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Fulltext De novo assembly of transcriptomes, mining, and development of novel EST-SSR markers in Curcuma alismatifolia (Zingiberaceae family) through Illumina sequencing

Taheri S, Abdullah TL, Rafii MY, Harikrishna JA, Werbrouck SPO, Teo CH, et al.

Sci Rep, 2019 Feb 28;9(1):3047.
PMID: 30816255 DOI: 10.1038/s41598-019-39944-2

Curcuma alismatifolia widely used as an ornamental plant in Thailand and Cambodia. This species of herbaceous perennial from the Zingiberaceae family, includes cultivars with a wide range of colours and long postharvest life, and is used as an ornamental cut flower, as a potted plant, and in exterior landscapes. For further genetic improvement, however, little genomic information and no specific molecular markers are available. The present study used Illumina sequencing and de novo transcriptome assembly of two C. alismatifolia cvs, 'Chiang Mai Pink' and 'UB Snow 701', to develop simple sequence repeat markers for genetic diversity studies. After de novo assembly, 62,105 unigenes were generated and 48,813 (78.60%) showed significant similarities versus six functional protein databases. In addition, 9,351 expressed sequence tag-simple sequence repeats (EST-SSRs) were identified with a distribution frequency of 12.5% total unigenes. Out of 8,955 designed EST-SSR primers, 150 primers were selected for the development of potential molecular markers. Among these markers, 17 EST-SSR markers presented a moderate level of genetic diversity among three C. alismatifolia cultivars, one hybrid, three Curcuma, and two Zingiber species. Three different genetic groups within these species were revealed using EST-SSR markers, indicating that the markers developed in this study can be effectively applied to the population genetic analysis of Curcuma and Zingiber species. This report describes the first analysis of transcriptome data of an important ornamental ginger cultivars, also provides a valuable resource for gene discovery and marker development in the genus Curcuma.

Matched MeSH terms: Molecular Sequence Annotation
The complete mitogenome of the soldier crab Mictyris longicarpus (Latreille, 1806) (Crustacea: Decapoda: Mictyridae)

Tan MH, Gan HM, Lee YP, Austin CM

Mitochondrial DNA A DNA Mapp Seq Anal, 2016 05;27(3):2121-2.
PMID: 25423510 DOI: 10.3109/19401736.2014.982585

The Mictyris longicarpus (soldier crab) complete mitochondrial genome sequence is reported making it the first for the family Mictyridae and the second for the superfamily Ocypodoidea. The mitogenome is 15,548 base pairs made up of 13 protein-coding genes, 2 ribosomal subunit genes, 22 transfer RNAs and a non-coding AT-rich region. The soldier crab mitogenome gene order is characteristic of brachyuran crabs with a base composition of 36.58% for T, 19.15% for C, 32.43% for A and 11.83% for G, with an AT bias of 69.01%.

Matched MeSH terms: Molecular Sequence Annotation
The complete mitogenome of the river blackfish, Gadopsis marmoratus (Richardson, 1848) (Teleostei: Percichthyidae)

Gan HM, Tan MH, Lee YP, Austin CM

Mitochondrial DNA A DNA Mapp Seq Anal, 2016 05;27(3):2030-1.
PMID: 25329292 DOI: 10.3109/19401736.2014.974174

The mitogenome of the Australian freshwater blackfish, Gadopsis marmoratus was recovered coverage by genome skimming using the MiSeq sequencer (GenBank Accession Number: NC_024436). The blackfish mitogenome has 16,407 base pairs made up of 13 protein-coding genes, 2 ribosomal subunit genes, 22 transfer RNAs, and a 819 bp non-coding AT-rich region. This is the 5th mitogenome sequence to be reported for the family Percichthyidae.

