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1.
Lianming Du Qin Liu Kelei Zhao Jie Tang Xiuyue Zhang Bisong Yue Zhenxin Fan 《Molecular ecology resources》2020,20(1):283-291
Microsatellites are widely distributed throughout nearly all genomes which have been extensively exploited as powerful genetic markers for diverse applications due to their high polymorphisms. Their length variations are involved in gene regulation and implicated in numerous genetic diseases even in cancers. Although much effort has been devoted in microsatellite database construction, the existing microsatellite databases still had some drawbacks, such as limited number of species, unfriendly export format, missing marker development, lack of compound microsatellites and absence of gene annotation, which seriously restricted researchers to perform downstream analysis. In order to overcome the above limitations, we developed PSMD (Pan‐Species Microsatellite Database, http://big.cdu.edu.cn/psmd/ ) as a web‐based database to facilitate researchers to easily identify microsatellites, exploit reliable molecular markers and compare microsatellite distribution pattern on genome‐wide scale. In current release, PSMD comprises 678,106,741 perfect microsatellites and 43,848,943 compound microsatellites from 18,408 organisms, which covered almost all species with available genomic data. In addition to interactive browse interface, PSMD also offers a flexible filter function for users to quickly gain desired microsatellites from large data sets. PSMD allows users to export GFF3 formatted file and CSV formatted statistical file for downstream analysis. We also implemented an online tool for analysing occurrence of microsatellites with user‐defined parameters. Furthermore, Primer3 was embedded to help users to design high‐quality primers with customizable settings. To our knowledge, PSMD is the most extensive resource which is likely to be adopted by scientists engaged in biological, medical, environmental and agricultural research. 相似文献
2.
Identification of CR1 retroposons in Arborophila rufipectus and their application to Phasianidae phylogeny 下载免费PDF全文
Tianlin Sun Jing Li Bisong Yue Xiuyue Zhang Jing Li 《Molecular ecology resources》2016,16(4):1037-1049
Chicken repeat 1 (CR1), a member of non‐LTR retroposon, is an important phylogenetic marker in avian systematics. In this study, we reported several characteristics of CR1 elements in a draft genome of Arborophila rufipectus (Sichuan partridge). According to the analyses of RepeatMasker, approximately 254 966 CR1 elements were identified in A. rufipectus, covering 6.7% of the genome. Subsequently, we selected eighteen novel CR1 elements by comparing the chicken genome, turkey genome and assembled A. rufipectus scaffolds. Here, a combined data set comprising of 22 CR1 loci, mitochondrial genomes and eight unlinked introns was analysed to infer the evolutionary relationships of twelve Phasianidae species. The applicability of CR1 sequences for inferring avian phylogeny relative to mtDNA and intron sequences was investigated as well. Our results elucidated the position of A. rufipectus in Phasianidae with robust supports that it presented a sister clade to Arborophila ardens/Arborophila brunneopectus, and implied that genus Arborophila was in a basal phylogenetic position within Phasianidae and a phylogenetic affinity between Meleagris gallopavo and Pucrasia macrolopha. Therefore, this work not only resolved some of the confounding relationships among Phasianidae, but also suggested CR1 sequences could provide powerful complementary data for phylogeny reconstruction. 相似文献
3.
美洲大蠊Periplaneta americana胸腺素基因具有THY1、THY2和THY3三个不同剪接体,其中THY3结构域最多。本研究使用实时荧光定量PCR技术比较分析了THY3在美洲大蠊不同性别、不同发育阶段及不同组织中的表达差异,以及大肠杆菌Escherichia coli诱导对美洲大蠊血淋巴和脂肪体中THY3表达的影响。结果表明:THY3在成虫期的表达量显著高于其他虫期,雌虫表达量显著高于雄虫,脂肪体表达量显著高于血淋巴、头部、肌肉、体壁组织。雌性成虫体腔注射大肠杆菌3 h后血淋巴中THY3表达量显著增高,而在脂肪体中12 h后才检测到THY3表达明显上调,研究结果为进一步研究美洲大蠊胸腺素的功能打下了基础。 相似文献
4.
Jin Yanjun He Kun Xiang Peng Wang Xiaodong Tong Lintian Wei Zhen Zhang Xiuyue Song Zhaobin 《Environmental Biology of Fishes》2022,105(9):1139-1151
Environmental Biology of Fishes - We investigated the temporal dynamics of population genetics of the Chinese longsnout catfish (Leiocassis longirostris) given wild population decline due to... 相似文献
5.
Molecular phylogenetic relationships among Asiatic shrewlike moles inferred from the complete mitogenomes 下载免费PDF全文
Robert W. Murphy Shunde Chen Xiuyue Zhang Chaochao Yan Yang Liu Zhiyu Sun Jianrong Fu Shaoying Liu Bisong Yue 《Journal of Zoological Systematics and Evolutionary Research》2015,53(2):155-160
Asiatic shrewlike moles are distributed almost entirely in south‐west China; four of the five species of the genus Uropsilus, Uropsilus aequodonenia, U. andersoni, U. investigator and U. soricipes are endemic to China. Excluding the five species, three cryptic species (U. sp. 1, U. sp. 2 and U. sp. 3) and two putative species, U. nivatus and U. atronates, are recognized. The phylogenetic relationships among the species remain unclear and these preclude investigations of their potential adaptations for living in high altitudes. We sequenced the complete mitochondrial DNA genomes of three species of Asiatic shrewlike moles (U. aequodonenia, U. andersoni and U. nivatus). Phylogenetic analyses of 16 published and our de novo mitogenomes yield single, robust trees with the relationships being (U. soricipes (U. sp. 1 (U. nivatus (U. andersoni, U. aequodonenia)))). Further, the tree verifies the validity of recently described U. aequodonenia. Analyses of selection pressure suggest that the 13 mtDNA‐encoding genes of species in the genus Uropsilus all have experienced strong purifying selection, although ATP8 accumulated a higher ratio of non‐synonymous substitutions than the other loci, which might reflect adaptation of the genus Uropsilus to different environments/elevations. 相似文献
6.
