Genome-wide analysis of restriction-modification system in unicellular and filamentous cyanobacteria

Cyanobacteria are an ancient group of gram-negative bacteria with strong genome size variation ranging from 1.6 to 9.1 Mb. Here, we first retrieved all the putative restriction-modification (RM) genes in the draft genome of Spirulina and then performed a range of comparative and bioinformatic analyses on RM genes from unicellular and filamentous cyanobacterial genomes. We have identified 6 gene clusters containing putative Type I RMs and 11 putative Type II RMs or the solitary methyltransferases (MTases). RT-PCR analysis reveals that 6 of 18 MTases are not expressed in Spirulina, whereas one hsdM gene, with a mutated cognate hsdS, was detected to be expressed. Our results indicate that the number of RM genes in filamentous cyanobacteria is significantly higher than in unicellular species, and this expansion of RM systems in filamentous cyanobacteria may be related to their wide range of ecological tolerance. Furthermore, a coevolutionary pattern is found between hsdM and hsdR, with a large number of site pairs positively or negatively correlated, indicating the functional importance of these pairing interactions between their tertiary structures. No evidence for positive selection is found for the majority of RMs, e. g., hsdM, hsdS, hsdR, and Type II restriction endonuclease gene families, while a group of MTases exhibit a remarkable signature of adaptive evolution. Sites and genes identified here to have been under positive selection would provide targets for further research on their structural and functional evaluations.

Genome-wide analysis of restriction-modification system in unicellular and filamentous cyanobacteria

Cyanobacteria are an ancient group of gram-negative bacteria with strong genome size variation ranging from 1.6 to 9.1 Mb. Here, we first retrieved all the putative restriction-modification (RM) genes in the draft genome of Spirulina and then performed a range of comparative and bioinformatic analyses on RM genes from unicellular and filamentous cyanobacterial genomes. We have identified 6 gene clusters containing putative Type I RMs and 11 putative Type II RMs or the solitary methyltransferases (MTases). RT-PCR analysis reveals that 6 of 18 MTases are not expressed in Spirulina, whereas one hsdM gene, with a mutated cognate hsdS, was detected to be expressed. Our results indicate that the number of RM genes in filamentous cyanobacteria is significantly higher than in unicellular species, and this expansion of RM systems in filamentous cyanobacteria may be related to their wide range of ecological tolerance. Furthermore, a coevolutionary pattern is found between hsdM and hsdR, with a large number of site pairs positively or negatively correlated, indicating the functional importance of these pairing interactions between their tertiary structures. No evidence for positive selection is found for the majority of RMs, e. g., hsdM, hsdS, hsdR, and Type II restriction endonuclease gene families, while a group of MTases exhibit a remarkable signature of adaptive evolution. Sites and genes identified here to have been under positive selection would provide targets for further research on their structural and functional evaluations.

Studies on hybridization effects of different geographic populations of Chlamys farreri - II. The medium-term growth and development of Chlamys farreri populations from China and Russia and their reciprocal crosses

Based on the research of juvenile (2, 3, 4 months) growth and survival of three populations of two different geographic areas in Chlamys farreri from Russian and China and their F, hybrids derived from Chinese cultural population (CC) female x Russian population (RW) male, Chinese wild population (CW) female x Russian population (RW) male, Russian population (RW) female x Chinese wild population (CW) the study of the medium-term (6, 8, 10, 12 months) growth and development of Chlamys farreri was carried out. The four determined results indicated that there existed different extent heterosis (3% similar to 52 %) for the growth in three types of F-1 hybrids, and the offspring derived from CC female X Rmale had a stronger heterosis among the crosses at the medium-term; the uptrend among traits are wet weight > shell width > shell length > shell height, Chinese cultural population could be recognized as excellent parent, and seasonal variations influence very much on the daily increment and growth rate of each trait of Chlamys farreri and it is only able to survive and could barely grow in winter (6 similar to 8 months), but grows fast in temperate season (10similar to12 months).

Transient expression of lacZ in bombarded unicellular green alga Haematococcus pluvialis

This paper reports for the first time the transient expression of a reporter gene, LacZ, in the unicellular green alga Haematococcus pluvialis. By employing the micro-particle bombardment method, motile cells in the exponential phase showed transient expression of lacZ. This was detected in bombarded motile cells under the rupture-disc pressures of 3103 KPa and 4137 KPa. Transient expression of LacZ gene could not be observed in non-motile cells of this alga under the same transformation condition. No LacZ background was found in either the motile cells or the non-motile cells. The study suggests a promising potential of the SV40 promoter and the lacZ reporter gene in genetic engineering of unicellular green algae.

