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Sequencing Plant Genomes

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  • Chromosome-level assembly of the mangrove plant Aegiceras corniculatum genome generated through Illumina, PacBio and Hi-C sequencing technologies
  • Whole genome sequence insight of two plant growth-promoting bacteria (B. subtilis BS87 and B. megaterium BM89) isolated and characterized from sugarcane rhizosphere depicting better crop yield potentiality
  • Recent advances in understanding mitochondrial genome diversity.
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Chromosome-level assembly of the mangrove plant Aegiceras corniculatum genome generated through Illumina, PacBio and Hi-C sequencing technologies

Chromosome-level assembly of the mangrove plant Aegiceras corniculatum genome generated through Illumina, PacBio and Hi-C sequencing technologies

Antibody, Assay Kit, Default, Detection Kit, DNA, Elisa Kit, Genome Sequencing of SAV3 Reveals Repeated Seeding Events of Viral Strains in Norwegian Aquaculture., Kit, Lab Product, Lab Reagent, Lentivirus, Medium, Monoclonal Antibody, NATtrol, Particles, Polyclonal Antibody, Protein, Reagent, Recent advances in understanding mitochondrial genome diversity., Recombinant Protein, RNA, Stain, Systematic Identification and Analysis of Light-Responsive Circular RNA and Co-expression Networks in Lettuce (Lactuca sativa)., Tips, Tissue, Tissue Array / By Leslie Obrien

Aegiceras corniculatum is a significant mangrove plant species tailored to waterlogging and saline circumstances, grows in the coastal intertidal zone of tropical and subtropical areas. Here, we current a chromosome-level genome assembly of A. corniculatum by incorporating PacBio long-read sequencing and Hi-C expertise. The outcomes confirmed that the PacBio draft genome measurement is 906.63 Mb. Hi-C scaffolding anchored 885.06 Mb contigs (97.62% of draft assembly) onto 24 pseudo-chromosomes. The contig N50 and scaffold N50 have been 7.1 Mb and 37.74 Mb, respectively.

Out of 40,727 protein-coding genes predicted in the research, 89% have practical annotations in public databases. We additionally confirmed that of the 603.93 Mb repetitive sequences predicted in the assembled genome, lengthy terminal repeat retrotransposons represent 41.52%. The genome evolution evaluation confirmed that the A. corniculatum genome skilled two whole-genome duplication occasions and shared the historical γ whole-genome triplication occasion.

A comparative genomic evaluation revealed an incidence of enlargement in 1,488 gene households related to important metabolism and biosynthetic pathways, together with photosynthesis, oxidative phosphorylation, phenylalanine, glyoxylate, dicarboxylate metabolism, and DNA replication, which possible represent adaptation traits that enable the A. corniculatum to outlive in the intertidal zone. Also, the systematic characterization of genes related to flavonoid biosynthesis pathway and the AcNHX gene household performed on this research will present perception into the adaptation mechanism of A. corniculatum to intertidal environments.

The high-quality genome reported right here can present historic insights into genomic transformations that assist the survival of A. corniculatum beneath harsh intertidal habitats. Availability of plant genome sequences has led to vital advances. However, with few exceptions, the nice majority of current genome assemblies are derived from brief learn sequencing technologies with extremely uneven learn coverages indicative of sequencing and assembly points that would considerably impression any downstream evaluation of plant genomes. In tomato for instance, 0.6% (5.1 Mb) and 9.7% (79.6 Mb) of short-read primarily based assembly had considerably larger and decrease protection in comparison with background, respectively.

To perceive what the causes could also be for such uneven protection, we first established machine studying fashions succesful of predicting genomic areas with variable coverages and discovered that prime protection areas are inclined to have larger easy sequence repeat and tandem gene densities in comparison with background areas. To decide if the excessive protection areas have been misassembled, we examined a not too long ago obtainable tomato long-read primarily based assembly and discovered that 27.8% (1.41 Mb) of excessive protection areas have been doubtlessly misassembled of duplicate sequences, in comparison with 1.4% in background areas.

