Eight intact LTR retrotransposons (Nbr1-Nbr8) have been previously characterized from the genome of Nosema bombycis, a eu- karyotic parasite with a compact and reduced genome. Here we describe six novel transcribed ...Eight intact LTR retrotransposons (Nbr1-Nbr8) have been previously characterized from the genome of Nosema bombycis, a eu- karyotic parasite with a compact and reduced genome. Here we describe six novel transcribed Nbr elements (Nbr9-Nbr14) identified through either cDNA library or RT-PCR. Like previously determined ones, all of them belong to the Ty3/Gypsy superfamily. Retrotransposon diversity and incomplete domains with insertions (Nbr12), deletions (Nbrll) and in-frame stop codons in coding regions (Nbr9) were detected, suggesting that both defective and loss events of LTR retrotransposon have happened in N. bornbycis genome. Analysis of selection showed that strong purifying selection acts on all elements except Nbr11. This implies that selective pressure keeps both these Nbrs and their functions in genome. Interestingly, Nbrll is under positive selection and some positively selected codons were identified, indicating that new functionality might have evolved in the Nbrll retrotransposon. Unlike other transposable elements, Nbrll has integrated into a conserved syntenic block and probably resulted in the inversion of both flanking regions. This demonstrates that transposable element is an important factor for the reshuffling and evolution of their host genomes, and may be maintained under natural selection.展开更多
The ribosomal proteins are crucial for the maintenance of ribosomal translational efficiency and fidelity.In the study,we characterized the ribosomal protein S30(RPS30)gene from Arachis hypogaea that has been isolated...The ribosomal proteins are crucial for the maintenance of ribosomal translational efficiency and fidelity.In the study,we characterized the ribosomal protein S30(RPS30)gene from Arachis hypogaea that has been isolated through Genefishing analysis during defense responses to Ralstonia solanacearum.The cDNA of RPS 30 contained a 189 base pair(bp)open-reading frame encoding 62 amino acids.The genomic DNA consists of 272 bp containing two exons and one 83 bp intron.The RPS 30 mRNA transcript was mainly expressed in roots and leaves.The expression level of the RPS 30 mRNA transcripts was up-regulated sharply 6 h after bacterial challenge and was 12 times greater than that of the control group.The phylogenetic analysis for genes encoding proteins showed that RPS30 were conserved within dicotyledonous and monocotyledonous plants.d S extremely exceeded d N in all branches of the tree(d N/d S<1.0),indicating that functional constraint have acted on RPS 30 throughout evolution.展开更多
The major histocompatibility complex (MHC) is a dynamic genetic region with an essential role in the adaptive immunity of jawed vertebrates. The MHC polymorphism is affected by many processes such as birth-and- deat...The major histocompatibility complex (MHC) is a dynamic genetic region with an essential role in the adaptive immunity of jawed vertebrates. The MHC polymorphism is affected by many processes such as birth-and- death evolution, gene conversion, and concerted evolution. Studies investigating the evolution of MHC class I genes have been biased toward a few particular taxa and model species. However, the investigation of this region in nonavian reptiles is still in its infancy. We present the first characterization of MHC class I genes in a species from the family Lacertidae. We assessed genetic diversity and a role of selection in shaping the diversity of MHC class I exon 4 among 37 individuals of Eremias multiocellata from a population in Lanzhou, China. We generated 67 distinct DNA sequences using cloning and sequencing methods, and identified 36 putative functional variants as well as two putative pseudogene-variants. We found the number of variants within an individual varying between two and seven, indicating that there are at least four MHC class I loci in this species. Gene duplication plays a role in increasing copy numbers of MHC genes and allelic diversity in this species. The class I exon 4 sequences are characteristic of low nucleotide diversity. No signal of recombination is detected, but purifying selection is detected in β2-microglobulin interaction sites and some other silent sites outside of the function-constraint regions. Certain identical alleles are shared by Eremias multiocellata and E. przewalskii and E. brenchleyi, suggesting trans-species polymorphism. The data are compatible with a birth-and-death model of evolution.展开更多
