Integrated transcriptome catalog of Tenualosa ilisha as a resource for gene discovery and expression profiling.

The silver pride of Bangladesh, migratory shad, Tenualosa ilisha (Hilsa), makes the highest contribution to the total fish production of Bangladesh. Despite its noteworthy contribution, a well-annotated transcriptome data is not available. Here we report a transcriptomic catalog of Hilsa, constructed by assembling RNA-Seq reads from different tissues of the fish including brain, gill, kidney, liver, and muscle.

Influence of contraceptive use and other socio-demographic factors on under-five child mortality in Bangladesh: semi-parametric and parametric approaches.

Background: The under-five child mortality rate is a widely accepted indicator of the development of a country as well as reflects the country's health care system and quality of life. Although the child mortality rate is decreasing over time in Bangladesh, the rate is still high among South Asian countries. The target of the Sustainable Development Goal-3.

Optimized Prediction Models from Fundus Imaging and Genetics for Late Age-Related Macular Degeneration.

Age-related macular degeneration (AMD) is a leading cause of blindness in the developed world. In this study, we compare the performance of retinal fundus images and genetic-information-based machine learning models for the prediction of late AMD. Using data from the Age-related Eye Disease Study, we built machine learning models with various combinations of genetic, socio-demographic/clinical, and retinal image data to predict late AMD using its severity and category in a single visit, in 2, 5, and 10 years.

Shotgun proteomics of Brassica rapa seed proteins identifies vicilin as a major seed storage protein in the mature seed.

Proteins make up a large percentage of the Brassica seed and are second only to the oil in economic importance with uses for both animal and human nutrition. The most abundant proteins reported in the seeds of Brassica are the seed storage proteins cruciferin and napin, belonging to the 12S globulin and 2S albumin families of proteins, respectively. To gain insight into the Brassica rapa seed proteome and to confirm the presence and relative quantity of proteins encoded by candidate seed storage genes in the mature seed, shotgun proteomics was carried out on protein extracts from seeds of B.

Machine learning prediction of sleep stages in dairy cows from heart rate and muscle activity measures.

Sleep is important for cow health and shows promise as a tool for assessing welfare, but methods to accurately distinguish between important sleep stages are difficult and impractical to use with cattle in typical farm environments. The objective of this study was to determine if data from more easily applied non-invasive devices assessing neck muscle activity and heart rate (HR) alone could be used to differentiate between sleep stages. We developed, trained, and compared two machine learning models using neural networks and random forest algorithms to predict sleep stages from 15 variables (features) of the muscle activity and HR data collected from 12 cows in two environments.

Challenges for FAIR-compliant description and comparison of crop phenotype data with standardized controlled vocabularies.

Crop phenotypic data underpin many pre-breeding efforts to characterize variation within germplasm collections. Although there has been an increase in the global capacity for accumulating and comparing such data, a lack of consistency in the systematic description of metadata often limits integration and sharing. We therefore aimed to understand some of the challenges facing findable, accesible, interoperable and reusable (FAIR) curation and annotation of phenotypic data from minor and underutilized crops.

Pests, diseases, and aridity have shaped the genome of Corymbia citriodora.

Corymbia citriodora is a member of the predominantly Southern Hemisphere Myrtaceae family, which includes the eucalypts (Eucalyptus, Corymbia and Angophora; ~800 species). Corymbia is grown for timber, pulp and paper, and essential oils in Australia, South Africa, Asia, and Brazil, maintaining a high-growth rate under marginal conditions due to drought, poor-quality soil, and biotic stresses. To dissect the genetic basis of these desirable traits, we sequenced and assembled the 408 Mb genome of Corymbia citriodora, anchored into eleven chromosomes.

Goat Genomic Resources: The Search for Genes Associated with Its Economic Traits.

Goat plays a crucial role in human livelihoods, being a major source of meat, milk, fiber, and hides, particularly under adverse climatic conditions. The goat genomics related to the candidate gene approach is now being used to recognize molecular mechanisms that have different expressions of growth, reproductive, milk, wool, and disease resistance. The appropriate literature on this topic has been reviewed in this article.