Genome sequencing and evaluation of plant growth-promoting attributes from Leclercia adecarboxylata

 

Plant growth-promoting micro organism are ecological options for fertilization, primarily for gramineous. Since plant x micro organism interplay is genotype and pressure dependent, trying to find new strains might contribute to the improvement of new biofertilizers. We purpose to characterize plant growth-promoting capability of Leclercia adecarboxylata pressure Palotina, previously remoted by our group in corn. A single remoted colony was taken and its genome was sequenced utilizing Illumina expertise.

The complete genome was in comparison with different Leclercia adecarboxylata strains, and their organic and growth-promoting traits, comparable to P solubilization and auxin manufacturing, have been examined. Following that, a 4.8 Mb genome of L. adecarboxylata pressure Palotina was assembled and the practical annotation was carried out. This paper is the first to report the genes related to plant progress promotion demonstrating in vitro indole acid manufacturing by this pressure. These outcomes venture the endophyte as a possible biofertilizer for additional industrial exploitation.

Coffea canephora is a paramount financial plant with nice financial worth. The full chloroplast (cp) genome is 154,751 bp in size, together with a big single copy (LSC) area of 84,850 bp, a small single copy (SSC) area of 18,131 bp and a pair of inverted repeats (IRs) of 25,885bp. This cp genome comprises 131 genes, comprising of 86 protein-coding genes, 37 tRNAs and Eight rRNAs. The majority of these genes have been single copy genes, whereas 18 genes existed as double copies, together with 6 protein-coding genes (ndhB, rpl2, rpl23, rps12, rps7 and ycf2), Eight tRNA genes (trnA-UGC, trnG-GCC, trnI-CAU, trnI-GAU, trnL-CAA, trnN-GUU, trnR-ACG and trnV-GAC) and Four rRNA genes (rrn4.5, rrn5, rrn16 and rrn23).

A neighbour-joining phylogenetic tree was reconstructed to point that Coffea canephora is evolutionarily near Olea europaea inside Asterids. The full cp genome will present intragenic data for molecular phylogeny and organic research of the Rubiales. In addition, utilizing a predictive mannequin that may distinguish accurately and incorrectly assembled excessive protection areas, we discovered that misassembled, excessive protection areas are typically flanked by easy sequence repeats, pseudogenes, and transposon parts.

Chromosome-level assembly of the mangrove plant Aegiceras corniculatum genome generated through Illumina, PacBio and Hi-C sequencing technologies

Complete genome sequence of plant growth-promoting and heavy metal-tolerant Enterobacter tabaci 4M9 (CCB-MBL 5004)

 

Enterobacter tabaci 4M9 (CCB-MBL 5004) was reported to have plant growth-promoting and heavy steel tolerance traits. It was in a position to tolerate greater than 300 mg/L Cd, 600 mg/L As, and 500 mg/L Pb and nonetheless maintained the means to provide plant growth-promoting substances beneath steel stress circumstances. To discover the genetic foundation of these useful traits, the full genome sequencing of 4M9 was carried out utilizing Pacific Bioscience (PacBio) sequencing expertise.

