Displaying publications 1 - 20 of 120 in total

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  1. Fulltext Serological prevalance of leptospiral infection in captive Malayan porcupiness (Hystrix brachyura)
    Siti-Nurdyana, A.K., Bahaman, A.R., Sharma, R.S.K., Azlan, C.M., Abdul Razak, M.F.A.
    Jurnal Veterinar Malaysia, 2016;28(2):1-3.
    MyJurnal
    Leptospirosis is recognised as one of the leading zoonotic diseases and rodents have been implicated as one of the natural reservoirs of the disease. The Malayan porcupines (Hystrix brachyura) which are also a rodent could possibly be a carrier of leptospiral organisms. This study was conducted to determine the serological prevalence of leptospiral infection among captive Malayan porcupines and to disclose the possibility of porcupines as a reservoir for leptospiral infection. Fifty serum samples were obtained from the Malayan porcupines kept in captivity at the Wildlife Conservation Centre, Sungai Dusun, Malaysia. The microscopic agglutination test (MAT) was performed on the serum samples to detect the presence of agglutinating antibodies to a panel of 16 Leptospira serovars (Australis, Autumnalis, Ballum, Bataviae, Canicola, Celledoni, Djasiman, Hardjobovis, Hardjopratjino, Hebdomadis, Hurstbridge, Icterohaemorrhagiae, Javanica, Pomona, Pyrogenes and Sejroe). From the serological test, 18% (n=9/50) of the Malayan porcupines tested had leptospiral antibodies to serovars Javanica (8%), Hurstbridge (4%), Ballum (2%), Celledoni (2%) and Hardjoprajitno (2%). It is seen that this study disclosed a high prevalence of leptospiral infection in the Malayan porcupines tested and indicated that the Malayan porcupines could possibly be a source of leptospirosis to other animals including humans and that they might play an important role in the epidemiology of leptospiral infection in the country.
    Matched MeSH terms: Brachyura
  2. Identification of the major allergens of Charybdis feriatus (red crab) and its cross-reactivity with Portunus pelagicus (blue crab)
    Misnan R, Murad S, Yadzir ZH, Abdullah N
    Asian Pac J Allergy Immunol, 2012 Dec;30(4):285-93.
    PMID: 23393908
    Tropomyosin and arginine kinase have been identified as the major allergens in multiple species of crab. Charybdis feriatus is an important commercial crab in this country.
    Matched MeSH terms: Brachyura/immunology*; Brachyura/chemistry
  3. Fulltext The adsorption of reactive orange 16 and basic blue 3 from aqueous solution using quaternized blue swimmer crab carapace
    Chuah, Y.J., Tan, Y.P., Abdullah, H.A.
    Pertanika Journal of Science & Technology, 2018;26(4):2045-2062.
    MyJurnal
    The crab carapace is a waste which cannot be decomposed. This waste was used to
    remove the Reactive Orange 16 (RO16) and Basic Blue 3 (BB3) from aqueous solution
    at different operational parameters such as pH, mass load, the concentrations of dye and
    the temperature. The crab collected was modified to obtain quaternized crab (QC) using
    (3-chloro-2-hydroxypropyl) trimethylammonium chloride solution (C6H15Cl2NO, 65% w/w
    in water). The pH of the dyes solution was varied from pH 4 to 10. The highest adsorption
    percentage was achieved at pH 7 for both dyes. Increasing the QC mass for the adsorption
    process had granted an increase of dyes removal percentage. The highest adsorption
    percentage was achieved at 91.00% for RO16 and 29.40% for BB3 dyes with 7.5 g/L QC
    used. However, the adsorption capacity of QC decreased with higher QC mass because the
    dye molecules occupied on the surface and prevented other molecules to diffuse into the
    QC. At higher concentration beyond 20 mg/L and 10 mg/L of RO16 and BB3, respectively,
    the maximum adsorption was achieved at 2.5362 mg/g and 0.6812 mg/g. The adsorption of
    both dyes by QC was best fitted using Langmuir isotherm model, explaining the adsorption
    mainly occurred as a single layer on the surface of QC. Comparison to the results obtained
    from the kinetic models, the adsorption was
    chemisorption in nature. According to the
    thermodynamic studies, the adsorption of
    RO16 was an exothermic, while BB3 was
    an endorthermic process.
