Cloning, characterization, and gene expression analysis of a novel cadmium metallothionein gene in Tetrahymena pigmentosa

A novel cadmium-inducible metallothionein (MT) gene (Tpig-MT1) was cloned and sequenced from the ciliate Tetrahymena pigmentosa. The number of deduced amino acids is 118. The polypeptide possesses CCC and CC clusters characteristic of typical Tetrahymena Cd-inducible MTs. The structure of Tpig-MT1 is different from the reported Cd-MT in T. pyriformis, T. thermophila and T. pigmentosa. Tpig-MT1 contains two intragenic tandem repeats with 72.9% identity described as Tpig-MT1 (repeat A1) and Tpig-MT1 (repeat A2). The transcriptional response of Tpig-MT1 gene to different heavy metals (Cd, Cu, Zn, Hg, Pb) and oxidative stress (H2O2) was measured using real-time quantitative PCR. The results showed that the gene was quickly induced (1 h) by the five heavy metals and the order of expression level was Hg>Pb>Cd>Cu>Zn. The induction effect of H2O2 was 5-fold after about 15 min, but soon decreased to a non-significant level (30 min). The genetic diversity of Tetrahymena MT genes is discussed in relation to the unique structure of the Tpig-MT1 gene and other reported Cd-MT isoforms. (C) 2008 Elsevier B.V. All rights reserved.

Cloning and sequence analysis of Sox genes in a tetraploid cyprinid fish, Tor douronensis

A PCR survey for Sox genes in a young tetraploid fish Tor douronensis (Teleostei: Cyprinidae) was performed to access the evolutionary fates of important functional genes after genome duplication caused by polyploidization event. Totally 13 Sox genes were obtained in Tor douronensis, which represent SoxB, SoxC and SoxE groups. Phylogenetic analysis of Sox genes in Tor douronensis provided evidence for fish-specific genome duplication, and suggested that Sox19 might be a teleost specific Sox gene member. Sequence analysis revealed most of the nucleotide substitutions between duplicated copies of Sox genes caused by tetraploidization event or their orthologues in other species are silent substitutions. It would appear that the sequences are under purifying selective pressure, strongly suggesting that they represent functional genes and supporting selection against all null allele at either of two duplicated loci of Sox4a, Sox9a and Sox9b. Surprising variations of the intron length and similarities of two duplicated copies of Sox9a and Sox9b, suggest that Tor douronensis might be an allotetraploidy.

PCR survey of Hox genes in the goldfish Carassius auratus auratus

A tetraploidization event took place in the cyprinid lineage leading to goldfishes about 15 million years ago. A PCR survey for Hox genes in the goldfish Carassius auratus auratus (Actinopterygii: Cyprinidae) was performed to assess the consequences of this genome duplication. Not surprisingly, the genomic organization of the Hox gene clusters of goldfish is similar to that of the closely related zebrafish (Danio rerio). However, the goldfish exhibits a much larger number of recent pseudogenes, which are characterized by indels. These findings are consistent with the hypothesis that dosage effects cause selection pressure to rapidly silence crucial developmental regulators after a tetraploidization event.

Identification of three duplicated Spin genes in medaka (Oryzias latipes)

Gene and genomic duplications are very important and frequent events in fish evolution, and the divergence of duplicated genes in sequences and functions is a focus of research on gene evolution. Here, we report the identification and characterization of three duplicated Spindlin (Spin) genes from medaka (Oryzias latipes): OlSpinA, OlSpinB, and OlSpinC. Molecular cloning, genomic DNA Blast analysis and phylogenetic relationship analysis demonstrated that the three duplicated OlSpin genes should belong to gene duplication. Furthermore, Western blot analysis revealed significant expression differences of the three OlSpins among different tissues and during embryogenesis in medaka, and suggested that sequence and functional divergence might have occurred in evolution among them. © 2005 Elsevier B.V. All rights reserved.

