2016, 35(12): 38-50.
doi: 10.1007/s13131-016-0957-z
Keywords:
nrDNA ,
Cynoglossus lineolatus ,
tandem repeat ,
pseudogene ,
polymorphism ,
non-concerted evolution
Although 18S rDNA sequence is extremely conservative, the polymorphism still has been found in few species. In the present study, three types (Type A, B and C) of 18S rDNA sequence coexisted in Cynoglossus lineolatus genome, suggesting a non-concerted evolution process, rather than a strictly concerted evolution fashion. Based on the differences of sequence variation, GC content, secondary structure and minimum free energy, Types A and B were speculated as the potential pseudogenes. Additionally, a fascinating finding was a 189-bp duplication of 18S rDNA in Type A sequence. To our knowledge, this is the first report on such a long duplication in teleostean ribosomal DNA. Compared with several theories accounting for the formation of tandem repeats, the unequal crossing over model was thought to be the most likely mechanism to generate the 189-bp duplication of 18S rDNA. These results not only provide a novel molecular evidence for the unequal crossing over model, but also benefit for the further study on 18S rDNA in fishes.
2022, 41(11): 108-114.
doi: 10.1007/s13131-022-1985-5
Published：2022-11-01
Since 2015, green tides with Ulva prolifera as the dominant species in the Qinhuangdao coastal waters have continued to occur. In this study, the relationship between green tides in Qinhuangdao and the Yellow Sea (setting sites in Rudong and Qingdao) was evaluated by genetic analyses of U. prolifera. Single nucleotide polymorphism (SNP) markers were used to analyze genetic diversity and genetic relationships among groups. Genetic differentiation was lower among floating U. prolifera populations in Rudong and Qingdao than in Qinhuangdao. The floating U. prolifera population had higher genetic diversity and polymorphism levels in Qingdao and Rudong than in Qinhuangdao. Physiological experiments showed that the growth rate and net buoyancy of floating U. prolifera were highest in Qinhuangdao and Qingdao, respectively, under the same environmental conditions (temperature and light). Overall, these findings showed that U. prolifera populations in the Qinhuangdao and Yellow Sea green tides (Rudong and Qingdao) differ significantly at the molecular and physiological levels. Therefore, the Qinhuangdao green tide is not correlated with the Yellow Sea green tide and has a different origin and development mode. This study provides insight into the mechanism underlying green tide blooms in coastal waters of China.
2010(6): 121-124.
doi: 10.1007/s13131-010-0083-2
Ten novel polymorphic microsatellite loci were developed using an enrichment and colony hybridization protocol and characterized for the cuttlefish, Sepiella maindroni. Polymorphism was explored by using 30 individuals from the coastal waters of Zhanjiang, Guangdong province, China, in December 2007. The number of alleles ranged from 5 to 13. The ranges of observed and expected heterozygosity were from 0.578 9 to 1.000 0 and 0.682 8 to 0.925 7, respectively, and the average polymorphic information content (PIC) was 0.778 5. These microsatellite loci will certainly facilitate the detection of the genetic variation and population structure of S. maindroni.
2003(3): 453-457.
Genetic variation of 11 lines of Porphyra yezoensis from the coastline of Kagoshima ofJapan, Qingdao, Nantong, Putuo and Nanji Islands of China were studied by using amplified fragment length polymorphism (AFLP).778 bands were obtained with AFLP analysis of 16 primer combinations, among which 15 were unique, about 98.07% were polymorphic. The AFLP data showed that the closest genetic distance was 0.180 between two Kagoshima samples, and the farthest one was 0.397 between Kagoshima No.1 and Nantong No.9 line. The genetic distance showed that the variation was within the inner species scope. Neighbor-joining cluster and UPGMA cluster indicated that samples from Kagoshima and Qingdao were with high similarity and either with the samples of Nantong, Putuo and Nanji Islands. P. yezoensis in China shared high genetic diversity, and the genetic distance showed positive correlation with the geographic distance.
2015, 34(2): 36-44.
doi: 10.1007/s13131-015-0588-9
In this study, the gene encoding hemocyanin subunit L, LvHcL, was cloned from Litopenaeus vannamei and the genomic organization was characterized. This gene was diverse with many SNPs and also had at least four isoforms, while one of them (LvHcL4) only had two exons and the exon2 was missed. Transcription analysis showed that these isoforms of LvHcL were up-regulated after WSSV challenge in WSSV-resistant shrimp, while the transcriptions were decreased constantly in WSSV-susceptible shrimp. It is suggested that the hemocyanin had rich polymorphism and was involved in the antiviral response. These results could extend our previous findings and provide insights into the immune feature of hemocyanin, which would be helpful for further studies aimed at antiviral mechanism in inver-tebrate.