Molecular cloning, characterization and evolutionary analysis of phytoene desaturase (PDS) gene from Haematococcus pluvialis

Phytoene desaturase is one of the most important enzymes necessary for the biosynthesis of carotenoids in some cyanobacteria, green algae and plants. In this study, genomic DNA and cDNA of pds were cloned from unicellular green alga Haematococcus pluvialis strain323 using PCR and RT-PCR methods. The cDNA was cloned into plasmid pET-28a and efficiently expressed in Escherichia coli BL21. The complete genomic PDS gene of H. pluvialis, 3.3 kb in size, included eight exons and seven introns. To locate transcriptional regulation elements, an approximate 1 kb of 5'-flanking region was isolated by genome-walking method. Results of bioinformatic analysis showed several putative cis-elements e.g. the ABRE motif (abscisic acid responsive element), the C-repeat/DRE (dehydration responsive element) motif and the GCN4 motif were located in 5'-flanking region of pds. Results of phylogenetic analyses reveal that different sources of PDS genes form a separate clade, respectively, with 100% bootstrap support. Moreover, a maximum likelihood approach was employed to detect evidence of positive selection in the evolution of PDS genes. Results of branch-site model analysis suggest that 7.9% of sites along the green algal branch are under positive selection, and the PDS gene in green algae exhibits a different evolutionary pattern from its counterparts in cyanobacteria and plants.

There are two 5 '-flanking regions of bkt encoding beta-carotene ketolase in Haematococcus pluvialis

The unicellular green alga Haematococcus pluvialis accumulates a commercially valuable astaxanthin, with levels reaching up to 4% dry weight under environmental stress. In recent years, much effort has been devoted to understanding the molecular mechanisms regulating astaxanthin biosynthetic pathways. Beta-carotene ketolase (bkt), with control being exhibited at the transcription level, plays an important role in astaxanthin biosynthesis by H. pluvialis. Here we demonstrate the presence of two separate 5'-flanking regions [1.5 kilobase (kb) and 2 kb] of bkt (bkt1 and bkt2) that possess regulatory elements similar to those of known stress-responsive genes in plants. Results of 5'-deletion constructs and transient beta-galactosidase expression assays demonstrate that there may be positive regulatory elements governing expression in the shorter promoter at -1060/-900 from the 1.5 kb 5' region, and in the longer promoter at -1838/-1219 and at -1046/ -734 from the 2 kb 5' region relative to each homologous ATG start codon. Furthermore, our present studies reveal that the first intron (+371/+497) downstream from the 1.5 kb 5' untranslated region of bkt1 may function as a negative regulatory element to regulate its own promoter.

