Enriching Genomic Resources and Marker Development from Transcript Sequences ofJatropha curcasfor Microgravity Studies

Jatropha (Jatropha curcasL.) is an economically important species with a great potential for biodiesel production. To enrich the jatropha genomic databases and resources for microgravity studies, we sequenced and annotated the transcriptome of jatropha and developed SSR and SNP markers from the transcriptome sequences. In total 1,714,433 raw reads with an average length of 441.2 nucleotides were generated. De novo assembling and clustering resulted in 115,611 uniquely assembled sequences (UASs) including 21,418 full-length cDNAs and 23,264 new jatropha transcript sequences. The whole set of UASs were fully annotated, out of which 59,903 (51.81%) were assigned with gene ontology (GO) term, 12,584 (10.88%) had orthologs in Eukaryotic Orthologous Groups (KOG), and 8,822 (7.63%) were mapped to 317 pathways in six different categories in Kyoto Encyclopedia of Genes and Genome (KEGG) database, and it contained 3,588 putative transcription factors. From the UASs, 9,798 SSRs were discovered with AG/CT as the most frequent (45.8%) SSR motif type. Further 38,693 SNPs were detected and 7,584 remained after filtering. This UAS set has enriched the current jatropha genomic databases and provided a large number of genetic markers, which can facilitate jatropha genetic improvement and many other genetic and biological studies.

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Development of EST-Molecular Markers from RNA Sequencing for Genetic Management and Identification of Growth Traits in Potato Grouper (Epinephelus tukula)

Biology ◽

10.3390/biology10010036 ◽

2021 ◽

Vol 10 (1) ◽

pp. 36

Author(s):

Te-Hua Hsu ◽

Yu-Ting Chiu ◽

Hung-Tai Lee ◽

Hong-Yi Gong ◽

Chang-Wen Huang

Keyword(s):

Molecular Markers ◽

Expressed Sequence Tag ◽

De Novo ◽

Growth Traits ◽

Gene Diversity ◽

Snp Markers ◽

Cdna Libraries ◽

Functional Markers ◽

Genetic Management ◽

Ssr And Snp Markers

The accuracy and efficiency of marker-assisted selection (MAS) has been proven for economically critical aquaculture species. The potato grouper (Epinephelus tukula), a novel cultured grouper species in Taiwan, shows large potential in aquaculture because of its fast growth rate among other groupers. Because of the lack of genetic information for the potato grouper, the first transcriptome and expressed sequence tag (EST)-derived simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) markers were developed. Initially, the transcriptome was obtained from seven cDNA libraries by using the Illumina platform. De novo transcriptome of the potato grouper yielded 51.34 Gb and 111,490 unigenes. The EST-derived SSR and SNP markers were applied in genetic management, in parentage analysis, and to discover the functional markers of economic traits. The F1 juveniles were identified as siblings from one pair of parents (80 broodstocks). Fast- and slow-growth individuals were analyzed using functional molecular markers and through their association with growth performance. The results revealed that two SNPs were correlated with growth traits. The transcriptome database obtained in this study and its derived SSR and SNP markers may be applied not only for MAS but also to maintain functional gene diversity in the novel cultured grouper.

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Development of EST-based SSR and SNP markers in Gastrodia elata (herbal medicine) by sequencing, de novo assembly and annotation of the transcriptome

3 Biotech ◽

10.1007/s13205-019-1823-4 ◽

2019 ◽

Vol 9 (8) ◽

Cited By ~ 3

Author(s):

Yunsheng Wang ◽

Muhammad Qasim Shahid ◽

Fozia Ghouri ◽

Sezai Ercişli ◽

Faheem Shehzad Baloch

Keyword(s):

Herbal Medicine ◽

De Novo Assembly ◽

De Novo ◽

Snp Markers ◽

Gastrodia Elata ◽

Ssr And Snp Markers

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Structural catalog of core Atg proteins opens new era of autophagy research

The Journal of Biochemistry ◽

10.1093/jb/mvab017 ◽

2021 ◽

Author(s):

