27 research outputs found
Comparison of Chloroplast Genomes among Species of Unisexual and Bisexual Clades of the Monocot Family Araceae
The chloroplast genome provides insight into the evolution of plant species. We de novo assembled and annotated chloroplast genomes of four genera representing three subfamilies of Araceae: Lasia spinosa (Lasioideae), Stylochaeton bogneri, Zamioculcas zamiifolia (Zamioculcadoideae), and Orontium aquaticum (Orontioideae), and performed comparative genomics using these chloroplast genomes. The sizes of the chloroplast genomes ranged from 163,770 bp to 169,982 bp. These genomes comprise 113 unique genes, including 79 protein-coding, 4 rRNA, and 30 tRNA genes. Among these genes, 17–18 genes are duplicated in the inverted repeat (IR) regions, comprising 6–7 protein-coding (including trans-splicing gene rps12), 4 rRNA, and 7 tRNA genes. The total number of genes ranged between 130 and 131. The infA gene was found to be a pseudogene in all four genomes reported here. These genomes exhibited high similarities in codon usage, amino acid frequency, RNA editing sites, and microsatellites. The oligonucleotide repeats and junctions JSB (IRb/SSC) and JSA (SSC/IRa) were highly variable among the genomes. The patterns of IR contraction and expansion were shown to be homoplasious, and therefore unsuitable for phylogenetic analyses. Signatures of positive selection were seen in three genes in S. bogneri, including ycf2, clpP, and rpl36. This study is a valuable addition to the evolutionary history of chloroplast genome structure in Araceae
Complete Chloroplast Genomes of Anthurium huixtlense and Pothos scandens (Pothoideae, Araceae) : Unique Inverted Repeat Expansion and Contraction Affect Rate of Evolution
The subfamily Pothoideae belongs to the ecologically important plant family Araceae. Here, we report the chloroplast genomes of two species of the subfamily Pothoideae:Anthurium huixtlense(size: 163,116 bp) andPothos scandens(size: 164,719 bp). The chloroplast genome ofP. scandensshowed unique contraction and expansion of inverted repeats (IRs), thereby increasing the size of the large single-copy region (LSC: 102,956 bp) and decreasing the size of the small single-copy region (SSC: 6779 bp). This led to duplication of many single-copy genes due to transfer to IR regions from the small single-copy (SSC) region, whereas some duplicate genes became single copy due to transfer to large single-copy regions. The rate of evolution of protein-coding genes was affected by the contraction and expansion of IRs; we found higher mutation rates for genes that exist in single-copy regions as compared to those in IRs. We found a 2.3-fold increase of oligonucleotide repeats inP. scandenswhen compared withA. huixtlense, whereas amino acid frequency and codon usage revealed similarities. The ratio of transition to transversion mutations was 2.26 inP. scandensand 2.12 inA. huixtlense. Transversion mutations mostly translated in non-synonymous substitutions. The phylogenetic inference of the limited species showed the monophyly of the Araceae subfamilies. Our study provides insight into the molecular evolution of chloroplast genomes in the subfamily Pothoideae and family Araceae.Peer reviewe
Chloroplast genome evolution in the Dracunculus clade (Aroideae, Araceae)
Chloroplast (cp) genomes are considered important for the study of lineage-specific molecular evolution, population genetics, and phylogenetics. Our aim here was to elucidate the molecular evolution in cp genomes of species in the Dracunculus clade (Aroideae, Araceae). We report de novo assembled cp genomes for eight species from eight genera and also retrieved cp genomes of four species from the National Center for Biotechnology Information (NCBI). The cp genomes varied in size from 162,424 bp to 176,835 bp. Large Single Copy (LSC) region ranged in size from 87,141 bp to 95,475 bp; Small Single Copy (SSC) from 14,338 bp to 23,981 bp; and Inverted Repeats (IRa and IRb) from 25,131 bp to 32,708 bp. The expansion in inverted repeats led to duplication of ycf1 genes in four species. The genera showed high similarity in gene content and yielded 113 unique genes (79 protein-coding, 4 rRNA, and 30 tRNA genes). Codon usage, amino acid frequency, RNA editing sites, microsatellites repeats, transition and transversion substitutions, and synonymous and non-synonymous substitutions were also similar across the clade. A previous study reported deletion of ycf1, accD, psbE, trnL-CAA, and trnG-GCC genes in four Amorphophallus species. Our study supports conservative structure of cp genomes in the Dracunculus clade including Amorphophallus species and does not support gene deletion mentioned above. We also report suitable polymorphic loci based on comparative analyses of Dracunculus clade species, which could be useful for phylogenetic inference. Overall, the current study broad our knowledge about the molecular evolution of chloroplast genome in aroids.Peer reviewe
Clinical characteristics of women captured by extending the definition of severe postpartum haemorrhage with 'refractoriness to treatment': a cohort study
Background: The absence of a uniform and clinically relevant definition of severe postpartum haemorrhage
hampers comparative studies and optimization of clinical management. The concept of persistent postpartum
haemorrhage, based on refractoriness to initial first-line treatment, was proposed as an alternative to common
definitions that are either based on estimations of blood loss or transfused units of packed red blood cells
(RBC). We compared characteristics and outcomes of women with severe postpartum haemorrhage captured
by these three types of definitions.
