Genetic differentiation and distribution of Pyropia acanthophora (Bangiales,Rhodophyta) in the Philippines

Pyropia acanthophora is a foliose Bangiales with widely known endemic populations in Indo-Pacific region. This alga has expanded its range recently as a consequence of introduction. In an attempt to explore the genetic diversity of Py. acanthophora within the Philippines and the impact of the introduction of the species from elsewhere, an examination of molecular differentiation and distribution was undertaken using the mitochondrial COI-5P and plastid rbcL gene sequences. The results revealed that the populations of Py. acanthophora in the Philippines exhibited high haplotypic and genetic diversities, and were found to be distinct from those previously reported as conspecific populations found in Taiwan, India, Japan, Hawaii, and from those introduced populations from Brazil. The network analyses as inferred from rbcL and from the combined COI-5P and rbcL genes showed evidence that the Philippine populations of Py. acanthophora exhibited a chaotic patchiness pattern characterized by a population with highly site-exclusive haplotypes, wide genetic variability and lack of local geographic patterns. The distribution of Py. acanthophora within the Philippines was also found to be greater than what was previously known, ranging from the extreme northwest to extreme northeast mainland Luzon coasts, including Camiguin Is., Cagayan. Understanding the genetic diversity and distribution of Py. acanthophora in the Philippines provides valuable information in relation to the conservation and effective resource management of native populations of Py. acanthophora in the tropical Asian region.     

Molecular determination of kleptoplast origins from the sea slug Plakobranchus ocellatus (Sacoglossa,Gastropoda) reveals cryptic bryopsidalean (Chlorophyta) diversity in the Hawaiian Islands

The sacoglossan sea slug species complex Plakobranchus ocellatus is a common algivore throughout the tropical Pacific, including the Hawaiian Islands. Plakobranchus ocellatus is kleptoplastic—it sequesters and retains algal chloroplasts—a characteristic that can be exploited to molecularly characterize diminutive bryopsidalean algae that are typically difficult to locate, collect, and identify. Previous DNA barcode analyses of both P. ocellatus and its kleptoplasts have been conducted primarily in the western Pacific and have only minimally sampled the most eastern populations in the Hawaiian Islands. Using two chloroplast markers, rbcL and tufA, kleptoplast samples from an Oahu population of P. ocellatus were amplified and cloned to identify their algal sources. Plakobranchus ocellatus sequester chloroplasts from up to 11 bryopsidalean algal species, all but one being diminutive in thallus size. Notably, eight of the detected algal species were new records to the Hawaiian Islands. A sequestration preference study demonstrated that the O‘ahu population of P. ocellatus preferentially sequesters chloroplasts from diminutive, epilithic taxa. Using coxI barcoding of P. ocellatus, we showed the O‘ahu population to be part of a clade that includes sequences from the neighboring island Maui, Australia, and the Philippines. The use of P. ocellatus as a novel sampling tool allows the exploration of the green algal community diversity and composition at a fine scale.     

金粉蕨属的分子系统学研究——基于5种叶绿体DNA序列片段

金粉蕨属（Onychium Kaulfuss）隶属广义凤尾蕨科中的凤尾蕨亚科。迄今为止,该属属下分组及种间界定等仍有诸多问题亟待解决。本研究选取5个叶绿体DNA 序列片段 （rbcL/atpA/matK/trnL-trnF/trnG-trnR）,采用最大似然法（ML）和贝叶斯法（BI）构建金粉蕨属的系统发育树。结果表明：（1）金粉蕨属的9个成员被分置于两大支上。其中野雉尾金粉蕨（Onychium japonicum(Thunberg) Kunze）、西藏金粉蕨（O.tibeticum Ching & S.K.Wu）、木坪金粉蕨（O.moupinense Ching）、湖北金粉蕨（O.moupinense var. ipii(Ching) K.H.Shing）、栗柄金粉蕨（O.japonicum var. lucidum(D.Don) Christ）、黑足金粉蕨（O.cryptogrammoides Christ）、繁羽金粉蕨（O.plumosum Ching）聚为一支;而金粉蕨（O.siliculosum(Desvaux) C.Christensen）和蚀盖金粉蕨（O.tenuifrons Ching）则聚为另一支,可为该属的属下分组提供分子系统学证据;（2）野雉尾金粉蕨与栗柄金粉蕨在系统树中并没有聚在一起,而是被其它类群分割开来,不支持将后者作为野雉尾金粉蕨的变种,建议将栗柄金粉蕨提升为种的等级;（3）系统树上木坪金粉蕨与湖北金粉蕨的样本聚在一个细支上,支持《中国植物志》将湖北金粉蕨作为木坪金粉蕨变种的分类处理;（4）西藏金粉蕨与野雉尾金粉蕨聚在一起,并得到较高的支持,说明两者的关系近缘。     

