Assembly of the durian chloroplast genome using long PacBio reads.

We have assembled the complete sequence of the Durio zibethinus chloroplast genome using long PacBio reads. Durian is a valuable commercial tree that produces durian fruit, which is popular in Southeast Asia. The chloroplast genome assembled into a single 143 kb cyclic contig that contained 111 genes. There were 46 short direct repeats (45 to 586 bp) and five short inverted repeats (63 to 169 bp). The long reads that were used for the assembly span the entire chloroplast with > 10 kb overlaps and multiple long reads join the start of the contig to the end of the contig. The durian chloroplast was found to lack the large inverted repeat that is common in chloroplast genomes. An additional 24 durian varieties were sequenced and compared to the assembly and found to also lack the large inverted repeat. There were nine SNPs among the varieties.

Identification of an Important Odorant Precursor in Durian: First Evidence of Ethionine in Plants.

On the basis of the following data from the literature, we hypothesized the presence of ethionine in durian pulp: (1) the major odorants in terms of quantity as well as odor potency in durian pulp are ethanethiol and its derivatives; (2) genome analysis of durian assigned methionine γ-lyase (MGL), the enzyme that converts methionine to methanethiol, a key role for durian odor formation; and (3) MGL accepts not only methionine but also ethionine as a substrate. A targeted search by liquid chromatography-tandem mass spectrometry allowed us to confirm the presence of ethionine in durian pulp. Quantitation of ethionine in samples of different varieties (Monthong, Krathum, Chanee, and Kanyao) showed concentrations (621-9600 µg/kg) in the same range but below the methionine concentrations (16100-30200 µg/kg). During fruit ripening, the ethionine concentration increased as well as the ethanethiol concentration. Final evidence for the role of ethionine as an ethanethiol precursor was provided by demonstrating the formation of (2H5)ethanethiol after adding (2H5)ethionine to durian pulp.

The draft genome of tropical fruit durian (Durio zibethinus).

Durian (Durio zibethinus) is a Southeast Asian tropical plant known for its hefty, spine-covered fruit and sulfury and onion-like odor. Here we present a draft genome assembly of D. zibethinus, representing the third plant genus in the Malvales order and first in the Helicteroideae subfamily to be sequenced. Single-molecule sequencing and chromosome contact maps enabled assembly of the highly heterozygous durian genome at chromosome-scale resolution. Transcriptomic analysis showed upregulation of sulfur-, ethylene-, and lipid-related pathways in durian fruits. We observed paleopolyploidization events shared by durian and cotton and durian-specific gene expansions in MGL (methionine γ-lyase), associated with production of volatile sulfur compounds (VSCs). MGL and the ethylene-related gene ACS (aminocyclopropane-1-carboxylic acid synthase) were upregulated in fruits concomitantly with their downstream metabolites (VSCs and ethylene), suggesting a potential association between ethylene biosynthesis and methionine regeneration via the Yang cycle. The durian genome provides a resource for tropical fruit biology and agronomy.

Phenology, seed dispersal and difficulties in natural recruitment of the canopy tree Pachira quinata (Malvaceae).

Life history and recruitment information of tropical trees in natural populations is scarce even for important commercial species. This study focused on a widely exploited Neotropical canopy species, Pachira quinata (Malvaceae), at the southernmost, wettest limit of its natural distribution, in the Colombian Amazonia. We studied phenological patterns, seed production and natural densities; assessed the importance of seed dispersal and density-dependent effects on recruitment, using field experiments. At this seasonal forest P. quinata was overrepresented by large adult trees and had very low recruitment caused by the combination of low fruit production, high seed predation and very high seedling mortality under continuous canopies mostly due to damping off pathogens. There was no evidence of negative distance or density effects on recruitment, but a clear requirement of canopy gaps for seedling survival and growth, where pathogen incidence was drastically reduced. In spite of the strong dependence on light for survival of seedlings, seeds germinated readily in the dark. At the study site, the population of P. quinata appeared to be declining, likely because recruitment depended on the rare combination of large gap formation with the presence of reproductive trees nearby. The recruitment biology of this species makes it very vulnerable to any type of logging in natural populations.

