In the past two decades, many studies have focused on the classification within genus Laminaria, ultimately trying to divide it into two subgroups or genera: Laminaria and Saccharina. A significant debate still surrounds the question of its division, as the conflicting phylogenetic hypotheses that have resulted from the classification studies are based on different taxon sampling, molecular markers, or analysis methods. It is aimed at elucidate the molecular phylogeny within Laminaria and Saccharina. The nine species of Laminariales are sampled from northern Asia and Europe, and 23 new sequences in the nuclear, plastid, and mitochondrial genomes are determined to identify their taxonomic status. The phylogenetic analyses of 71 species are performed, including representatives from six of the seven families of the order Laminariales, based on three separate data sets. An evidence is provided to strongly support a clear split that maintains the two recognized genera, Laminaria and Saccharina, with Laminaria appearing to be the ancestor group. Further, analyses indicate that all taxa in Saccharina and Laminaria did not form a monophyletic lineage, instead Laminariaceae and Lessoniaceae grouped together interlacedly, and Costariaceae appeared as the sister taxon of the Lessoniaceae-Laminariaceae clade. In the phylogenetic analysis, mitochondrial c oxidase I (COI) sequences appeared to be the most credible molecular marker which was more befitting than nuclear encoded internal transcribed spacer (ITS) and plastid encoded rbcL for establishment of Laminariales systematics. It is the most comprehensive phylogeny of the order Laminariales, and contributes to an enhanced understanding and estimation of the phylogenetic relationships for the economically important seaweeds, Laminaria and Saccharina.

To clarify cuttlefish phylogeny,mitochondrial cytochrome c oxidase subunit Ⅰ (COI) gene and partial 16S rRNA gene are sequenced for 13 cephalopod species.Phylogenetic trees are constructed,with the neighbor-joining method.Coleoids are divided into two main lineages,Decabrachia and Octobrachia.The monophyly of the order Sepioidea,which includes the families Sepiidae,Sepiolidae and Idiosepiidae,is not supported.From the two families of Sepioidea examined,the Sepiolidae are polyphyletic and are excluded from the order.On the basis of 16S rRNA and amino acid of COI gene sequences data,the two genera (Sepiella and Sepia) from the Sepiidae can be distinguished,but do not have a visible boundary using COI gene sequences.The reason is explained.This suggests that the 16S rDNA of cephalopods is a precious tool to analyze taxonomic relationships at the genus level,and COI gene is fitter at a higher taxonomic level (i.e.,family).

In order to clarify the phylogeny and relationships of the most confused hypotrichous ciliates, Holosticha-complex, four closely related holostichids (five populations), Holosticha bradburyae, H. diademata, Anteholosticha sp., and A. manca, were compared and analyzed using ITS2 secondary structures, ITS1-5.8S-ITS2 region and SSrRNA gene sequences. The ITS1-5.8S-ITS2 region sequences of these four species were first sequenced, and they shared sequence identities ranging from 68.0% to 90.1%, while two populations of Anteholosticha sp. differed in three nucleotides (sequence identity 99.8%). There were several minor differences among ITS2 secondary structures of these species, while two populations of Anteholosticha sp. had the identical secondary structure. Phylogenetic trees inferred from the ITS1-5.8S-ITS2 region sequences of stichotrichs using multiple algorithms (Neighbor-Joining, Maximum Parsimony and Bayesian) revealed similar topologies. The results show that:(1) Holosticha bradburyae and H. diademata firmly clustered together with strong bootstrap supports, forming a sister clade with Anteholosticha sp., (2) Anteholosticha appeared to be a paraphyletic assemblage, in which the morphotype A. manca was more closely related to Diaxonella trimarginata than to its congener Anteholosticha sp. Phylogenetic analyses based on the SSrRNA gene and the combined sequences of SSrRNA gene and ITS1-5.8S-ITS2 region revealed the similar relationships between Holosticha and Anteholosticha, nevertheless their positions within the subclass Stichotrichia differed from each other inferred from different genes.