    Matched MeSH terms: Brachyura
  4. Fulltext Experimental data on behavioral, hepatosomatic, gonadosomatic indeces and total lipid of mud crab, Scylla olivacea at different velocity levels
    Muhammad T, Ismail S, Ikhwanuddin M, Abol-Munafi AB
    Data Brief, 2019 Aug;25:104205.
    PMID: 31338400 DOI: 10.1016/j.dib.2019.104205
    The data collected in the present work correspond to the behavioral, Hepatosomatic Index (HSI), Gonadosomatic Index (GSI) and total lipid analysis between male and female mud crabs, Scylla olivacea at different water velocities. A total of 56 immature male and female crabs were used in this data article. The important criteria for estimating the selective habitat facing by S. olivacea is a considerate of (1) the behavioral range in response to abiotic factors (and how it adapt ontogenetically) and (2) the movement of the crab under wild velocities situations. This work purposes to recognize the performance, locomotion rate and escaping capability of S. olivacea under stagnant and flowing water situations and to discuss the significance of horizontal walking to habitat choice. The collective outcomes clearly show that the locomotor activities and escaping capabilities of S. olivacea were influenced by water flow in the mangrove habitats. For the HSI data, velocities of 20 cm/s were the highest increased mean HSI percentage and highest mean HSI percentage in males and females was recorded on the end of the experiment. For GSI percentage of male and female crabs, 20 cm/s dominates the highest increases mean GSI, followed by 60, 40 and 0 cm/s. For total lipid percentage, the results showed that, the mean total lipid of hepatopancrease, muscle and gonad were increased at the beginning and decreased at the final in each water velocities except for 20 cm/s over a culture period of 60 days. Velocities of 20 cm/s were the highest increased mean total lipid percentage followed by 40, 60, and lastly 0 cm/s. The high flow velocities inhibit the production of hepatopancrease and gonad, in terms of nutrients from food used to endeavor the stress condition faced.
    Matched MeSH terms: Brachyura
  5. Thermal tolerance and locomotor activity of blue swimmer crab Portunus pelagicus instar reared at different temperatures
    Azra MN, Chen JC, Ikhwanuddin M, Abol-Munafi AB
    J Therm Biol, 2018 May;74:234-240.
    PMID: 29801633 DOI: 10.1016/j.jtherbio.2018.04.002
    Owing to its potential market value, the blue swimmer crab Portunus pelagicus is of great economic importance. The temperature of water significantly affects the physiological function and production efficiency of these crabs. The aim of the present study was therefore to examine the critical thermal minimum (CTMin), critical thermal maximum (CTMax), acclimation response ratio (ARR), escaping temperature (Tesc), and locomotor behavior of P. pelagicus instars at 20 °C, 24 °C, 28 °C, 32 °C, and 36 °C. The CTMax ranged from 39.05 °C to 44.38 °C, while the CTMin ranged from 13.05 °C to 19.30 °C, and both increased directly with temperature. The ARR ranged from 0.25 to 0.51. The movement of crabs (walking before molting) correlated positively with the acclimation temperature. These results indicate that the parameters evaluated varied with temperature. Furthermore, the high CTMax indicates the potential of this species to adapt to a wide range of temperatures. In addition, the implications of these findings for portunid crabs behavior and distribution in their natural habitat are also discussed.
    Matched MeSH terms: Brachyura/physiology*
  6. Fulltext Fatty Acid Composition of Hepatopancreas and Gonads in Both Sexes of Orange Mud Crab, Scylla olivacea Cultured at Various Water Flow Velocities
    Taufik M, Shahrul I, Mohd Nordin AR, Ikhwanuddin M, Abol-Munafi AB
    Trop Life Sci Res, 2020 Jul;31(2):79-105.