Chromosome-Scale Assembly and Annotation of the Macadamia Genome ( HAES 741).

is a representative of the large basal eudicot family Proteaceae and the main progenitor species of the Australian native nut crop macadamia. Since its commercialisation in Hawaii fewer than 100 years ago, global production has expanded rapidly. However, genomic resources are limited in comparison to other horticultural crops.

Abundant expression of maternal siRNAs is a conserved feature of seed development.

Small RNAs are abundant in plant reproductive tissues, especially 24-nucleotide (nt) small interfering RNAs (siRNAs). Most 24-nt siRNAs are dependent on RNA Pol IV and RNA-DEPENDENT RNA POLYMERASE 2 (RDR2) and establish DNA methylation at thousands of genomic loci in a process called RNA-directed DNA methylation (RdDM). In , RdDM is required in the maternal sporophyte for successful seed development.

Identification, characterization and epitope mapping of proteins encoded by putative allergenic napin genes from Brassica rapa.

Background: Brassica rapeseed crops contain high concentrations of oil in the seed. The remaining meal, following oil extraction, has a high protein content, but is of low value due to the presence of high amounts of napin seed storage proteins. These 2S albumin-like proteins are difficult to digest and have been identified as major allergens in humans.

Impact of Recurrent Floods on the Utilization of Maternal and Newborn Healthcare in Bangladesh.

Objective: Floods are one of the most common types of disasters in Bangladesh and lead to direct and indirect impacts on health. The aim of the study was to assess the impact of floods on Maternal and Newborn Healthcare (MNH) utilization in Bangladesh between the years 2011 and 2014.

Methods: We used variables from the Bangladesh Demographic and Health Survey 2014 data and georeferenced data of floods between 2011 and 2014 from the Emergency Events Database.

Maximising recombination across macadamia populations to generate linkage maps for genome anchoring.

The Proteaceae genus Macadamia has a recent history of domestication as a commercial nut crop. We aimed to establish the first sequence-based haploid-correlated reference genetic linkage maps for this primarily outcrossing perennial tree crop, with marker density suitable for genome anchoring. Four first generation populations were used to maximise the segregation patterns available within full-sib, biparental and self-pollinated progeny.

Genome-wide association studies for yield component traits in a macadamia breeding population.

Background: Breeding for new macadamia cultivars with high nut yield is expensive in terms of time, labour and cost. Most trees set nuts after four to five years, and candidate varieties for breeding are evaluated for at least eight years for various traits. Genome-wide association studies (GWAS) are promising methods to reduce evaluation and selection cycles by identifying genetic markers linked with key traits, potentially enabling early selection through marker-assisted selection.

Identification of SNP loci and candidate genes related to four important fatty acid composition in Brassica napus using genome wide association study.

Rapeseed oil (canola, Brassica napus L.) is an important healthy vegetable oil throughout the world, the nutritional and economical value of which largely depends on its seed fatty acid composition. In this study, based on 201,187 SNP markers developed from the SLAF-seq (specific locus amplified fragment sequencing), a genome wide association study of four important fatty acid content traits (erucic acid, oleic acid, linoleic acid and linolenic acid) in a panel of 300 inbred lines of rapeseed in two environments (JXAU and JXRIS) was carried out.

The complete mitochondrial genome of the New Zealand parasitic roundworm (Trichostrongyloidea: Haemonchidae) field strain NZ_Hco_NP.

The complete mitochondrial genome of the New Zealand parasitic nematode field strain NZ_Hco_NP was sequenced and annotated. The 14,001 bp-long mitogenome contains 12 protein-coding genes (atp8 gene missing), two ribosomal RNAs, 22 transfer RNAs, and a 583 bp non-coding region. Phylogenetic analysis showed that NZ_Hco_NP forms a monophyletic cluster with the remaining three Haemonchidae species, and further illustrates the high levels of diversity and gene flow among Trichostrongylidae.

Complete mitochondrial genome sequence of Black Bengal goat ().

