The complete chloroplast genomes of two species in threatened monocot genus Caldesia in China.

Caldesia is a genus in the family Alismataceae mainly found in the tropical and temperate regions of the Northern hemisphere. In China, two species, Caldesia parnassifolia, and Caldesia grandis are recorded as critically endangered in sporadic regions. Available protection of the genetic resource of these threatened species has been impeded due to limited genomic information. Here, we sequence the whole chloroplast (cp) genome of the two Caldesia species using high throughput sequencing technology. The whole cp genomes of C. parnassifolia and C. grandis were 167,647 bp and 168,500 bp, respectively with a typical quadripartite structure. There were 115 unique genes with 81 protein-coding genes, 31 tRNA genes, and four rRNA genes. Both species showed a GC content of 37.1%. A duplication of two tRNA genes and a ~ 6 kb inversion region in the LSC was noted in both species. Mononucleotide simple sequence repeats (SSRs) A/T were most abundant for both Caldesia species. High nucleotide variability was recorded in ycf1 gene and trnK-UUU/rps16 intergenic spacer region. All RNA editing conversions were C-U in 23 and 24 protein-coding genes for C. parnassifolia and C. grandis, respectively. Phylogenetic analysis placed both Caldesia species as sister to Sagittaria lichuanensis. This study will be useful for further evolutionary, systematic researches and conservation of the genus Caldesia.

Differential distribution of amino acids in plants.

Plants are a rich source of amino acids and their individual abundance in plants is of great significance especially in terms of food. Therefore, it is of utmost necessity to create a database of the relative amino acid contents in plants as reported in literature. Since in most of the cases complete analysis of profiles of amino acids in plants was not reported, the units used and the methods applied and the plant parts used were different, amino acid contents were converted into relative units with respect to lysine for statistical analysis. The most abundant amino acids in plants are glutamic acid and aspartic acid. Pearson's correlation analysis among different amino acids showed that there were no negative correlations between the amino acids. Cluster analysis (CA) applied to relative amino acid contents of different families. Alismataceae, Cyperaceae, Capparaceae and Cactaceae families had close proximity with each other on the basis of their relative amino acid contents. First three components of principal component analysis (PCA) explained 79.5% of the total variance. Factor analysis (FA) explained four main underlying factors for amino acid analysis. Factor-1 accounted for 29.4% of the total variance and had maximum loadings on glycine, isoleucine, leucine, threonine and valine. Factor-2 explained 25.8% of the total variance and had maximum loadings on alanine, aspartic acid, serine and tyrosine. 14.2% of the total variance was explained by factor-3 and had maximum loadings on arginine and histidine. Factor-4 accounted 8.3% of the total variance and had maximum loading on the proline amino acid. The relative content of different amino acids presented in this paper is alanine (1.4), arginine (1.8), asparagine (0.7), aspartic acid (2.4), cysteine (0.5), glutamic acid (2.8), glutamine (0.6), glycine (1.0), histidine (0.5), isoleucine (0.9), leucine (1.7), lysine (1.0), methionine (0.4), phenylalanine (0.9), proline (1.1), serine (1.0), threonine (1.0), tryptophan (0.3), tyrosine (0.7) and valine (1.2).

First record of the aquatic plant Echinodorus scaber Rataj (Alismataceae) for the State of Maranhão, Northeastern Brazil.

Echinodorus is the second largest genus of the aquatic plant family Alismataceae, comprising 28 species, of which 24 occur in Brazil. This study represents the first record of Echinodorus scaber Rataj for the State of Maranhão, based on material collected in the Municipality of Brejo, eastern Maranhão. Echinodorus scaber shares morphological similarities with E. macrophyllus (Kunth) Micheli, but it can be distinguished by (I) a highly branched inflorescence, (II) scabrous peduncles and petioles covered by stellate trichomes, and (II) small flowers with reflexed petals. This new record of E. scaber contributes to a better understanding of this genus' diversity and distribution in Maranhão and underscores the necessity to broaden collection efforts for a better comprehension of the state's flooded zones. Comprehensive collection efforts, with a special focus on aquatic plants and in locations far from the state's main urban center, São Luís, may result in a significant knowledge increase of the flora, especially of the genus Echinodorus, which needs a broad taxonomic study. These recommendations may result in new records, range extensions, and species descriptions, contributing to the conservation of the aquatic environments of Maranhão.

