Genome survey and microsatellite motif identification of Pogonophryne albipinna

The genus Pogonophryne is a speciose group that includes 28 species inhabiting the coastal or deep waters of the Antarctic Southern Ocean. The genus has been divided into five species groups, among which the P. albipinna group is the most deep-living group and is characterized by a lack of spots on the top of the head. Here, we carried out genome survey sequencing of P. albipinna using the Illumina HiSeq platform to estimate the genomic characteristics and identify genome-wide microsatellite motifs. The genome size was predicted to be ~883.8 Mb by K-mer analysis (K=25), and the heterozygosity and repeat ratio were 0.289% and 39.03%, respectively. The genome sequences were assembled into 571,624 contigs, covering a total length of ~819.3 Mb with an N50 of 2,867 bp. A total of 2,217,422 simple sequence repeat motifs were identified from the assembly data, and the number of repeats decreased as the length and number of repeats increased. These data will provide a useful foundation for the development of new molecular markers for the P. albipinna group as well as for further whole genome sequencing of P. albipinna.

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Identification and expression pattern of chemosensory genes in the transcriptome of Propsilocerus akamusi

PeerJ ◽

10.7717/peerj.9584 ◽

2020 ◽

Vol 8 ◽

pp. e9584

Author(s):

Chuncai Yan ◽

Xiaoya Sun ◽

Wei Cao ◽

Ruoqun Li ◽

Cong Zhao ◽

...

Keyword(s):

Differential Expression Analysis ◽

Odorant Receptors ◽

Indicator Organisms ◽

Illumina Hiseq ◽

Chemosensory Genes ◽

Chironomid Species ◽

Gene Level ◽

Illumina Hiseq Platform ◽

Odorant Binding ◽

Simple Sequence

Chironomidae is the most ecologically diverse insects in aquatic and semi-aquatic habitats. Propsilocerus akamusi (Tokunaga) is a dominant and ubiquitous chironomid species in Eastern Asia and its morphologically unique larvae are also considered as indicator organisms to detect water contamination, potential toxicity and waterborne pathogens. Since few studies to date have focused on the olfactory system of P. akamusi, our study aims to elucidate the potential functions of chemosensory genes in P. akamusi. In our study, we found that although signals released from male groups might attract female swarmers, it was a completely male-dominated mating process. Sequencing the transcriptome of P. akamusi on an Illumina HiSeq platform generated 4.42, 4.46 and 4.53 Gb of clean reads for heads, legs, and antennae, respectively. 27,609 unigenes, 20,379 coding sequences (CDSs), and 8,073 simple sequence repeats were finally obtained. The gene-level differential expression analysis demonstrated variants among three different tissues, including 2,019 genes specifically expressed in heads, 1,540 genes in legs, and 2,071 genes in antennae. Additionally, we identified an assortment of putative olfactory genes consisting of 34 odorant binding proteins, 17 odorant receptors, 32 gustatory receptors, 22 ionotropic receptors, six chemosensory proteins as well as 3 sensory neuron membrane proteins; their relative abundances in the above three tissues were also determined by RT-qPCR. Our finding could allow a more plausible understanding of certain olfaction-mediated behaviors in groups of this macroinvertebrate.

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Genome-wide SSR marker development and application in genetic diversity analysis of the red swamp crayfish, Procambarus clarkii (Girard, 1852) in China

Crustaceana ◽

10.1163/15685403-bja10076 ◽

2021 ◽

Vol 94 (2) ◽

pp. 189-205

Author(s):

Junxiao Sun ◽

Guohui Peng ◽

Lijing Xiong ◽

Cong Tan ◽

Yanhe Li ◽

...