线蕨属（水龙骨科）的系统发育研究：来自叶绿体rbcL和rps4-trnS序列的证据

线蕨属Colysis 植物主要分布于亚洲热带和亚热带地区,少数种类分布至非洲、澳大利亚(昆士兰)及新几内亚地区.自1849年成立以来,线蕨属的分类范畴和系统位置一直有待确定.本文利用叶绿体基因组的rbcL、rps4基因和rps4-trnS基凶间隔区序列,运用最大简约法和贝叶斯方法分析了线蕨属及其近缘类群的系统演化关系.研究结果显示:(1)线蕨属和薄唇蕨属Leptochilus(含似薄唇蕨属Paraleptochilus)组成一个支持率很高的单系分支(C-L Clade),但是薄唇蕨属的成员位于线蕨属的不同支系内,支持线蕨属和薄唇蕨属合并为一个属;(2)瘤蕨属Phymatosorus单独形成一个单系分支;(3)星蕨属Microsorum是一个多系类群,除Microsorium linguiforme、M.varians和M.pustulatum与马来群岛的Lecanopteris聚在一起外,其他的星蕨属成员均位于不同的支系上.本文的系统发育分析结果为线蕨属和薄唇蕨属的分类处理提供了分子系统学的证据.     

Characterization of the crustose red alga Peyssonnelia japonica (Rhodophyta,Gigartinales) and its taxonomic relationship with Peyssonnelia boudouresquei based on morphological and molecular data

The vegetative and reproductive morphology of the crustose red alga Peyssonnelia japonica (Segawa) Yoneshigue was re‐examined based on the holotype specimen and recent collections from various localities in Japan, including the type locality, and Hawaii. This species is characterized by the following features: thallus with appressed margins, perithallial filaments arising from the entire upper surface of each hypothallial cell (the Peyssonnelia rubra‐type), easily separable perithallial filaments in a gelatinous matrix, hypothallial filaments arranged in parallel rows, unicellular rhizoids, hypobasal calcification, gonimoblasts derived mainly from connecting filaments, and spermatangia produced in a series of whorls comprised of one to four paired spermatangia surrounding each central cell (the Peyssonnelia dubyi‐type). In addition to these features, the dimensions of the vegetative and reproductive structures of Peyssonnelia boudouresquei Yoneshigue described from Brazil were consistent with those of P. japonica. Molecular phylogenetic analyses using partial 26S rDNA, rbcL, and cox2‐3 spacer DNA sequences also supported the monophyly of P. japonica (from 16 localities in Japan and one locality in Hawaii) and P. boudouresquei (from two localities in Brazil). Therefore, P. boudouresquei may be a taxonomic synonym of P. japonica. However, considering the relatively high sequence divergences between the two taxa (2.1–2.5% in partial 26S rDNA, 5.9–6.7% in rbcL, and 5.8–6.7% in cox2‐3 spacer), and the relatively limited geographic sampling ranges, we reserve the taxonomic conclusion until further morphological and genetic data of the specimens from other geographic areas connecting Japan and Brazil become available.     

New species of freshwater Ulva, Ulva limnetica (Ulvales, Ulvophyceae) from the Ryukyu Islands, Japan

Ulva limnetica Ichihara et Shimada, sp. nov. (Ulvales, Ulvophyceae) is described from the Ryukyu Islands, Japan, and is characterized by thalli that are: (i) branched, tubular, fragile and wrinkled; (ii) up to 80 cm in height and up to 2 cm in diameter; (iii) light to yellowish green in color; and (iv) having an asexual reproduction by means of quadriflagellate swarmers. Rhizoidal cells bear tubular extensions on the outside of the cell layer in the stipe. Ulva limnetica is distinguished from species with similar thalli by chloroplast disposition, branching pattern, number of pyrenoids per cell and gross morphology. It is also distinguished by sequences of the nuclear-encoded 18S ribosomal RNA gene, internal transcribed spacer 2 region and the plastid-encoded large subunit of ribulose-1,5-bisphosphate carboxylase/oxgenase gene ( rbc L). Ulva limnetica was clustered with other Ulva species in an early diverging lineage within the genus.     