sequencing unit 33x45 cm
ESEQ1100-SYS Consort ea
EUR 1535
sequencing system 20x50 cm
ESEQ1200-SYS Consort ea
EUR 1535
Trypin for Mass & Sequencing
T9600-025 GenDepot 25ug
EUR 145
Trypin for Mass & Sequencing
T9600-100 GenDepot 100ug
EUR 219
Trypin for Mass & Sequencing
T9600-112 GenDepot 12x100ug
EUR 1657
Trypin for Mass & Sequencing
T9600-400 GenDepot 4x100ug
EUR 651
SequaGel Sequencing System 1L Kit
NAT1136 National Diagnostics 1KIT
EUR 143
SequaGel Sequencing System 2.2L Kit
NAT1138 National Diagnostics EACH
EUR 211
PCR Clean Up for DNA Sequencing
BT5100 Bio Basic 100preps
EUR 95.68
  • Product category: PCR Related/PCR Kits (Cleanup)
PCR Clean Up for DNA Sequencing
BT5101 Bio Basic 1000Preps, 1000prep
EUR 461.08
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DNA Library Prep Kit for IIlumina Sequencing
K1475-12 Biovision 12 Rxns
EUR 480
U1 Primers
MP00001 ABM 150 ul / 10 uM
EUR 121
SNORD44 Primers
MPH00003 ABM 150 ul / 10 uM
EUR 121
SNORD47 Primers
MPH00004 ABM 150 ul / 10 uM
EUR 121
SNORD48 Primers
MPH00005 ABM 150 ul / 10 uM
EUR 121
RNU43 Primers
MPM00003 ABM 150 ul / 10 uM
EUR 121
snoRNA142 Primers
MPM00004 ABM 150 ul / 10 uM
EUR 121
Random Primers
S300 GeneOn 30 µg
EUR 46
Random Primers
S305 GeneOn 5x30 µg
EUR 102
U6-2 Primers
MPH00001 ABM 150 ul / 10 uM
EUR 121
U6 snRNA Primers
MPM00002 ABM 150 ul / 10 uM
EUR 121
U1 snRNA Primers
MPM00006 ABM 150 ul / 10 uM
EUR 121
mmu-miR-30f Primers
MPM01166 ABM 150 ul / 10 uM
EUR 121
mmu-miR-3154 Primers
MPM01188 ABM 150 ul / 10 uM
EUR 121
mmu-miR-344i Primers
MPM01226 ABM 150 ul / 10 uM
EUR 121
mmu-miR-3473b Primers
MPM01229 ABM 150 ul / 10 uM
EUR 121
mmu-miR-3473c Primers
MPM01230 ABM 150 ul / 10 uM
EUR 121
mmu-miR-3473d Primers
MPM01231 ABM 150 ul / 10 uM
EUR 121
mmu-miR-3473e Primers
MPM01232 ABM 150 ul / 10 uM
EUR 121
mmu-miR-3473f Primers
MPM01233 ABM 150 ul / 10 uM
EUR 121
mmu-miR-3473g Primers
MPM01234 ABM 150 ul / 10 uM
EUR 121
mmu-miR-3535 Primers
MPM01245 ABM 150 ul / 10 uM
EUR 121
mmu-miR-3552 Primers
MPM01250 ABM 150 ul / 10 uM
EUR 121
mmu-miR-378c Primers
MPM01282 ABM 150 ul / 10 uM
EUR 121
mmu-miR-378d Primers
MPM01283 ABM 150 ul / 10 uM
EUR 121
mmu-miR-451a Primers
MPM01313 ABM 150 ul / 10 uM
EUR 121
mmu-miR-451b Primers
MPM01314 ABM 150 ul / 10 uM
EUR 121
mmu-miR-466q Primers
MPM01321 ABM 150 ul / 10 uM
EUR 121
mmu-miR-496b Primers
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EUR 121
mmu-miR-497b Primers
MPM01363 ABM 150 ul / 10 uM
EUR 121
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MPM01372 ABM 150 ul / 10 uM
EUR 121
mmu-miR-5098 Primers
MPM01373 ABM 150 ul / 10 uM
EUR 121
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EUR 121
mmu-miR-5100 Primers
MPM01375 ABM 150 ul / 10 uM
EUR 121
mmu-miR-5101 Primers
MPM01376 ABM 150 ul / 10 uM
EUR 121
mmu-miR-5103 Primers
MPM01377 ABM 150 ul / 10 uM
EUR 121
mmu-miR-5104 Primers
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EUR 121