Cloning and expression analysis in mature individuals of two chicken type-II GnRH (cGnRH-II) genes in common carp (Cyprinus carpio)

Gonadotropin-releasing hormone (GnRH) is a conservative neurodecapeptide family, which plays a crucial role in regulating the gonad development and in controlling the final sexual maturation in vertebrate. Two differing cGnRH-II cDNAs of common carp, namely cGnRH-II cDNA1 and cDNA2, were firstly cloned from the brain by rapid amplification of cDNA end (RACE) and reverse transcription- polymerase chain reaction (RT-PCR). The length of cGnRH-II cDNA1 and cDNA2 was 622 and 578 base pairs (bp), respectively. The cGnRH-II precursors encoded by two cDNAs consisted of 86 amino acids, including a signal peptide, cGnRH-II decapeptide and a GnRH-associated peptide (GAP) linked by a Gly-Lys-Arg proteolytic site. The results of intron trapping and Southern blot showed that two differing cGnRH-II genes in common carp genome were further identified, and that two genes might exist as a single copy. The multi-gene coding of common carp cGnRH-II gene offered novel evidence for gene duplication hypothesis. Using semi-quantitative RT-PCR, expression and relative expression levels of cGnRH-II genes were detected in five dissected brain regions, pituitary and gonad of common carp. With the exception of no mRNA2 in ovary, two cGnRH-II genes could be expressed in all the detected tissues. However, expression levels showed an apparent difference in different brain regions, pituitary and gonad. According to the expression characterization of cGnRH-II genes in brain areas, it was presumed that cGnRH-II might mainly work as the neurotransmitter and neuromodulator and also operate in the regulation for the GnRH releasing. Then, the expression of cGnRH-II genes in pituitary and gonad suggested that cGnRH-II might act as the autocrine or paracrine regulator.

Motilin/ghrelin荷尔蒙基因家族及其受体基因家族的分子进化研究和云南闭壳龟（Cuorayunnanensis）的分子鉴定及进化地位研究

哺乳动物motilin/ghrelin荷尔蒙基因家族编码产生三种多肽荷尔蒙，motilin、ghrelin和obestatin。这三种荷尔蒙分别结合各自特异性受体MLNR、GHSR和GPR39，调控不尽相同，但类似或相关的生理生化过程，并且它们的受体相互之间也高度同源。根据达尔文的进化论，任何复杂的生物系统都是在原有基础上，在自然选择的作用下逐步调整优化而来（Darwin 1859）。一方面，一个系统中相互作用的各个组分在进化过程中同时发生或变化的概率微乎其微；另一方面，紧密相互关联的系统中一个组分的孤立存在看起来又是毫无意义的。本研究中，我们基于系统发育分析重建了荷尔蒙基因家族及其受体基因家族的进化历史，探讨它们在进化中的关系。从而了解在一个整合的系统中，基因复制（gene duplication）后产生的新的组分是如何演化的，是如何形成新的分子间相互作用（如荷尔蒙–受体间特异性相互作用）和发生功能分化的。 我们的研究结果表明，preproghrelin（GHRL）和prepromotilin（MLN）源于一个祖先基因，是由基因重复而来，基因重复发生在C端两个新的翻译后剪辑位点演化出现之后，既两栖动物与羊膜动物分歧之后（而后产生了新的多肽荷尔蒙，例如高等哺乳动物GHRL中的obestatin）。受体与配体的进化历史并不一致。受体GPR39最先分歧，然后类似GHSR的祖先基因经历先后两次重复，产生了硬骨鱼世袭特异的基因簇A，MLNR和GHSR，基因重复事件的发生早于硬骨鱼与四足动物的分歧。Ghrelin/GHSR信号通路系统从硬骨鱼到哺乳动物的进化过程中十分保守，结构和功能几乎都没有发生太大变化。Motilin和MLNR间的特异性相互作用是荷尔蒙基因重复发生后，配体、受体间协同进化的结果，自此形成了新的Motilin/MLNR信号通路系统。 我们提出了一个复杂系统（分子间相互作用网络）进化的模型：基因重复或酶饰作用后产生了新的组分，它们通常是先前已有组分的一种结构上的变异，能与之前已经存在的分子形成新的分子间相互作用，从而演化出新的功能。基因重复之前，通常存在基因共享，即一种分子参与到多个过程、多种分子间相互作用。基因重复或酶饰作用生成了新组分，新的分子间相互作用，为功能上的专化和特化提供了条件。 此外我们还对新近发现的活的云南闭壳龟进行了分子鉴定，并探讨了云南闭壳龟的系统发育地位。云南闭壳龟（Cuora yunnanensis，Boulenger，1906）曾被认为已经灭绝，在保护生物学上受到广泛的关注。我们测定了三只活的云南闭壳龟线粒体COI和ND4及His、Ser、Leu tRNA序列片断，共1725碱基序列。结合闭壳龟属其它物种序列，包括之前测定的一只云南闭壳龟标本（MNHN 1907.10）的DNA序列，进行了分子系统学分析。与100年前的标本比较，无论是形态上、还是本文的分子系统结果都显示，新发现的活的云南闭壳龟确实是云南闭壳龟。同时，我们的结果确证了标本序列的可信性，揭示云南闭壳龟不是近期杂交形成的，代表了进化上独立的遗传谱系，且种内仍存在一定的遗传多样度。本文是分子系统学在濒危物种保护应用中的成功案例。我们的结果为推翻云南闭壳龟已经灭绝的观点提供了进一步强有力的分子生物学证据，但该物种极其稀少的状况提示其前景不容乐观，必须尽快采取有力的措施予以重点保护。