    PMID: 32922670 DOI: 10.21315/tlsr2020.31.2.5
    Nutritional quality of the hepatopancreas and gonads of orange portunid mud crab, Scylla olivacea was evaluated for each gender under four treatment of different water velocities (0, 20, 40 and 60 cm s-1), in terms of nutrient reserve and nutrient for reproduction. About 56 crabs were used in this study in which fatty acids composition was analysed using gas chromatography mass-spectrometry (GC-MS). For hepatopancreas analysis, monounsaturated fatty acids (MUFAs) were present in the highest fatty acids concentration, followed by polyunsaturated fatty acids (PUFAs) and, saturated fatty acids (SFAs). However, long-chain polyunsaturated fatty acids (LC-PUFAs) were displayed in low concentration in the hepatopancreas. Total fatty acid (TFAs) composition was significantly higher at moderate velocity of 20 cm s-1 compared to other water velocity treatments. For gonad analysis, 20 cm s-1 showed the highest TFA concentration of 93.34 mg g-1 while, the lowest concentration of 3.90 mg g-1 occurred at 0 cm s-1. There were significant differences in male and female crab's fatty acids contents of gonads at all flow velocities challenged (p < 0.05). PUFAs and MUFAs were dominant while, SFAs were observed at low concentration. This study revealed that, concentration of PUFAs increased as gonad maturation increased. The decreasing concentration of hepatopancreas fatty acids over the culture period indicated that nutrient was shifted from the hepatopancreas, to be used as energy reserved to gonads for further growth of eggs and offspring. The linkages between water flow strength, hepatopancreas, and gonad fatty acids concentrations, is fundamental knowledge useful in establishing efficient habitat velocities selection which will improve aquaculture production of mud crabs with high quality broodstock.
    Matched MeSH terms: Brachyura
  7. Fulltext Behavioural data on instar crab movement at different thermal acclimation
    Azra MN, Ikhwanuddin M, Abol-Munafi AB
    Data Brief, 2019 Feb;22:998-1002.
    PMID: 30740484 DOI: 10.1016/j.dib.2019.01.026
    This article investigated how crabs responded to different culture temperatures especially dislocation before molting using a combination of large recording files and computer software. In this novel approach of video recording portunid crab behavioral data, crab culture was recorded at five different acclimation temperatures of 20, 24, 28, 32 and 36 °C. Crabs were reared until the instar stage before being acclimatized for video recording. Large video files (MPEG-TS) were then analyzed using the latest version of Solomon Coder software developed by A. Peter and programmed with Embarcadero® Delphi® XE [1]. Recorded data was analyzed by calculating and marking movements of crabs using the time sequence tool. Additionally, a total movement was counted 30 min before crabs molted from instar stage 8 to instar stage 9. Part of the data is associated with the research article "Thermal tolerance and locomotor activity of blue swimmer crab Portunus pelagicus instar reared at different temperatures" (Azra et al., 2018) [2] and provided here as raw data of Supplementary materials.
    Matched MeSH terms: Brachyura
  8. Fecundity, embryonic and ovarian development of blue swimming crab, Portunus pelagicus (Linnaeus, 1758) in coastal water of Johor, Malaysia
    Ikhwanuddin M, Azra MN, Siti-Aimuni H, Abol-Munafi AB
    Pak J Biol Sci, 2012 Aug 01;15(15):720-8.
    PMID: 24171257
    Blue swimming crab, Portunus pelagicus is widely study and research throughout the Indo-West Pacific, but little is known of its reproductive biology in Malaysia. The present study describes the fecundity, embryonic development and ovarian development stages of the P. pelagicus from Johor coastal water, Malaysia. Carapace width range of berried crabs sampled was from 9.64 to 13.32 cm, while the body weight range was from 75 to 235 g. The mean number of egg produced by females in different sizes ranged from 105443.333 +/- 35448.075 per eggs batch. Mean egg size during embryonic development at stage 1 was 0.307 +/- 0.037, while 0.386 +/- 0.039 and 0.396 +/- 0.033 for stage 2 and stage 3, respectively. Study showed that there was significant (p < 0.05) relationship between the number of eggs and carapace width/body weight. Mean diameter oocyte during ovarian development at stage 1 was 97.732 +/- 12.391 while for stage 2 was 149.516 +/- 23.287. Stage 3 showed increasingly of size with mean diameter was 158.506 +/- 27.616 and 181.013 +/- 24.339 for stage 4.
