The complete chloroplast genome of (Jacq.) Schott 1829 (Alismatales: Araceae).

(Jacq.) Schott 1829, a species of the Araceae family, is a foliage plant of ornamental value. The complete chloroplast genome sequence of was obtained by the assembly of NovaSeq 6000 (Illumina Co.

The complete chloroplast genome of Kimnach & Moran 1980 (Saxifragales: Crassulaceae).

Kimnach & Moran 1980 is a succulent plant having ornamental and ecological importance. In this study, the first complete chloroplast genome of a species belonging to the Crassulaceae family, was characterized from the assembly of Illumina NovaSeq 6000 paired-end sequencing data. The chloroplast genome of is 150,080 bp in length, which includes a large single-copy (LSC) region of 81,741 bp, a small single-copy (SSC) region of 16,747 bp, and a pair of identical inverted repeat regions (IRs) of 25,796 bp each.

The complete mitochondrial genome of (Trochida: Turbinidae) and its phylogeny analysis.

The complete mitochondrial genome sequence of , a species of the family, was characterized from the assembly of Illumina paired-end sequencing data. The complete mitochondrial genome of was 17,297 bp in length and comprised of 13 protein-coding genes, 25 tRNAs, and two rRNAs. The base composition of exhibited a high A + T content of 71.

Complete chloroplast genome of Miq. (Caryophyllales: Caryophyllaceae).

The complete chloroplast genome sequence of Miq., a species of the family, was assembled and analyzed from the assembly of Illumina paired-end sequencing data. The total length of the chloroplast genome of was 152,675 bp including a large single-copy (LSC) region of 83,552 bp, a small single-copy (SSC) region of 17,349 bp, and a pair of identical inverted repeat regions (IRs) of 25,887 bp.

Revealing immune responses in the Mycobacterium avium subsp. paratuberculosis-infected THP-1 cells using single cell RNA-sequencing.

Mycobacterium avium subsp. paratuberculosis (MAP) is a causative agent of Johne's disease, which is a chronic and debilitating disease in ruminants. MAP is also considered to be a possible cause of Crohn's disease in humans.

Transcriptomic responses of Aspergillus flavus to temperature and oxidative stresses during aflatoxin production.

Aflatoxin is a group of polyketide-derived carcinogenic and mutagenic secondary metabolites produced by Aspergillus flavus that negatively impact global food security and threaten the health of both humans and livestock. Aflatoxin biosynthesis is strongly affected by the fungal developmental stage, cultivation conditions, and environmental stress. In this study, a novel float culture method was used to examine the direct responses of the A.

The complete chloroplast genome of (Araceae).

The complete chloroplast genome sequence of , a species of the Araceae family, was characterized from the assembly of HiSeq (Illumina Co.) paired-end sequencing data. The chloroplast genome of was 165,289 bp in length, with a large single-copy (LSC) region of 91,747 bp, a small single-copy (SSC) region of 22,550 bp, and a pair of identical inverted repeat regions (IRs) of 25,496 bp.

The complete chloroplast genome of (Menispermaceae).

We generated the complete chloroplast genome sequence of , a species of the Menispermaceae family, and characterized from the assembly of Illumina HiSeq paired-end sequencing data. The total length of the chloroplast genome of was 162,787 bp with a large single-copy (LSC) region of 91,430 bp, a small single-copy (SSC) region of 21,245 bp, and a pair of identical inverted repeat regions (IRs) of 25,056 bp. The total of 131 genes were annotated in the chloroplast genome of , including 85 protein-coding genes, 38 transfer RNA (tRNA) genes, and 8 ribosomal RNA (rRNA) genes.

The complete chloroplast genome of .

We have sequenced the complete chloroplast genome of , a species of the Asphodelaceae family, through Illumina HiSeq paired-end sequencing. The total size of chloroplast genome of was 155,855 bp with a large single-copy (LSC) region of 84,607 bp, a small single-copy (SSC) region of 18,508 bp, and a pair of identical inverted repeat regions (IRs) of 26,370 bp. The genome contained a total of 112 genes, including 79 protein-coding genes, 29 transfer RNA (tRNA) genes, and 4 ribosomal RNA (rRNA) genes.

The complete chloroplast genome of (Ranunculaceae).

The complete chloroplast genome sequence of , a species of the family, was characterized from the assembly of HiSeq (Illumina Co.) paired-end sequencing data. The chloroplast genome of was 155,292 bp in length, with a large single-copy (LSC) region of 84,120 bp, a small single-copy (SSC) region of 18,342 bp, and a pair of identical inverted repeat regions (IRs) of 26,415 bp.

The complete chloroplast genome of (Campanulaceae).

The complete chloroplast genome sequence of was determined by next generation sequencing. The total length of chloroplast genome of was 169,447 bp long, including a large single-copy (LSC) region of 85,253 bp, a small single-copy (SSC) region of 8060 bp, and a pair of identical inverted repeat regions (IRs) of 38,067 bp. A total of 110 genes was annotated, resulting in 79 protein-coding genes, 27 tRNA genes, and 4 rRNA genes.