Keyword(s):

Genetic Diversity ◽

Ssr Markers ◽

Genetic Basis ◽

Molecular Breeding ◽

Procambarus Clarkii ◽

Genome Survey ◽

Red Swamp Crayfish ◽

Genome Wide ◽

Ssr Loci ◽

Simple Sequence

Abstract The red swamp crayfish, Procambarus clarkii (Girard, 1852), is currently an economically important aquaculture animal. Its genetic basis has been scarcely reported, however, partly due to the absence of abundant molecular markers in the genome. In this study, Simple Sequence Repeat (SSR) loci were mined, based on genome survey sequencing via the next generation sequence of the red swamp crayfish. A total of 4897 SSR loci were identified, with the most abundant type being the di-nucleotide repeat motifs (75.2%), followed by tri- (20.4%), tetra- (3.8%), penta- (0.5%), and hexanucleotide (0.2%) repeats. In total, 1546 SSR markers were validated to be amplified, and 721 of these were identified as polymorphic SSR markers. Fifty polymorphic SSR markers were randomly selected for the identification of the genetic diversity of the 14 red swamp crayfish populations in China. The expected and observed heterozygosity and polymorphism information content were 0.39, 0.30, and 0.29, respectively, on average. The results indicated a medium genetic diversity among the 14 investigated populations. These probably cluster into three genetic populations. The current study provides abundant genetic markers and information on the 14 populations, which can be helpful for genetic diversity estimation and molecular breeding of the red swamp crayfish.

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Genome-wide identification of conserved and novel microRNAs in one bud and two tender leaves of tea plant (Camellia sinensis) by small RNA sequencing, microarray-based hybridization and genome survey scaffold sequences

BMC Plant Biology ◽

10.1186/s12870-017-1169-1 ◽

2017 ◽

Vol 17 (1) ◽

Cited By ~ 22

Author(s):

Anburaj Jeyaraj ◽

Xiao Zhang ◽

Yan Hou ◽

Mingzhu Shangguan ◽

Prabu Gajjeraman ◽

...

Keyword(s):

Rna Sequencing ◽

Camellia Sinensis ◽

Small Rna ◽

Tea Plant ◽

Small Rna Sequencing ◽

Genome Survey ◽

Genome Wide

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Genome wide simple sequence repeats development and their application in genetic diversity analysis in wax gourd ( Benincasa hispida )

Plant Breeding ◽

10.1111/pbr.12990 ◽

2022 ◽

Author(s):

Qianmei Hu ◽

Haiping Wang ◽

Biao Jiang ◽

Huayu Zhu ◽

Xiaoming He ◽

...

Keyword(s):

Genetic Diversity ◽

Simple Sequence Repeats ◽

Diversity Analysis ◽

Genetic Diversity Analysis ◽

Genome Wide ◽

Benincasa Hispida ◽

Wax Gourd ◽

Simple Sequence

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Development of genome-wide simple sequence repeat markers in Codonopsis lanceolata using next-generation sequencing

Horticulture Environment and Biotechnology ◽

10.1007/s13580-021-00389-0 ◽

2021 ◽

Author(s):

Serim Kim ◽

Namsu Jo ◽

Jinsu Gil ◽

Sung Cheol Koo ◽

Yurry Um ◽

...

Keyword(s):

Next Generation Sequencing ◽

Simple Sequence Repeat ◽

Next Generation ◽

Sequence Repeat ◽

Codonopsis Lanceolata ◽

Simple Sequence Repeat Markers ◽

Genome Wide ◽

Generation Sequencing ◽

Simple Sequence

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An amended description of two Gyrodactylus species (Platyhelminthes: Monogenea) parasitizing Antarctic Notothenioid fish

Journal of Helminthology ◽

10.1017/s0022149x18001098 ◽

2018 ◽

Vol 94 ◽

Cited By ~ 1

Author(s):

I. Heglasová ◽

V. Nezhybová ◽

I. Přikrylová

Keyword(s):

