Checklist of Orchidaceae from Caquetá, Colombia.

A checklist of Orchidaceae from Caquetá, Colombia is presented here. We recorded 98 genera and 418 species, exceeding a previous inventory by 276 species. The checklist is conservative in the number of genera and species by including only taxa that were fully and reliably identified and that are either linked to a corresponding herbarium voucher, a living collection specimen or a photo taken in the field and published in iNaturalist by one of the authors or a collaborator. The documented species diversity in the region could dramatically increase in the next few years with additional collecting efforts in the eastern slopes of the Andes nested in Caquetá. About 9% (418/4600) of all Orchidaceae species recorded for Colombia are reported for this area, showing the important contribution to orchid diversity of Andean-Amazonian foothills of Caquetá.

Dual-transcriptomic datasets evaluating the effect of the necrotrophic fungus Alternaria brassicicola on Arabidopsis germinating seeds.

Many fungal pathogens are carried and transmitted by seeds. These pathogens affect germination and seed quality. Their transmission from the germinating seed to seedling causes many diseases in crops. Seed defense mechanisms during germination are poorly documented. RNA-seq experiments were used to describe the molecular mechanisms involved in seed interaction with a necrotrophic fungus. Here the Arabidopsis thaliana/Alternaria brassicicola pathosystem was used to perform dual-transcriptomic approach. Arabidopsis thaliana seeds and necrotrophic fungus transcripts were identified at critical germination and seedling establishment stages. Total RNA was extracted from healthy and infected germinating seeds and seedlings at 3, 6 and 10 days after sowing. Transcript libraries were made and sequenced, then fungal and plant short reads were mapped and quantified respectively against Arabidopsis thaliana and Alternaria brassicicola reference transcriptomes. This dual-transcriptomic approach revealed that 3409, 7506 and 8589 Arabidopsis thaliana genes showed a differential expression at respectevely 3, 6 and 10 days after sowing between healthy and infected seeds, including 1192 genes differentially expressed at the three studied stages. Moreover, in this experiement, we also identified the dynamic of the transcript changes occurring at the same stages in the necrotrophic fungus concomitantly during germination and seedling establishment.

Seed Transmission of Pathogens: Non-Canonical Immune Response in Arabidopsis Germinating Seeds Compared to Early Seedlings against the Necrotrophic Fungus Alternaria brassicicola.

The transmission of seed-borne pathogens by the germinating seed is responsible for major crop diseases. The immune responses of the seed facing biotic invaders are poorly documented so far. The Arabidopsis thaliana/Alternaria brassicicola patho-system was used to describe at the transcription level the responses of germinating seeds and young seedling stages to infection by the necrotrophic fungus. RNA-seq analyses of healthy versus inoculated seeds at 3 days after sowing (DAS), stage of radicle emergence, and at 6 and 10 DAS, two stages of seedling establishment, identified thousands of differentially expressed genes by Alternaria infection. Response to hypoxia, ethylene and indole pathways were found to be induced by Alternaria in the germinating seeds. However, surprisingly, the defense responses, namely the salicylic acid (SA) pathway, the response to reactive oxygen species (ROS), the endoplasmic reticulum-associated protein degradation (ERAD) and programmed cell death, were found to be strongly induced only during the latter post-germination stages. We propose that this non-canonical immune response in early germinating seeds compared to early seedling establishment was potentially due to the seed-to-seedling transition phase. Phenotypic analyses of about 14 mutants altered in the main defense pathways illustrated these specific defense responses. The unexpected germination deficiency and insensitivity to Alternaria in the glucosinolate deficient mutants allow hypothesis of a trade-off between seed germination, necrosis induction and Alternaria transmission to the seedling. The imbalance of the SA and jasmonic acid (JA) pathways to the detriment of the JA also illustrated a non-canonical immune response at the first stages of the seedling.

Genome-wide diversity analysis to infer population structure and linkage disequilibrium among Colombian coconut germplasm.

