa subfamily and related proteins. Bootstrap values from 1000 trials are indicated at each branch node. The scale bar indicates 0.05 amino acid replacements per site. C elegans Ce-GLH-1 was used as an outgroup. The transcript encoding Chvasa, indicated by a red open box, is properly aligned to the clade of molluscan Vasa colored by green. The Vasa subfamily proteins are enclosed by the dotted lines. For the GenBank accession numbers of the reference sequences, see S3 Table. (C) Expression profile of C.hongkongensis vasa ortholog (Chvasa) in adult tissues with mean ± s.e.m. as error bars (n = 5).
Fig 4.
Analysis of Nanos ortholog identified in C.hongkongensis transcriptome.
(A) Amino acid sequence alignment of the nanos RNA-binding domain predicted in the Ch-nanos with that of other Nanos orthologs. Two highly conserved CCHC zinc finger motifs are indicated by asterisks. For the GenBank accession numbers of the reference sequences, see S3 Table. (B) Domain structure of Ch-nanos. (C) Expression profile of in Ch-nanos adult tissues by qRT-PCR with mean±s.e.m. as error bars (n = 5). nd: not detected. (D) Histological analysis of C.hongkongensis female gonad at early developing stage. (E) Expression profile of Ch-nanos in early developing stage female gonad detected by ISH with antisense and sense probe. (F) Positive cells are stained in purple.OG: oogonia; EO: early vitellogenic oocyte.
Fig 5.
Analysis of Piwi genes identified in C.hongkongensis transcriptome.
(A) Domain structure of the C.hongkongensis Piwi orthologs. (B) Phylogenetic tree constructed using the neighbor-joining method on the basis of the amino acid sequences alignment of C.hongkongensis Piwi ortholog with Piwi-like proteins of vertebrates. A total of 1000 bootstrap trials were run. Bootstrap values were indicated at each branch node. The scale bar represents an evolutionary distance of 0.1 amino acid substitutions per position. The transcript encoding C.hongkongensis Piwi ortholog, colored by red, was aligned to the clade of vertebrate Piwil1proteins. For the GenBank accession numbers of the reference sequences, see S3 Table. (C) Expression profile of ChPiwil1 in adult tissues by qRT-PCR with mean±s.e.m. as error bars (n = 5). (D-L) Expression profile of ChPiwil1during C.hongkongensis oogenesis by ISH. Histological analysis of C.hongkongensis female gonad at early developing stage (D), late developing stage (E) and mature stage (F) stained with HE. Expression profile of ChPiwil1during C.hongkongensis oogenesis by ISH with antisense (G-I) and sense probe (J-L). Positive cells are stained with brown or purple. OG: oogonia; EO: early vitellogenic oocyte; MO: mature ova.
Table 4.
Presence of sex determination/differentiation genes from Caenorhabditis elegans, Drosophila melanogaster, Danio rerio, Mus musculus and Crassostrea hongkongensis.
Fig 6.
Heat map of sex determination/differentiation genes expressed at different adult tissues of C.hongkongensis.
Genes showing similar expression profiles on all samples (columns) were clustered together. Color represents the normalized expression after variance-stabilizing transformation. Expression levels are depicted with a color scale, in which shades of red represent higher expression and shades of green represent lower expression.
Fig 7.
Amino acid sequence alignment of the ADD domain from C.hongkongensis ATRX ortholog with vertebrate ATRX.
The highly conserved C2-C2 zinc finger and C4-C4 zinc finger are indicated by asterisks.
Fig 8.
Classification of single nucleotide polymorphisms (SNPs) identified from the C.hongkongensis transcriptome.
Transitions occurred more frequently than transversions. The overall frequency of all types of SNPs including indels was one per 392 bp.
Table 5.
Frequency distribution of SSRs by motif length in the C.hongkongensis transcriptome.