mmu-miR-5106 Primers
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EUR 121
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EUR 121
mmu-miR-5110 Primers
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EUR 121
mmu-miR-5112 Primers
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EUR 121
mmu-miR-5113 Primers
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EUR 121
mmu-miR-5114 Primers
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EUR 121
mmu-miR-5116 Primers
MPM01387 ABM 150 ul / 10 uM
EUR 121
mmu-miR-5118 Primers
MPM01388 ABM 150 ul / 10 uM
EUR 121
mmu-miR-5119 Primers
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EUR 121
mmu-miR-5120 Primers
MPM01390 ABM 150 ul / 10 uM
EUR 121
mmu-miR-5121 Primers
MPM01391 ABM 150 ul / 10 uM
EUR 121
mmu-miR-5122 Primers
MPM01392 ABM 150 ul / 10 uM
EUR 121
mmu-miR-5123 Primers
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EUR 121
mmu-miR-5124a Primers
MPM01394 ABM 150 ul / 10 uM
EUR 121
mmu-miR-5124b Primers
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EUR 121
mmu-miR-5125 Primers
MPM01396 ABM 150 ul / 10 uM
EUR 121
mmu-miR-5126 Primers
MPM01397 ABM 150 ul / 10 uM
EUR 121
mmu-miR-5127 Primers
MPM01398 ABM 150 ul / 10 uM
EUR 121
mmu-miR-5128 Primers
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EUR 121
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MPM01402 ABM 150 ul / 10 uM
EUR 121
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MPM01403 ABM 150 ul / 10 uM
EUR 121
mmu-miR-5133 Primers
MPM01406 ABM 150 ul / 10 uM
EUR 121
mmu-miR-5134 Primers
MPM01407 ABM 150 ul / 10 uM
EUR 121
mmu-miR-5135 Primers
MPM01410 ABM 150 ul / 10 uM
EUR 121
mmu-miR-5136 Primers
MPM01411 ABM 150 ul / 10 uM
EUR 121
mmu-miR-5710 Primers
MPM01447 ABM 150 ul / 10 uM
EUR 121
mmu-miR-6236 Primers
MPM01454 ABM 150 ul / 10 uM
EUR 121
mmu-miR-6237 Primers
MPM01455 ABM 150 ul / 10 uM
EUR 121
mmu-miR-6238 Primers
MPM01456 ABM 150 ul / 10 uM
EUR 121
mmu-miR-6239 Primers
MPM01457 ABM 150 ul / 10 uM
EUR 121
mmu-miR-6240 Primers
MPM01458 ABM 150 ul / 10 uM
EUR 121
mmu-miR-6241 Primers
MPM01459 ABM 150 ul / 10 uM
EUR 121
mmu-miR-6243 Primers
MPM01460 ABM 150 ul / 10 uM
EUR 121
mmu-miR-6244 Primers
MPM01461 ABM 150 ul / 10 uM
EUR 121
mmu-miR-6335 Primers
MPM01462 ABM 150 ul / 10 uM
EUR 121
mmu-miR-6336 Primers
MPM01463 ABM 150 ul / 10 uM
EUR 121
mmu-miR-6337 Primers
MPM01464 ABM 150 ul / 10 uM
EUR 121
mmu-miR-6338 Primers
MPM01465 ABM 150 ul / 10 uM
EUR 121
mmu-miR-6339 Primers
MPM01466 ABM 150 ul / 10 uM
EUR 121
mmu-miR-6340 Primers
MPM01467 ABM 150 ul / 10 uM
EUR 121
mmu-miR-6341 Primers
MPM01468 ABM 150 ul / 10 uM
EUR 121
mmu-miR-6342 Primers
MPM01469 ABM 150 ul / 10 uM
EUR 121
mmu-miR-6343 Primers
MPM01470 ABM 150 ul / 10 uM
EUR 121
mmu-miR-6344 Primers
MPM01471 ABM 150 ul / 10 uM
EUR 121
mmu-miR-6345 Primers
MPM01472 ABM 150 ul / 10 uM
EUR 121