    Matched MeSH terms: Brachyura/embryology*; Brachyura/physiology*
  9. Fulltext Chitosan extracted from mud crab (Scylla olivicea) shells: physicochemical and antioxidant properties
    Sarbon NM, Sandanamsamy S, Kamaruzaman SF, Ahmad F
    J Food Sci Technol, 2015 Jul;52(7):4266-75.
    PMID: 26139891 DOI: 10.1007/s13197-014-1522-4
    The aim of this study is to report the yield of extraction, as well as the physicochemical and antioxidant properties of extracted chitosan from mud crabs (S.olivacea) as compared to commercial chitosan. The yield obtained for extracted chitosan was 44.57 ± 3.44 % with a moisture and ash content of 9.48 ± 0.59 % and 5.97 ± 0.90 %, respectively. Commercial chitosan demonstrated a higher degree of deacetylation (58.42 ± 2.67 %), water (250 ± 9.90 %) and fat (329 ± 7.07 %) binding capacity, solubility (73.85 %), viscosity (463.25 ± 13.10 %) and also the whiteness value (77.8 ± 0.47) compared to the extracted chitosan, which were only 53.42 ± 0.88 %, 180 ± 0.00 %, 260 ± 0.00 %, 53.38 %, 383.9 ± 28.43 % and 62.1 ± 7.52 %, respectively. The structure of extracted and commercial chitosan was also investigated using Fourier Transform Infrared Spectroscopy (FTIR). In conclusion, the extracted chitosan possessed potential properties similar to the commercial chitosan with high reducing power but low in the scavenging activity on the DPPH and hydroxyl radicals compared to the commercial chitosan.
    Matched MeSH terms: Brachyura
  10. Fulltext Allergens derived from shrimp
    Mary Margaret, P.D.S., Jinap, S., Ahmad Faizal, A.R.
    International Food Research Journal, 2015;22(5):1751-1754.
    MyJurnal
    Allergy caused by food is usually type 1 allergy of four types of allergic reactions. One of the most widespread allergic is those that are caused by crustacean shellfish. Crustaceans are classified among arthropods which include crab, crayfish, lobster, prawn and shrimp. Shrimp which are broadly consumed as nutritional food is one of the most important food that contribute to allergy. Thus, reducing the allergenicity of shrimp allergen will be helpful to individuals who are sensitive to shrimp and for this reason the characteristics of each allergen need to be studied. Those sensitized individuals can develop urticaria, angiodema, laryngospasm, asthma and life threatening anaphylaxis. To date, four main allergens contribute to allergic reactions. They are tropomyosin (TM), a highly conserved and heat stable myofibrillar protein of 35-38 kDa followed by arginine kinase (AK) which is also known as Pen m 2 or Lit v 2 with 40 kDa. Two other contributing allergens are sarcoplasmic calcium-binding protein (SCP) also known as Lit v 4 with 22 kDa and myosin light chain (MLC) which is also termed as Lit v 3 with 20 kDa. This mini-review will provide a better understanding of each allergen derived from shrimp which subsequently will help to reduce the allergenicity.
    Matched MeSH terms: Brachyura
  11. Study on Carapace Width Growth Band Counts Relationship of Orange Mud Crab, Scylla olivacea (Herbst, 1796) from Terengganu Coastal Waters, Malaysia
    Hasyima Ismail N, Amin Safwan A, Fairuz Fozi N, Megat FH, Muhd Farouk H, Kamaruddin SA, et al.
    Pak J Biol Sci, 2017;20(3):140-146.
    PMID: 29023005 DOI: 10.3923/pjbs.2017.140.146
    BACKGROUND: Orange mud crab Scylla olivacea is one of the most important fisheries resources. A new development in ageing technique of crustaceans has been introduced. The detection of growth band deposited in hard structure of gastric mill in the cardiac stomach are found retained after moulting process can be used as age indicator and growth estimation.

    OBJECTIVE: This study was carried out to determine the comparison between carapace width and growth band count of S. olivacea in Malaysia.

