Multi‐gene phylogenetic analyses of New Zealand coralline algae: Corallinapetra Novaezelandiae gen. et sp. nov. and recognition of the Hapalidiales ord. nov.

Coralline red algae from the New Zealand region were investigated in a study focused on documenting regional diversity. We present a multi‐gene analysis using sequence data obtained for four genes (nSSU, psaA, psbA, rbcL) from 68 samples. The study revealed cryptic diversity at both genus and species levels, confirming and providing further evidence of problems with current taxonomic concepts in the Corallinophycidae. In addition, a new genus Corallinapetra novaezelandiae gen. et sp. nov. is erected for material from northern New Zealand. Corallinapetra is excluded from all currently recognized families and orders within the Corallinophycidae and thus represents a previously unrecognized lineage within this subclass. We discuss rank in the Corallinophycidae and propose the order Hapalidiales.     

DNA methylation changes in photoperiod-thermo-sensitive male sterile rice PA64S under two different conditions

Epigenetic modification can occur at a high frequency in crop plants and might generate phenotypic variation without changes in DNA sequences. DNA methylation is an important epigenetic modification that may contribute to environmentally-induced phenotypic variations by regulating gene expression. Rice Photoperiod-Thermo-Sensitive Genic Male Sterile (PTGMS) lines can transform from sterility to fertility under lower temperatures and short-day (SD) conditions during anther development. So far, little is known about the DNA methylation variation of PTGMS throughout the genome in rice. In this study, we investigated DNA cytosine methylation alterations in the young panicles of PTGMS line PA64S under two different conditions using methylation sensitive amplified polymorphism (MSAP) method. Compared with the DNA methylation level of PA64S under lower temperatures and SD conditions (fertility), higher methylation was observed in PA64S (sterility). The sequences of 25 differentially amplified fragments were successfully obtained and annotated. Three methylated fragments, which are homologous to D2, NAD7 and psaA, were confirmed by bisulfite sequencing and their expression levels were also evaluated by qPCR. Real time quantitative PCR analysis revealed that five of the six selected methylated genes were downregulated in PA64S (sterility). These results suggested that DNA methylation may be involved in the sterility–fertility transition of PA64S under two different environmental conditions.     

A phylogenetic re‐appraisal of the family Liagoraceae sensu lato (Nemaliales,Rhodophyta) based on sequence analyses of two plastid genes and postfertilization development

The marine red algal family Liagoraceae sensu lato is shown to be polyphyletic based on analyses of a combined rbcL and psaA data set and the pattern of carposporophyte development. Fifteen of eighteen genera analyzed formed a monophyletic lineage that included the genus Liagora. Nemalion did not cluster with Liagoraceae sensu stricto, and Nemaliaceae is reinstated, characterized morphologically by the formation of the primary gonimolobes by longitudinal divisions of the gonimoblast initial. Yamadaella and Liagoropsis, previously placed in the Dermonemataceae, are shown to be independent lineages and are recognized as two new families Yamadaellaceae and Liagoropsidaceae. Yamadaellaceae is characterized by two gonimoblast initials cut off bilaterally from the fertilized carpogonium and diffusely spreading gonimoblast filaments. Liagoropsidaceae is characterized by at least three gonimoblast initials cut off by longitudinal septa from the fertilized carpogonium. In contrast, Liagoraceae sensu stricto is characterized by a single gonimoblast initial cut off transversely or diagonally from the fertilized carpogonium. Reproductive features, such as diffuse gonimoblasts and unfused carpogonial branches following postfertilization, appear to have evolved on more than one occasion in the Nemaliales and are therefore not taxonomically diagnostic at the family level, although they may be useful in recognizing genera.     

Two adjacent nuclear genes are required for functional complementation of a chloroplast trans-splicing mutant from Chlamydomonas reinhardtii

