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ABSTRACT: Amphioxus is a promising model animal for evolutionary and developmental studies. However, as an emerging model organism, amphioxus lacks most molecular techniques applied in other well-developed model animals. Microinjection is a powerful technique for gene manipulation, and thus it undoubtedly is one of useful approaches in the studies of gene function and embryonic development. Although the method has been exploited in Florida and European amphioxus, it still remains to be optimized and introduced into other amphioxus species. In order to introduce the technique into our lab, we followed and optimized the previous description and successfully performed microinjection on unfertilized eggs of Asian amphioxus Branchiostoma belcheri. We made six solutions for practice: 200 mM KCl, 100 ng/μl actin-LacZ or 100 ng/μl actin-RFP vectors, LacZ or RFP vectors without promoter and RFP capped mRNA. More than 99.2 % of eggs injected with KCl were able to be fertilized, 94.3 % of them could hatch normally and 55.9 % survived until 2-day larvae, all of which were nearly equivalent to those obtained from normally fertilized eggs. Embryos injected with two plasmid constructs also showed very high fertilizing and hatching ratios, but normally developing ratios were slightly lower than that of KCl injection. Of those injected embryos, 91.8 % expressed exogenous gene LacZ and 80.5 % exhibited foreign RFP expression, which were driven by a promoter from amphioxus β-actin gene. The data indicated a successful modified microinjection method for the unfertilized eggs of Asian amphioxus, and those modifications improved the feasibility and efficiency of microinjection on amphioxus.
Archiv für Entwickelungsmechanik der Organismen 04/2013; · 1.77 Impact Factor
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ABSTRACT: In addition to protein coding sequence, the organism genome contains a significant amount of regulatory DNA. Comparative genomics reveals that the organism genomes of vertebrates, tunicate, cephalochordate, flies, and nematodes contain cis-regulatory elements with highly conserved non-coding elements (CNEs). CNEs that cluster around trans-dev genes are part of core gene regulatory networks (GRNs), and usually, they can act as transcriptional enhancers. In this review, we described the identification of CNEs and summarized their key properties across the metazoans, and then discussed the evolution of CNEs after large-scale genome duplication events and the role of CNEs in the evolution of ani-mal body plan.
Hereditas (Beijing) 01/2013; 35(1):35-44.
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ABSTRACT: Endogenous green fluorescent proteins (GFPs) have recently been found in amphioxus, where different characteristics of light production in different development stages and between different individuals have manifested. We identified the GFP genes in an amphioxus species Branchiostoma belcheri and monitored real time fluorescence signals of GFPs during different developmental stages to provide an insight on the GFP function in amphioxus. We found there are at least 12 endogenous GFP genes in amphioxus genome, and fluorescent expression changes in body position during different developmental stages. Additionally, GFP expression after metamorphosis development differed significantly among different amphioxus individuals, suggesting that there are multiple GFP homologous genes responsible for fluorescent expression. Expression levels of these genes varied significantly during different developmental stages, indicating that different GFP genes may have their unique functions in the development of amphioxus during specific phases of growth.
Zoological Research 06/2012; 33(3):304-13.
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ABSTRACT: A series of signal transduction pathways have been found to regulate the polarity establishment and formation of animal primary body axis. Among them, Wnt signaling pathway is extremely conserved and several key components in the pathway have been identified in the demosponge lineage. This implies that it is one of the earliest pathways involved in the ancestral metazoan axis development and might play an important role in specification and development of posterior and ventral fate of animal axis. Recently, with the establishment of functional experiments in vitro, the body plan formation has been found to be affected, in varying degrees, by many genes in the Wnt signaling pathway, such as members of wnt gene family, maternal gene beta-catenin and some transcription factor encoding genes. In this review, we analyzed the evolutionary origin of the wnt gene family involved in development of metazoan body plans, and then made a brief review on the roles of canonical Wnt/beta-catenin signaling in the polarity establishment and formation of primary body axis in diverse deuterostomes including sea urchin, amphioxus, zebrafish, frog, and mouse.
Hereditas (Beijing) 07/2011; 33(7):684-94.