    MATERIALS AND METHODS: Samples were collected from Setiu Wetlands, Terengganu, Malaysia from February until August, 2016. Samples were categorized based on their morphological measurements. The mesocardiac and zygocardiac ossicles in the gastric mill of S. olivacea was dissected out and preserved in solutions and underwent a cross sectioning process. A total of 76 of wild S. olivacea ranging from 6.56 to 12.84 cm in carapace width were analysed. The growth band counts were examined for each individual and ranging from 1 to 3 band counts.

    RESULTS: A positive linear relation was observed between CW and GBC with r2 = 0.5178, p<0.01. Overall, there was a strong, positive correlation between CW and GBC. Increase in CW were correlated with increases in GBC respectively for this species.

    CONCLUSION: Therefore, the carapace width, growth band counts and body weight can be used to improve data on growth, recruitment, maturation and mortality. Thus, this study would able to improve new ageing technique and contribute greatly to improve the conservation and management of S. olivacea in Setiu Wetlands, Terengganu, Malaysia.

    Matched MeSH terms: Brachyura/growth & development*
  12. Testis maturation stages of mud crab (scylla olivacea) broodstock on different diets
    Ghazali Azmie, Mohamad N. Azra, Mhd Ikhwanuddin, Siti Fatimah Nahar, Wendy Wee, Ambok-Bolong Abol-Munaf
    Sains Malaysiana, 2018;47:427-432.
    The aim of this study was to investigate how various diets influence testis maturation stages in mud crab (Scylla olivacea)
    broodstock. Morphological and histological assessments were performed in triplicate (10 male crabs each). Daily,
    subject crabs were fed a squid (Loligo sp.) and a fish (Decapterus sp.) diet at 5-10% of body weight. Diets were analyzed
    following methods from the Association of Analytical Communities (AOAC). In comparison to control (wild) crabs, the
    two diets generally did not cause significant differences (p>0.05) in body weight, carapace width and gonadosomatic
    index (GSI), except in the GSI of squid-fed crabs (p<0.05). At the end of the experiment, crabs that reached Stage 3 testis
    maturation included were 6 fish-fed individuals and 23 squid-fed individuals. Additionally, differences in crude protein
    and fat levels across diets influenced the nature of male gonadal development. In conclusion, a squid diet was sufficient
    to induce Stage 3 testis maturation in Scylla olivacea within 60 days of culture. Our results prove the usefulness in
    developing appropriate feeding regimes for male Scylla olivacea broodstock.
    Matched MeSH terms: Brachyura
  13. Species delimitation of crab-eating frogs (Fejervarya cancrivora complex) clarifies taxonomy and geographic distributions in mainland Southeast Asia
    Yodthong S, Stuart BL, Aowphol A
    Zookeys, 2019;883:119-153.
    PMID: 31719776 DOI: 10.3897/zookeys.883.37544
    The taxonomy and geographic distributions of species of crab-eating frogs (Fejervarya cancrivora complex) in mainland Southeast Asia have been highly uncertain. Three taxonomic names are used in recent literature (F. cancrivora, F. raja, and F. moodiei) but the applications of these names to localities has been inconsistent, especially owing to the lack of available molecular data for F. raja. Morphometric and mitochondrial DNA variation was examined in these frogs, including name-bearing types and topotypes of all three species. Findings corroborate evidence for the existence of two species in coastal mainland Southeast Asia, with F. moodiei having a wide geographic distribution and F. cancrivora sensu stricto occurring only in extreme southern Thailand and peninsular Malaysia. Fejervarya raja is shown to be only a large-bodied population of F. cancrivora sensu stricto and is synonymized with that species. Revised descriptions of F. moodiei and F. cancrivora sensu stricto are provided.
    Matched MeSH terms: Brachyura
  14. Fulltext Analysis of the relations between allergen specific LgG antibody and allergic dermatosis of 14 kinds foods
    Yin'e H, Shufang D, Bin W, Wei Q, Junling G, Ashraf MA
    Open Med (Wars), 2015;10(1):405-409.
