OL-032 Identification of miRNAs in Aedes albopictus and determination of their expression profiles during developmental stages and blood feeding using Solexa sequencing

Flowering is the first committed step of plant sexual reproduction. While the developing flower is a strong sink requiring large quantity of sugars from photosynthetic source tissues, this process is under-temper-spatially controlled via hormone signaling pathway and nutrient availability. Sugar transporters SUT/SUC and SWEET mediate sugars movement across membranes and play a significant role in various physiological processes, including reproductive organ development. In Petunia axillaris, a model ornamental plant, 5 SUT/SUC and 36 SWEET genes are identified in the current version of the genome. Analysis of their gene structure and chromosomal locations reveal that SWEET family is moderately expanded. Most of the transporter genes are abundantly expressed in the flower than in other organs. During the five flower developmental stages, transcript levels of PaSUT1, PaSUT3, PaSWEET13c, PaSWEET9a, PaSWEET1d, PaSWEET5a and PaSWEET14a increase with the maturation of the flower and reach their maximum in the fully open flowers. PaSWEET9c, the nectar-specific PhNEC1 orthologous, is expressed in matured and fully opened flowers. Moreover, determination of sugar concentrations and phytohormone dynamics in flowers at the five developmental stages shows that glucose is the predominant form of sugar in young flowers at the early stage but depletes at the later stage, whereas sucrose accumulates only in maturated flowers prior to the corolla opening. On the other hand, GA3 content and to a less extent IAA and zeatin decreases with the flower development; however, JA, SA and ABA display a remarkable peak at mid- or later flower developmental stage.

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Systematic identification of autophagy-related proteins in Aedes albopictus

PLoS ONE ◽

10.1371/journal.pone.0245694 ◽

2021 ◽

Vol 16 (1) ◽

pp. e0245694

Author(s):

Yu Wang ◽

Jialu Qiao ◽

Dandan Zhang ◽

Chunyan Zhong ◽

Shengya Wang ◽

...

Keyword(s):

Aedes Albopictus ◽

Developmental Stages ◽

Expression Profiles ◽

Basic Information ◽

Research Attention ◽

Autophagy Pathway ◽

Arbovirus Infection ◽

Related Proteins ◽

Systematic Identification

Autophagy is a conserved cellular process playing a role in maintenance of cellular homeostasis and response to changing nutrient conditions via degradation and recirculation of cellular redundant components. Autophagy-related proteins (Atg) play important function in autophagy pathway. Aedes albopictus mosquito is an effective vector transmitting multiple viruses which cause serious human diseases. Moreover, Aedes albopictus mosquito is becoming a serious threat to human health due to its widening distribution in recent years and thus worth of more research attention. It was reported that autophagy might play a role in viral infection in Aedes mosquito. To better understand the interaction between autophagy and arbovirus infection in mosquito system, it is necessary to identify autophagy pathway in the system. However, autophagy in Aedes albopictus mosquito is still poorly understood so far. We recently identified AaAtg8, the first Atg protein reported in Aedes albopictus mosquito. This work further identified twelve atg genes in Aedes albopictus mosquito. Sequence and phylogenetic analysis of the twelve atg genes were performed. Expression profiles of all the twelve Aaatg genes in different developmental stages and genders of Aedes albopictus mosquito were conducted. Effects of chemicals inhibiting or inducing autophagy on the levels of eight identified AaAtg proteins were examined. The function of two identified AaAtg proteins AaAtg6 and AaAtg16 and their response to arbovirus SINV infection were studied preliminarily. Taken together, this work systematically identified Aedes albopictus atg genes and provided basic information which might help to elucidate the autophagy pathway and the role of autophagy in arbovirus infection in Aedes mosquito system.

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Single cell transcriptome atlas of mouse mammary epithelial cells across development

Breast Cancer Research ◽

10.1186/s13058-021-01445-4 ◽

2021 ◽

Vol 23 (1) ◽

Author(s):

Bhupinder Pal ◽

Yunshun Chen ◽

Michael J. G. Milevskiy ◽

François Vaillant ◽

Lexie Prokopuk ◽

...