酵母基因组进化中一些重要新性状的产生及其效应

本论文用生物信息学的方法对酵母基因组进化中产生的新性状进行了系统 深入的研究。首先，在大多数的真核生物中，线粒体是生物能量生成所必需的细 胞器。但当葡萄糖的含量丰富的时候，即使是在有氧条件下，经过基因组重复 （WGD，whole genome duplication）后的大多酵母也都可以不需要线粒体而执行 发酵过程，而且甚至在线粒体基因组缺陷的情况下仍可以生存。在本次研究中， 我们揭示核编码的线粒体相关基因的进化速率在基因组重复后的物种中比其在 基因组重复前的物种中显著加快。而且这些基因的密码子使用偏好也在基因组重 复后的物种中减弱。密码子使用偏好的模式和一个特殊转录调控因子的分布显示 在基因组重复后的进化支系中，有效的有氧发酵过程的起源时间大致是在 Kluyveromyces polysporus 和 Saccharomyces castellii 从它们的共同祖先分化之 后。根据上述结果我们得出结论，可能正是这种新的能量策略的产生导致了线粒 体相关基因的功能在基因组重复后的物种中选择性放松。 其次，我们系统地研究了一个多细胞真菌Ashbya gossypii 和九个单细胞酵母 之间密码子使用偏好性的差异。细胞周期调控基因一直被认为是它们形态差异的 关键基因。由于A. gossypii 和典型的单细胞酵母Saccharomyces cerevisiae 有几乎 完全一样的细胞周期调控基因，因此形态上的差异可能是由于直系同源基因的表 达调控差异造成的。我们发现在A. gossypii 中细胞周期基因的翻译效率比在其他 单细胞酵母中显著增高，同时也发现单细胞酵母中的新陈代谢基因比其在A. gossypii 中有显著增高的翻译效率。因为基因的翻译效率和该基因在物种中的重 要性密切相关，所以我们观察到的这些基因翻译效率的显著差异可能可以阐明 A. gossypii 和单细胞酵母的形态差异的原因。同时我们的结果对理解真核生物多 细胞的起源过程也有提示意义。