Genetic diversity and relatedness of accessions for coconut growing in Colombia was unknown until this study. Here we develop single nucleotide polymorphisms (SNPs) along the coconut genome based on Genotyping by Sequencing (GBS) with the goal of analyze the genetic diversity, population structure, and linkage disequilibrium (LD) of a diverse coconut panel consisting of 112 coconut accessions from the Atlantic and Pacific coasts of Colombia. A comprehensive catalog of approximately 40,000 SNPs with a minor allele frequency (MAF) of > 0.05 is presented. A total of 40,614 SNPs were found but only 19,414 anchored to chromosomes. Of these, 10,338 and 4606 were exclusive to the Atlantic and Pacific gene pools, respectively, and 3432 SNPs could differentiate both gene pools. A filtered subset of unlinked and anchored SNPs (1271) showed a population structure at K = 4, separating accessions from the Pacific and Atlantic coasts that can also be distinguished by palm height, as found in previous studies. The Pacific groups had a slow LD decay, low Fixation Index (Fst) and low nucleotide diversity (π), while the Atlantic group had slightly higher genetic diversity and faster LD decay. Genome-wide diversity analyses are of importance to promote germplasm conservation and breeding programs aimed at developing new cultivars better adapted to the region.

The Mitochondrial Genome of a Plant Fungal Pathogen Pseudocercospora fijiensis (Mycosphaerellaceae), Comparative Analysis and Diversification Times of the Sigatoka Disease Complex Using Fossil Calibrated Phylogenies.

Mycosphaerellaceae is a highly diverse fungal family containing a variety of pathogens affecting many economically important crops. Mitochondria play a crucial role in fungal metabolism and in the study of fungal evolution. This study aims to: (i) describe the mitochondrial genome of Pseudocercospora fijiensis, and (ii) compare it with closely related species (Sphaerulina musiva, S. populicola, P. musae and P. eumusae) available online, paying particular attention to the Sigatoka disease's complex causal agents. The mitochondrial genome of P. fijiensis is a circular molecule of 74,089 bp containing typical genes coding for the 14 proteins related to oxidative phosphorylation, 2 rRNA genes and a set of 38 tRNAs. P. fijiensis mitogenome has two truncated cox1 copies, and bicistronic transcription of nad2-nad3 and atp6-atp8 confirmed experimentally. Comparative analysis revealed high variability in size and gene order among selected Mycosphaerellaceae mitogenomes likely to be due to rearrangements caused by mobile intron invasion. Using fossil calibrated Bayesian phylogenies, we found later diversification times for Mycosphaerellaceae (66.6 MYA) and the Sigatoka disease complex causal agents, compared to previous strict molecular clock studies. An early divergent Pseudocercospora fijiensis split from the sister species P. musae + P. eumusae 13.31 MYA while their sister group, the sister species P. eumusae and P. musae, split from their shared common ancestor in the late Miocene 8.22 MYA. This newly dated phylogeny suggests that species belonging to the Sigatoka disease complex originated after wild relatives of domesticated bananas (section Eumusae; 27.9 MYA). During this time frame, mitochondrial genomes expanded significantly, possibly due to invasions of introns into different electron transport chain genes.

Plastid phylogenomics resolves ambiguous relationships within the orchid family and provides a solid timeframe for biogeography and macroevolution.