mmu-miR-6346 Primers
MPM01473 ABM 150 ul / 10 uM
EUR 121
mmu-miR-6347 Primers
MPM01474 ABM 150 ul / 10 uM
EUR 121
mmu-miR-6348 Primers
MPM01475 ABM 150 ul / 10 uM
EUR 121
mmu-miR-6349 Primers
MPM01476 ABM 150 ul / 10 uM
EUR 121
mmu-miR-6350 Primers
MPM01477 ABM 150 ul / 10 uM
EUR 121
mmu-miR-6351 Primers
MPM01478 ABM 150 ul / 10 uM
EUR 121
mmu-miR-6352 Primers
MPM01479 ABM 150 ul / 10 uM
EUR 121
mmu-miR-6353 Primers
MPM01480 ABM 150 ul / 10 uM
EUR 121
mmu-miR-6354 Primers
MPM01481 ABM 150 ul / 10 uM
EUR 121
mmu-miR-6355 Primers
MPM01482 ABM 150 ul / 10 uM
EUR 121
mmu-miR-6356 Primers
MPM01483 ABM 150 ul / 10 uM
EUR 121
mmu-miR-6357 Primers
MPM01484 ABM 150 ul / 10 uM
EUR 121
mmu-miR-6358 Primers
MPM01485 ABM 150 ul / 10 uM
EUR 121
mmu-miR-6359 Primers
MPM01486 ABM 150 ul / 10 uM
EUR 121
mmu-miR-6360 Primers
MPM01487 ABM 150 ul / 10 uM
EUR 121
mmu-miR-6361 Primers
MPM01488 ABM 150 ul / 10 uM
EUR 121
mmu-miR-6362 Primers
MPM01489 ABM 150 ul / 10 uM
EUR 121
mmu-miR-6363 Primers
MPM01490 ABM 150 ul / 10 uM
EUR 121
mmu-miR-6364 Primers
MPM01491 ABM 150 ul / 10 uM
EUR 121
mmu-miR-6365 Primers
MPM01492 ABM 150 ul / 10 uM
EUR 121
mmu-miR-6366 Primers
MPM01493 ABM 150 ul / 10 uM
EUR 121
mmu-miR-6367 Primers
MPM01494 ABM 150 ul / 10 uM
EUR 121
mmu-miR-6368 Primers
MPM01495 ABM 150 ul / 10 uM
EUR 121
mmu-miR-6369 Primers
MPM01496 ABM 150 ul / 10 uM
EUR 121
mmu-miR-6370 Primers
MPM01497 ABM 150 ul / 10 uM
EUR 121
mmu-miR-6371 Primers
MPM01498 ABM 150 ul / 10 uM
EUR 121
mmu-miR-6372 Primers
MPM01499 ABM 150 ul / 10 uM
EUR 121
mmu-miR-6373 Primers
MPM01500 ABM 150 ul / 10 uM
EUR 121

The full genome consisted of one chromosome of 4,654,430 bp with a GC content material of 54.6% and one plasmid of 51,135 bp with a GC content material of 49.4%. Genome annotation revealed a number of genes concerned in plant growth-promoting traits, together with the manufacturing of siderophore, indole acetic acid, and 1-aminocyclopropane-1-carboxylate deaminase; solubilization of phosphate and potassium; and nitrogen metabolism. Similarly, genes concerned in heavy metals tolerance have been detected.

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Recent Posts

  • Chromosome-level assembly of the mangrove plant Aegiceras corniculatum genome generated through Illumina, PacBio and Hi-C sequencing technologies
  • Whole genome sequence insight of two plant growth-promoting bacteria (B. subtilis BS87 and B. megaterium BM89) isolated and characterized from sugarcane rhizosphere depicting better crop yield potentiality
  • Systematic Identification and Analysis of Light-Responsive Circular RNA and Co-expression Networks in Lettuce (Lactuca sativa).
  • Genome Sequencing of SAV3 Reveals Repeated Seeding Events of Viral Strains in Norwegian Aquaculture.
  • Recent advances in understanding mitochondrial genome diversity.

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