Matched MeSH terms: Molecular Sequence Annotation
The complete mitogenome of the Australian tadpole shrimp Triops australiensis (Spencer & Hall, 1895) (Crustacea: Branchiopoda: Notostraca)

Gan HM, Tan MH, Lee YP, Austin CM

Mitochondrial DNA A DNA Mapp Seq Anal, 2016 05;27(3):2028-9.
PMID: 25329290 DOI: 10.3109/19401736.2014.974173

The mitochondrial genome sequence of the Australian tadpole shrimp, Triops australiensis is presented (GenBank Accession Number: NC_024439) and compared with other Triops species. Triops australiensis has a mitochondrial genome of 15,125 base pairs consisting of 13 protein-coding genes, 2 ribosomal subunit genes, 22 transfer RNAs, and a non-coding AT-rich region. The T. australiensis mitogenome is composed of 36.4% A, 16.1% C, 12.3% G and 35.1% T. The mitogenome gene order conforms to the primitive arrangement for Branchiopod crustaceans, which is also conserved within the Pancrustacean.

Matched MeSH terms: Molecular Sequence Annotation
The complete mitogenome of the moon crab Ashtoret lunaris (Forskal, 1775), (Crustacea; Decapoda; Matutidae)

Tan MH, Gan HM, Lee YP, Austin CM

Mitochondrial DNA A DNA Mapp Seq Anal, 2016;27(2):1313-4.
PMID: 25090387 DOI: 10.3109/19401736.2014.945572

The complete mitochondrial genome of the moon crab Ashtoret lunaris was obtained from a partial genome scan using the MiSeq sequencing system. The Ashtoret lunaris mitogenome is 15,807 base pairs in length (70% A + T content) and made up of 13 protein-coding genes, 2 ribosomal subunit genes, 22 transfer RNAs, and a putative 956 bp non-coding AT-rich region. This A. lunaris mitogenome sequence is the first for the genus, as well as the family Matutidae and superfamily Calappoidea.

Matched MeSH terms: Molecular Sequence Annotation
The complete mitogenome of Cherax monticola (Crustacea: Decapoda: Parastacidae), a large highland crayfish from New Guinea

Gan HM, Tan MH, Eprilurahman R, Austin CM

Mitochondrial DNA A DNA Mapp Seq Anal, 2016;27(1):337-8.
PMID: 24617471 DOI: 10.3109/19401736.2014.892105

The complete mitochondrial genome of a highland freshwater crayfish, Cherax monticola, was recovered by shotgun sequencing. The mitogenome consists of 15,917 base pairs containing 13 protein-coding genes, 2 ribosomal subunit genes, 22 transfer RNAs and a non-coding AT-rich region. The base composition of C. monticola is 33.46% for T, 21.48% for C, 33.71% for A and 11.35% for G, with an AT bias of 67.17%.

Matched MeSH terms: Molecular Sequence Annotation
Molecular and allergenic characterization of recombinant tropomyosin from mud crab Scylla olivacea

Azemi NFH, Misnan R, Keong BP, Mokhtar M, Kamaruddin N, Fah WC, et al.

Mol Biol Rep, 2021 Oct;48(10):6709-6718.
PMID: 34427887 DOI: 10.1007/s11033-021-06661-x

BACKGROUND: Tropomyosin is a major allergen in crustaceans, including mud crab species, but its molecular and allergenic properties in Scylla olivacea are not well known. Thus, this study aimed to produce the recombinant tropomyosin protein from S. olivacea and subsequently investigate its IgE reactivity.
METHODS AND RESULTS: The tropomyosin gene was cloned and expressed in the Escherichia coli system, followed by SDS-PAGE and immunoblotting test to identify the allergenic potential of the recombinant protein. The 855-base pair of tropomyosin gene produced was found to be 99.18% homologous to Scylla serrata. Its 284 amino acids matched the tropomyosin of crustaceans, arachnids, insects, and Klebsiella pneumoniae, ranging from 79.03 to 95.77%. The tropomyosin contained 89.44% alpha-helix folding with a tertiary structure of two-chain alpha-helical coiled-coil structures comprising a homodimer heptad chain. IPTG-induced histidine tagged-recombinant tropomyosin was purified at the size of 42 kDa and confirmed as tropomyosin using anti-tropomyosin monoclonal antibodies. The IgE binding of recombinant tropomyosin protein was reactive in 90.9% (20/22) of the sera from crab-allergic patients.
CONCLUSIONS: This study has successfully produced an allergenic recombinant tropomyosin from S. olivacea. This recombinant tropomyosin may be used as a specific allergen for the diagnosis of allergy.