Internal Transcribed Spacer ◽

Host Record ◽

Sister Group ◽

Weddell Sea ◽

Locality Record ◽

New Host ◽

New Host Record ◽

Notothenia Coriiceps ◽

Species Groups ◽

The Antarctic

Abstract Species identification based on the morphometry of opisthaptoral hard parts, in combination with internal transcribed spacer ribosomal DNA (ITS rDNA) region sequences, confirmed the presence of four viviparous Gyrodactylus von Nordman, 1832 (Plathyhelminthes, Monogenea) species on Nototheniid fish from the Prince Gustav Channel (Weddell Sea, Antarctica). Gyrodactylus antarcticus Gusev, 1967 was found mostly on Trematomus newnesi Boulenger (93 specimens) but also on T. bernacchii Boulenger (one specimen), the latter representing a new host record for this species. Gyrodactylus byrdi Hargis & Dillon, 1968 and G. coriicepsi Rokicka, Lumme & Ziętara, 2009 were recorded on their type hosts, T. newnesi and Notothenia coriiceps Richardson, respectively. Gyrodactylus wilkesi Hargis & Dillon, 1968 was found mostly on the fins of T. bernacchii (29 specimens), but also on T. hansoni Boulenger (one specimen) and T. newnesi (three specimens). The finding of G. wilkesi on T. newnesi represents a new host record. The low number of Gyrodactylus specimens may indicate an accidental infection. The occurence of all four Gyrodactylus species in the Prince Gustav Channel represents a new locality record. According to phylogentic methods, the newly redescribed monogeneans belong to the Antarctic lineage, forming a sister group to North American and European marine Gyrodactylus species, and consist of two species groups, one comprising G. coriicepsi and G. nudifronsi Rokicka, Lumme & Ziętara, 2009, and the other G. anarcticus and G. wilkesi.

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Genome survey sequencing and identification of genomic SSR markers for Batocera horsfieldi (Coleoptera: Cerambycidae)

10.21203/rs.3.rs-498077/v1 ◽

2021 ◽

Author(s):

Xin Peng ◽

Zhende Yang ◽

Lei Xu ◽

Hantang Wang ◽

Chunhui Guo ◽

...

Keyword(s):

Microsatellite Markers ◽

Gc Content ◽

Pcr Amplification ◽

Repeat Sequence ◽

Survey Analysis ◽

Genome Survey ◽

Fundamental Information ◽

Genome Wide ◽

Genomic Ssr ◽

Batocera Horsfieldi

Abstract The white-striped longhorn beetle Batocera horsfieldi (Coleoptera: Cerambycidae) is a polyphagous wood-boring pest that causes substantial damage to the lumber, fruit and nut industry. Here, next-generation sequencing was used to generate a whole genome survey dataset to provide fundamental information of its genome and develop genome-wide microsatellite markers for it. The genome size of B. horsfieldi was estimated as approximate 520 Mb by using K-mer analyses, and its heterozygosity ratio and repeat sequence ratio were 0.26% and 51.03%, respectively. The assembled genome was 528.56Mb with GC content of 35.40%. A total of 121750 microsatellite motifs were identified. The most frequent repeat motif was mononucleotide with a frequency of 85.84%, followed by 8.08% of dinonucleotide, 5.04% of trinonucleotide, 0.73% of tetranonucleotide, 0.20% of pentanonucleotide and 0.12% of hexanonucleotide motifs. The AT/AT, TA/TAand GA/TC repeats were the most abundant motifs of dinucleotide motifs, and AAT/ATT, TAA/TTA and ATA/TAT were the most abundant motifs of trinucleotide motifs, respectively. ninety six pairs of SSR primers were randomly selected for PCR amplification and agarose gel electrophoresis detection, among which 56 pairs of primers can be effectively amplified to obtain the target fragment. In summary, various candidate microsatellite markers were identified and characterized in this study using genome survey analysis.