    PMID: 28352727 DOI: 10.1515/med-2015-0070
    To use food-specific IgG antibody detection to explore its application in the allergy dermatoses. 181 patients were included from January 2014 to September 2014. Fourteen food-specific IgG antibodies were detected by ELISA. The positive rates of IgG antibody of the patient group and the healthy group were significantly different. The positive rates of IgG antibody of egg, milk, shrimp and crab took a large proportion in three groups of patients with three kinds of allergy dermatoses of urticaria, eczema and allergic dermatitis, the proportion of which was respectively 70.2%, 77.8% and 71.7%. There was mild and moderate intolerance of food in the allergic dermatitis group while there was no distribution difference of food intolerance in urticaria group and eczema group. Among urticaria and allergic dermatitis patients with positive antibody, the positive rate of children was significantly higher than that of adults while there was no significant difference between children and adults among eczema patients with positive antibody. Allergy dermatoses are closely related to food-specific IgG antibody and the allergy dermatoses patients have a high incidence rate of food intolerance; detecting IgG antibody in patients is of great significance for the diagnosis and treatment of allergy dermatoses.
    Matched MeSH terms: Brachyura
  15. 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: Brachyura/immunology*
  16. The complete mitogenome of purple mottled shore crab Cyclograpsus granulosus H. Milne-Edwards, 1853 (Crustacea: Decapoda: Grapsoidea)
    Tan MH, Gan HM, Lee YP, Austin CM
    Mitochondrial DNA A DNA Mapp Seq Anal, 2016 11;27(6):3981-3982.
    PMID: 25541307
    The mitochondrial genome sequence of the purple mottled shore crab, Cyclograpsus granulosus, is documented (GenBank accession number: LN624373), which makes it the third for genera of the superfamily Grapsoidea. Cyclograpsus granulosus has a mitogenome of 16,300 bp consisting of 13 protein-coding genes, two ribosomal subunit genes, 22 transfer RNAs and a non-coding AT-rich region. The base composition of the C. granulosus mitogenome is 36.15% for T, 19.54% for C, 33.14% for A and 11.17% for G, with an AT bias of 69.29%. The mitogenome gene order is atypical for the brachyuran crabs, but is identical to species of the genus Eriocheir from the same family.
    Matched MeSH terms: Brachyura/genetics*
  17. The complete mitogenome of the ghost crab Ocypode ceratophthalmus (Pallas, 1772) (Crustacea: Decapoda: Ocypodidae)
    Tan MH, Gan HM, Lee YP, Austin CM
    Mitochondrial DNA A DNA Mapp Seq Anal, 2016 05;27(3):2123-4.
    PMID: 25423512 DOI: 10.3109/19401736.2014.982587
    The mitochondrial genome sequence of the ghost crab, Ocypode ceratophthalmus, is documented (GenBank accession number: LN611669) in this article. This is the first mitogenome for the family Ocypodidae and the second for the order Ocypodoidea. Ocypode ceratophthalmus has a mitogenome of 15,564 base pairs consisting of 13 protein-coding genes, two ribosomal subunit genes, 22 transfer RNAs and a non-coding AT-rich region. The base composition of the O. ceratophthalmus mitogenome is 35.78% for T, 19.36% for C, 33.73% for A and 11.13% for G, with an AT bias of 69.51% and the gene order is the typical arrangement for brachyuran crabs.
    Matched MeSH terms: Brachyura/genetics*
  18. 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: Brachyura/genetics*
  19. ORDER within the chaos: Insights into phylogenetic relationships within the Anomura (Crustacea: Decapoda) from mitochondrial sequences and gene order rearrangements
    Tan MH, Gan HM, Lee YP, Linton S, Grandjean F, Bartholomei-Santos ML, et al.
    Mol Phylogenet Evol, 2018 10;127:320-331.
