Interspecific hybridization is a driving force in evolution and speciation of higher plants. Interspecific hybridization often induces immediate and saltational changes in gene expression, a phenomenon collectively te...Interspecific hybridization is a driving force in evolution and speciation of higher plants. Interspecific hybridization often induces immediate and saltational changes in gene expression, a phenomenon collectively termed ＂transcriptome shock＂. Although transcriptome shock has been reported in various plant and animal taxa, the extent and pattern of shock-induced expression changes are often highly idiosyncratic, and hence entails additional investigations. Here, we produced a set of interspecific F1 triploid hybrid plants between Oryza sativa, ssp. japonica （2n=2x=24, genome AA） and the tetraploid form of O. punctata （2n=4x =48, genome, BBCC）, and conducted RNA-seq transcriptome profiling of the hybrids and their exact parental plants. We analyzed both homeolog expression bias and overall gene expression level difference in the hybrids relative to the in silico ＂hybrids＂ （parental mixtures）. We found that approximately 16% （2,541） of the 16,112 expressed genes in leaf tissue of the F1 hybrids showed nonadditive expression, which were specifically enriched in photosynthesis-related pathways. Interestingly, changes in the maternal homeolog expression, including non-stochastic silencing, were the major causes for altered homeolog expression partitioning in the F1 hybrids. Our findings have provided further insights into the tran- scriptome response to interspecific hybridization and heterosis.展开更多
Established allopolyploid species often contain specific gene(s)dedicated to suppressing the pairing of homoeologous chromosomes during meiosis.A longstanding question is whether such genes in allopolyploids with lowe...Established allopolyploid species often contain specific gene(s)dedicated to suppressing the pairing of homoeologous chromosomes during meiosis.A longstanding question is whether such genes in allopolyploids with lower ploidy levels can retain full functionality when the ploidy level rises following the addition of a new subgenome during outcrossing.Here,we addressed this question by generating a synthetic allohexaploid wheat species,Triticum kiharae(GGAADD),by crossing the allotetraploid Triticum timopheevii(GGAA)to the diploid Aegilops tauschii(DD),followed by colchicine-induced chromosomal doubling.The gene Pairing homoeologous 1(Ph1)inherited from T.timopheevii was likely hypofunctional in nascent T.kiharae,as evidenced by irregularities during meiotic chromosome pairing and organismal numerical and structural chromosome variation in selfed progeny populations.The allohexaploidization event also induced substantial rewiring of gene expression among homoeologs and nonadditive gene expression,leading to distinct predicted biological functions for differentially expressed genes(DEGs)when they were partitioned into the subgenomes.F1hybrids from a cross between T.kiharae and bread wheat(T.aestivum,BBAADD)were male-sterile but female-fertile,confirming intrinsic postzygotic reproductive isolation between the two species while enabling backcrossing of these sterile F1hybrids to bread wheat.These features provide a feasible route to simultaneously introgress standing congeneric genetic variations from both T.timopheevii and Ae.tauschii,as well as heritable de novo variations that have arisen in T.kiharae into bread wheat.展开更多
Brucella melitensis is a facultative intracellular bacterium that replicates within macrophages. The ability of Brucella to survive and multiply in the hostile environment of host macrophages is essential for its viru...Brucella melitensis is a facultative intracellular bacterium that replicates within macrophages. The ability of Brucella to survive and multiply in the hostile environment of host macrophages is essential for its virulence. The cold shock protein Csp A plays an important role in the virulence of B. melitensis. To analyze the genes regulated by Csp A, the whole transcriptomes of B. melitensis NI?csp A and its parental wild-type strain, B. melitensis NI, were sequenced and analyzed using the Solexa/Illumina sequencing platform. A total of 446 differentially expressed genes were identified, including 324 up-regulated and 122 down-regulated genes. Numerous genes identified are involved in amino acid, fatty acid, nitrogen, and energy metabolism. Interestingly, all genes involved in the type IV secretion system and Lux R-type regulatory protein Vjb R were significantly down-regulated in NI?csp A. In addition, an effector translocation assay confirmed that the function of T4 SS in NI?csp A is influenced by deletion of the csp A gene. These results revealed the differential phenomena associated with virulence and metabolism in NI?csp A and NI, providing important information for understanding detailed Csp A-regulated interaction networks and Brucella pathogenesis.展开更多