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The mitochondrial genome and phylogenetic analysis of the tick Haemaphysalis qinghaiensis Teng, 1980 (Acari:Ixodidae)

Systematic and Applied Acarology ◽

10.11158/saa.27.1.9 ◽

2022 ◽

Author(s):

Tianhong Wang ◽

Zihao Wang ◽

Ruwei Bai ◽

Zhijun Yu ◽

Jingze Liu

Keyword(s):

Phylogenetic Analysis ◽

Mitochondrial Genome ◽

Complete Mitochondrial Genome ◽

Rrna Genes ◽

Trna Genes ◽

Illumina Hiseq ◽

Protein Coding ◽

Haemaphysalis Qinghaiensis ◽

Mitogenome Sequence ◽

Illumina Hiseq Platform

Haemaphysalis qinghaiensis is an endemic species and mainly inhabiting in the northwestern plateau of China, which can transmit many zoonotic pathogens and cause great harm to animals. In this study, the complete mitochondrial genome (mitogenome) of H. qinghaiensis was assembled through the Illumina HiSeq platform. The mitogenome was 14,533 bp in length, consisting of 13 protein-coding genes (PCGs), 22 tRNA genes, 2 rRNA genes and 3 noncoding regions (NCRs). The bias towards a high A+T content with 77.65% in mitogenome of H. qinghaiensis. The rearrangement of mitochondrial genes in H. qinghaiensis was consistent with other hard ticks. The phylogenetic analysis based on the concatenation of 13 PCGs from 65 tick mitogenomes showed that the H. qinghaiensis was clustered into a well-supported clade within the Haemaphysalis genus. This is the first complete mitogenome sequence of H. qinghaiensis, which provides a useful reference for understanding of the taxonomic and genetics of ticks.

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Comparative Analysis of Whole-Genome and Methylome Profiles of a Smooth and a Rough Mycobacterium abscessus Clinical Strain

G3 Genes|Genome|Genetics ◽

10.1534/g3.119.400737 ◽

2019 ◽

Vol 10 (1) ◽

pp. 13-22 ◽

Cited By ~ 2

Author(s):

Chiranjibi Chhotaray ◽

Shuai Wang ◽

Yaoju Tan ◽

Amjad Ali ◽

Muhammad Shehroz ◽

...

Keyword(s):

Single Molecule ◽

Gene Clusters ◽

Mycobacterium Abscessus ◽

Clinical Strain ◽

Comparative Genomic ◽

Illumina Hiseq ◽

Clinical Strains ◽

Synonymous Mutations ◽

Pan Genome ◽

Genome Wide

Mycobacterium abscessus is a fast growing Mycobacterium species mainly causing skin and respiratory infections in human. M. abscessus is resistant to numerous drugs, which is a major challenge for the treatment. In this study, we have sequenced the genomes of two clinical M. abscessus strains having rough and smooth morphology, using the single molecule real-time and Illumina HiSeq sequencing technology. In addition, we reported the first comparative methylome profiles of a rough and a smooth M. abscessus clinical strains. The number of N4-methylcytosine (4mC) and N6-methyladenine (6mA) modified bases obtained from smooth phenotype were two-fold and 1.6 fold respectively higher than that of rough phenotype. We have also identified 4 distinct novel motifs in two clinical strains and genes encoding antibiotic-modifying/targeting enzymes and genes associated with intracellular survivability having different methylation patterns. To our knowledge, this is the first report about genome-wide methylation profiles of M. abscessus strains and identification of a natural linear plasmid (15 kb) in this critical pathogen harboring methylated bases. The pan-genome analysis of 25 M. abscessus strains including two clinical strains revealed an open pan genome comprises of 7596 gene clusters. Likewise, structural variation analysis revealed that the genome of rough phenotype strain contains more insertions and deletions than the smooth phenotype and that of the reference strain. A total of 391 single nucleotide variations responsible for the non-synonymous mutations were detected in clinical strains compared to the reference genome. The comparative genomic analysis elucidates the genome plasticity in this emerging pathogen. Furthermore, the detection of genome-wide methylation profiles of M. abscessus clinical strains may provide insight into the significant role of DNA methylation in pathogenicity and drug resistance in this opportunistic pathogen.

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