Expression Profiles of Housekeeping Genes and Tissue-Specific Genes in Different Tissues of Chinese Sturgeon ().

The Chinese sturgeon () is an ancient, complex autooctoploid fish species that is currently facing conservation challenges throughout its distribution. To comprehensively characterize the expression profiles of genes and their associated biological functions across different tissues, we performed a transcriptome-scale gene expression analysis, focusing on housekeeping genes (HKGs), tissue-specific genes (TSGs), and co-expressed gene modules in various tissues. We collected eleven tissues to establish a transcriptomic repository, including data from Pacific Biosciences isoform sequencing (PacBio Iso-seq) and RNA sequencing (RNA-seq), and then obtained 25,434 full-length transcripts, with lengths from 307 to 9515 bp and an N50 of 3195 bp.

Genome architecture of the allotetraploid wild grass Aegilops ventricosa reveals its evolutionary history and contributions to wheat improvement.

The allotetraploid wild grass Aegilops ventricosa (2n = 4x = 28, genome DDNN) has been recognized as an important germplasm resource for wheat improvement owing to its ability to tolerate biotic stresses. In particular, the 2NS segment from Ae. ventricosa, as a stable and effective resistance source, has contributed greatly to wheat improvement.

The Spatio-Temporal Expression Profiles of Silkworm Pseudogenes Provide Valuable Insights into Their Biological Roles.

Background: Pseudogenes are sequences that have lost the ability to transcribe RNA molecules or encode truncated but possibly functional proteins. While they were once considered to be meaningless remnants of evolution, recent researches have shown that pseudogenes play important roles in various biological processes. However, the studies of pseudogenes in the silkworm, an important model organism, are limited and have focused on single or only a few specific genes.

Polyploidization of Indotyphlops braminus: evidence from isoform-sequencing.

Background: Indotyphlops braminus, the only known triploid parthenogenetic snake, is a compelling species for revealing the mechanism of polyploid emergence in vertebrates.

Methods: In this study, we applied PacBio isoform sequencing technology to generate the first full-length transcriptome of I. braminus, aiming to improve the understanding of the molecular characteristics of this species.

Large-scale snake genome analyses provide insights into vertebrate development.

Snakes are a remarkable squamate lineage with unique morphological adaptations, especially those related to the evolution of vertebrate skeletons, organs, and sensory systems. To clarify the genetic underpinnings of snake phenotypes, we assembled and analyzed 14 de novo genomes from 12 snake families. We also investigated the genetic basis of the morphological characteristics of snakes using functional experiments.

Systematic identification of smORFs in domestic silkworm ().

The silkworm () is not only an excellent model species, but also an important agricultural economic insect. Taking it as the research object, its advantages of low maintenance cost and no biohazard risks are considered. Small open reading frames (smORFs) are an important class of genomic elements that can produce bioactive peptides.

Reference genome assemblies reveal the origin and evolution of allohexaploid oat.

Common oat (Avena sativa) is an important cereal crop serving as a valuable source of forage and human food. Although reference genomes of many important crops have been generated, such work in oat has lagged behind, primarily owing to its large, repeat-rich polyploid genome. Here, using Oxford Nanopore ultralong sequencing and Hi-C technologies, we have generated a reference-quality genome assembly of hulless common oat, comprising 21 pseudomolecules with a total length of 10.

Genomic adaptations for arboreal locomotion in Asian flying treefrogs.

SignificanceTo adapt to arboreal lifestyles, treefrogs have evolved a suite of complex traits that support vertical movement and gliding, thus presenting a unique case for studying the genetic basis for traits causally linked to vertical niche expansion. Here, based on two de novo-assembled Asian treefrog genomes, we determined that genes involved in limb development and keratin cytoskeleton likely played a role in the evolution of their climbing systems. Behavioral and morphological evaluation and time-ordered gene coexpression network analysis revealed the developmental patterns and regulatory pathways of the webbed feet used for gliding in .

RNA-binding protein Hfq plays a vital role in cellulose decomposition throughout affecting cellulase gene expression.

Objective: To study the function of the RNA-binding protein Hfq in Bacillus subtilis cellulose decomposition.

Results: In the medium with sodium carboxymethylcellulose (Na-CMC) as the sole carbon source, the knockout of Hfq resulted in a 38.0% ± 2.