基金supported by the National Natural Science Foundation of China (NSFC#30990243)the State Key Basic Research and Development Plan of China (2013CBA01404)+1 种基金the Program for Introducing Talents to Universities (#B07017)a Graduate Student Innovation Fund (12SSXT130)
文摘Interspecific hybridization is a driving force in evolution and speciation of higher plants. Interspecific hybridization often induces immediate and saltational changes in gene expression, a phenomenon collectively termed ＂transcriptome shock＂. Although transcriptome shock has been reported in various plant and animal taxa, the extent and pattern of shock-induced expression changes are often highly idiosyncratic, and hence entails additional investigations. Here, we produced a set of interspecific F1 triploid hybrid plants between Oryza sativa, ssp. japonica （2n=2x=24, genome AA） and the tetraploid form of O. punctata （2n=4x =48, genome, BBCC）, and conducted RNA-seq transcriptome profiling of the hybrids and their exact parental plants. We analyzed both homeolog expression bias and overall gene expression level difference in the hybrids relative to the in silico ＂hybrids＂ （parental mixtures）. We found that approximately 16% （2,541） of the 16,112 expressed genes in leaf tissue of the F1 hybrids showed nonadditive expression, which were specifically enriched in photosynthesis-related pathways. Interestingly, changes in the maternal homeolog expression, including non-stochastic silencing, were the major causes for altered homeolog expression partitioning in the F1 hybrids. Our findings have provided further insights into the tran- scriptome response to interspecific hybridization and heterosis.
基金supported by the National Natural Science Foundation of China(31991211 to Bao Liu)the China Postdoctoral Science Foundation(2024 M760322 to Ruili Lyu)。
文摘Established allopolyploid species often contain specific gene(s)dedicated to suppressing the pairing of homoeologous chromosomes during meiosis.A longstanding question is whether such genes in allopolyploids with lower ploidy levels can retain full functionality when the ploidy level rises following the addition of a new subgenome during outcrossing.Here,we addressed this question by generating a synthetic allohexaploid wheat species,Triticum kiharae(GGAADD),by crossing the allotetraploid Triticum timopheevii(GGAA)to the diploid Aegilops tauschii(DD),followed by colchicine-induced chromosomal doubling.The gene Pairing homoeologous 1(Ph1)inherited from T.timopheevii was likely hypofunctional in nascent T.kiharae,as evidenced by irregularities during meiotic chromosome pairing and organismal numerical and structural chromosome variation in selfed progeny populations.The allohexaploidization event also induced substantial rewiring of gene expression among homoeologs and nonadditive gene expression,leading to distinct predicted biological functions for differentially expressed genes(DEGs)when they were partitioned into the subgenomes.F1hybrids from a cross between T.kiharae and bread wheat(T.aestivum,BBAADD)were male-sterile but female-fertile,confirming intrinsic postzygotic reproductive isolation between the two species while enabling backcrossing of these sterile F1hybrids to bread wheat.These features provide a feasible route to simultaneously introgress standing congeneric genetic variations from both T.timopheevii and Ae.tauschii,as well as heritable de novo variations that have arisen in T.kiharae into bread wheat.
基金supported by the National Natural Science Foundation of China (31402197, 31372446)
文摘Brucella melitensis is a facultative intracellular bacterium that replicates within macrophages. The ability of Brucella to survive and multiply in the hostile environment of host macrophages is essential for its virulence. The cold shock protein Csp A plays an important role in the virulence of B. melitensis. To analyze the genes regulated by Csp A, the whole transcriptomes of B. melitensis NI?csp A and its parental wild-type strain, B. melitensis NI, were sequenced and analyzed using the Solexa/Illumina sequencing platform. A total of 446 differentially expressed genes were identified, including 324 up-regulated and 122 down-regulated genes. Numerous genes identified are involved in amino acid, fatty acid, nitrogen, and energy metabolism. Interestingly, all genes involved in the type IV secretion system and Lux R-type regulatory protein Vjb R were significantly down-regulated in NI?csp A. In addition, an effector translocation assay confirmed that the function of T4 SS in NI?csp A is influenced by deletion of the csp A gene. These results revealed the differential phenomena associated with virulence and metabolism in NI?csp A and NI, providing important information for understanding detailed Csp A-regulated interaction networks and Brucella pathogenesis.