Keyword(s):

Epithelial Cells ◽

Single Cell ◽

Developmental Stages ◽

Mammary Epithelial Cells ◽

Expression Profiles ◽

Single Cells ◽

Chromatin Accessibility ◽

Mammary Epithelial ◽

Cell Transcriptome ◽

Single Cell Transcriptome

Abstract Background Heterogeneity within the mouse mammary epithelium and potential lineage relationships have been recently explored by single-cell RNA profiling. To further understand how cellular diversity changes during mammary ontogeny, we profiled single cells from nine different developmental stages spanning late embryogenesis, early postnatal, prepuberty, adult, mid-pregnancy, late-pregnancy, and post-involution, as well as the transcriptomes of micro-dissected terminal end buds (TEBs) and subtending ducts during puberty. Methods The single cell transcriptomes of 132,599 mammary epithelial cells from 9 different developmental stages were determined on the 10x Genomics Chromium platform, and integrative analyses were performed to compare specific time points. Results The mammary rudiment at E18.5 closely aligned with the basal lineage, while prepubertal epithelial cells exhibited lineage segregation but to a less differentiated state than their adult counterparts. Comparison of micro-dissected TEBs versus ducts showed that luminal cells within TEBs harbored intermediate expression profiles. Ductal basal cells exhibited increased chromatin accessibility of luminal genes compared to their TEB counterparts suggesting that lineage-specific chromatin is established within the subtending ducts during puberty. An integrative analysis of five stages spanning the pregnancy cycle revealed distinct stage-specific profiles and the presence of cycling basal, mixed-lineage, and 'late' alveolar intermediates in pregnancy. Moreover, a number of intermediates were uncovered along the basal-luminal progenitor cell axis, suggesting a continuum of alveolar-restricted progenitor states. Conclusions This extended single cell transcriptome atlas of mouse mammary epithelial cells provides the most complete coverage for mammary epithelial cells during morphogenesis to date. Together with chromatin accessibility analysis of TEB structures, it represents a valuable framework for understanding developmental decisions within the mouse mammary gland.

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Monte Carlo determination of dose coefficients at different developmental stages of zebrafish (Danio rerio) in experimental condition

Journal of Environmental Radioactivity ◽

10.1016/j.jenvrad.2021.106667 ◽

2021 ◽

Vol 237 ◽

pp. 106667

Author(s):

Huiyuan Xue ◽

Yefeng Zhang ◽

Na Chen ◽

Han Gao ◽

Qixuan Zhang ◽

...

Keyword(s):

Monte Carlo ◽

Danio Rerio ◽

Developmental Stages ◽

Dose Coefficients

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Genome-Wide Identification of Soybean ABC Transporters Relate to Aluminum Toxicity

International Journal of Molecular Sciences ◽

10.3390/ijms22126556 ◽

2021 ◽

Vol 22 (12) ◽

pp. 6556

Author(s):

Junjun Huang ◽

Xiaoyu Li ◽

Xin Chen ◽

Yaru Guo ◽

Weihong Liang ◽

...

Keyword(s):

Gene Expression ◽

Abc Transporters ◽

Developmental Stages ◽

Aluminum Toxicity ◽

Expression Profiles ◽

Gene Expression Profiles ◽

Purifying Selection ◽

Biotic Stresses ◽

Genome Wide ◽

New Germplasm

ATP-binding cassette (ABC) transporter proteins are a gene super-family in plants and play vital roles in growth, development, and response to abiotic and biotic stresses. The ABC transporters have been identified in crop plants such as rice and buckwheat, but little is known about them in soybean. Soybean is an important oil crop and is one of the five major crops in the world. In this study, 255 ABC genes that putatively encode ABC transporters were identified from soybean through bioinformatics and then categorized into eight subfamilies, including 7 ABCAs, 52 ABCBs, 48 ABCCs, 5 ABCDs, 1 ABCEs, 10 ABCFs, 111 ABCGs, and 21 ABCIs. Their phylogenetic relationships, gene structure, and gene expression profiles were characterized. Segmental duplication was the main reason for the expansion of the GmABC genes. Ka/Ks analysis suggested that intense purifying selection was accompanied by the evolution of GmABC genes. The genome-wide collinearity of soybean with other species showed that GmABCs were relatively conserved and that collinear ABCs between species may have originated from the same ancestor. Gene expression analysis of GmABCs revealed the distinct expression pattern in different tissues and diverse developmental stages. The candidate genes GmABCB23, GmABCB25, GmABCB48, GmABCB52, GmABCI1, GmABCI5, and GmABCI13 were responsive to Al toxicity. This work on the GmABC gene family provides useful information for future studies on ABC transporters in soybean and potential targets for the cultivation of new germplasm resources of aluminum-tolerant soybean.

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Genome-Wide Analysis and Characterization of the Aux/IAA Family Genes Related to Floral Scent Formation in Hedychium coronarium

International Journal of Molecular Sciences ◽

10.3390/ijms20133235 ◽

2019 ◽

Vol 20 (13) ◽

pp. 3235 ◽

Cited By ~ 2

Author(s):

Yanguo Ke ◽

Farhat Abbas ◽

Yiwei Zhou ◽

Rangcai Yu ◽

Yuechong Yue ◽

...

