Supplementary Materials Supplemental Material supp_29_11_1805__index. = 48) and (topmouth culter [TC]; 2n = 2x = 48), family Cyprinidae, are economically important freshwater fish (Chen 1998; Zhou et al. 2008). The BSB and the TC have distinct feeding habits (the BSB is usually herbivorous, whereas the TC is usually carnivorous) and shapes (the BSB has a higher dorsal fin and a shorter body than the TC). Furthermore, the progenies of intergeneric reciprocal crosses between these fishes (BSB [] TC [] and TC [] BSB []) show different degrees of phenotypic variation. For example, the hybrid lineages of reciprocal crosses had intermediate shapes between those of their parents (Xiao et al. 2014). Hybrid lineages of BSB and TC also show many physiological advantages over their parents, such as faster growth rates, higher hypoxia tolerance, and greater disease resistance (Xiao et al. 2014; Li et al. 2018), as observed in other hybrid fishes, including tilapia hybrids ( conversation by modifying the activity or expression of transcription factors (Wittkopp et al. 2004; Maheshwari and Barbash 2012). The co-evolution always occurred in the conversation of [BSB]; 2n = 48) and topmouth culter ([TC]; 2n = 48), which reached sexual maturity AZD2014 distributor in natural waters of the Yangtze River in China, were collected for the hybrid experiments. The AZD2014 distributor procedure for generating the hybrid lineages investigated in this study is usually shown in Physique 1. BSB and TC were used as the parents in the reciprocal cross hybrids to form two types of hybrid lineages. In the first cross group, a BSB () TC () cross was performed to produce F1 hybrids (BT, HYAL1 2n = 48). Then, the intercrossing within F1 females and males produce F2 hybrids, which generated F3, forming the hybrid lineage (F1CF3). In the second cross group, a TC () BSB () cross was performed to produce F1 hybrids (TB, 2n = 48). Then, the intercrossing within F1 females and males produce F2 hybrids, which generated F3, establishing the hybrid lineage (F1CF3) (Supplemental Methods). Open in a separate window Physique 1. Procedure for generating the reciprocal cross hybrids of BSB and TC. (TC, zebrafish (and gynogenetic genome Open in a separate window Genome development A phylogenetic tree was constructed using 796 single-copy genes from 10 species (Fig. 2A). The results indicated that this ancestral lineage AZD2014 distributor of the BSB and the TC diverged from that of the grass carp 27.35 million years ago (MYA) (Fig. 2A; Supplemental Desk S10; Supplemental Strategies). The distribution of had been extracted from Schartl et al. (2013). (= 0.0026) (Fig. 3D,E; Supplemental Fig. S26; Supplemental Strategies), disclosing the TC expression dominance in TB and BT. Great ratios of TC appearance dominance in AZD2014 distributor up-regulated genes and BSB appearance dominance in down-regulated genes had been observed predicated on even more genes in patterns II (75.89%) and IX (58.24%) than in XI (24.11%) and IV (41.76%) in BT and TB (Supplemental Fig. S26). On the other hand, some gradual lowering tendencies of additive (I and XII) and appearance dominance (II, XI, IV, and IX) genes and a growing craze of Transgressive up-/down-regulation (III, VII, X, V, VI, and VIII) genes had been discovered from F1 to F3, disclosing a continuous weakening of parental impact in hybrids. Appearance appearance and divergence bias To research the coregulation of alleles produced from two subgenomes in the hybrids, 9753 orthologous genes had been selected through recognition of 103,190 species-specific SNPs, as well as the distribution of species-specific SNPs in each gene was proven (Supplemental Fig. S27; Supplemental Strategies). After evaluating the TC and BSB allelic appearance, AZD2014 distributor the seven genes with TC allelic silencing had been distributed in the liver organ of TBF1-TBF3, and eight had been distributed in BTF1-BTF3 (Supplemental Fig. S28). A cluster evaluation of allelic appearance data was performed, disclosing the close romantic relationship in BSB and TC allelic appearance from the hybrids, however a clear parting was discovered in allelic appearance of the liver organ of BTF3 (Supplemental Fig. S29). Concentrating on the path and magnitude of allelic appearance, the log2 (TC/BSB) beliefs in hybrids had been calculated predicated on the amounts from the depth of.