The chloroplast tscA gene from Chlamydomonas reinhardtii encodes a co-factor RNA that is involved in trans-splicing of exons 1 and 2 of the psaA mRNA encoding a core polypeptide of photosystem I. Here we provide molecular and genetic characterization of the trans-splicing mutant TR72, which is defective in the 3'-end processing of the tscA RNA and consequently defective in splicing exons 1 and 2 of the psaA mRNA. Using genomic complementation, two adjacent nuclear genes were identified, Rat1 and Rat2, that are able to restore the photosynthetic growth of mutant TR72. Restoration of the photosynthesis phenotype, however, was successful only with a DNA fragment containing both genes, while separate use of the two genes did not rescue the wild-type phenotype. This was further confirmed by using a set of 10 gene derivatives in complementation tests. The deduced amino acid sequence of Rat1 shows significant sequence homology to the conserved NAD+-binding domain of poly(ADP-ribose) polymerases of eukaryotic organisms. However, mutagenesis of conserved residues in this putative NAD+-binding domain did not reveal any effect on restoration efficiency. Immunodetection analyses with enriched fractions of chloroplast proteins indicated that Rat1 is associated with chloroplast membranes. Using the yeast three-hybrid system, we were able to demonstrate the specific binding of tscA RNA by the Rat1 polypeptide. We propose that the two nuclear factors Rat1 and Rat2 are involved in processing of chloroplast tscA RNA and in subsequent splicing of psaA exons 1 and 2.     

球形棕囊藻(Phaeocystis globosa)叶绿体psaA基因片段的序列分析

根据GenBank中检索到的南极棕囊藻(Phaeocystis globosa)psaA基因序列设计psaAL和psaAR引物,对球形棕囊藻(Phaeocystis globosa),的psaA基因片段进行PCR扩增并测序,获得了629bp的DNA序列。应用clustal X对球形棕囊藻P1、P2株系和南极棕囊藻的psaA基因片段序列进行比对,结果表明,球形棕囊藻psaA基因片段序列无插入／缺失,核苷酸差异率为3.34％。应用DNAstar分析软件推断球形棕囊藻和南极棕囊藻的psaA基因对应的氨基酸序列和RNA二级结构,发现它们的氨基酸序列差异不大,序列中209个氨基酸只有1个发生了变化,其氨基酸变异率为0．48％;除部分结构域比较相似外,RNA二级结构上体现一定程度的差异,这可能对棕囊藻的分子分类研究有参考价值。因所获得的psaA基因片段序列及氨基酸序列具有种的极端保守性,不适宜用作Phaeocystis属种间的分子分类研究。     

Comparative analysis of zygospore transcripts during early germination in Chlamydomonas reinhardtii

The unicellular green alga Chlamydomonas reinhardtii has a haplontic life cycle, and forms diploid zygotes for reproduction. The zygospore, a sporulating zygote, begins germination in response to light signals, generating haploid progenies and inducing several cell-biological events; e.g., DNA synthesis and meiotic division, successively. Their regulatory mechanisms remain largely unknown, so we focused on the early stages of germination and analyzed the dynamics of gene expression associated with the germination process. The gene expression levels of zygospores at 1 and 6 h after light exposure were analyzed by a next-generation sequencing platform, the 454 GS Junior. At 6 h, the photosynthesis pathway, including its antenna proteins and two methionine metabolism-related genes (methionine synthase and sulfite reductase), were up-regulated compared to 1 h after light exposure. Meanwhile, three uncharacterized genes that contained an antibiotic biosynthesis monooxygenase domain and an HSP20/alpha crystallin family protein were specifically expressed at 1 h after light exposure. These gene expressions were also verified by quantitative real-time PCR analysis. These results suggest that the photosynthesis and methionine synthesis pathways, both of which occur in the chloroplast, are activated in zygospores at around 6 h after light exposure, and that some polyketides and/or a small heat shock protein may be related to the initiation of zygospore germination.     

A NEW AGAROPHYTE SPECIES,GELIDIUM EUCORNEUM SP. NOV. (GELIDIALES,RHODOPHYTA), BASED ON MOLECULAR AND MORPHOLOGICAL DATA1

Gelidium is an economically and ecologically important agar‐producing genus. Although the taxonomy of Gelidium has been the focus of many published studies, there is still a need to reevaluate species‐level diversity. Herein, we describe Gelidium eucorneum sp. nov. based on specimens collected off Geojedo on the southern coast of Korea. G. eucorneum is distinguished by cartilaginous thalli with brush‐like haptera, rhizoidal filaments concentrated in the medulla, and globose cytocarps that are horned with multiple determinate branchlets. The species occurs in wave‐exposed intertidal sites, sometimes in association with other mat‐forming algae. Phylogenetic analyses (rbcL, psaA, and cox1) reveal that G. eucorneum is unique and clearly distinct from other species of the genus. The clade containing Gelidium vagum and Acanthopeltis longiramulosa was resolved as a sister group to G. eucorneum. We suggest that the diverse morphologies of G. eucorneum, G. vagum, and Acanthopeltis developed from a common ancestor in East Asian waters. This study shows that even in well‐studied areas, more agarophyte species are to be added to the world inventory of red algae.