Development of a Genetic Map for Onion ( L.) Using Reference-Free Genotyping-by-Sequencing and SNP Assays.

Single nucleotide polymorphisms (SNPs) play important roles as molecular markers in plant genomics and breeding studies. Although onion ( L.) is an important crop globally, relatively few molecular marker resources have been reported due to its large genome and high heterozygosity.

Transcriptome Analysis of Spartina pectinata in Response to Freezing Stress.

Prairie cordgrass (Spartina pectinata), a perennial C4 grass native to the North American prairie, has several distinctive characteristics that potentially make it a model crop for production in stressful environments. However, little is known about the transcriptome dynamics of prairie cordgrass despite its unique freezing stress tolerance. Therefore, the purpose of this work was to explore the transcriptome dynamics of prairie cordgrass in response to freezing stress at -5°C for 5 min and 30 min.

Validating DNA Polymorphisms Using KASP Assay in Prairie Cordgrass (Spartina pectinata Link) Populations in the U.S.

Single nucleotide polymorphisms (SNPs) are one of the most abundant DNA variants found in plant genomes and are highly efficient when comparing genome and transcriptome sequences. SNP marker analysis can be used to analyze genetic diversity, create genetic maps, and utilize marker-assisted selection breeding in many crop species. In order to utilize these technologies, one must first identify and validate putative SNPs.

The complete chloroplast genomes of three Korean Echinochloa crus-galli accessions.

The complete chloroplast (cp) genomes of three Echinochloa crus-galli accessions (KR822684, KR822685, and KR822686) are reported in this work. The cp genome size is similar in three accessions, ranging from 139 846 bp to 139 860 bp. All three genomes have two inverted repeats (IR) of 22 748 bp per each IR with a large single copy (LSC) region of 81 833-81 844 bp and a small single copy (SSC) region of 12 517-12 520 bp.

Complete chloroplast genomes of two Miscanthus species.

The complete chloroplast (cp) genomes of two Miscanthus species, M. sinensis and M. sacchariflorus, were sequenced and investigated for genes, genome size variation, and polymorphisms.

An Epigenetic Role for Disrupted Paternal Gene Expression in Postzygotic Seed Abortion in Arabidopsis Interspecific Hybrids.

Interspecific hybrids often increase the levels of heterozygosity and hybrid vigor, but some interspecific hybrid seeds are aborted shortly after fertilization. The mechanism behind this postzygotic seed abortion is poorly understood. Here, we report genome-wide analysis of allelic expression changes in developing siliques and seeds in three F1 interspecific crosses between Arabidopsis thaliana (Col, Ler, or C24) and Arabidopsis arenosa.

Uncovering the differential molecular basis of adaptive diversity in three Echinochloa leaf transcriptomes.

Echinochloa is a major weed that grows almost everywhere in farmed land. This high prevalence results from its high adaptability to various water conditions, including upland and paddy fields, and its ability to grow in a wide range of climates, ranging from tropical to temperate regions. Three Echinochloa crus-galli accessions (EC-SNU1, EC-SNU2, and EC-SNU3) collected in Korea have shown diversity in their responses to flooding, with EC-SNU1 exhibiting the greatest growth among three accessions.

Metabolomic and transcriptomic insights into how cotton fiber transitions to secondary wall synthesis, represses lignification, and prolongs elongation.

Background: The morphogenesis of single-celled cotton fiber includes extreme elongation and staged cell wall differentiation. Designing strategies for improving cotton fiber for textiles and other uses relies on uncovering the related regulatory mechanisms. In this research we compared the transcriptomes and metabolomes of two Gossypium genotypes, Gossypium barbadense cv Phytogen 800 and G.

Uncovering the novel characteristics of Asian honey bee, Apis cerana, by whole genome sequencing.

Background: The honey bee is an important model system for increasing understanding of molecular and neural mechanisms underlying social behaviors relevant to the agricultural industry and basic science. The western honey bee, Apis mellifera, has served as a model species, and its genome sequence has been published. In contrast, the genome of the Asian honey bee, Apis cerana, has not yet been sequenced.

Transcriptome analysis of extant cotton progenitors revealed tetraploidization and identified genome-specific single nucleotide polymorphism in diploid and allotetraploid cotton.

Background: The most widely cultivated cotton (Gossypium hirsutum L., AD-genome) is derived from tetraploidization between A- and D-genome species. G.

High-throughput RNA-seq for allelic or locus-specific expression analysis in Arabidopsis-related species, hybrids, and allotetraploids.

With the next generation sequencing technology, RNA-Seq (RNA sequencing) becomes one of the most powerful tools in quantification of global transcriptomes, discovery of new transcripts and alternative isoforms, as well as detection of single nucleotide polymorphisms (SNPs). RNA-Seq is advantageous over hybridization-based gene quantification methods: (1) it does not require prior information about genomic sequences, (2) it avoids high background problem caused by cross-hybridization, and (3) it is highly sensitive and avoids background and saturation of signals; and finally it is capable of detecting allelic expression differences in hybrids and allopolyploids. We used the RNA-Seq method to determine the genome-wide transcriptome changes in Arabidopsis allotetraploids and their parents, A.