Keyword(s):

Gene Family ◽

Developmental Stages ◽

Floral Scent ◽

Expression Profiles ◽

Expression Patterns ◽

Regulatory Elements ◽

Virus Induced Gene Silencing ◽

Cut Flowers ◽

Flower Opening ◽

Hedychium Coronarium

Auxin plays a key role in different plant growth and development processes, including flower opening and development. The perception and signaling of auxin depend on the cooperative action of various components, among which auxin/indole-3-acetic acid (Aux/IAA) proteins play an imperative role. In a recent study, the entire Aux/IAA gene family was identified and comprehensively analyzed in Hedychium coronarium, a scented species used as an ornamental plant for cut flowers. Phylogenetic analysis showed that the Aux/IAA gene family in H. coronarium is slightly contracted compared to Arabidopsis, with low levels of non-canonical proteins. Sequence analysis of promoters showed numerous cis-regulatory elements related to various phytohormones. HcIAA genes showed distinct expression patterns in different tissues and flower developmental stages, and some HcIAA genes showed significant responses to auxin and ethylene, indicating that Aux/IAAs may play an important role in linking hormone signaling pathways. Based on the expression profiles, HcIAA2, HcIAA4, HcIAA6 and HcIAA12, were selected as candidate genes and HcIAA2 and HcIAA4 were screened for further characterization. Downregulation of HcIAA2 and HcIAA4 by virus-induced gene silencing in H. coronarium flowers modified the total volatile compound content, suggesting that HcIAA2 and HcIAA4 play important roles in H. coronarium floral scent formation. The results presented here will provide insights into the putative roles of HcIAA genes and will assist the elucidation of their precise roles during floral scent formation.

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Transcriptional Profiles of Secondary Metabolite Biosynthesis Genes and Cytochromes in the Leaves of Four Papaver Species

Data ◽

10.3390/data3040055 ◽

2018 ◽

Vol 3 (4) ◽

pp. 55 ◽

Cited By ~ 5

Author(s):

Dowan Kim ◽

Myunghee Jung ◽

In Ha ◽

Min Lee ◽

Seok-Geun Lee ◽

...

Keyword(s):

Secondary Metabolite ◽

Developmental Stages ◽

Expression Profiles ◽

Bioinformatics Analyses ◽

Kegg Pathways ◽

Benzylisoquinoline Alkaloid ◽

Development Life Cycle ◽

The Family ◽

Leaf Transcriptome ◽

Secondary Metabolite Biosynthesis

Poppies are well-known plants in the family Papaveraceae that are rich in alkaloids. This family contains 61 species, and in this study we sequenced the transcriptomes of four species’ (Papaver rhoeas, Papaver nudicaule, Papaver fauriei, and Papaver somniferum) leaves. These transcripts were systematically assessed for the expression of secondary metabolite biosynthesis (SMB) genes and cytochromes, and their expression profiles were assessed for use in bioinformatics analyses. This study contributed 265 Gb (13 libraries with three biological replicates) of leaf transcriptome data from three Papaver plant developmental stages. Sequenced transcripts were assembled into 815 Mb of contigs, including 226 Mb of full-length transcripts. The transcripts for 53 KEGG pathways, 55 cytochrome superfamilies, and benzylisoquinoline alkaloid biosynthesis (BIA) were identified and compared to four other alkaloid-rich genomes. Additionally, 22 different alkaloids and their relative expression profiles in three developmental stages of Papaver species were assessed by targeted metabolomics using LC-QTOF-MS/MS. Collectively, the results are given in co-occurrence heat-maps to help researchers obtain an overview of the transcripts and their differential expression in the Papaver development life cycle, particularly in leaves. Moreover, this dataset will be a valuable resource to derive hypotheses to mitigate an array of Papaver developmental and secondary metabolite biosynthesis issues in the future.

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Comparative Transcriptomic Analysis of Riptortus pedestris (Hemiptera: Alydidae) to Characterize Wing Formation across All Developmental Stages

Insects ◽

10.3390/insects12030226 ◽

2021 ◽

Vol 12 (3) ◽

pp. 226

Author(s):

Siying Fu ◽

Yujie Duan ◽

Siqi Wang ◽

Yipeng Ren ◽

Wenjun Bu

Keyword(s):