同源四倍体水稻雌配子体发育特性及变异胚囊研究

通过秋水仙素诱导获得同源四倍体水稻10个株系，包括6个恢复系、3个保持系和1个不育系，这些株系具有加倍的染色体组。田间观察表明10个株系具有特殊的农艺性状：茎杆变粗壮、植株颜色加深、叶片变厚、叶宽适度增加、分蘖数减少、有效分蘖的比率下降等。根尖有丝分裂鉴定表明，同源四倍体水稻10个株系具有正常的有丝分裂，观察细胞的染色体数目皆为2n=48。花粉母细胞减数分裂鉴定表明10个株系具有比较理想的减数分裂行为，后期I染色体滞后、末期I微核生成和末期II异常小孢子比率较低，能较好的完成减数分裂过程，其中后期I染色体滞后比率约为10%-20%，末期I微核生成比率约为1%-6%，末期II异常小孢子比率约为1%-8%。这提示，染色体联合和分离不规则导致三价体、单价体 和落后染色体等产生，并进一步导致在后期和末期不均横分离产生异常小孢子，这可能是同源四倍体株系结实率不高的原因之一。 同源四倍体水稻正常胚囊为蓼型，变异胚囊具有多种类型，其比率显著高于二倍体对照，变化范围为39.62%－69.85%。按变异胚囊的结构特点和形成方式，分为四种类型：退化型，结构变异型，无融合生殖型和反足细胞增殖型。退化型胚囊的平均比率为29.17%，包括小胚囊（15.04%）和完全退化胚囊（14.13%），前者仍有较小胚囊腔而后者胚囊腔缺失。结构变异胚囊包括结构缺失、结构重复和位置异常，反映了蓼型胚囊八核七细胞结构的变异，其在各株系的平均比率为18.96%。无融合生殖胚囊发生比率极低，平均比率为1.77%，类型包括反足胚和卵细胞胚。反足细胞增殖胚囊是反足细胞团频繁增殖形成，伴随上述三种变异发生使异常胚囊的多样性进一步增加，其在各株系的平均比率为10.62%。相关分析表明，同源四倍体水稻结实可能主要来自三部分：正常胚囊、正常型小胚囊和反足细胞增殖型胚囊。这三种胚囊具有相对完整的蓼型结构，可能具有较好的育性，其对结实率的贡献程度估计值分别为72.44%、15.12%、12.44%。此外，完全退化型胚囊和位置异常型胚囊对结实率分别表现出显著（-0.66）和极显著（-0.92）的负相关，这表明二者可能是结实性的抑制因素。 Ten autotetraploid strains, which include six restoring lines, three maintaining lines and a sterile line, are derived from artificial induction by colchicine treatments. Variations of agronomical traits are observed which include large organs, sturdy plants, long panicle length and deep leaf color and so on. It has been confirmed that autotetraploid strains exhibit normal chromosome behaviors in mitosis and the chromosome numbers are all 48. Moreover, abnormal chromosome behaviors are investigated in meiosis including univalent, trivalent, quatrivalent, chromosome lagging and microkernel and so on. It evaluates that the percentage of chromosome lagging in anaphase I is about 10%-20%, the percentage of microkernel in telophase I is about 1%-6% and the percentage of abnormal microspore in telophase II is about 1%-8%. In all, abnormal behaviors of chromosomes could induce univalent, trivalent and et al. and subsequently induce infertile microspore. That may be one of the causes of low seed sets in autotetraploid strains. Embryo sacs of autotetraploid strains are formed according to the Polygonum type. However, these strains exhibit variations of abnormal embryo sacs at high frequencies (39.62% - 69.85%). The variations are frequently involved in the spikelets of the main panicles and the first tillers, leading to obvious decreases of the percentages of normal embryo sacs among the strains. Four types of abnormal embryo sacs are classified basing on their different structures and origins: degenerated embryo sac (DES), structure variation (SV), apomixis (Apo) and antipodal cell proliferation (ACP). Embryo sacs of DES (29.17%) exhibit small embryo sacs (15.04%) or no embryo sac (14.13%), the former showing embryo sacs with decreased size and the latter showing no sac. Embryo sacs of AS (18.96%) include three subtypes: structure deletion, structure duplication and location variation, which suggests abnormalities of the eight nuclei, seven celled pattern of the Polygonum type. Embryo sacs of Apo (only 1.77%) include two origins of apomictic embryos: antipodal embryo and egg embryo. Embryo sacs of ACP are observed frequently (10.62%) in autotetraploid strains which subsequently increase the variations of abnormal embryo sacs. It evaluates by the Pearson’s correlation analysis that seed set is probably contributed by three origins of embryo sacs: normal embryo sacs, small embryo sacs (normal pattern) and embryo sacs of ACP. These three origins exhibit comparatively good structure of the Polygonum type and could account for seed set at a percentage of 72.44%, 15.12%, 12.44%, respectively. Moreover, the subtype of no embryo sac (NES) negatively related to seed set at the P>0.01 level (-0.92) and the subtype of location variation (LV) negatively related to seed set at the P>0.05 level (-0.66). Which suggest the two subtypes may have strong stress on seed set.