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ABSTRACT: Amphioxus (lancelet) is an important model animal in the field of Evo-Devo study. However, the specimens for laboratorial experiments are usually sampled directly from the field. Thus, it is necessary to correctly identify species and evaluate the genetic diversity of geographic populations. In the present investigation, we amplified and sequenced COX I gene of amphioxus collected from various localities of the West Pacific Ocean and downloaded all available sequences of the gene from NCBI. Based on those sequences data, we constructed NJ tree to decide the taxonomic status of those amphioxus and performed AMOVA analysis to estimate genetic diversities among geographic populations and individuals. The current results supported the validity of the three amphioxus species, Branchiostoma malayanum, B. belcheri and B. japonicum. We also proposed that some amphioxus species names recorded in NCBI sequence database might be inaccurate. Genetic analysis on the geographic populations of amphioxus species suggested that each examined amphioxus species have a high level of genetic diversity. However, the genetic divergences among geographic populations of the same species are indetectable, indicating a frequent gene flow among them.
Zoological Research 08/2010; 31(4):375-80.
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ABSTRACT: Bone morphogenetic proteins (BMPs) are responsible for regulating embryo development and tissue homeostasis beyond osteogenesis. However, the precise biological roles of BMP3 and BMP3b remain obscure to a certain extent. In the present study, we cloned an orthologous gene (AmphiBMP3/3b) from amphioxus (Branchiostoma japonicum) and found its exon/intron organization is highly conserved. Further, in situ hybridization revealed that the gene was strongly expressed in the dorsal neural plate of the embryos. The gene also appeared in Hatschek's left diverticulum, neural tube, preoral ciliated pit and gill slit of larvae, and adult tissues including ovary, neural tube and notochordal sheath. Additionally, real-time quantitative polymerase chain reaction (RTqPCR) analysis revealed that the expression displayed two peaks at gastrula and juvenile stages. These results indicated that AmphiBMP3/3b, a sole orthologue of vertebrate BMP3 and BMP3b, might antagonize ventralizing BMP2 orthologous signaling in embryonic development, play a role in the evolutionary precursors of adenohypophysis, as well as act in female ovary physiology in adult.
Embryologia 02/2010; 52(2):157-67. · 2.21 Impact Factor
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ABSTRACT: The Pax gene family encodes a group of transcription factors whose evolution has accompanied the major morphological and functional innovations of vertebrate species. The evolutionary conservation throughout diverse lineages of metazoan and the functional importance in development rendered Pax family an ideal system to address the relationship inside Chordata phylum. In the present study, we sequenced and annotated four genomic regions containing Chinese amphioxus (Branchiostoma belcheri) Pax genes, and retrieved homologous sequences from public database. In comparison with vertebrate homologues, the predicted amphioxus Pax proteins display high sequence conservation. Evidences from the molecular phylogenetic studies and gene organization analyses supports cephalochordates have a much closer relationship to vertebrates than that between tunicates and vertebrates, contrasting to urochordate relatives hypothesis proposed by several latest studies. Analysis of phylogenetic topology derived from concatenated subfamily datasets uncovered a potential statistical bias of supermatrix approach. Furthermore, we deduced an evolutionary scenario of Pax gene family. This scenario provided a plausible explanation for the origin and dynamics of the Pax gene members.
Genes & Genetic Systems 01/2010; 85(3):193-206. · 0.95 Impact Factor
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ABSTRACT: As one of the closest living invertebrate relatives of vertebrates, amphioxus (subphylum Cephalochordata) occupies a key position in animal evolution and is becoming the best available proxy and model animal for studying the last common ancestor of all chordates, especially vertebrates. As long-term continuous culturing of amphioxus in laboratory became reliable, for pushing this animal to be a more successful model system, whole-genome sequencing of one or more species derived from this branch will be another urgent issue needed to address. In the present study, we described the construction and characterization of a bacterial artificial chromosome (BAC) library, using a single individual of Chinese amphioxus (Branchiostoma belcheri). High quality genomic DNA extracted from the spermary was partially digested with EcoRand EcoRmethylase. Desirable DNA fragments were isolated by pulsed field gel electrophoresis (PFGE), ligated to linearized and phosphorylased carrier pCC1BAC, and then transformed to Escherichia coli EPI300. The constructed library consists of 44 706 clones with the average insert fragment size around 80 kb as estimated by PFGE. The representation of the library is about 9 equivalents to the amhioxus genome. These results indicate that the BAC library will be useful for functional genomic studies and facilitate the whole-genome sequencing of Chinese amphioxus.