Molecular Mechanisms ◽

Developmental Stages ◽

Average Length ◽

Transcriptome Assembly ◽

Expression Profiles ◽

Economic Losses ◽

Future Research ◽

Economic Damage ◽

Wing Formation ◽

Riptortus Pedestris

Riptortus pedestris (Hemiptera: Alydidae) is a major agricultural pest in East Asia that causes considerable economic losses to the soybean crop each year. However, the molecular mechanisms governing the growth and development of R. pedestris have not been fully elucidated. In this study, the Illumina HiSeq6000 platform was employed to perform de novo transcriptome assembly and determine the gene expression profiles of this species across all developmental stages, including eggs, first-, second-, third-, fourth-, and fifth-instar nymphs, and adults. In this study, a total of 60,058 unigenes were assembled from numerous raw reads, exhibiting an N50 length of 2126 bp and an average length of 1199 bp, and the unigenes were annotated and classified with various databases, such as the Kyoto Encyclopedia of Genes and Genomes (KEGG), Clusters of Orthologous Groups (COG), and Gene Ontology (GO). Furthermore, various numbers of differentially expressed genes (DEGs) were calculated through pairwise comparisons of all life stages, and some of these DEGs were associated with immunity, metabolism, and development by GO and KEGG enrichment. In addition, 35,158 simple sequence repeats (SSRs) and 715,604 potential single nucleotide polymorphisms (SNPs) were identified from the seven transcriptome libraries of R. pedestris. Finally, we identified and summarized ten wing formation-related signaling pathways, and the molecular properties and expression levels of five wing development-related genes were analyzed using quantitative real-time PCR for all developmental stages of R. pedestris. Taken together, the results of this study may establish a foundation for future research investigating developmental processes and wing formation in hemimetabolous insects and may provide valuable data for pest control efforts attempting to reduce the economic damage caused by this pest.

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Recherches sur le rôle de la température dans la réalisation du phénotype chez des embryons de l'Amphibien Pleurodeles waltlii homozygotes pour la mutation thermosensible ac (ascite caudale)

Development ◽

10.1242/dev.34.1.221 ◽

1975 ◽

Vol 34 (1) ◽

pp. 221-252

Author(s):

Par Maria Fernandez ◽

Jean-Claude Beetschen

Keyword(s):

Embryonic Development ◽

Developmental Stages ◽

Fluid Collection ◽

Temperature Shift ◽

Temperature Sensitive ◽

Tail Bud ◽

Dorsal Fin ◽

Second Shift ◽

Pleurodeles Waltlii

1. At the feeding stage (st. 38), a high percentage (79 %) of Pleurodeles homozygous ac/ac larvae show bent tails after a persistent ascitic blister in the dorsal part of the fin, when embryonic development occurred at 12°C; about only 25 % of them are affected by abdominal and pericardic ascites; about 40 % can feed and survive. The larval phenotype is very different when embryonic development occurred at 23 °C, in which case tail growth appears to be normal, but 95 % larvae die, due to ascitic fluid collection in the abdominal and heart regions, marked anaemia and microcephaly. 2. The exchange of posterior neural plates and dorso-lateral epidermis between normal and mutant neurulae has shown that the localization of the blister in the dorsal fin is not dependent on autonomous properties of the mutant dorsal tissues, but should be considered as resulting from general disturbances in the mutant organism. 3. Experiments were performed, involving a temperature shift from 12 to 23°C or 23 to 12°C, occurring at various developmental stages from the end of gastrulation (stage 13) to the stage of spontaneous embryonic muscle contractions (stage 26). When the temperature shift was applied after the end of neurulation (stage 21), the caudal phenotype was statistically similar to that of larvae which had been bred continuously at the first temperature. Thus temperature-sensitive phases can be characterized between neurula stages 15 and 18 (for a 12–23° shift) or 15 and 21 (for a 23–12° shift). Similarly, abdominal ascites can be induced when embryos are kept at 23 °C till stage 23 (early tail-bud) only, and occurs much less frequently when embryos are kept at 12°C till stage 23 and then transferred to 23°C. 4. It could be concluded from these experiments that the caudal mutant phenotype is already temperature-determined during neurulation, before stage 21. Nevertheless, double temperature-shift experiments showed that the second shift could modify the results which would be obtained if the first shift only occurred. Paradoxical results were obtained, more than 90 % of the tail phenotypes being of the ‘warm type’ when the embryos were first kept at 12°C, then shifted up to 23 °C between stages 22 and 26, and shifted down again to 12°C. Such a treatment markedly lowers the percentage of bent tails (‘cold type’) from the percentage which would occur if ac/ac embryos were constantly kept at 23 °C after stage 21, but this longer warm treatment is of no effect of itself as compared to the case when the whole development occurs at 12°C (bent tails are predominant in this latter case). Thus, whereas the early determination of the position of the caudal blister can be considered as a stable phenomenon under given temperature conditions, it is not irreversible. 5. As compared to cold-bred larvae, thrice as many completely anaemic larvae (66 %) were obtained from ac/ac embryos kept at 23 °C between stages 21 and 26; this offers an opportunity for the experimental study of this anaemia. 6. Implications of these results for further analysis of temperature-sensitive mutations in cold-blooded vertebrates are suggested.

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