Generic phylogeny and historical biogeography of Alismataceae, inferred from multiple DNA sequences.

Alismataceae is an aquatic or semi-aquatic herb family with a subcosmopolitan distribution. The family is one of the oldest lineages within monocots and plays an important role in the systematics, biogeography and evolutionary processes of flowering plants. However, the generic relationships of the family are still a subject of debate, and its historical biogeography is less studied. In the present study, we carried out a comprehensive phylogenetic analysis based on multiple DNA sequences (nuclear: ITS; chloroplast: psbA, rbcL, matK, rpoB, rpoC1, trnK 5' intron and trnK 3' intron; mitochondria: cob and atp1). The result supports merging Limnocharitaceae into Alismataceae as one family. Two well-supported clades were obtained based on the combined ITS, psbA, rbcL and matK dataset. Clade B consists of Luronium, Damasonium, Baldellia and Alisma; and clade A consists of the remaining genera of Alismataceae as well as Limnocharitaceae. Biogeographic analysis and bayesian molecular dating suggested that Alismataceae originated in West Palearctic or Afrotropical area during the Late Cretaceous, and subsequently split into two clades. Clade A and clade B diversified in Afrotropical area and West Palearctic area, respectively. The intercontinental distribution of this family mainly resulted from dispersals involving migration across land bridges and long-distance dispersal.

Phylogenetics and phylogeography of the monocot genus Baldellia (Alismataceae): Mediterranean refugia, suture zones and implications for conservation.

Aquatic plants, and especially the emblematic genus Baldellia (Alismataceae), are among the most threatened organisms, due to unprecedented human-driven habitat destructions. Therefore protection plans are crucially needed and call for thoroughly documenting the genetic diversity and clarifying the taxonomy of this endangered genus. Our sampling included 282 individuals from 42 natural populations and covered the whole geographical range of the genus, across Europe and the Mediterranean. We combined sequencing of nuclear internal transcribed spacer (ITS) and chloroplastic trnL-ndhF regions with amplified fragment length polymorphism (AFLP) genotyping to investigate the Alismataceae phylogeny, and produce a phylogeography of Baldellia. Our phylogeny strongly supported the monophyly of Baldellia and placed it as the sister clade to Luronium and Alisma, therefore excluding, as previously supposed, a close genetic relatedness to the predominantly neotropical genus Echinodorus. The phylogeography of Baldellia outlined patterns consistent with a hypothesis considering glacial refugia located in the Iberian Peninsula and the Italy/Balkan region from which two distinct genetic lineages re-colonized Europe. These two lineages corresponded respectively to Baldellia ranunculoides (Italy/Balkan derived populations) and Baldellia repens (populations recovered from the Iberian Peninsula refuge), therefore supporting differences outlined between the two taxa in previous ecological and morphological studies. These results allowed clarifying taxonomic uncertainties by confirming the genetic distinctness of B. repens according to B. ranunculoides. A third lineage, Baldellia alpestris, originated and remained endemic to the mountainous regions of the Iberian Peninsula. Unexpectedly, B. repens populations collected in northern Africa, appeared to be genetically distinct from their European counterparts, this calls for further investigation to fully address their genetic and conservation status. Finally, we detected a large hybridization zone in northwestern Europe between B. repens and B. ranunculoides. These results were discussed in light of conservation approaches for Baldellia populations.

Environmental state and tendencies of the Puerto Morelos CARICOMP site, Mexico.

The CARICOMP site at Puerto Morelos, Mexico was monitored from 1993 to 2005. No significant changes in air temperature, wind patterns, periodicity and quantity of rainfall, sea-surface temperature and water transparency were observed between sampling years. During the study four hurricane impacts were registered. At the coral reef site overall mean cover of fleshy algae (47%) and turf algae (36%) were high, whereas cover of corals (2%) and sponges (3%), and abundance of sea-urchins (0.04 org m(-2)) were consistently low. Gorgonians were dominant and showed changes in their community structure; the number of species increased from 1993 to 1995, their abundance decreased after Hurricane Roxanne (1995) and recovered by 2001. At four seagrass sites total community biomass remained constant (707.1-929.6 g dry m(-2)) but the above-ground biomass of the seagrass Syringodium filiforme and fleshy algae increased gradually. Total biomass (531-699 g dry m(-2)) and leaf productivity (0.89-1.56 g dry m(-2) d(-1)) of the seagrass Thalassia testudinum remained constant, but the species invested proportionally more biomass in above-ground leaf tissues at the end of the study. The minor hurricanes from 1993 until 2005 had no detectable impacts on the seagrass beds, however, the major Hurricane Wilma (October 2005) changed the community composition at three stations and caused complete burial of the vegetation at a coastal station. The gradual changes in the seagrass and reef communities recorded in the 12 years of continuous monitoring of the CARICOMP site may reflect the increased pollution caused by the rapid augment in urban and tourist developments along the coasts and inland from Puerto Morelos, coupled with poor water management practices.

