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Sunday, September 22, 2019

Genomic analysis of Picochlorum species reveals how microalgae may adapt to variable environments.

Understanding how microalgae adapt to rapidly changing environments is not only important to science but can help clarify the potential impact of climate change on the biology of primary producers. We sequenced and analyzed the nuclear genome of multiple Picochlorum isolates (Chlorophyta) to elucidate strategies of environmental adaptation. It was previously found that coordinated gene regulation is involved in adaptation to salinity stress, and here we show that gene gain and loss also play key roles in adaptation. We determined the extent of horizontal gene transfer (HGT) from prokaryotes and their role in the origin of novel functions in the…

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Sunday, September 22, 2019

Whole-genome sequencing of Chinese yellow catfish provides a valuable genetic resource for high-throughput identification of toxin genes.

Naturally derived toxins from animals are good raw materials for drug development. As a representative venomous teleost, Chinese yellow catfish (Pelteobagrus fulvidraco) can provide valuable resources for studies on toxin genes. Its venom glands are located in the pectoral and dorsal fins. Although with such interesting biologic traits and great value in economy, Chinese yellow catfish is still lacking a sequenced genome. Here, we report a high-quality genome assembly of Chinese yellow catfish using a combination of next-generation Illumina and third-generation PacBio sequencing platforms. The final assembly reached 714 Mb, with a contig N50 of 970 kb and a scaffold…

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Sunday, September 22, 2019

An improved genome assembly for Larimichthys crocea reveals hepcidin gene expansion with diversified regulation and function.

Larimichthys crocea (large yellow croaker) is a type of perciform fish well known for its peculiar physiological properties and economic value. Here, we constructed an improved version of the L. crocea genome assembly, which contained 26,100 protein-coding genes. Twenty-four pseudo-chromosomes of L. crocea were also reconstructed, comprising 90% of the genome assembly. This improved assembly revealed several expansions in gene families associated with olfactory detection, detoxification, and innate immunity. Specifically, six hepcidin genes (LcHamps) were identified in L. crocea, possibly resulting from lineage-specific gene duplication. All LcHamps possessed similar genomic structures and functional domains, but varied substantially with respect to…

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Sunday, September 22, 2019

First draft genome for red sea bream of family Sparidae.

Reference genomes for all organisms on earth are now attainable owing to advances in genome sequencing technologies (Goodwin et al., 2016). Generally, species that contribute considerably to the economy or human welfare are sequenced and are considered more important than others. Furthermore, coastal indigenous people mainly depend on marine species for their food sources, which has resulted in the extinction of several marine species (Cisneros-Montemayor et al., 2016). Of these, an extinction risk assessment of marine fishes, mainly for sea breams (Family: Sparidae), has recently been conducted by way of a global extinction risk assessment from the dataset of the…

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Sunday, September 22, 2019

Genome of Tenualosa ilisha from the river Padma, Bangladesh.

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.The genome of Tenualosa ilisha collected from the river Padma of Rajshahi, Bangladesh has been sequenced and its de novo hybrid assembly and structural annotations are being reported here. Illumina and PacBio sequencing platforms were used for high depth sequencing and the draft…

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Saturday, September 21, 2019

Multi-Locus Variable number of tandem repeat Analysis (MLVA) of Yersinia ruckeri confirms the existence of host-specificity, geographic endemism and anthropogenic dissemination of virulent clones.

A Multi-Locus Variable number of tandem repeat Analysis (MLVA) assay was developed for epizootiological study of the internationally significant fish pathogen Yersinia ruckeri, which causes yersiniosis in salmonids. The assay involves amplification of ten Variable Number of Tandem Repeat (VNTR) loci in two five-plex PCR reactions, followed by capillary electrophoresis. A collection of 484 Y. ruckeri isolates, originating from various biological sources and collected from four continents over seven decades, was analysed. Minimum spanning tree cluster analysis of MLVA profiles separated the studied population into nine major clonal complexes, and a number of minor clusters and singletons. The major clonal…

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