    PMID: 29800651 DOI: 10.1016/j.ympev.2018.05.015
    The infraorder Anomura consists of a morphologically and ecologically heterogeneous group of decapod crustaceans, and has attracted interest from taxonomists for decades attempting to find some order out of the seemingly chaotic diversity within the group. Species-level diversity within the Anomura runs the gamut from the "hairy" spindly-legged yeti crab found in deep-sea hydrothermal vent environments to the largest known terrestrial invertebrate, the robust coconut or robber crab. Owing to a well-developed capacity for parallel evolution, as evidenced by the occurrence of multiple independent carcinization events, Anomura has long tested the patience and skill of both taxonomists attempting to find order, and phylogeneticists trying to establish stable hypotheses of evolutionary inter-relationships. In this study, we performed genome skimming to recover the mitogenome sequences of 12 anomuran species including the world's largest extant invertebrate, the robber crab (Birgus latro), thereby over doubling these resources for this group, together with 8 new brachyuran mitogenomes. Maximum-likelihood (ML) and Bayesian-inferred (BI) phylogenetic reconstructions based on amino acid sequences from mitogenome protein-coding genes provided strong support for the monophyly of the Anomura and Brachyura and their sister relationship, consistent with previous studies. The majority of relationships within families were supported and were largely consistent with current taxonomic classifications, whereas many relationships at higher taxonomic levels were unresolved. Nevertheless, we have strong support for a polyphyletic Paguroidea and recovered a well-supported clade of a subset of paguroids (Diogenidae + Coenobitidae) basal to all other anomurans, though this requires further testing with greater taxonomic sampling. We also introduce a new feature to the MitoPhAST bioinformatics pipeline (https://github.com/mht85/MitoPhAST) that enables the extraction of mitochondrial gene order (MGO) information directly from GenBank files and clusters groups based on common MGOs. Using this tool, we compared MGOs across the Anomura and Brachyura, identifying Anomura as a taxonomic "hot spot" with high variability in MGOs among congeneric species from multiple families while noting the broad association of highly-rearranged MGOs with several anomuran lineages inhabiting extreme niches. We also demonstrate the value of MGOs as a source of novel synapomorphies for independently reinforcing tree-based relationships and for shedding light on relationships among challenging groups such as the Aegloidea and Lomisoidea that were unresolved in phylogenetic reconstructions. Overall, this study contributes a substantial amount of new genetic material for Anomura and attempts to further resolve anomuran evolutionary relationships where possible based on a combination of sequence and MGO information. The new feature in MitoPhAST adds to the relatively limited number of bioinformatics tools available for MGO analyses, which can be utilized widely across animal groups.
    Matched MeSH terms: Brachyura/classification; Brachyura/genetics
  20. Two reads to rule them all: Nanopore long read-guided assembly of the iconic Christmas Island red crab, Gecarcoidea natalis (Pocock, 1888), mitochondrial genome and the challenges of AT-rich mitogenomes
    Gan HM, Linton SM, Austin CM
    Mar Genomics, 2019 Jun;45:64-71.
    PMID: 30928201 DOI: 10.1016/j.margen.2019.02.002
    Despite recent advances in sequencing technology, a complete mitogenome assembly is still unavailable for the gecarcinid land crabs that include the iconic Christmas Island red crab (Gecarcoidea natalis) which is known for its high population density, annual mass breeding migration and ecological significance in maintaining rainforest structure. Using sequences generated from Nanopore and Illumina platforms, we assembled the complete mitogenome for G. natalis, the first for the genus and only second for the family Gecarcinidae. Nine Nanopore long reads representing 0.15% of the sequencing output from an overnight MinION Nanopore run were aligned to the mitogenome. Two of them were >10 kb and combined are sufficient to span the entire G. natalis mitogenome. The use of Illumina genome skimming data only resulted in a fragmented assembly that can be attributed to low to zero sequencing coverage in multiple high AT-regions including the mitochondrial protein-coding genes (NAD4 and NAD5), 16S ribosomal rRNA and non-coding control region. Supplementing the mitogenome assembly with previously acquired transcriptome dataset containing high abundance of mitochondrial transcripts improved mitogenome sequence coverage and assembly reliability. We then inferred the phylogeny of the Eubrachyura using Maximum Likelihood and Bayesian approaches, confirming the phylogenetic placement of G. natalis within the family Gecarcinidae based on whole mitogenome alignment. Given the substantial impact of AT-content on mitogenome assembly and the value of complete mitogenomes in phylogenetic and comparative studies, we recommend that future mitogenome sequencing projects consider generating a modest amount of Nanopore long reads to facilitate the closing of problematic and fragmented mitogenome assemblies.
    Matched MeSH terms: Brachyura/classification; Brachyura/genetics*
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