Matched MeSH terms: Molecular Sequence Annotation
Fulltext COGNAC: a web server for searching and annotating hydrogen-bonded base interactions in RNA three-dimensional structures

Firdaus-Raih M, Hamdani HY, Nadzirin N, Ramlan EI, Willett P, Artymiuk PJ

Nucleic Acids Res, 2014 Jul;42(Web Server issue):W382-8.
PMID: 24831543 DOI: 10.1093/nar/gku438

Hydrogen bonds are crucial factors that stabilize a complex ribonucleic acid (RNA) molecule's three-dimensional (3D) structure. Minute conformational changes can result in variations in the hydrogen bond interactions in a particular structure. Furthermore, networks of hydrogen bonds, especially those found in tight clusters, may be important elements in structure stabilization or function and can therefore be regarded as potential tertiary motifs. In this paper, we describe a graph theoretical algorithm implemented as a web server that is able to search for unbroken networks of hydrogen-bonded base interactions and thus provide an accounting of such interactions in RNA 3D structures. This server, COGNAC (COnnection tables Graphs for Nucleic ACids), is also able to compare the hydrogen bond networks between two structures and from such annotations enable the mapping of atomic level differences that may have resulted from conformational changes due to mutations or binding events. The COGNAC server can be accessed at http://mfrlab.org/grafss/cognac.

Matched MeSH terms: Molecular Sequence Annotation
Identification of polyunsaturated fatty acid and diterpenoid biosynthesis pathways from draft genome of Aureispira sp. CCB-QB1

Furusawa G, Lau NS, Shu-Chien AC, Jaya-Ram A, Amirul AA

Mar Genomics, 2015 Feb;19:39-44.
PMID: 25468060 DOI: 10.1016/j.margen.2014.10.006

The genus Aureispira consisting of two species, Aureispira marina and Aureispira maritima is an arachidonic acid-producing bacterium and produces secondary metabolites. In this study, we isolated a new Aureispira strain, Aureispira sp. CCB-QB1 from coastal area of Penang, Malaysia and the genome sequence of this strain was determined. The draft genome of this strain is composed of 185 contigs for 7,370,077 bases with 35.6% G+C content and contains 5911 protein-coding genes and 76 RNA genes. Linoleoyl-CoA desaturase, the key gene in arachidonic acid biosynthesis, is present in the genome. It was found that this strain uses mevalonate pathway for the synthesis of geranylgeranyl diphosphate (GGPP), which is precursor of diterpenoid, and novel pathway via futalosine for the synthesis of menaquinones. This is the first draft genome sequence of a member of the genus Aureispira.

Matched MeSH terms: Molecular Sequence Annotation
Cupriavidus malaysiensis sp. nov., a novel poly(3-hydroxybutyrate-co-4-hydroxybutyrate) accumulating bacterium isolated from the Malaysian environment

Ramachandran H, Shafie NAH, Sudesh K, Azizan MN, Majid MIA, Amirul AA

Antonie Van Leeuwenhoek, 2018 Mar;111(3):361-372.
PMID: 29022146 DOI: 10.1007/s10482-017-0958-8