The Black Bengal goat ( is a native breed found in Bangladesh, popular due to its economic contribution. Here, we report the complete mitochondrial genome sequence of Black Bengal goat. The circular genome is 16,640 bp long, comprising of 60.

The Genome Sequence of the Anthelmintic-Susceptible New Zealand Haemonchus contortus.

Internal parasitic nematodes are a global animal health issue causing drastic losses in livestock. Here, we report a H. contortus representative draft genome to serve as a genetic resource to the scientific community and support future experimental research of molecular mechanisms in related parasites.

The genome of the Black Bengal goat (Capra hircus).

Objectives: Black Bengal goat (Capra hircus), a member of the Bovidae family with the unique traits of high prolificacy, skin quality and low demand for food is the most socioeconomically significant goat breed in Bangladesh. Furthermore, the aptitude of adaptation and disease resistance capacity of it is highly notable which makes its whole genome information an area of research interest.

Data Description: The genomic DNA of a local (Chattogram, Bangladesh) healthy male Black Bengal goat (Capra hircus) was extracted and then sequenced.

Genome of Tenualosa ilisha from the river Padma, Bangladesh.

Objective: Hilsa shad (Tenualosa ilisha), is a popular fish of Bangladesh belonging to the Clupeidae family. An anadromous species, like the salmon and many other migratory fish, it is a unique species that lives in the sea and travels to freshwater rivers for spawning. During its entire life, Tenualosa ilisha migrates both from sea to freshwater and vice versa.

Transcriptional response of rice flag leaves to restricted external phosphorus supply during grain filling in rice cv. IR64.

Plant phosphorus (P) remobilisation during leaf senescence has fundamental implications for global P cycle fluxes. Hypothesising that genes involved in remobilisation of P from leaves during grain filling would show altered expression in response to P deprivation, we investigated gene expression in rice flag leaves at 8 days after anthesis (DAA) and 16 DAA in plants that received a continuous supply of P in the nutrient solution vs plants where P was omitted from the nutrient solution for 8 consecutive days prior to measurement. The transcriptional response to growth in the absence of P differed between the early stage (8 DAA) and the later stage (16 DAA) of grain filling.

Maternal components of RNA-directed DNA methylation are required for seed development in Brassica rapa.

Small RNAs trigger repressive DNA methylation at thousands of transposable elements in a process called RNA-directed DNA methylation (RdDM). The molecular mechanism of RdDM is well characterized in Arabidopsis, yet the biological function remains unclear, as loss of RdDM in Arabidopsis causes no overt defects, even after generations of inbreeding. It is known that 24 nucleotide Pol IV-dependent siRNAs, the hallmark of RdDM, are abundant in flowers and developing seeds, indicating that RdDM might be important during reproduction.

Annotation of the Corymbia terpene synthase gene family shows broad conservation but dynamic evolution of physical clusters relative to Eucalyptus.

Terpenes are economically and ecologically important phytochemicals. Their synthesis is controlled by the terpene synthase (TPS) gene family, which is highly diversified throughout the plant kingdom. The plant family Myrtaceae are characterised by especially high terpene concentrations, and considerable variation in terpene profiles.

Genome and transcriptome sequencing characterises the gene space of Macadamia integrifolia (Proteaceae).

Background: The large Gondwanan plant family Proteaceae is an early-diverging eudicot lineage renowned for its morphological, taxonomic and ecological diversity. Macadamia is the most economically important Proteaceae crop and represents an ancient rainforest-restricted lineage. The family is a focus for studies of adaptive radiation due to remarkable species diversification in Mediterranean-climate biodiversity hotspots, and numerous evolutionary transitions between biomes.

Transcriptome of the Australian Mollusc Dicathais orbita Provides Insights into the Biosynthesis of Indoles and Choline Esters.

Dicathais orbita is a mollusc of the Muricidae family and is well known for the production of the expensive dye Tyrian purple and its brominated precursors that have anticancer properties, in addition to choline esters with muscle-relaxing properties. However, the biosynthetic pathways that produce these secondary metabolites in D. orbita are not known.