Recent phylogenomic analyses based on the maternally inherited plastid organelle have enlightened evolutionary relationships between the subfamilies of Orchidaceae and most of the tribes. However, uncertainty remains within several subtribes and genera for which phylogenetic relationships have not ever been tested in a phylogenomic context. To address these knowledge-gaps, we here provide the most extensively sampled analysis of the orchid family to date, based on 78 plastid coding genes representing 264 species, 117 genera, 18 tribes and 28 subtribes. Divergence times are also provided as inferred from strict and relaxed molecular clocks and birth-death tree models. Our taxon sampling includes 51 newly sequenced plastid genomes produced by a genome skimming approach. We focus our sampling efforts on previously unplaced clades within tribes Cymbidieae and Epidendreae. Our results confirmed phylogenetic relationships in Orchidaceae as recovered in previous studies, most of which were recovered with maximum support (209 of the 262 tree branches). We provide for the first time a clear phylogenetic placement for Codonorchideae within subfamily Orchidoideae, and Podochilieae and Collabieae within subfamily Epidendroideae. We also identify relationships that have been persistently problematic across multiple studies, regardless of the different details of sampling and genomic datasets used for phylogenetic reconstructions. Our study provides an expanded, robust temporal phylogenomic framework of the Orchidaceae that paves the way for biogeographical and macroevolutionary studies.

A 10-Gene Classifier for Indeterminate Thyroid Nodules: Development and Multicenter Accuracy Study.

BACKGROUND: In most of the world, diagnostic surgery remains the most frequent approach for indeterminate thyroid cytology. Although several molecular tests are available for testing in centralized commercial laboratories in the United States, there are no available kits for local laboratory testing. The aim of this study was to develop a prototype in vitro diagnostic (IVD) gene classifier for the further characterization of nodules with an indeterminate thyroid cytology. METHODS: In a first stage, the expression of 18 genes was determined by quantitative polymerase chain reaction (qPCR) in a broad histopathological spectrum of 114 fresh-tissue biopsies. Expression data were used to train several classifiers by supervised machine learning approaches. Classifiers were tested in an independent set of 139 samples. In a second stage, the best classifier was chosen as a model to develop a multiplexed-qPCR IVD prototype assay, which was tested in a prospective multicenter cohort of fine-needle aspiration biopsies. RESULTS: In tissue biopsies, the best classifier, using only 10 genes, reached an optimal and consistent performance in the ninefold cross-validated testing set (sensitivity 93% and specificity 81%). In the multicenter cohort of fine-needle aspiration biopsy samples, the 10-gene signature, built into a multiplexed-qPCR IVD prototype, showed an area under the curve of 0.97, a positive predictive value of 78%, and a negative predictive value of 98%. By Bayes' theorem, the IVD prototype is expected to achieve a positive predictive value of 64-82% and a negative predictive value of 97-99% in patients with a cancer prevalence range of 20-40%. CONCLUSIONS: A new multiplexed-qPCR IVD prototype is reported that accurately classifies thyroid nodules and may provide a future solution suitable for local reference laboratory testing.

An ultrasound model to discriminate the risk of thyroid carcinoma.

RATIONALE AND OBJECTIVES: Thyroid nodules are common on ultrasonographic examination and are mostly benign. Ultrasound characteristics may help discriminate thyroid carcinoma (TC) from benign nodules. The aims of this study were to identify ultrasonographic characteristics associated with TC and to validate a previously proposed model based on the presence of three ultrasonographic characteristics. MATERIALS AND METHODS: From a protocolized prospective registry of 1108 fine needle aspiration biopsies performed during a 16-month period at an ambulatory center, the ultrasonographic characteristics of TC and non-TC biopsies were compared. Adjusted odds ratios (ORs) and likelihood ratios for TC were estimated for eight combinations of three previously identified characteristics (microcalcifications, hypoechogenicity, and irregular borders). RESULTS: Microcalcifications (OR, 6.6; 95% confidence interval [CI], 4.4-9.9), hypoechogenicity (OR, 4.7; 95% CI, 2.8-8.0), and irregular borders (OR, 4.3; 95% CI, 2.8-6.5) were independently associated with TC. When added to a logistic regression model, the three ultrasonographic characteristics remained statistically significant. In the absence of these three features, the likelihood ratio for TC was 0.1 (95% CI, 0.0-0.2), while in their simultaneous presence, the likelihood ratio was 11 (95% CI, 6.6-19.0). CONCLUSIONS: The absence or simultaneous presence of three simple ultrasonographic characteristics generates a large change of pretest probability of TC and could avoid unnecessary fine needle aspiration biopsy.