2011(6): 104-111.
doi: 10.1007/s13131-011-0167-7
The diversity of modular polyketide synthase (PKS) genes in sediments of Ardley Island in Antarctica, was studied by restriction fragment length polymorphism (RFLP) analysis. Phylogenetic analysis of 14 amino acid (AA) sequences indicates that the identified ketosynthase (KS) domains were clustered with those from diverse bacterial groups, including Cyanobacteria, γ-Proteobacteria, Actinobacteria, Firmicutes, and some unidentified microorganisms from marine sponge, bryozoan and other environmental samples. The obtained KS domains showed 43%-81% similarity at the AA level to reference sequences in GenBank. Six identified KS domains showed diverse sequences of the motif (VQTACSTS) that was used to identify the hybrid PKS/nonribosomal peptide synthetase (NRPS) enzyme complex, and formed a new branch. These results reveal a high diversity and novelty of PKS genes in antarctic sediments.
2007(1): 93-100.
Keywords:
Chlamys farreri ,
farrer's scallop ,
internal transcribed spacer (ITS-1) ,
DNA sequence ,
genetic variation
Sequence variation of the first internal transcribed spacer of ribosomal DNA (ITS-1) was examined and its application to the study of genetic variation was explored in four populations of farrer's scallop Chlamys farreri.ITS-1 fragments, with a length of about 300 bp, of 78 individuals collected from Dalian, Qingdao, Yantai in China and Korea respectively were amplified via PCR, cloned and sequenced.Intra-genomic variation was examined by sequencing several clones of single individuals.Alignment and polymorphism analysis detected 44 haplotypes and 50 polymorphic sites which consist of 30 substitutions and 20 indels, indicating a high level of polymorphisms.Sequence analysis also showed a very low level of intra-individual variation.All these features validated the feasibility of application of ITS-1 fragment to population analysis.Polymorphism analysis showed that the Korea sample has the richest genetic variation, followed by Yantai and Qingdao samples.AMOVA (analysis of molecular variance) showed that the majority (96.26%) of genetic variation was distributed within populations and 3.74% resulted from among populations, but with P<0.05 (=0.042), indicating that the populations in this study have significant divergence.This output was basically concordant with the result arising from RAPD data and different from that from mitochondrial 16S rDNA sequence data.Discussion on this inconsistency was made accordingly.
2005(4): 107-113.
The AFLP(amplified fragment length polymorphism)technique was used to analyse the genetic diversity in four scallop species,Patinopecten yessoensis,Argopecten irradians,Chlamys nobilis and C.farreri.The genetic similarity indexes of these four species are 0.841 5,0.786 3,0.719 0 and 0.673 1,while Shannon diversity indexes are 43.52,58.87,80.16 and 92.83,respectively.As analyzed,the genetic diversities in two native species,i.e.,C.farreri and C.nobilis,are higher than those in other two introduced species,A.irradians and P.yessoensis.The results also showed that C.nobilis and C.farreri shared the most common loci.The genetic distance indicated that C.nobilis and C.farreri are closely related.Moreover,out of 510 AFLP markers,21 specific bands are found to distinguish the four species scallops and these markers may be applied to the specific germplasm characterization and molecular assistant classification in scallops.
2005(5): 127-138.
A depth profile of bacterial community structure in one deep-sea sediment core of the western Pacific "warm pool" (WP) was investigated and compared with that in a sediment sample from the eastern Pacific (EP) by phylogenetic analysis of 16S rDNA fragments.Five bacterial 16S rDNA clone libraries were constructed, and t33 clones with different restriction fragment length polymorphism(RFLP) patterns were sequenced.A phylogenetic analysis of these sequences revealed that the bacterial diversity in a sample from the WP was more abundant than that in the EP sample.The bacterial population in the sediment core of WP was composed of eight major lineages of the domain bacteria.Among them the γ-Proteobacteria was the predominant and most diverse group in each section of WP sediment core, followed by the α-Proteobacteria.The genus Colwellia belonging to γ-Proteobacteria was predominant in this sample.The shift of bacterial communities among different sections of the WP sediment core was δ-, ε-Proteobacteria, and Cytopahga-Flexibacteria-Bacteroides (CFB) group.The ratios between them in the bacterial communities all showed inversely proportional to the depth of sediment.The sequences related to sulphate reducing bacteria (SRB) were detected in every section.The bacterial community structure in this sediment core might be related to the environmental characteristics of the surface seawater of the western Pacific WP.
2006(5): 151-157.
Two microsatellite DNA loci were used to trace the pedigree structure of six families in the shrimp Fenneropenaeus chinensis.Four of the families were natural mating, and the others were mated by artificial insemination.Eleven alleles were acquired at two microsatellite DNA loci (locus RS0622 and locus EN0033) by investigating 145 offsprings and 11 parents.Five alleles were acquired from locus RS0622 and six from locus EN0033.As analyzed, the gene frequencies were between 0.024 1 and 0.493 1, the heterozygosity was 0.652 2 and 0.688 8, and the polymorphism information content (PIC) was 0.585 7 and 0.652 9 for the locus RS0622 and the locus EN0033, respectively.Twenty-three genotypes were detected and the genotypes of the losing parents were also inferred.The pedigrees of three F1 and three F2 generations were determined by matching the genotype at each locus.
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