Environmental state and tendencies of the Puerto Morelos CARICOMP site, Mexico

The CARICOMP site at Puerto Morelos, Mexico was monitored from 1993 to 2005. No significant changes in air temperature, wind patterns, periodicity and quantity of rainfall, sea-surface temperature and water transparency were observed between sampling years. During the study four hurricane impacts were registered. At the coral reef site overall mean cover of fleshy algae (47%) and turf algae (36%) were high, whereas cover of corals (2%) and sponges (3%), and abundance of sea-urchins (0.04 org m-2) were consistently low. Gorgonians were dominant and showed changes in their community structure; the number of species increased from 1993 to 1995, their abundance decreased after Hurricane Roxanne (1995) and recovered by 2001. At four seagrass sites total community biomass remained constant (707.1-929.6 g dry m-2) but the above-ground biomass of the seagrass Syringodium filiforme and fleshy algae increased gradually. Total biomass (531-699 g dry m-2) and leaf productivity (0.89-1.56 g dry m-2 d-1) of the seagrass Thalassia testudinum remained constant, but the species invested proportionally more biomass in above-ground leaf tissues at the end of the study. The minor hurricanes from 1993 until 2005 had no detectable impacts on the seagrass beds, however, the major Hurricane Wilma (October 2005) changed the community composition at three stations and caused complete burial of the vegetation at a coastal station. The gradual changes in the seagrass and reef communities recorded in the 12 years of continuous monitoring of the CARICOMP site may reflect the increased pollution caused by the rapid augment in urban and tourist developments along the coasts and inland from Puerto Morelos, coupled with poor water management practices. Rev. Biol. Trop. 58 (Suppl. 3): 23-43. Epub 2010 October 01.

El sitio CARICOMP en Puerto Morelos, México, se monitoreo de 1993 a 2005. No se registraron cambios significativos en la temperatura del aire, los patrones de viento, la periodicidad y cantidad de lluvia, la temperatura superficial del mar y la transparencia del agua entre los años de muestreo. Durante el estudio se registraron cuatro huracanes menores. En el sitio del arrecife coralino la cobertura global promedio de algas carnosas (47%) y de algas tipo tapete (36%) fue elevada, mientras que la cobertura de corales (2%), esponjas (3%) y la abundancia de erizos (0.04 m-2) fue consistentemente baja. Los gorgonáceos fueron dominantes y mostraron cambios en su estructura comunitaria; el número de especies aumentó de 1993 a 1995, su abundancia disminuyó después del Huracán Roxanne (1995) y se recuperó en el 2001. En cuatro estaciones de pastos marinos la biomasa total de la comunidad permaneció constante (707.1-929.6 gps m-2) pero la biomasa sobre el sustrato del pasto Syringodium filiforme y de algas carnosas aumentó gradualmente. La biomasa total (531-699 gps m-2) y productividad de hojas (0.89-1.56 gps m-2 d-1) del pasto Thalassia testudinum permaneció constante, pero la especie invirtió proporcionalmente más biomasa en el tejido de hojas sobre el sustrato al final del estudio. Los huracanes menores entre 1993 y 2005 no produjeron impactos detectables en las camas de pastos, sin embargo, el huracán mayor Wilma (Octubre 2005) cambió la composición de la comunidad en tres estaciones y causó el enterramiento completo de la vegetación en la estación costera. El cambio gradual en las comunidades de pastos marinos y arrecife registrado en 12 años de monitoreo continuo en el sitio CARICOMP puede reflejar un aumento en la contaminación causada por el rápido incremento en desarrollo urbano y turístico a lo largo de la costa y tierra adentro de Puerto Morelos, acompañado por malas prácticas de manejo del agua.