Six genes encoding light-harvesting complex (LHC) protein have been characterized in the multicellular red alga Griffithsia japonica EST analysis. Three of them were full sequences while others were partial sequences with 3'-UTRs. The cleavage sites between signal peptide and mature LHC protein were analyzed on these three full sequences. The sequence characteristics, calculated molecular weights and isoelectric point (pI) values and hydrophobieity of the mature proteins were deduced and analyzed. Comparing the LHC sequences of G. japonica with higher plant, Chlorophyta, chromophytes and other red algae, the high conservation of the chlorophyll (Chl) binding site among chromophytes and red algae were revealed. Phylogenetic analysis on LHC proteins from higher plant, green algae, euglena, brown algae, diatom, cryptomonad, Raphidophyte and red algae reveals that (1) there are two distinct groups of Chl a/b and Chl a/c -binding LHC; (2) Chl a binding proteins of red algae share greater similarities with the Chl a/c-binding proteins of the chromophytes and dinoflagellate than with the Chl a/b-binding proteins of the green algae and higher plants; (3) chromophyte's LHC is supposed to be evolved from red algae LHC.

The study aims to reveal phylogenetic and evolutionary relationship between aerobic anoxygenic phototrophic bacteria (AAnPB) and their relatives, anaerobic anoxygenic phototrophic bacteria (AnAnPB) and nonphototrophic bacteria (NPB, which had high homology of 16S rDNA gene with AAnPB and fell into the same genus), and validate reliability and usefulness of farnesyl pyrophosphate synthase (FPPS) gene for the phylogenetic determination. FPPS genes with our modified primers and 16S rDNA genes with general primers, were amplified and sequenced or retrieved from GenBank database. In contrast to 16S rDNA gene phylogenetic tree, AAnPB were grouped into two clusters and one branch alone with no intermingling with NPB and AnAnPB in the tree constructed on FPPS. One branch of AAnPB, in both trees, was located closer to outgroup species than AnAnPB, which implicated that some AAnPB would be diverged earlier in FPPS evolutionary history than AnAnPB and NPB. Some AAnPB and NPB were closer located in both trees and this suggested that they were the closer relatives than AnAnPB. Combination codon usage in FPPS with phylogenetic analysis, the results indicates that FPPS gene and 16S rRNA gene have similar evolutionary pattern but the former seems to be more reliable and useful in determining the phylogenic and evolutionary relationship between AAnPB and their relatives. This is the first attempt to use a molecular marker beside 16S rRNA gene for studying the phylogeny of AAnPB, and the study may also be helpful in understanding the evolutionary relationship among phototrophic microbes and the trends of photosynthetic genes transfer.

Harmful algal blooms often occurred in the East China Sea (ECS) and the German coastal waters of the North Sea but Karlodinium veneficum had not been taxonomically reported. Two strains of Karlodinium (LAMB090611 and LAMB010601) were isolated from the two areas in 2009. The morphological characteristics and molecular phylogeny of two strains are compared on the basis of observation of a light microscope, a scanning electron microscope (SEM), a laser scanning microscope (LSM) and an internal transcribed spacer (ITS) sequence data. The mean cell length of strain LAMB090611 is (14.2±1.8) μm (range 11.1-18.7 μm) and mean width is (10.8±1.5) μm (range 8.2-14.7 μm). The mean cell length of strain LAMB010601 is (15.1±1.2) μm (range 12.7-17.9 μm) and the mean width is (11.4±1.1) μm (range 9.1-14.7 μm), respectively. The two strains are similar in morphological characteristics, including a straight apical groove, distinct ventral pore, sulcal extension, cingulum displacement, two or four irregular shaped chloroplasts within the cell and almost equal sized epicone and hypocone. The large and round nucleus is located at the center or at the hypocone of the cell. The sequence length of the ECS strain LAMB090611 and the German strain LAMB010601 is 640 and 646 bp, respectively. The GC content is 49%. The nucleotide similarity of the two strains is 98.1%. The sequence divergence is 0.003. Both strains are confirmed as Karlodinium veneficum (D. Ballantine) J. Larsen and this is the first taxonomic report from China and Germany coastal waters. The population dynamics of this toxic species in the ECS and German coastal waters needs to be investigated in the near future.