The complete mitochondrial DNA genome of the Sichuan taimen (Hucho bleekeri) was determined by the long and accurate polymerase chain reaction (LA-PCR) and primer walking sequence method. The entire mitochondrial genome of this species is 16,997 bp in length, making it the longest among the completely sequenced Salmonidae mitochondrial genomes. It consists of two ribosomal RNA (rRNA) genes, 13 protein-coding genes, 22 transfer RNA (tRNA) genes, and one control region (CR). The gene arrangement, nucleotide composition, and codon usage pattern of the mitochondrial genome are similar to those of other teleosts. A T-type mononucleotide microsatellite and an 82 bp tandem repeat were identified in the control region, which were almost identical among the three H. bleekeri individuals examined. Both phylogenetic analyses based on 12 concatenated protein-coding genes of the heavy strand and on just the control region show that H. bleekeri is a basal species in Salmoninae. In addition, Salmo, Salvelinus and Oncorhynchus all represent monophyletic groups, respectively. All freshwater species occupied basal phylogenetic positions, and also possessed various tandem repeats in their mitochondrial control regions. These results support established phylogenetic relationships among genera in Salmonidae based on morphological and molecular analyses, and are consistent with the hypothesis that Salmonidae evolved from freshwater species. 相似文献
7.
The Chevrier's field mouse (Apodemus chevrieri) is an endemic species to China and is an important pest in agriculture and human diseases. In this study, the complete mitochondrial genome of this species was sequenced and its size was 16,298 bases (accession no.: HQ896683). The mitogenome structure was similar compared with other reported rodent mitochondrial genomes and includes 13 protein-coding genes, 2 rRNA genes (12S rRNA and 16S rRNA), 22 tRNA genes, and 1 control region. This was the first complete mitogenome sequenced in genus Apodemus. The phylogenetic analyses based on the sequences of 12 heavy-strand protein-coding genes demonstrated that A. chevrieri clustered together with genus Mus. Additionally, extremely high haplotype and nucleotide diversities (h=0.978, π=2.6%) were observed based on 44 mitochondrial cytochrome b (cyt b) gene sequences. This suggests adaptive divergence of this species to a variety of living habitats and potential refuges in the eastern margin of the Hengduan Mountains during the Quaternary ice ages. No population expansions or genetic bottlenecks were observed in demographic analyses. The phylogenetic analysis of cyt b sequences and haplotypes revealed a genetic differentiation between north and south populations. The divergence between north clade and south clade occurred probably in the middle Pleistocene 1.1815 million years ago (Mya) (95% highest posterior density 2.3189-0.2737 Mya), which was congruent with the periods of the most tense uplift events in the Tibetan Plateau. 相似文献
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9.
Zhenxin Fan Shaoying Liu Yang Liu Bo Zeng Xiuyue Zhang Cong Guo Bisong Yue 《Molecular phylogenetics and evolution》2009,51(3):447-453
Although the subfamily Zapodinae (Rodentia, Dipodidae) contains only five species, the phylogeny and taxonomy of these species are still being disputed. First, whether Eozapus and Napaeozapus should be treated as independent genera or subgenera of Zapus has been argued for a long period. Second, the subspecific genetic differentiation of Chinese jumping mouse (Eozapus setchuanus) has not been studied in detail, neither from morphological nor molecular aspects. In this study, the phylogenetic relationship among all the five species of Zapodinae was reconstructed using DNA sequence data from the mitochondrial cytochrome b gene and the nuclear interphotoreceptor retinoid binding protein gene. Bayesian inference, maximum parsimony and maximum likelihood analyses were conducted. The results showed that two major clades could be recognized within Zapodinae. Eozapus setchuanus, is the species endemic to China, strongly formed a monophyletic clade. In the other clade, genus Zapus received significant support in all analyses to be the sister group of the genus Napaeozapus. By comparing genetic distances among these three genera, we conclude that both Eozapus and Napaeozapus should be considered as valid genera rather than subgenera of Zapus. Furthermore, we observed that the two subspecies of E. setchuanus did not form reciprocally monophyletic groups, thus the traditional taxonomy which divided E. setchuanus into two subspecies based on only one morphological character was questionable. 相似文献
10.
Fifteen new microsatellite markers were isolated in rock carp, Procypris rabaudi (Tchang), from an AC-enriched genomic library. The allele number of these loci ranged from three to 13 (average 6.87 per
locus) in the tested 24 individuals. Polymorphism information content (PIC) ranged from 0.453 to 0.821 with an average of
0.719. Average observed and expected heterozygosities were 0.712 (range 0.565–0.917) and 0.772 (range 0.542–0.855), respectively.
These microsatellite markers could be useful in the population genetic study of rock carp. 相似文献