PVA降解菌的产酶条件及特性研究

目前对PVA生物降解研究重点逐渐转移到对PVA降解菌和PVA降解酶的研究开发上，随着对PVA降解高效新菌株的不断发现和PVA降解酶作用机理和分泌机制的深入了解，利用高效微生物或酶法治理PVA这类高聚物的污染将具有较大的应用潜力。本论文研究工作正是基于这种客观条件下进行的，对本实验室前期分离的PVA降解菌株P1、共生菌B1+B2、Pa、Pb为研究对象，重点研究了菌株P1和共生菌B1+B2的产酶条件和产酶特性，验证找出了影响菌株P1产酶的生长因子，论证了菌株B1+B2的产酶特性，优化得出了菌株B1+B2的最佳产酶条件；然后对共生菌B1+B2的PVA降解酶的稳定性进行了研究；最后研究了最佳组合菌的产酶特性和最佳产酶条件。主要研究结果如下： 1 通过对菌株P1产酶因子的研究，找出了核黄素是菌株P1产酶的必须因子，在以淀粉为碳源时，核黄素只是产酶的必须因子，而不是菌体生长的必须因子；在以PVA为碳源时，核黄素既是生长的必须因子，也是产酶的必须因子，是菌株P1的生长因子。 2 对共生菌B1+B2的产酶条件和产酶特性进行了研究，并通过正交实验找出了影响菌株产酶的主要条件和菌株产酶的最佳条件。 3 对共生菌PVA降解酶的稳定性进行了研究，确定了影响酶稳定性的主要理化条件。 4 通过对菌株降解性能的比较，确定菌株Pa、Pb、共生菌、P1的作为组合菌的组成菌，然后通过复配实验确定出菌株的最佳组合为菌株Pa、P1、共生菌，最后通过正交实验确定最佳组合菌的最佳配比。 5对影响组合菌产酶的因素进行了研究，通过正交实验确定了影响组合菌产酶的主要因素和最佳产酶条件。 本文通过对PVA降解菌株产酶条件和特性的研究，旨在为PVA降解菌生产酶制剂及进一步优化PVA降解菌在PVA废水治理中的应用提供理论和应用依据。 Now the PVA-degrading bacteria and polyvinyl alcohol-degrading enzyme are the key studies on the PVA biological degradation. It has great application potential using special bacteria and enzyme to treat pollution of PVA, with some high efficient Strain and enzyme were found. The study of this paper was based on that objective condition. The stain P1, symbiotic bacteria B1+B2, stain Pa and strain Pb were studied .The conditions of enzyme production and enzyme production characteristic of stain P1, symbiotic bacteria B1+B2 were our key study, we tested and verified the growth factor which effected enzyme production of strain P1, demonstrated enzyme production characteristic of symbiotic bacteria B1+B2, optimized and obtained the optimum conditions of enzyme production; then we studied the stability of polyvinyl alcohol-degrading enzyme of strain B1+B2; last the enzyme characteristic and the optimum conditions of alcohol-degrading enzyme production of optimum combination stains were studied. The main study results are below: 1. Through the study of enzyme production factor we found that lactoflavin is the necessary factor in strain P1 enzyme production. When we used starch to be carbon energy, lactoflavin is only the necessary factor of enzyme production, but not growth factor. When we used PVA to be carbon energy, lactoflavin was not only the necessary growth factor ,but also the necessary enzyme production factor.So it was the growth factor of strain P1 2. The enzyme production conditions and enzyme production characteristic of symbiotic bacteria B1+B2 were studied. Through the orthogonal experimental design, the main conditions which effected the enzyme production and the optimum conditions of enzyme production were obtained 3. Through the study of the stability of polyvinyl alcohol-degrading enzyme, the main physical and chemical conditions which effected the enzyme stability were 4. The stain P1,symbiotic bacteria B1+B2, stain Pa and strain Pb were selected to form combination bacteria. The stain P1,symbiotic bacteria B1+B2,stain Pa were the optimum combination through duplication experiment. Then the optimum ratio was obtained through orthogonal experiment. 5. Studied the factors which effected the polyvinyl alcohol-degrading enzyme activity, then through orthogonal experiment, the main factors and condition of enzyme production which effected the combination bacteria were achieved. The result of the study was valuable for the ferment of the PVA-degrading enzyme and the optimization of the PVA-degrading performance in the PVA wastewater.