Cytochrome P450 monooxygenase genes in the wild silkworm, .

Wild ( and domestic silkworms () are good models for investigating insect domestication, as 5000 years of artificial breeding and selection have resulted in significant differences between and . In this study, we improved the genome assemblies to the chromosome level and updated the protein-coding gene annotations for . Based on this updated genome, we identified 68 cytochrome P450 genes in .

Genome-wide signatures of mammalian skin covering evolution.

Animal body coverings provide protection and allow for adaptation to environmental pressures such as heat, ultraviolet radiation, water loss, and mechanical forces. Here, using a comparative genomics analysis of 39 mammal species spanning three skin covering types (hairless, scaly and spiny), we found some genes (e.g.

The Genome of Shaw's Sea Snake (Hydrophis curtus) Reveals Secondary Adaptation to Its Marine Environment.

The transition of terrestrial snakes to marine life ∼10 Ma is ideal for exploring adaptive evolution. Sea snakes possess phenotype specializations including laterally compressed bodies, paddle-shaped tails, valvular nostrils, cutaneous respiration, elongated lungs, and salt glands, yet, knowledge on the genetic underpinnings of the transition remains limited. Herein, we report the first genome of Shaw's sea snake (Hydrophis curtus) and use it to investigate sea snake secondary marine adaptation.

Building an octaploid genome and transcriptome of the medicinal plant Pogostemon cablin from Lamiales.

The Lamiales order presents highly varied genome sizes and highly specialized life strategies. Patchouli, Pogostemon cablin (Blanco) Benth. from the Lamiales, has been widely cultivated in tropical and subtropical areas of Asia owing to high demand for its essential oil.

Endangered Père David's deer genome provides insights into population recovering.

The Milu (Père David's deer, ) were once widely distributed in the swamps (coastal areas to inland areas) of East Asia. The dramatic recovery of the Milu population is now deemed a classic example of how highly endangered animal species can be rescued. However, the molecular mechanisms that underpinned this population recovery remain largely unknown.

Adaptive evolution to a high purine and fat diet of carnivorans revealed by gut microbiomes and host genomes.

Carnivorous members of the Carnivora reside at the apex of food chains and consume meat-only diets, rich in purine, fats and protein. Here, we aimed to identify potential adaptive evolutionary signatures compatible with high purine and fat metabolism based on analysis of host genomes and symbiotic gut microbial metagenomes. We found that the gut microbiomes of carnivorous Carnivora (e.

Complete Chloroplast Genome Sequence of Franch. and Its Evolutionary History.

The Franch. is an important medicinal plant from the Ranunculales. We used next generation sequencing technology to determine the complete chloroplast genome of .

The Complete Chloroplast Genome Sequences of the Medicinal Plant Pogostemon cablin.

Pogostemon cablin, the natural source of patchouli alcohol, is an important herb in the Lamiaceae family. Here, we present the entire chloroplast genome of P. cablin.

Survey of the genome of Pogostemon cablin provides insights into its evolutionary history and sesquiterpenoid biosynthesis.

Pogostemon cablin (Blanco) Benth. (Patchouli) is an important traditional Chinese medicinal plant that has both essential oil value and a broad range of therapeutic effects. Here we report the first de novo assembled 1.

The Dendrobium catenatum Lindl. genome sequence provides insights into polysaccharide synthase, floral development and adaptive evolution.

Orchids make up about 10% of all seed plant species, have great economical value, and are of specific scientific interest because of their renowned flowers and ecological adaptations. Here, we report the first draft genome sequence of a lithophytic orchid, Dendrobium catenatum. We predict 28,910 protein-coding genes, and find evidence of a whole genome duplication shared with Phalaenopsis.

The WRKY transcription factor genes in eggplant (Solanum melongena L.) and Turkey Berry (Solanum torvum Sw.).

WRKY transcription factors, which play critical roles in stress responses, have not been characterized in eggplant or its wild relative, turkey berry. The recent availability of RNA-sequencing data provides the opportunity to examine WRKY genes from a global perspective. We identified 50 and 62 WRKY genes in eggplant (SmelWRKYs) and turkey berry (StorWRKYs), respectively, all of which could be classified into three groups (I-III) based on the WRKY protein structure.