Hereditas (Beijing) 01/2010; 32(1):67-72.
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ABSTRACT: Green fluorescent protein (GFP) has been widely used as a molecular marker in modern biological research. Before the recent report of one GFP gene in Branchiostoma floridae, GFP family members were cloned only from other two groups of species: Cnidaria and Copepoda. Here we describe the complete GFP gene repertoire of B. floridae which includes 13 functional genes and 2 pseudogenes, representing the largest GFP family found so far. Coupling with nine other GFP sequences from another two species of genus Branchiostoma and the sequences from Cnidaria and Copepoda, we made a deep-level phylogenetic analysis for GFP genes in cephalochordates and found: 1) GFP genes have experienced a divergent evolution in cephalochordates; 2) all amphioxus GFP genes form four main clades on the tree which had diverged before the radiation of the last common ancestor of all extant cephalochordates; 3) GFP genes in amphioxus shared a common ancestor with that in Copepoda rather than being derived from horizontal gene transfer, which indicates that our ancestor was derived from a fluorescent organism and lost this ability after its separation from Cephalochordata, and also makes GFP a rare gene which has a rather unusual evolutionary path. In addition, we also provided evidence indicating that GFP genes have evolved divergent functions by specializing their expression profile, and different fluorescent spectra by changing their emission peaks. These findings spark two interesting issues: what are GFP in vivo functions in cephalochordates and why they are lost in other examined deuterostomes?
Gene 08/2009; 446(1):41-9. · 2.34 Impact Factor
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ABSTRACT: The rice frog, Fejervarya multistriata, is an amphibian widely distributed in China. In this study, we sampled the species across its distributional area in China and sequenced the mtDNA D-loop to investigate the genetic diversity and geographical pattern of the frog population. The results revealed 38 haplotypes in the population, with K2P values varying from 0.19% to 4.22%. Both a phylogenetic analysis and a nested clade analysis (NCA) detected two geographically isolated lineages respectively distributed around the Yangtze drainage (Yangtze lineage) and the south of China (southern lineage). NCA inferred a contiguous range expansion within the Yangtze lineage and allopatric fragmentation within the southern lineage, which might be partly due to the limited samples from this lineage. Accordingly, Fu's Fs test also indicated a population expansion after glacial movement. Therefore, we assumed that the species history responding to glacial events shaped the present population pattern of F. multistriata on the Chinese mainland.
ZOOLOGICAL SCIENCE 09/2008; 25(8):811-20. · 0.95 Impact Factor
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ABSTRACT: Previous studies showed that the vertebrate ABCA subfamily, one subgroup of the ATP-binding-cassette superfamily, has evolved rapidly in terms of gene duplication and loss. To further uncover the evolutionary history of the ABCA subfamily, we characterized ABCA members of two amphioxus species (Branchiostoma floridae and B. belcheri), the closest living invertebrate relative to vertebrates. Phylogenetic analysis indicated that these two species have the same set of ABCA genes (both containing six members). Five of these genes have clear orthologs in vertebrate, including one cephalochordate-specific duplication and one vertebrate-specific duplication. In addition, it is found that human orthologs of amphioxus ABCA1/4/7 and its neighboring genes mainly localize on chromosome 1, 9, 19 and 5. Considering that most of analyzed amphioxus genes have clear orthologs in zebrafish, we conclude these four human paralogous regions might derive from a common ancestral region by genome duplication occurred prior to teleost/tetrapod split. Therefore, the present results provide new evidence for 2R hypothesis.
Gene 01/2008; 405(1-2):88-95. · 2.34 Impact Factor
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ABSTRACT: C-type lectins found in many animals are non-enzymatic proteins and able to bind with mono- and oligosaccharides in a Ca(2+)-dependent fashion. Here, we report the cloning of two C-type lectins named BML-1 and BML-2 from the venom gland of Bungarus multicinctus, and expression of their mature peptides with 135 and 137 amino acids as inclusion bodies. Recombinant BML-1 and BML-2 proteins with 135 amino acids formed monomers, and those with 137 amino acids formed homodimers and monomers and both of them displayed certain hemagglutinating activity to rabbit erythrocytes. The results of Western blotting and immuno-affinity chromatography demonstrated that C-type lectins in B. multicinctus formed dimers in physiological conditions, and their molecular weight is lower than previous predictions. This is the first report of the cloning of the BML-2 gene from the venom gland of B. multicinctus, as well as an investigation of its confirmation and biological functions.