Cflec-4, a multidomain C-type lectin involved in immune defense of Zhikong scallop Chlamys farreri

C-type lectins are a superfamily of carbohydrate-recognition proteins which play crucial roles in the innate immunity. In this study, a novel multidomain C-type lectin gene from scallop Chlamys farreri (designated as Cflec-4) was cloned by RACE approach based on EST analysis. The full-length cDNA of Cflec-4 was of 2086 bp. The open reading frame was of 1830 bp and encoded a polypeptide of 609 amino acids, including a signal sequence and four dissimilar carbohydrate-recognition domains (CRDs). The deduced amino acid sequence of CflecA shared high similarities to other C-type lectin family members. The phylogenetic analysis revealed the divergence between the three N-terminal CRDs and the C-terminal one, suggesting that the four CRDs in Cflec-4 originated by repeated duplication of different primordial CRD. The potential tertiary structure of each CRD in Cflec-4 was typical double-loop structure with Ca2+-binding site 2 in the long loop region and two conserved disulfide bridges at the bases of the loops. The tissue distribution of Cflec-4 mRNA was examined by fluorescent quantitative real-time PCR. In the healthy scallops, the Cflec-4 transcripts could be only detected in gonad and hepatopancreas, whereas in the Listonella anguillarum challenged scallops, it could be also detected in hemocytes. These results collectively suggested that CflecA was involved in the immune defense of scallop against pathogen infection and provided new insight into the evolution of C-type lectin superfamily. (C) 2009 Elsevier Ltd. All rights reserved.

Expression of human epidermal growth factor gene in cyanobacteria

The human epidermal growth factor (hEGF) is a small single-chain polypeptide of 53 amino acid residues. It can stimulate the proliferation of many cell types, mainly those of epidermal and epithelial tissues both in vivo and in vitro. A vector pRL-hEGF was constructed using plasmids pRL-489 and pUC-hEGF. The synthetic hEGF gene was recombined into the downstream of strong promoter psbA in plasmids pRL-489. Then, the vector was introduced into Synechococcus sp. PCC 7002 and Anabaena sp. PCC 7120 by triparental conjugative transfer. The transformation was confirmed by PCR amplification. The pRL-hEGF is thought to be retained as a plasmid form in the transgenic Anabaena sp. PCC 7120, since it can be recovered. However, it has been integrated into the chromosome of Synechococcus sp. PCC 7002 as there is no duplication origin in the pRL-hEGF in this cyanobacterium. and plasmid cannot be isolated from the Synechococcus sp. PCC 7002 either. The radioimmunoassay (RIA) proved that the hEGF gene has been expressed as the protein existed in these two strains of transgenic cyanobacteria, and the hEGF protein in Anabaena sp. PCC 7002 could be secreted into the medium.

Phycobilisomes linker family in cyanobacterial genomes: divergence and evolution

Cyanobacteria are the oldest life form making important contributions to global CO2 fixation on the Earth. Phycobilisomes (PBSs) are the major light harvesting systems of most cyanobacteria species. Recent availability of the whole genome database of cyanobacteria provides us a global and further view on the complex structural PBSs. A PBSs linker family is crucial in structure and function of major light-harvesting PBSs complexes. Linker polypeptides are considered to have the same ancestor with other phycobiliproteins (PBPs), and might have been diverged and evolved under particularly selective forces together. In this paper, a total of 192 putative linkers including 167 putative PBSs-associated linker genes and 25 Ferredoxin-NADP oxidoreductase (FNR) genes were detected through whole genome analysis of all 25 cyanobacterial genomes (20 finished and 5 in draft state). We compared the PBSs linker family of cyanobacteria in terms of gene structure, chromosome location, conservation domain, and polymorphic variants, and discussed the features and functions of the PBSs linker family. Most of PBSs-associated linkers in PBSs linker family are assembled into gene clusters with PBPs. A phylogenetic analysis based on protein data demonstrates a possibility of six classes of the linker family in cyanobacteria. Emergence, divergence, and disappearance of PBSs linkers among cyanobacterial species were due to speciation, gene duplication, gene transfer, or gene loss, and acclimation to various environmental selective pressures especially light.