Methods: In this large retrospective cohort study in 61 hospitals in the Netherlands we included 1391 consecutive
women with postpartum haemorrhage who received either ≥4 units of RBC or a multicomponent transfusion. Clinical
characteristics and outcomes of women with severe postpartum haemorrhage defined as persistent postpartum
haemorrhage were compared to definitions based on estimated blood loss or transfused units of RBC within 24 h
following birth. Adverse maternal outcome was a composite of maternal mortality, hysterectomy, arterial embolisation
and intensive care unit admission.
Results: One thousand two hundred sixty out of 1391 women (90.6%) with postpartum haemorrhage fulfilled the
definition of persistent postpartum haemorrhage. The majority, 820/1260 (65.1%), fulfilled this definition within 1 h
following birth, compared to 819/1391 (58.7%) applying the definition of ≥1 L blood loss and 37/845 (4.4%) applying
the definition of ≥4 units of RBC. The definition persistent postpartum haemorrhage captured 430/471 adverse maternal
outcomes (91.3%), compared to 471/471 (100%) for ≥1 L blood loss and 383/471 (81.3%) for ≥4 units of RBC. Persistent
postpartum haemorrhage did not capture all adverse outcomes because of missing data on timing of initial, first-line
treatment.
Conclusion: The definition persistent postpartum haemo
Mutational Dynamics of Aroid Chloroplast Genomes II
The co-occurrence among single nucleotide polymorphisms (SNPs), insertions-deletions (InDels), and oligonucleotide repeats has been reported in prokaryote, eukaryote, and chloroplast genomes. Correlations among SNPs, InDels, and repeats have been investigated in the plant family Araceae previously using pair-wise sequence alignments of the chloroplast genomes of two morphotypes of one species, Colocasia esculenta belonging to subfamily Aroideae (crown group), and four species from the subfamily Lemnoideae, a basal group. The family Araceae is a large family comprising 3,645 species in 144 genera, grouped into eight subfamilies. In the current study, we performed 34 comparisons using 27 species from 7 subfamilies of Araceae to determine correlation coefficients among the mutational events at the family, subfamily, and genus levels. We express strength of the correlations as: negligible or very weak (0.10-0.19), weak (0.20-0.29), moderate (0.30-0.39), strong (0.40-0.69), very strong (0.70-0.99), and perfect (1.00). We observed strong/very strong correlations in most comparisons, whereas a few comparisons showed moderate correlations. The average correlation coefficient was recorded as 0.66 between "SNPs and InDels," 0.50 between "InDels and repeats," and 0.42 between "SNPs and repeats." In qualitative analyses, 95-100% of the repeats at family and sub-family level, while 36-86% of the repeats at genus level comparisons co-occurred with SNPs in the same bins. Our findings show that such correlations among mutational events exist throughout Araceae and support the hypothesis of distribution of oligonucleotide repeats as a proxy for mutational hotspots.Peer reviewe
La NeuropsicologÃa en América Central
The countries of Central America represent
a wide diversity of ethnic groups,
languages, and political realities with their
accompanying social and medical structures
and needs. These factors have influenced
the development (or lack thereof) of
neuropsychology across the region and
within each country. This article presents a
brief summary from each country of the
history of neuropsychology and the current state of practice and instruction. These
reveal a growing recognition across
disciplines of the importance of a
neuropsychological perspective yet a spotty
development of actual practice and a limited
number of practitioners with heterogeneous
training, and limited access to services for
the general population. Professional training
is limited to courses within other programs,
occasional workshops, or study abroad. The
article concludes with a call for more
regional coordination particularly around
research, development of instruments
tailored to the populations, and, most
importantly, a more standardized program of professional training.Los paÃses de Centro América representan
una diversidad amplia de grupos étnicos,
lenguajes, realidades polÃticas y
necesidades sociales y médicas. Estos
factores han impactado el desarrollo de
NeuropsicologÃa (o falta de tal) en la región
y en cada paÃs. Este artÃculo presenta una
breve reseña de cada paÃs de la historia y el
estado actual de la práctica y enseñanza de
NeuropsicologÃa. Revelan un
reconocimiento de una perspectiva
neuropsicológica pero con aplicación muy
irregular, un número limitado de
practicantes con niveles de formación muy
heterogéneo, y poco acceso a los servicios
para la población general. Formación
profesional está limitada a cursos dentro de
otros programas, talleres de vez en cuando,
o estudios al exterior. El artÃculo concluye
con una llamada por mayor coordinación
regional, particularmente en cuanto a la
necesidad de investigación, el desarrollo de
instrumentos adaptados a las poblaciones,
y, sobre todo, un programa más estandarizado de formación profesional
Relict inland mangrove ecosystem reveals Last Interglacial sea levels.