Toxicon 10/2007; 50(3):411-9. · 2.51 Impact Factor
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ABSTRACT: The lancelet is considered to be a promising laboratory model animal. To establish laboratory colonies of lancelet, we collected parental lancelets of Branchiostoma belcheri and B. japonicum (previously named as B. belcheri tsingtauense) with fully developed gonads from Xiamen Rare Marine Creature Conservation Areas (Fujian, China) on dates just before their spawning in the field in 2005. Those parental lancelets spawned spontaneously in the laboratory and produced thousands upon thousands of fertilized eggs. After carefully hatching and maintaining for almost 1 year, we successfully obtained about 500 first generation (F1) adults of B. belcheri and 3,300 of B. japonicum. Part of those F1 lancelets ripened and spontaneously spawned in 2006, and several thousands of second generation (F2) individuals of both species were produced. The young F2 lancelets are growing in good condition and some of B. japonicum initiated gonad development in December, 2006. Our experience emphasizes that cleanness of settlement substratum and sufficient food supply are important factors for long-term culture of lancelets in the laboratory.
Journal of Experimental Zoology Part B Molecular and Developmental Evolution 08/2007; 308(4):464-72. · 2.42 Impact Factor
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ABSTRACT: Identification of conserved genomic regions within and between different genomes is crucial when studying genome evolution. Here, we described regions of strong synteny conservation between vertebrate deuterostomes (tetrapods and teleosts) and invertebrate deuterostomes (amphioxus and sea urchin). The shared gene contents across phylogenetically distant species demonstrate that the conservation of the regions stemmed from an ancestral segment instead of a series of independent convergent events. Comparison of the syntenic regions allows us to postulate the primitive gene organization in the last common ancestor of deuterostomes and the evolutionary events that occurred to the 3 distinct lineages of sea urchin, amphioxus, and vertebrates after their separation. In addition, alignment of the syntenic regions led to the identification of 8 noncoding evolutionarily conserved regions shared between amphioxus and vertebrates. To our knowledge, this is the first report of conserved noncoding sequences shared by vertebrates and nonvertebrates. These noncoding sequences have high possibility of being elements that regulate neighboring genes. They are likely to be a factor in the maintenance of conserved synteny over long phylogenetic distance in different deuterostome lineages.
Molecular Biology and Evolution 04/2007; 24(3):784-91. · 5.55 Impact Factor
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ABSTRACT: The ATP-binding cassette (ABC) superfamily of genes encodes membrane proteins that transport many kinds of substrates across membranes. Based on amino acid sequence similarities and phylogeny, 48 ABC genes in the human genome were divided into seven subfamilies: ABCA to ABCG. Among them, ABCA transporters have a unique topology and the members of this subfamily had expanded twice by gene duplication after the divergences between amphibian and mammal, respectively. The new duplicated genes are well retained in rodent and carnivore, while half of them became pseudogenes or were absent in primate genome. Transporters of the ABCA subclass were responsible for critical physiological functions in the transmembrane transport of endogenous lipid and cholesterol substrates. Mutations of members of ABCA are associated with human genetic diseases.
Hereditas (Beijing) 09/2006; 28(8):1015-22.
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ABSTRACT: Chinese alligator (Alligator sinensis) is one of the most critically endangered species among 23 extant crocodiles in the world. To prevent the extinction of the
species, a captive propagation started at early 1980s, and the total number of alligator was brought up to 10 thousands from
dozens of founder in 2000. But several genetic investigations showed those alligators were under an extremely low genetic
diversity status with few detectible polymorphic loci. To get more insight into its genetic diversity for the management of
captive Chinese alligator, AFLP was adopted to characterize variations in the population. Total of 347 bands were generated
from 47 individuals using 3 primer combinations, of which 203 (58.50%) were polymorphic, and 35 AFLP phenotypes were revealed
from those individuals. Comparing the results between RAPD and AFLP analysis on almost same sample set clearly indicated that
AFLP is more efficient in revealing polymorphic loci, especially in those populations with extremely low genetic diversity.