Kazuaki Matoba ◽

Nobuo N Noda

Keyword(s):

De Novo ◽

Structural Information ◽

Membrane Dynamics ◽

Autophagosome Formation ◽

New Era ◽

Intracellular Degradation ◽

Atg Proteins ◽

Biological Studies ◽

Evolutionarily Conserved ◽

Biological Methods

Summary Autophagy, which is an evolutionarily conserved intracellular degradation system, involves de novo generation of autophagosomes that sequester and deliver diverse cytoplasmic materials to the lysosome for degradation. Autophagosome formation is mediated by approximately 20 core autophagy-related (Atg) proteins, which collaborate to mediate complicated membrane dynamics during autophagy. To elucidate the molecular functions of these Atg proteins in autophagosome formation, many researchers have tried to determine the structures of Atg proteins by using various structural biological methods. Although not sufficient, the basic structural catalog of all core Atg proteins was established. In this review article, we summarize structural biological studies of core Atg proteins, with an emphasis on recently unveiled structures, and describe the mechanistic breakthroughs in autophagy research that have derived from new structural information.

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Long-Term Waterlogging as Factor Contributing to Hypoxia Stress Tolerance Enhancement in Cucumber: Comparative Transcriptome Analysis of Waterlogging Sensitive and Tolerant Accessions

Genes ◽

10.3390/genes12020189 ◽

2021 ◽

Vol 12 (2) ◽

pp. 189

Author(s):

Kinga Kęska ◽

Michał Wojciech Szcześniak ◽

Izabela Makałowska ◽

Małgorzata Czernicka

Keyword(s):

Stress Tolerance ◽

De Novo ◽

Average Length ◽

Marker Genes ◽

Long Term Memory ◽

Low Oxygen ◽

Waterlogging Tolerance ◽

Pre Treatment ◽

Waterlogging Treatment

Waterlogging (WL), excess water in the soil, is a phenomenon often occurring during plant cultivation causing low oxygen levels (hypoxia) in the soil. The aim of this study was to identify candidate genes involved in long-term waterlogging tolerance in cucumber using RNA sequencing. Here, we also determined how waterlogging pre-treatment (priming) influenced long-term memory in WL tolerant (WL-T) and WL sensitive (WL-S) i.e., DH2 and DH4 accessions, respectively. This work uncovered various differentially expressed genes (DEGs) activated in the long-term recovery in both accessions. De novo assembly generated 36,712 transcripts with an average length of 2236 bp. The results revealed that long-term waterlogging had divergent impacts on gene expression in WL-T DH2 and WL-S DH4 cucumber accessions: after 7 days of waterlogging, more DEGs in comparison to control conditions were identified in WL-S DH4 (8927) than in WL-T DH2 (5957). Additionally, 11,619 and 5007 DEGs were identified after a second waterlogging treatment in the WL-S and WL-T accessions, respectively. We identified genes associated with WL in cucumber that were especially related to enhanced glycolysis, adventitious roots development, and amino acid metabolism. qRT-PCR assay for hypoxia marker genes i.e., alcohol dehydrogenase (adh), 1-aminocyclopropane-1-carboxylate oxidase (aco) and long chain acyl-CoA synthetase 6 (lacs6) confirmed differences in response to waterlogging stress between sensitive and tolerant cucumbers and effectiveness of priming to enhance stress tolerance.

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Initiation and maturation of I-Z-I bodies in the growth tips of transfected myotubes

Journal of Cell Science ◽

10.1242/jcs.112.22.4101 ◽

1999 ◽

Vol 112 (22) ◽

pp. 4101-4112 ◽

Cited By ~ 3

Author(s):

K. Ojima ◽

Z.X. Lin ◽

Z.Q. Zhang ◽

T. Hijikata ◽

S. Holtzer ◽

...