中国对虾育种方法研究与遗传连锁图谱的构建

本研究以中国对虾为材料，以杂交育种和选择育种为目标，进行了系统的中国对虾杂交育种试验、生长性状遗传参数试验及其分子遗传连锁图谱的构建工作。结果表明以不同地理群体杂交作为基础群体，然后采用系统的选择育种方法可以获得较好的选择效果。构建的遗传连锁图谱为中国对虾分子辅助育种提供一定的基础。这些试验结果为中国对虾合理系统的育种工作提供了理论基础和数据支持。其具体结果如下： 1. 试验对中国对虾黄渤海水域乳山湾群体（WYP）和朝鲜半岛南海群体（WKN）的2个群体及其杂交后代不同月龄生长情况和存活率进行了研究，测量体长（TL）、头胸甲长（CL）、头胸甲宽（CW）、第2、3腹节高（HST）、第2、3腹节宽（WST）、体重（BW）和存活率共7个性状，计算各项指标的杂种优势率，并对各性状进行了方差分析和多重比较。其3月龄生长情况和存活率研究结果表明，存活率在乳山湾群体（WYP♀）× 朝鲜半岛南海群体（WKN♂）杂交后代出现杂种劣势外，其他指标都表现出不同程度的杂种优势(4.37%～23.96% )。除了存活率外，杂交后代生长性状均显著高于亲本，乳山湾群体（WYP♀）×朝鲜半岛南海群体（WKN♂）杂交后代高于朝鲜半岛南海群体（WKN♀）× 乳山湾群体（WYP♂）杂交后代，黄渤海水域乳山湾群体高于朝鲜半岛南海群体后代。为确定测量性状与中国对虾体重的相关程度，建立了用体长(X1)，头胸甲宽(X2)，第2、3腹节宽(X3)，头胸甲长(X4)，第2、3腹节高(X5)估计体重的多元回归方程：Y = －2.056 + 0.03X1 + 0.076X2 + 0.078X3 + 0.033X4 + 0.043X5。 2. 中国对虾黄渤海水域乳山湾群体（WYP）和朝鲜半岛南海群体（WKN）2个群体及其杂交后代在4月龄时期的6个生长指标和存活率的杂种优势范围在0.514%到14.95%之间，WYP♀×WKN♂杂交后代在这7个指标中都高于WKN♀×WYP♂杂交后代。5月龄杂交后代也表现出一定程度的杂种优势，其范围在-9.000%～19.090%之间，但头胸甲长、第2、3腹节处高和存活率3个指标出现杂种劣势。不同杂交组合各个阶段生长发育情况和存活率在杂种优势表现出一定的规律。随着月龄的增加，WKN♀×WYP♂杂交后代杂种优势率有所增加，而WYP♀×WKN♂杂交后代的却有所降低。ANOVA分析结果表明，杂交后代在存活率方面与双亲差异不显著。4月龄的分析结果发现杂交后代在WST和BW这2个指标上存在显著差异。LSD多重比较结果显示，WYP♀×WKN♂杂交后代在BW指标上与亲本存在显著差异，在WST指标方面与其他3个组合的后代差异显著。5月龄的数据分析结果发现，杂交后代除体重存在显著差异外，其他各项指标差异均不显著。LSD多重比较结果发现，WKN♀×WYP♂杂交后代体重与其亲本WKN存在显著差异。 3. 对2个野生群体——朝鲜半岛南海岸群体（WKN）和黄渤海群体（WYP）和3个养殖群体——朝鲜半岛群体的养殖一代（FKN），黄海1号（HH1）和即抗98（JK98）进行杂交试验的研究，结果表明JK98 (♀)  WKN (♂)组合在存活率方面最高，其余的依次为WYP (♀) WKN (♂)，WKN (♀) WYP (♂)，FKN (♀)HH1 (♂) 和 WYP (♀) FKN (♂)。而在体重方面FKN(♀)  HH1(♂)组合最高，其余的依次为WKN (♀) WYP (♂)，WYP (♀) WKN (♂)，WYP (♀)FKN (♂) 和 JK98 (♀)WKN (♂)。在所有生长性状方面，JK98 (♀)  WKN (♂)在5个组合中是最低的。方差检测结果表明，TL、CL、HST、LL和BW这5个指标在不同组合间存在差异，而其他指标不存在差异。多重比较结果发现JK98 (♀)WKN (♂)组合的TL与其他组合间差异极显著，HST指标与WKN (♀) WYP (♂)，FKN(♀)  HH1(♂)和 WYP (♀)  WKN (♂)这3个组合差异显著，BW指标与WKN (♀) WYP (♂) 和 FKN(♀)  HH1(♂)差异显著。 4. 通过人工授精的方法建立了中国对虾21个半同胞家系，测量了中国对虾21个半同胞（46个全同胞）家系的TL、CL、CW、HST、WST、第1腹节长（FL）、第6腹节长（LL）。利用MTDFREML软件得到生长性状遗传力在0.15~0.35之间，属于中度遗传力范围。TL的遗传力为0.34±0.071，CL的为0.30±0.070，CW为0.35±0.077，WST为0.33±0.073，HST为0.33±0.073，FL的最低为0.15±0.044，LL的为0.24±0.059。各个性状间表现出高的正相关，其中CW和TL以及HST的遗传相关最大，FL和WST的遗传相关最小。 通过以上杂交育种和选择育种的研究，认为单纯的依靠杂交育种来改善中国对虾的育种工作可能具有一定的局限性。所以在实际的育种过程中，以中国对虾不同群体的杂交后代作为基础群体，并以此为基础进行系统的选择育种应该具有更大的潜力。 5. 本试验利用中国对虾F2群体和AFLP分子标记技术进行了遗传连锁图谱的构建。利用55对AFLP引物组合对F2家系的110个个体进行了研究，结果检测到532个符合作图策略的AFLP标记。利用卡方检验检测分离位点是否符合孟德尔分离定律。对于符合3：1比例的分离位点利用F2自交模型构建性别平均连锁图谱，对于符合1：1比例的分离位点利用拟测交理论分别构建中国对虾的雌性和雄性遗传连锁图谱。雌性、雄性和性别平均遗传图谱分别有28、35和44个连锁群，图谱实际长度分别为1090、1617和1772.1 cM。中国对虾遗传连锁图谱估计基因组长度为2420 cM，符合与人类基因组相比的对虾类基因组长度。中国对虾雄性遗传连锁图谱比雌性遗传连锁图谱长32.6%，这可能说明中国对虾不同性别存在不同的重组率。通过皮尔逊相关系数检测认为AFLP标记在中国对虾图谱上分布均匀。本文利用AFLP标记构建的中国对虾遗传连锁图谱为中国对虾基因组研究和遗传改良提供一定的基础，同时也应该开发微卫星等共显性标记，为遗传连锁图谱的整合提供条件。

