Multiple cotton genomes (diploid and tetraploid) have been assembled. However, genomic variations between cultivars of allotetraploid upland cotton ( Gossypium hirsutum L.), the most widely planted cotton species in the world, remain unexplored. Here, we use single-molecule long read and Hi-C sequencing technologies to assemble genomes of the two upland cotton cultivars TM-1 and zhongmiansuo24 (ZM24). Comparisons among TM-1 and ZM24 assemblies and the genomes of the diploid ancestors reveal a large amount of genetic variations. Among them, the top three longest structural variations are located on chromosome A08 of the tetraploid upland cotton, which account for ~30% total length of this chromosome. Haplotype analyses of the mapping population derived from these two cultivars and the germplasm panel show suppressed recombination rates in this region. This study provides additional genomic resources for the community, and the identified genetic variations, especially the reduced meiotic recombination on chromosome A08, will help future breeding.

BackgroundWUSCHEL-related homeobox (WOX) family members play significant roles in plant growth and development, such as in embryo patterning, stem-cell maintenance, and lateral organ formation. The recently published cotton genome sequences allow us to perform comprehensive genome-wide analysis and characterization of WOX genes in cotton.ResultsIn this study, we identified 21, 20, and 38 WOX genes in Gossypium arboreum (2n = 26, A2), G. raimondii (2n = 26, D5), and G. hirsutum (2n = 4x = 52, (AD)t), respectively. Sequence logos showed that homeobox domains were significantly conserved among the WOX genes in cotton, Arabidopsis, and rice. A total of 168 genes from three typical monocots and six dicots were naturally divided into three clades, which were further classified into nine sub-clades. A good collinearity was observed in the synteny analysis of the orthologs from At and Dt (t represents tetraploid) sub-genomes. Whole genome duplication (WGD) and segmental duplication within At and Dt sub-genomes played significant roles in the expansion of WOX genes, and segmental duplication mainly generated the WUS clade. Copia and Gypsy were the two major types of transposable elements distributed upstream or downstream of WOX genes. Furthermore, through comparison, we found that the exon/intron pattern was highly conserved between Arabidopsis and cotton, and the homeobox domain loci were also conserved between them. In addition, the expression pattern in different tissues indicated that the duplicated genes in cotton might have acquired new functions as a result of sub-functionalization or neo-functionalization. The expression pattern of WOX genes under different stress treatments showed that the different genes were induced by different stresses.ConclusionIn present work, WOX genes, classified into three clades, were identified in the upland cotton genome. Whole genome and segmental duplication were determined to be the two major impetuses for the expansion of gene numbers during the evolution. Moreover, the expression patterns suggested that the duplicated genes might have experienced a functional divergence. Together, these results shed light on the evolution of the WOX gene family, and would be helpful in future research.Electronic supplementary materialThe online version of this article (doi:10.1186/s12870-017-1065-8) contains supplementary material, which is available to authorized users.

This study aimed to evaluate the protein-sparing effect of dietary lipid on digestive and metabolic responses of fingerling Megalobrama amblycephala. Fish were fed nine practical diets with three protein levels (270, 310 and 350 g kg(-1)) and three lipid levels (40, 70 and 100 g kg(-1)) for 8 weeks. Weight gain was significantly affected only by dietary lipid levels with the highest found in fish fed 70 g kg(-1) lipid. Relative feed intake and whole-body protein content showed little difference among all the treatments. Activities of intestine lipase and amylase increased significantly as dietary lipid levels increased, whereas little difference was observed in protease activities. Liver lipid content was significantly affected only by protein levels with the lowest found in fish fed 310 g kg(-1) protein. Liver aspartate aminotransferase (GOT) activities increased significantly with decreasing lipid levels, whereas the highest GOT activity was obtained in fish fed 310 g kg(-1) protein in terms of dietary protein levels. Activities of liver lipoprotein lipase, total lipase and plasma cholesterol concentration of fish fed 350 g kg(-1) protein were significantly lower than that of the other groups, whereas the same was true for plasma 3, 5, 3'-triiodothyronine level of fish fed 270 g kg(-1) protein. The results indicated that an increase of dietary lipid content from 40 to 70 g kg(-1) can enhance the growth and digestive enzyme activities of this species and reduce the proportion of dietary protein catabolized for energy without inducing hepatic steatosis; meanwhile, decreasing protein level from 350 to 310 g kg(-1) leads to the increase of lipase activities both in intestine and liver coupled with the reduced liver lipid content.

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