Testing four proposed barcoding markers for the identification of species within Ligustrum L. (Oleaceae)

DNA barcoding is a biological technique that uses short and standardized genes or DNA regions to facilitate species identification. DNA barcoding has been used successfully in several animal and plant groups. Ligustrum (Oleaceae) species occur widely throughout the world and are used as medicinal plants in China. Therefore, the accurate identification of species in this genus is necessary. Four potential DNA barcodes, namely the nuclear ribosomal internal transcribed spacer (ITS) and three chloroplast (cp) DNA regions (rbcL, matK, and trnH–psbA), were used to differentiate species within Ligustrum. BLAST, character-based method, tree-based methods and TAXONDNA analysis were used to investigate the molecular identification capabilities of the chosen markers for discriminating 92 samples representing 20 species of this genus. The results showed that the ITS sequences have the most variable information, followed by trnH–psbA, matK, and rbcL. All sequences of the four regions correctly identified the species at the genus level using BLAST alignment. At the species level, the discriminating power of rbcL, matK, trnH–psbA, and ITS based on neighbor-joining (NJ) trees was 36.8%, 38.9%, 77.8%, and 80%, respectively. Using character-based and maximum parsimony (MP) tree methods together, the discriminating ability of trnH–psbA increased to 88.9%. All species could be differentiated using ITS when combining the NJ tree method with character-based or MP tree methods. Overall, the results indicate that DNA barcoding is an effective molecular identification method for Ligustrum species. We propose the nuclear ribosomal ITS as a plant barcode for plant identification and trnH–psbA as a candidate barcode sequence.     

Molecular identification of species in Prunus sect. Persica (Rosaceae), with emphasis on evaluation of candidate barcodes for plants

Abstract Species of Prunus L. sect. Persica are not only important fruit trees, but also popular ornamental and medicinal plants. Correct identification of seedlings, barks, or fruit kernels is sometimes required, but no reliable morphological characters are available. Nowadays, the technique of DNA barcoding has the potential to meet such requirements. In this study, we evaluated the suitability of 11 DNA loci (atpB‐rbcL, trnH‐psbA, trnL‐F, trnS‐G, atpF‐H, rbcL, matK, rpoB, rpoC1, nad1, and internal transcribed spacer [ITS]) as candidate DNA barcodes for peaches, using samples from 38 populations, covering all the species in sect. Persica. On the whole, the primers worked well in this group and sequencing difficulties were met only in the case of ITS locus. Five loci (rbcL, matK, rpoB, rpoC, and nad1) have very low variation rates, whereas atpB‐rbcL, atpF‐H, trnH‐psbA, trnL‐F and trnS‐G show more variability. The most variable loci, atpB‐rbcL and trnH‐psbA, can distinguish three of the five species. Two two‐locus combinations, atpB‐rbcL+trnL‐F and atpB‐rbcL+atpF‐H, can resolve all five species. We also find that identification powers of the loci are method‐dependent. The NeighborNet method shows higher species identification power than maximum parsimony, neighbor joining, and unweighted pair group method with arithmetic mean methods.     

Testing four candidate barcoding markers in temperate woody bamboos (Poaceae: Bambusoideae)

Abstract Bambusoideae is an important subfamily of the grass family Poaceae that has considerable economic, ecologic and cultural value. In addition, Bambusoideae species are important constituents of the forest vegetation in China. Because of the paucity of flower‐bearing specimens and homoplasies of morphological characters, it is difficult to identify species of Bambusoideae using morphology alone, especially in the case of temperate woody bamboos (i.e. Arundinarieae). To this end, DNA barcoding has shown great potential in identifying species. The present study is the first attempt to test the feasibility of four proposed DNA barcoding markers (matK, rbcL, trnH–psbA, and internal transcribed spacer [ITS]) in identifying 27 species of the temperate woody bamboos. Three plastid markers showed high levels of universality, whereas the universality of ITS was comparatively low. A single plastid marker provided low levels of discrimination success at both the genus and species levels (<12%). Among the combinations of plastid markers, the highest discriminatory power was obtained using the combination of rbcL+matK (14.8%). Using a combination of three markers did not increase species discrimination. The nuclear region ITS alone could identify 66.7% of species, although fewer taxa were included in the ITS analyses than in the plastid analyses. When ITS was integrated with a single or combination of plastid markers, the species discriminatory power was significantly improved. We suggest that a combination of rbcL+ ITS, which exhibited the highest species identification power of all combinations in the present study, could be used as a potential DNA barcode for temperate woody bamboos.