Complete mitochondrial genomes (mitogenomes) can indicate phylogenetic relationships, as well as useful information for gene rearrangement mechanisms and molecular evolution. Currently, the phylogenetic location of the genus Varuna (Brachyura: Varunidae) has not been well resolved mainly because of limited representatives (only two extant species). Here, we determined a new mitogenome of this genus (Varuna litterata) and added the published mitogenomes to reconstruct the phylogeny of Varunidae. The 16 368-bp mitogenome contains the entire set of 37 genes and a putative control region. The characteristics of this newly sequenced mitogenome were described and compared with the other 15 Varunidae mitogenomes. All 16 analyzed mitogenomes have identical gene order and similar molecular features. The sliding window and genetic distance analyses demonstrate highly variable nucleotide diversity, with comparatively low variability of COI and COII, and high variability of ND6. The nonsynonymous/synonymous substitution rates (dN/dS ratio) analysis shows that all 13 PCGs are under purifying selection and ATP8 gene evolves under the least selective pressure. Twelve tRNA genes, two rRNAs, one PCG, and the putative control region are found to be rearranged with respect to the pancrustacean ground pattern gene order. Tandem duplication/random loss model is adopted to explain the large-scale gene rearrangement events occurring in Varunidae mitogenomes. Phylogenetic analyses show that all Varunidae species are placed into one group, and form a sister clade with Macrophthalmidae. Nevertheless, the phylogenetic relationships within Varunidae are not completely consistent based on the two different datasets used in this study. These findings will contribute to a better understanding of gene rearrangement and molecular evolution in Varunidae mitogenomes, as well as provide insights into the phylogenetic studies of Brachyura.

The mitochondrial genome (mitogenome) of hybrid grouper Epinephelus moara (♀)×Epinephelus tukula (♂), a new hybrid progeny, can provide valuable information for analyzing phylogeny and molecular evolution. In this study, the mitogenome was analyzed using PCR amplification and sequenced, then the phylogenetic relationship of E. moara (♀)×E. tukula (♂) and 35 other species were constructed using Maximum Likelihood and Neighbor-Joining methods with the nucleotide sequences of 13 conserved protein-coding genes (PCGs). The complete mitogenome of E. moara (♀)×E. tukula (♂) was 16 695 bp in length, which contained 13 PCGs, 2 rRNA genes, 22 tRNA genes, a replication origin and a control region. The composition and order of these genes were consistent with most other vertebrates. Of the 13 PCGs, 12 PCGs were encoded on the heavy strand, and ND6 was encoded on the light strand. The mitogenome of the E. moara (♀)×E. tukula (♂) had a higher AT nucleotide content, a positive AT-skew and a negative GC-skew. All protein initiation codons were ATG, except for COX and ND4 (GTG), ATP6 (CTG), and ND3 (ATA). ND2, COXII, ND3, ND4 and Cytb had T as the terminating codon, COXIII’s termination codon was TA, and the remaining PCGs of that were TAA. All tRNA genes, except for the lacking DHU-arm of tRNA^{Ser (AGN)}, were predicted to form a typical cloverleaf secondary structure. In addition, sequence similarity analysis (99% identity) and phylogenetic analysis (100% bootstrap value) indicated that the mitochondrial genome was maternally inherited. This study provides mitogenome data for studying genetic, phylogenetic relationships and breeding of grouper.

A molecular phylogenetic analysis was undertaken to evaluate the present systematic status of commercially familiar Pleuronectidae fishes in the northwestern Pacific Ocean.We sequenced a 529 bp fragment of the mitochondrial DNA (mtDNA) COI gene from 34 individuals of these familiar flatfishes from 11 species of nine genera collected in China and Japan.Genetic relationships among haplotypes of specimens from 11 species for COI gene data were reconstructed using the neighbour-joining method and the maximum parsimony (MP) method.The resulting molecular phylogeny of the 11 species, with a few exceptions, supported the existing taxonomy which was based largely on the morphological characteristics.The most noteworthy findings were that the genus Pleuronichthys diverged before deriving of the common ancestor for the other species; the stone flounder, Kareius biocoloratus, should belong to the genus Platichthys with the latin name Platichthys biocoloratus and the genus Verasper was not the extraordinary differentiation from the other species in family Pleuronectidae.The resultant phylogenetic trees were also consistent with multiple origins of direct development within family Pleuronectidae.New proof not only for further illuminating the multiple origins of Pleuronectidae but also for confirmation of the evolutionary relationships among groups in the family will be supported.

A new marine benthic diatom, Pleurosira nanjiensis sp. nov., is described from the rocky intertidal zone of the Xiaochaiyu Island of the Nanji Islands in China. Its morphology was examined with light and scanning electron microscopy. Molecular phylogeny was reconstructed based on SSU rRNA and rbcL gene sequences. Pleurosira nanjiensis differs from congeners in possession of a combination of morphological features including the domed valve with broadly lanceolate, elliptical or circular valve outline, two elevated marginal ocelli, two (rarely three) rimportulae, and radiate striae.