Bacterial classification on the basis of a polyphasic approach was conducted on three poly(3 hydroxybutyrate-co-4-hydroxybutyrate) [P(3HB-co-4HB)] accumulating bacterial strains that were isolated from samples collected from Malaysian environments; Kulim Lake, Sg. Pinang river and Sg. Manik paddy field. The Gram-negative, rod-shaped, motile, non-sporulating and non-fermenting bacteria were shown to belong to the genus Cupriavidus of the Betaproteobacteria on the basis of their 16S rRNA gene sequence analyses. The sequence similarity value with their near phylogenetic neighbour, Cupriavidus pauculus LMG3413T, was 98.5%. However, the DNA-DNA hybridization values (8-58%) and ribotyping analysis both enabled these strains to be differentiated from related Cupriavidus species with validly published names. The RiboPrint patterns of the three strains also revealed that the strains were genetically related even though they displayed a clonal diversity. The major cellular fatty acids detected in these strains included C15:0 ISO 2OH/C16:1 ω7c, hexadecanoic (16:0) and cis-11-octadecenoic (C18:1 ω7c). Their G+C contents ranged from 68.0 to 68.6 mol%, and their major isoprenoid quinone was Ubiquinone Q-8. Of these three strains, only strain USMAHM13 (= DSM 25816 = KCTC 32390) was discovered to exhibit yellow pigmentation that is characteristic of the carotenoid family. Their assembled genomes also showed that the three strains were not identical in terms of their genome sizes that were 7.82, 7.95 and 8.70 Mb for strains USMAHM13, USMAA1020 and USMAA2-4, respectively, which are slightly larger than that of Cupriavidus necator H16 (7.42 Mb). The average nucleotide identity (ANI) results indicated that the strains were genetically related and the genome pairs belong to the same species. On the basis of the results obtained in this study, the three strains are considered to represent a novel species for which the name Cupriavidus malaysiensis sp. nov. is proposed. The type strain of the species is USMAA1020T (= DSM 19416T = KCTC 32390T).

Matched MeSH terms: Molecular Sequence Annotation
Fulltext Draft genome sequence of the rubber tree Hevea brasiliensis

Rahman AY, Usharraj AO, Misra BB, Thottathil GP, Jayasekaran K, Feng Y, et al.

BMC Genomics, 2013;14:75.
PMID: 23375136 DOI: 10.1186/1471-2164-14-75

Hevea brasiliensis, a member of the Euphorbiaceae family, is the major commercial source of natural rubber (NR). NR is a latex polymer with high elasticity, flexibility, and resilience that has played a critical role in the world economy since 1876.

Matched MeSH terms: Molecular Sequence Annotation
Fulltext Extracellular Vesicle-derived circular RNAs confers chemoresistance in Colorectal cancer

Hon KW, Ab-Mutalib NS, Abdullah NMA, Jamal R, Abu N

Sci Rep, 2019 Nov 11;9(1):16497.
PMID: 31712601 DOI: 10.1038/s41598-019-53063-y

Chemo-resistance is associated with poor prognosis in colorectal cancer (CRC), with the absence of early biomarker. Exosomes are microvesicles released by body cells for intercellular communication. Circular RNAs (circRNAs) are non-coding RNAs with covalently closed loops and enriched in exosomes. Crosstalk between circRNAs in exosomes and chemo-resistance in CRC remains unknown. This research aims to identify exosomal circRNAs associated with FOLFOX-resistance in CRC. FOLFOX-resistant HCT116 CRC cells (HCT116-R) were generated from parental HCT116 cells (HCT116-P) using periodic drug induction. Exosomes were characterized using transmission electron microscopy (TEM), Zetasizer and Western blot. Our exosomes were translucent cup-shaped structures under TEM with differential expression of TSG101, CD9, and CD63. We performed circRNAs microarray using exosomal RNAs from HCT116-R and HCT116-P cells. We validated our microarray data using serum samples. We performed drug sensitivity assay and cell cycle analysis to characterize selected circRNA after siRNA-knockdown. Using fold change >2 and p

Matched MeSH terms: Molecular Sequence Annotation