In present three assays, electrophoresis profile also displayed 3 individuals possessing very highly polymorphic AFLP phenotypes
that were never been found by RAPD and mtDNA D-loop sequencing, implicating that we should offer these individuals more breeding
opportunities to maintain the genetic diversity in the population and restrict those carrying few polymorphic loci from reproduction.
Biodiversity and Conservation 07/2006; 15(9):2945-2955. · 2.24 Impact Factor
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ABSTRACT: Lancelets in Xiamen were reported as Branchiostoma belcheri in 1932, and subsequently were believed to comprise a single species. However, recent studies revealed that Xiamen lancelets actually represent two species, B. belcheri and B. japonicum. We observed thousands of lancelets from Xiamen beach to recognize these two species. Our observations showed that at least three morphological characters distinguish them: 1) the rostral fin is slightly round with the end obtuse in B. belcheri but elliptic with the end cuspate in B. japonicum; 2) the number of preanal fin-chambers is more than 80 in B. belcheri but less than 64 in B. japonicum, and the chambers are slender in the former but stout in the latter; 3) the caudal fin of B. belcheri is narrower than that of B. japonicum, and the angle between the dorsal and super-caudal fins, and between preanal and sub-caudal fins, is obtuse in B. belcheri but acute in B. japonicum. We also provide some ecological and distributional evidence to support the conclusion that there are two separate species in Xiamen waters.
ZOOLOGICAL SCIENCE 07/2006; 23(6):573-9. · 0.95 Impact Factor
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ABSTRACT: Alternative splicing, a fundamental and important regulatory mechanism in eukaryotes, allows one pre-mRNA to be processed into many different mature forms within a cell, each of which can have distinct functions. As alternative splicing is associated with human diseases, the study of alternative splicing becomes quite important. Bioinformatics is a new subject for the study of alternative splicing, especially for its regulatory mechanism, prediction and origin. Of course, bioinformatics must be combined with experimental research so as to clarify these aspects of alternative splicing. This paper reviewed the recent research progress in this field in the hope to gain a deeper understanding of eukaryotic gene expression regulation.
Hereditas (Beijing) 12/2005; 27(6):1001-6.
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ABSTRACT: Snake venom contains a number of small proteins,enzymes and other components,which displays a broad spectrum of biological activities. With the ability of specifically binding on acetylcholine acceptor, alpha-bungarotoxins are not only useful molecular probes in investigating the mechanism of neural signal transmission, but also potential pharmic preparations for neural disease treatment. In current research,cDNAs of Bungarus multicinutus venom gland were synthesized using SMART cDNA amplification kit and then, alpha-bungarotoxin genes were cloned and sequenced. Total of 20 clones were sequenced representing 14 isotoxin mRNAs of alpha-bungarotoxins. Among those clones, a novel isotoxin gene was subcloned into two expression plasmids, alpha-BgTX/pQE30a and alpha-BgTX/pGEX-4T-1, and transformed into E. coli. After inducing with IPTG, fused protein of GST-alpha-BgTX was successfully expressed at level of 30% gross proteins of bacteria. More than 25% of fused protein was in the soluble fraction and the rest in inclusion body.
Acta Genetica Sinica 08/2005; 32(7):682-8.
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ABSTRACT: Amphioxus is a crucial organism for the study of vertebrate evolution. Although a genomic BAC library of Branchiostoma floridae has been constructed, we report here another BAC library construction of its distant relative species Branchiostoma belcheri. The amphioxus BAC library established in present study consists of 45,312 clones arrayed in one hundred and eighteen 384-well plates. The average insert fragment size was 120 kb estimated by Pulsed Field Gel Electrophoresis (PFGE) analysis of 318 randomly selected clones. The representation of the library is about 12 equivalent to the genome, allowing a 99.9995% probability of recovering any specific sequence of interest. We further screened the library with 4 single copied Amphi-Pax genes and identified total of 26 positive clones with average of 6.5 clones for each gene. The result indicates this library is well suited for many applications and should also serve as a useful complemental resource for the scientific community.
Genes & Genetic Systems 07/2005; 80(3):233-6. · 0.95 Impact Factor