Lineage-specific domain fusion in the evolution of purine nucleotide cyclases in cyanobacteria

Cyclic nucleotides (both cAMP and cGMP) play extremely important roles in cyanobacteria, such as regulating heterocyst formation, respiration, or gliding. Catalyzing the formation of cAMP and cGMP from ATP and GTP is a group of functionally important enzymes named adenylate cyclases and guanylate cyclases, respectively. To understand their evolutionary patterns, in this study, we presented a systematic analysis of all the cyclases in cyanobacterial genomes. We found that different cyanobacteria had various numbers of cyclases in view of their remarkable diversities in genome size and physiology. Most of these cyclases exhibited distinct domain architectures, which implies the versatile functions of cyanobacterial cyclases. Mapping the whole set of cyclase domain architectures from diverse prokaryotic organisms to their phylogenetic tree and detailed phylogenetic analysis of cyclase catalytic domains revealed that lineage-specific domain recruitment appeared to be the most prevailing pattern contributing to the great variability of cyanobacterial cyclase domain architectures. However, other scenarios, such as gene duplication, also occurred during the evolution of cyanobacterial cyclases. Sequence divergence seemed to contribute to the origin of putative guanylate cyclases which were found only in cyanobacteria. In conclusion, the comprehensive survey of cyclases in cyanobacteria provides novel insight into their potential evolutionary mechanisms and further functional implications.

Characterization of amphioxus GDF8/11 gene, an archetype of vertebrate MSTN and GDF11

MSTN, also known as growth and differentiation factor 8 (GDF8), and GDF11 are members of the transforming growth factor-beta (TGF-beta) subfamily. They have been thought to be derived from one ancestral gene. In the present study, we report the isolation and characterization of an invertebrate GDF8/11 homolog from the amphioxus (Branchiostoma belcheri tsingtauense). The amphioxus GDF8/11 gene consists of five exons flanked by four introns, which have two more exons and introns than that of other species. In intron III, a possible transposable element was identified. This suggested that this intron might be derived from transposon. The amphioxus GDF8/11 cDNA encodes a polypeptide of 419 amino acid residues. Phologenetic analysis shows that the GDF8/11 is at the base of vertebrate MSTNs and GDF11s. This result might prove that the GDF8/11 derived from one ancestral gene and the amphioxus GDF8/11 may be the common ancestral gene, and also the gene duplication event generating MSTN and GDF11 occurred before the divergence of vertebrates and after or at the divergence of amphioxus from vertebrates. Reverse transcriptase polymerase chain reaction results showed that the GDF8/11 gene was expressed in new fertilized cell, early gastrulation, and knife-shaped embryo, which was different from that in mammals. It suggested that the GDF8/11 gene might possess additional functions other than regulating muscle growth in amphioxus.

Chromosomal rearrangement in Pectinidae revealed by rRNA loci and implications for bivalve evolution

Karyotype and chromosomal localization of major (18-5.8-28S) and minor (5S) ribosomal RNA genes were studied in two species of Pectinidae, zhikong (Chlamys farreri) and bay (Argopecten irradians irradians) scallops. using fluorescence in situ hybridization (FISH). C. farreri had a haploid number of 19 with a karyotype of 3m + 4sm + 7sm-st + 4st + 1st-t, and A. i. irradians had a haploid number of 16 with a karyotype of 5st + 11t. In C. farreri, the major and minor rRNA genes had one locus each and were mapped to the same chromosome-Chromosome 5. In A. i. irradians, the major rRNA genes had two loci, located on Chromosomes 4 and 8, and the 5S rRNA gene was found at a third chromosome-Chromosome 10. Results of this and other studies indicate that karyotype of A. i. irradians (n = 16, 21 arms) is secondary and derived from an ancestral karyotype similar to that of C. farreri (n = 19, 38 arms) through considerable chromosomal loss and rearrangements. The ability to tolerate significant chromosomal loss suggests that the modal karyotype of Pectinidae and possibly other bivalves with a haploid number of 19 is likely tetraploid; i.e., at least one genome duplication has occurred during the evolution of Bivalvia.