基金supported by the National Basic Research Program of China(No.2005CB121000)the project of Chongqing Science & Technology Commission(CSTC,No.2006AA5019 and 2009BB1241)+1 种基金the Programme of Introducing Talents of Discipline to Universities(No.B07045)State Development Fund at Risk of Callus Silk(No.M012005-000Y-00070)
文摘Eight intact LTR retrotransposons (Nbr1-Nbr8) have been previously characterized from the genome of Nosema bombycis, a eu- karyotic parasite with a compact and reduced genome. Here we describe six novel transcribed Nbr elements (Nbr9-Nbr14) identified through either cDNA library or RT-PCR. Like previously determined ones, all of them belong to the Ty3/Gypsy superfamily. Retrotransposon diversity and incomplete domains with insertions (Nbr12), deletions (Nbrll) and in-frame stop codons in coding regions (Nbr9) were detected, suggesting that both defective and loss events of LTR retrotransposon have happened in N. bornbycis genome. Analysis of selection showed that strong purifying selection acts on all elements except Nbr11. This implies that selective pressure keeps both these Nbrs and their functions in genome. Interestingly, Nbrll is under positive selection and some positively selected codons were identified, indicating that new functionality might have evolved in the Nbrll retrotransposon. Unlike other transposable elements, Nbrll has integrated into a conserved syntenic block and probably resulted in the inversion of both flanking regions. This demonstrates that transposable element is an important factor for the reshuffling and evolution of their host genomes, and may be maintained under natural selection.
基金Natural Science Funds for Young Scholar of Shandong Academy of Agricultural Sciences,China(No.2015YQN13)Natural Science Foundation of Shandong Province,China(ZR2015YL064)+2 种基金Qingdao Science and Technology Plan Basic Research Project,China(No.12-1-4-11-(1)-jch)China Agricultural Research System(No.CARS-13)Agricultural Scientific and Technological Innovation Project of Shandong Academy of Agricultural Sciences,China(No.CXGC2018E21)
文摘The ribosomal proteins are crucial for the maintenance of ribosomal translational efficiency and fidelity.In the study,we characterized the ribosomal protein S30(RPS30)gene from Arachis hypogaea that has been isolated through Genefishing analysis during defense responses to Ralstonia solanacearum.The cDNA of RPS 30 contained a 189 base pair(bp)open-reading frame encoding 62 amino acids.The genomic DNA consists of 272 bp containing two exons and one 83 bp intron.The RPS 30 mRNA transcript was mainly expressed in roots and leaves.The expression level of the RPS 30 mRNA transcripts was up-regulated sharply 6 h after bacterial challenge and was 12 times greater than that of the control group.The phylogenetic analysis for genes encoding proteins showed that RPS30 were conserved within dicotyledonous and monocotyledonous plants.d S extremely exceeded d N in all branches of the tree(d N/d S<1.0),indicating that functional constraint have acted on RPS 30 throughout evolution.
基金supported by the Science and Technology Project for Outstanding Youths in Life Science (KSCX2-EW-Q-6) from the Chinese Academy of SciencesNational Natural Science Foundation of China (31272281)
文摘The major histocompatibility complex (MHC) is a dynamic genetic region with an essential role in the adaptive immunity of jawed vertebrates. The MHC polymorphism is affected by many processes such as birth-and- death evolution, gene conversion, and concerted evolution. Studies investigating the evolution of MHC class I genes have been biased toward a few particular taxa and model species. However, the investigation of this region in nonavian reptiles is still in its infancy. We present the first characterization of MHC class I genes in a species from the family Lacertidae. We assessed genetic diversity and a role of selection in shaping the diversity of MHC class I exon 4 among 37 individuals of Eremias multiocellata from a population in Lanzhou, China. We generated 67 distinct DNA sequences using cloning and sequencing methods, and identified 36 putative functional variants as well as two putative pseudogene-variants. We found the number of variants within an individual varying between two and seven, indicating that there are at least four MHC class I loci in this species. Gene duplication plays a role in increasing copy numbers of MHC genes and allelic diversity in this species. The class I exon 4 sequences are characteristic of low nucleotide diversity. No signal of recombination is detected, but purifying selection is detected in β2-microglobulin interaction sites and some other silent sites outside of the function-constraint regions. Certain identical alleles are shared by Eremias multiocellata and E. przewalskii and E. brenchleyi, suggesting trans-species polymorphism. The data are compatible with a birth-and-death model of evolution.