Phenology, seed dispersal and difficulties in natural recruitment of the canopy tree Pachira quinata (Malvaceae)

Life history and recruitment information of tropical trees in natural populations is scarce even for important commercial species. This study focused on a widely exploited Neotropical canopy species, Pachiraquinata (Malvaceae), at the southernmost, wettest limit of its natural distribution, in the Colombian Amazonia. We studied phenological patterns, seed production and natural densities; assessed the importance of seed dispersal and density-dependent effects on recruitment, using field experiments. At this seasonal forest P. quinata was overrepresented by large adult trees and had very low recruitment caused by the combination of low fruit production, high seed predation and very high seedling mortality under continuous canopies mostly due to damping off pathogens. There was no evidence of negative distance or density effects on recruitment, but a clear requirement of canopy gaps for seedling survival and growth, where pathogen incidence was drastically reduced. In spite of the strong dependence on light for survival of seedlings, seeds germinated readily in the dark. At the study site, the population of P. quinata appeared to be declining, likely because recruitment depended on the rare combination of large gap formation with the presence of reproductive trees nearby. The recruitment biology of this species makes it very vulnerable to any type of logging in natural populations. Rev. Biol. Trop. 59 (2): 921-933. Epub 2011 June 01.

Información acerca de la historia de vida y reclutamiento de poblaciones naturales de árboles tropicales es escasa, incluso para especies de alto interés comercial. Este estudio se centró en una especie de dosel altamente explotada, Pachira quinata (Malvaceae), en la zona más húmeda de su distribución geográfica, en la Amazoní a colombiana. Estudiamos sus patrones fenológicos, producción de semillas y densidades naturales, además de la importancia de la dispersión de semillas y efectos denso-dependientes en el reclutamiento natural, todo lo anterior se logró con el uso de experimentos y observaciones en el campo. En este bosque estacional, la población de P. quinata estaba dominada por grandes árboles adultos y el reclutamiento era extremadamente bajo, como consecuencia de la baja producción de frutos, alta depredación de semillas y muy alta mortalidad de plántulas bajo el bosque por infección de patógenos. No encontramos evidencia de efectos de distancia al árbol parental o densidad de semillas en el reclutamiento, pero si hallamos un evidente requerimiento de claros de luz para la supervivencia y el crecimiento de plántulas, donde la mortalidad por patógenos se reduce drásticamente. Sin embargo, a pesar de la dependencia de la luz para la supervivencia, las semillas germinan en la oscuridad. En la zona de estudio, la población de P. quinata parece estar en claro declive, probablemente porque el reclutamiento depende de la coincidencia de la formación de grandes claros con la presencia cercana de árboles reproductivos. Los requerimientos de reclutamiento de esta especie la hacen muy vulnerable a cualquier actividad extractiva de árboles adultos en poblaciones naturales.

Dinámica de crecimiento de tubos polínicos en poblaciones de Pachira quinata (Jacq.) W. Alverson (Bombacaceae) / Dynamics of pollen tube growth in Pachira quinata W. Alverson (Bombacaceae) populations

La dinámica de crecimiento de tubos polínicos fue estudiada en dos poblaciones de Pachira quinata, incluyendo los factores que la afectan como: el tipo de cruce, autopolinización y polinización cruzada intra e interprocedencia. El tiempo de cosecha de las flores afecta el número de óvulos penetrados, pero no afecta la distancia máxima alcanzada por los tubos, ni el número de tubos polínicos a lo largo del estilo. El número de tubos polínicos y la proporción de óvulos penetrados fue significativamente mayor cuando el polen fue almacenado a temperatura ambiente, comparado con los valores de polen refrigerado. El número de tubos polínicos a lo largo del estilo es independiente del tipo de cruce utilizado, asi mismo, la proporción de óvulos penetrados es menor en las polinizaciones interprocedencia que en cruces intraprocedencia y autopolinización. La alta proporción de óvulos penetrados en autopolinización indica que la incompatibilidad en Pachira quinata es una reacción de acción tardía y ocurre a nivel del ovario. El mayor número de óvulos penetrados en cruces intraprocedencia comparado con cruces interprocedencia, sugieren un efecto de depresión en la fecundación entre individuos de distintas áreas geográficas.

The dynamics of pollen tube growth was studied in populations of Pachira quinata, as well as the factors that affect it, such as: the type off crossing, self-pollination and cross-pollination among and inside populations. It was found that the time ofgathering of the flowers determines the number of penetrated ovules, but it does not determine the maximum distance reached by the tubes, neither the number of pollen tubes along the style. The number of pollen tubes and the proportion of ovules penetrated were significantly bigger when the pollen was stored at environment temperature, compared with the values of refrigerated pollen. The number of pollen tubes along the style is independent of the type of crossing used; likewise, the proportion of penetrated ovules is smaller in the pollinations among populations than in crossing among populations and self-pollination. The high proportion of ovules penetrated in self-pollination indicates that the incompatibility in Pachira quinata is an auto-incompatibility of late action that occurs at the ovary zone. The biggest number of ovules penetrated throughout crossing inside populations compared with crossing among populations suggests the existence of an out-breeding depression effect among individuals from different geographical areas.