Climatic oscillations during the Pleistocene played a major role in shaping the spatial distribution and demographic dynamics of Earth's biota, including our own species. The Last Interglacial (LIG) or Eemian Period (ca. 130 to 115 thousand years B.P.) was particularly influential because this period of peak warmth led to the retreat of all ice sheets with concomitant changes in global sea level. The impact of these strong environmental changes on the spatial distribution of marine and terrestrial ecosystems was severe as revealed by fossil data and paleogeographic modeling. Here, we report the occurrence of an extant, inland mangrove ecosystem and demonstrate that it is a relict of the LIG. This ecosystem is currently confined to the banks of the freshwater San Pedro Mártir River in the interior of the Mexico-Guatemala El Petén rainforests, 170 km away from the nearest ocean coast but showing the plant composition and physiognomy typical of a coastal lagoon ecosystem. Integrating genomic, geologic, and floristic data with sea level modeling, we present evidence that this inland ecosystem reached its current location during the LIG and has persisted there in isolation ever since the oceans receded during the Wisconsin glaciation. Our study provides a snapshot of the Pleistocene peak warmth and reveals biotic evidence that sea levels substantially influenced landscapes and species ranges in the tropics during this period
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Experimental DNA Demethylation Associates with Changes in Growth and Gene Expression of Oak Tree Seedlings.
Epigenetic modifications such as DNA methylation, where methyl groups are added to cytosine base pairs, have the potential to impact phenotypic variation and gene expression, and could influence plant response to changing environments. One way to test this impact is through the application of chemical demethylation agents, such as 5-Azacytidine, which inhibit DNA methylation and lead to a partial reduction in DNA methylation across the genome. In this study, we treated 5-month-old seedlings of the tree, Quercus lobata, with foliar application of 5-Azacytidine to test whether a reduction in genome-wide methylation would cause differential gene expression and change phenotypic development. First, we demonstrate that demethylation treatment led to 3-6% absolute reductions and 6.7-43.2% relative reductions in genome-wide methylation across CG, CHG, and CHH sequence contexts, with CHH showing the strongest relative reduction. Seedlings treated with 5-Azacytidine showed a substantial reduction in new growth, which was less than half that of control seedlings. We tested whether this result could be due to impact of the treatment on the soil microbiome and found minimal differences in the soil microbiome between two groups, although with limited sample size. We found no significant differences in leaf fluctuating asymmetry (i.e., deviations from bilateral symmetry), which has been found in other studies. Nonetheless, treated seedlings showed differential expression of a total of 23 genes. Overall, this study provides initial evidence that DNA methylation is involved in gene expression and phenotypic variation in seedlings and suggests that removal of DNA methylation affects plant development
Recommended from our members
Experimental DNA Demethylation Associates with Changes in Growth and Gene Expression of Oak Tree Seedlings.
Epigenetic modifications such as DNA methylation, where methyl groups are added to cytosine base pairs, have the potential to impact phenotypic variation and gene expression, and could influence plant response to changing environments. One way to test this impact is through the application of chemical demethylation agents, such as 5-Azacytidine, which inhibit DNA methylation and lead to a partial reduction in DNA methylation across the genome. In this study, we treated 5-month-old seedlings of the tree, Quercus lobata, with foliar application of 5-Azacytidine to test whether a reduction in genome-wide methylation would cause differential gene expression and change phenotypic development. First, we demonstrate that demethylation treatment led to 3-6% absolute reductions and 6.7-43.2% relative reductions in genome-wide methylation across CG, CHG, and CHH sequence contexts, with CHH showing the strongest relative reduction. Seedlings treated with 5-Azacytidine showed a substantial reduction in new growth, which was less than half that of control seedlings. We tested whether this result could be due to impact of the treatment on the soil microbiome and found minimal differences in the soil microbiome between two groups, although with limited sample size. We found no significant differences in leaf fluctuating asymmetry (i.e., deviations from bilateral symmetry), which has been found in other studies. Nonetheless, treated seedlings showed differential expression of a total of 23 genes. Overall, this study provides initial evidence that DNA methylation is involved in gene expression and phenotypic variation in seedlings and suggests that removal of DNA methylation affects plant development
High-quality genome and methylomes illustrate features underlying evolutionary success of oaks.
The genus Quercus, which emerged ∼55 million years ago during globally warm temperatures, diversified into ∼450 extant species. We present a high-quality de novo genome assembly of a California endemic oak, Quercus lobata, revealing features consistent with oak evolutionary success. Effective population size remained large throughout history despite declining since early Miocene. Analysis of 39,373 mapped protein-coding genes outlined copious duplications consistent with genetic and phenotypic diversity, both by retention of genes created during the ancient γ whole genome hexaploid duplication event and by tandem duplication within families, including numerous resistance genes and a very large block of duplicated DUF247 genes, which have been found to be associated with self-incompatibility in grasses. An additional surprising finding is that subcontext-specific patterns of DNA methylation associated with transposable elements reveal broadly-distributed heterochromatin in intergenic regions, similar to grasses. Collectively, these features promote genetic and phenotypic variation that would facilitate adaptability to changing environments