Keyword(s):

Binding Sites ◽

Thin Filament ◽

Fluorescent Protein ◽

De Novo ◽

Actin Binding ◽

Double Staining ◽

Green Fluorescent ◽

Short Time ◽

Alpha Actin ◽

De Novo Assembling

While over a dozen I-Z-I proteins are expressed in postmitotic myoblasts and myotubes it is unclear how, when, or where these first assemble into transitory I-Z-I bodies (thin filament/Z-band precursors) and, a short time later, into definitive I-Z-I bands. By double-staining the growth tips of transfected myotubes expressing (a) MYC-tagged s-alpha-actinins (MYC/s-alpha-actinins) or (b) green fluorescent protein-tagged titin cap (GFP/T-cap) with antibodies against MYC and I-Z-I band proteins, we found that the de novo assembly of I-Z-I bodies and their maturation into I-Z-I bands involved relatively concurrent, cooperative binding and reconfiguration of, at a minimum, 5 integral Z-band molecules. These included s-alpha-actinin, nebulin, titin, T-cap and alpha-actin. Resolution of the approximately 1.0 microm polarized alpha-actin/nebulin/tropomyosin/troponin thin filament complexes occurred subsequent to the maturation of Z-bands into a dense tetragonal configuration. Of particular interest is finding that mutant MYC/s-alpha-actinin peptides (a) lacking spectrin-like repeats 1–4, or consisting of spectrin-like repeats 1–4 only, as well as (b) mutants/fragments lacking titin or alpha-actin binding sites, were promptly and exclusively incorporated into de novo assembling I-Z-I bodies and definitive I-Z-I bands as was exogenous full length MYC/s-alpha-actinin or GFP/T-cap.

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Transcriptome Analysis of Ramie (Boehmeria niveaL. Gaud.) in Response to Ramie Moth (Cocytodes coeruleaGuenée) Infestation

BioMed Research International ◽

10.1155/2016/3702789 ◽

2016 ◽

Vol 2016 ◽

pp. 1-10 ◽

Cited By ~ 5

Author(s):

Liangbin Zeng ◽

Airong Shen ◽

Jia Chen ◽

Zhun Yan ◽

Touming Liu ◽

...

Keyword(s):

Protein Function ◽

Molecular Mechanisms ◽

Defense Mechanism ◽

Natural Fiber ◽

De Novo ◽

Average Length ◽

Expression Patterns ◽

Transcriptome Profiling ◽

Cdna Libraries ◽

Pcr Analysis

The ramie mothCocytodes coeruleaGuenée (RM) is an economically important pest that seriously impairs the yield of ramie, an important natural fiber crop. The molecular mechanisms that underlie the ramie-pest interactions are unclear up to date. Therefore, a transcriptome profiling analysis would aid in understanding the ramie defense mechanisms against RM. In this study, we first constructed two cDNA libraries derived from RM-challenged (CH) and unchallenged (CK) ramie leaves. The subsequent sequencing of the CH and CK libraries yielded 40.2 and 62.8 million reads, respectively. Furthermore,de novoassembling of these reads generated 26,759 and 29,988 unigenes, respectively. An integrated assembly of data from these two libraries resulted in 46,533 unigenes, with an average length of 845 bp per unigene. Among these genes, 24,327 (52.28%) were functionally annotated by predicted protein function. A comparative analysis of the CK and CH transcriptome profiles revealed 1,980 differentially expressed genes (DEGs), of which 750 were upregulated and 1,230 were downregulated. A quantitative real-time PCR (qRT-PCR) analysis of 13 random selected genes confirmed the gene expression patterns that were determined by Illumina sequencing. Among the DEGs, the expression patterns of transcription factors, protease inhibitors, and antioxidant enzymes were studied. Overall, these results provide useful insights into the defense mechanism of ramie against RM.

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De novo transcriptome assembly of Pueraria montana var. lobata and Neustanthus phaseoloides for the development of eSSR and SNP markers: narrowing the US origin(s) of the invasive kudzu

BMC Genomics ◽

10.1186/s12864-018-4798-3 ◽

2018 ◽

Vol 19 (1) ◽

Cited By ~ 2

Author(s):

Matthew S. Haynsen ◽

Mohammad Vatanparast ◽

Gouri Mahadwar ◽

Dennis Zhu ◽

Roy Z. Moger-Reischer ◽

...