[An ultrasound score to predict the presence of papillary thyroid carcinoma. Preliminary report]. / Diseño de una escala ecográfica predictora de malignidad en nódulos tiroideos: comunicación preliminar.

BACKGROUND: Thyroid nodules are common and associated to a low risk of malignancy. Their clinical assessment usually includes a fine needle aspiration biopsy (FNAB). AIM: To identify ultrasonographic characteristics associated to papillary thyroid carcinoma (PTC) and generate a score that predicts the risk of PTC. MATERIAL AND METHODS: Retrospective review of all fine needle aspiration biopsies of the thyroid performed in a lapse of two years. Biopsies that were conclusive for PTC were selected and compared with an equal amount of randomly selected biopsies that disclosed a benign diagnosis. RESULTS: One hundred twenty two biopsies of a total of 1,498 were conclusive for PTC. Univariate analysis showed associations with PTC for the presence of micro-calcifications (Odds ratio (OR) 49.2: 95% confidence intervals (CI) 18.7-140.9), solid predominance (OR 25.1; 95% CI 6-220), hypoechogenicity (OR 23.5, 95% CI 6.5-122.6), irregular borders (OR 17, 95% CI 7.2-42.9), lymph node involvement (OR 12.3, 95% CI2.7-112), central vascularization (OR 12.2, 95% CI 4.8-33.3), local invasion and hyperechogenicity (OR 0.2; CI 95% CI 0.03-0.6). Multivariate analysis disclosed microcalcifications (OR 28.1; CI 95% 8.9-89), hypoechogenicity (OR 9.4; 95% CI 1.5-59.5) and irregular borders (OR 4.7; CI 95% 1.5-15) as the variables independently associated with the presence of PTC. The prevalence of PTC in the presence of the three variables was 97.6% (Likelihood ratio (LR) 45) and 5.4% in their absence (LR 0.06). CONCLUSIONS: This scale predicts the presence or absence of PTC using simple ultrasound characteristics.

Diseño de una escala ecográfica predictora de malignidad en nódulos tiroideos: Comunicación preliminar / An ultrasound score to predict the presence of papillary thyroid carcinoma: Preliminary report

Background: Thyroid nodules are common and associated to a low risk of malignancy. Their clinical assessment usually includes a fine neddle aspiration biopsy (FNAB). Aim To identify ultrasonographic characteristics associated to papillary thyroid carcinoma (PTC) and generate a score that predicts the risk of PTC. Material and methods: Retrospective review of all fine needle aspiration biopsies of the thyroid performed in a lapse of two years. Biopsies that were conclusive for PTC were selected and compared with an equal amount of randomly selected biopsies that disclosed a benign diagnosis. Results: One hundred twenty two biopsies of a total of 1,498 were conclusive for PTC. Univariate analysis showed associations with PTC for the presence of micro-calcifications (Odds ratio (OR) 49.2: 95 percent confidence intervals (CI) 18.7-140.9), solid predominance (OR 25.1; 95 percent CI 6-220), hypoechogenicity (OR 23.5, 95 percent CI 6.5-122.6), irregular borders (OR 17, 95 percent CI 7.2-42.9), lymph node involvement (OR 12.3, 95 percent CI2.7-112), central vascularization (OR 12.2, 95 percent CI 4.8-33.3), local invasion and hyperechogenicity (OR 0.2; CI95 percent CI 0.03-0.6). Multivariate analysis disclosed microcalcifications (OR 28.1; CI 95 percent 8.9-89), hypoechogenicity (OR 9.4; 95 percent CI 1.5-59.5) and irregular borders (OR 4.7; CI 95 percent 1.5-15) as the variables independently associated with the presence of PTC. The prevalence of PTC in the presence of the three variables was 97.6 percent (Likelihood ratio (LR) 45) and 5.4 percent in their absence (LR 0.06). Conclusions: This scale predicts the presence or absence of PTC using simple ultrasound characteristics.