Evolution of nutrient structure and phytoplankton composition in the Jiaozhou Bay ecosystem

The inventories of nutrients in the surface water and large phytoplankton( > 69 pm) were analyzed from the data set of JERS ecological database about a typical coastal waters, the Jiaozhou Bay, China, from 1960s for N, P and from 1980s; for Si. By examining long-term changes of nutrient concentration, calculating stoichiometric balance, and comparing diatom composition, Si limitation of diatom production was found to be more possible. The possibility of Si limitation was from 37% in 1980s to 50% in 1990s. Jiaozhou Bay ecosystem is becoming serious eutrophication, with notable increase of NO2-N, NO3-N and NH4-N from 0.1417 mumol/L, 0.5414 mumol/L, 1.7222 mumol/L in 1960s to 0.9551 mumol/L, 3.001 mumol/L, 8.0359 mumol/L in late 1990s respectively and prominent decrease of Si from 4.2614 mumol/L in 1980s to 1.5861 mumol/L in late 1990s; the nutrient structure is controlled by nitrogen; the main limiting nutrient is probably silicon; because of the Si limitation the phytoplankton community structure has changed drastically.

Genetic improvement on Chinese shrimp (Fenneropenaeus chinensis): growth and viability performance in F1 hybrids of different populations

Fenneropenaeus chinensis distributed in the Yellow Sea and Bohai Sea of China and the west coast of the Korean Peninsula. Different geographical populations represent potentially different genetic resources. To learn further the characteristics of different geographical population, crosses among two wild and three farmed populations were produced. The two wild populations were from the Yellow Sea and Bohai Sea (WYP), and the west coast of the Korean Peninsula and coast (WKN). The three farmed populations included the offspring of first generation of wild shrimp from coast in Korea (FKN), the Huang Hai (the Yellow Sea in Chinese) No.1 (HH1), and JK98. The phenotypes growth and survival rates of these populations were compared to confirm the feasibility for crossbreeding. The body length (BL), carapace length (CL), carapace width (CW), height of the second and third abdominal segment (HST), width of the second and third abdominal segment (WST), length of the first abdominal segment (LF), length of the last abdominal segment (LL), live body weight (BW), and survival rate were measured. Different combinations were statistically performed with ANOVA and Duncan's Multiple Range Test. The results show that the survival rate of JK98(a (TM) Euro)xWKN(a (TM),) was the highest, followed by WYP(a (TM) Euro)xWKN(a (TM),), FKN(a (TM) Euro)xWYP(a (TM),), FKN(a (TM) Euro)xHH1(a (TM),) and WYP(a (TM) Euro)xFKN(a (TM),); the body weight of FKN(a (TM) Euro)sxHH1(a (TM),) was the highest, followed by FKN(a (TM) Euro)xWYP(a (TM),), WYP(a (TM) Euro)xWKN(a (TM),), WYP(a (TM) Euro)xFKN(a (TM),) and JK98(a (TM) Euro)xWKN(a (TM),); the total length had the same ranking as the body weight. All growth traits in hybrids JK98(a (TM) Euro)xWKN(a (TM),) were the lowest among all combinations. F1 hybrids had significant difference (P < 0.05) in BL, CL, HST, LL, and BW; and insignificant difference (P > 0.05) in other growth traits and survival rate. The results of Duncan's Multiple Range Test are that BL and CL of JK98(a (TM) Euro)xWKN(a (TM),) were significantly different from the other combinations; HST different from the combination of FKN(a (TM) Euro)xWYP(a (TM),), FKN(a (TM) Euro)xHH1(a (TM),) and WYP(a (TM) Euro)xWKN(a (TM),); and BW different from FKN(a (TM) Euro)xWYP(a (TM),) and FKN(a (TM) Euro)xHH1(a (TM),). As a whole, the results indicate that the FKN(a (TM) Euro)xHH1(a (TM),) was the best combination in all growth traits. Therefore, hybridization can introduce the variation to base populations. The systematic selection program based on additive genetic performance may be more effective than crossbreeding.