Keyword(s):

De Novo ◽

Transcriptome Assembly ◽

Snp Markers ◽

De Novo Transcriptome Assembly ◽

De Novo Transcriptome ◽

The Us ◽

Pueraria Montana

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De novo Transcriptome Assembly and Comparative Analysis Highlight the Primary Mechanism Regulating the Response to Selenium Stimuli in Oats (Avena sativa L.)

Frontiers in Plant Science ◽

10.3389/fpls.2021.625520 ◽

2021 ◽

Vol 12 ◽

Author(s):

Tao Liu ◽

Xiaoting Liu ◽

Rangrang Zhou ◽

Hong Chen ◽

Huaigang Zhang ◽

...

Keyword(s):

Transcriptome Analysis ◽

Regulatory Mechanism ◽

De Novo ◽

Average Length ◽

Transcriptome Assembly ◽

Processing Technique ◽

Sodium Selenate ◽

Control Group ◽

Primary Mechanism ◽

High Selenium

Selenium is an essential microelement for humans and animals. The specific processing technique of oats can maximize the preservation of its nutrients. In this study, to understand the genetic response of oats in a high-selenium environment, oats were treated with sodium selenate for 24 h, and transcriptome analysis was performed. A total of 211,485,930 clean reads composing 31.30 Gb of clean data were retained for four samples. After assembly, 186,035 unigenes with an average length of 727 bp were generated, and the N50 length was 1,149 bp. Compared with that in the control group, the expression of 7,226 unigenes in the treatment group was upregulated, and 2,618 unigenes were downregulated. Based on the sulfur assimilation pathway and selenocompound metabolic pathway, a total of 27 unigenes related to selenate metabolism were identified. Among them, the expression of both key genes APS (ATP sulfurylase) and APR (adenosine 5′-phosphosulfate reductase) was upregulated more than 1,000-fold under selenate treatment, while that of CBL (cystathionine-β-synthase) was upregulated 3.12-fold. Based on the transcriptome analysis, we suspect that the high-affinity sulfur transporter Sultr1;2 plays a key role in selenate uptake in oats. A preliminary regulatory mechanism explains the oat response to selenate treatment was ultimately proposed based on the transcriptome analysis and previous research.

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De novo transcriptome assembly and analysis of the codon usage bias of the MADS-box gene family in Cymbidium kanran

Indian Journal of Genetics and Plant Breeding (The) ◽

10.31742/ijgpb.79.2.13 ◽

2019 ◽

Vol 79 (02) ◽

Author(s):

Boyun Yang ◽

Huolin Luo ◽

Yuan Tao ◽

Wenjing Yu ◽

Liping Luo

Keyword(s):

Codon Usage ◽

Codon Usage Bias ◽

De Novo ◽

Average Length ◽

Transcriptome Assembly ◽

Mads Box ◽

Illumina Hiseq ◽

Optimal Codons ◽

Mads Box Gene ◽

New Varieties

Cymbidium kanran is an important commercially grown member of the Chinese orchid family. However, little information regarding the molecular biology of this species is available. In this study, the C. kanran root, shoot, stem, leaf, and flower transcriptomes were sequenced with the Illumina HiSeq 4000 system, which resulted in 8.9 Gb of clean reads that were assembled into 74,620 unigenes, with an average length and N50 of 983 bp and 1,640 bp, respectively. The screening of seven databases (NR, NT, GO, KOG, KEGG, Swiss-Prot, and InterPro) for similar sequences resulted in the functional annotation of 49,813 unigenes. Additionally, 173 MADS-box genes, which help to control major aspects of plant development, were identified and their codon usage bias was analyzed. Only 26 genes had a low ENC (less than or equal to 35), suggesting the codon usage bias was weak. Base mutations were the major determinants of codon usage, although natural selection pressure also influenced codon usage bias. Moreover, 22 optimal codons were identified based on ΔRSCU, and 20 codons ended with A/U. The results of this study provide the foundation for the molecular breeding of new varieties

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