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Morphometric sex determination of Milky and Painted Storks in captivity

Ong HK, Chinna K, Khoo SK, Ng WL, Wong BY, Chow KL, et al.

Zoo Biol, 2012 Mar-Apr;31(2):219-28.
PMID: 21480370 DOI: 10.1002/zoo.20387

Logistic regression was applied to develop a morphometric sexing method of two closely related stork species that were previously sexed through amplification of the CHD gene. Tarsus length (TL) and bill length (BL) measurements were recorded from captive populations of adult Milky Stork (Mycteria cinerea) (n = 60) and Painted Stork (Mycteria leucocephala) (n = 58) at Zoo Negara Malaysia. Despite having monomorphic plumages, both stork species exhibited normal sexual size dimorphism in which males were significantly larger than females in the tested variables. Based on logistic regression analysis, BL correctly classified the sex of sampled individuals from Painted and Milky stork with an overall predicted accuracy of 94.8 and 90.0%, respectively. However, TL measurements generated a lower predicted accuracy level of 86.2% and a same accuracy level of 90% on the sex classification of individuals from Painted and Milky stork, respectively. By comparing the measurements of both species, only the average BL measurements of the Milky storks were significantly lower than that of Painted storks (t-test, P80.001). The logistic regression equation in this study may serve as a simple and more practical option for sexing Milky and Painted storks for their breeding and conservation programmes.
Fulltext Inhibition of euchromatic histone methyltransferase 1 and 2 sensitizes chronic myeloid leukemia cells to interferon treatment

Loh SW, Ng WL, Yeo KS, Lim YY, Ea CK

PLoS One, 2014;9(7):e103915.
PMID: 25079219 DOI: 10.1371/journal.pone.0103915

H3K9 methylation is one of the essential histone post-translational modifications for heterochromatin formation and transcriptional repression. Recently, several studies have demonstrated that H3K9 methylation negatively regulates the type I interferon response.
Molecular genetic variation and structure of Southeast Asian crocodile (Tomistoma schlegelii): Comparative potentials of SSRs versus ISSRs

Shafiei-Astani B, Ong AH, Valdiani A, Tan SG, Yien CY, Ahmady F, et al.

Gene, 2015 Oct 15;571(1):107-16.
PMID: 26112832 DOI: 10.1016/j.gene.2015.06.053

Tomistoma schlegelii, also referred to as the "false gharial", is one of the most exclusive and least known of the world's fresh water crocodilians, limited to Southeast Asia. Indeed, lack of economic value for its skin has led to neglect the biodiversity of the species. The current study aimed to investigate the mentioned case using 40 simple sequence repeat (SSR) primer pairs and 45 inter-simple sequence repeat (ISSR) primers. DNA analysis of 17 T. schlegelii samples using the SSR and ISSR markers resulted in producing a total of 49 and 108 polymorphic bands, respectively. Furthermore, the SSR- and ISSR-based cluster analyses both generated two main clusters. However, the SSR based results were found to be more in line with the geographical distributions of the crocodile samples collected across the country as compared with the ISSR-based results. The observed heterozygosity (HO) and expected heterozygosity (HE) of the polymorphic SSRs ranged between 0.588-1 and 0.470-0.891, respectively. The present results suggest that the Malaysian T. schlegelii populations had originated from a core population of crocodiles. In cooperation with the SSR markers, the ISSRs showed high potential for studying the genetic variation of T. schlegelii, and these markers are suitable to be employed in conservation genetic programs of this endangered species. Both SSR- and ISSR-based STRUCTURE analyses suggested that all the individuals of T. schlegelii are genetically similar with each other.
Fulltext A cell-based screening system for anti-influenza A virus agents

Wong WY, Loh SW, Ng WL, Tan MC, Yeo KS, Looi CY, et al.

Sci Rep, 2015;5:8672.
PMID: 25728279 DOI: 10.1038/srep08672

Emerging of drug resistant influenza A virus (IAV) has been a big challenge for anti-IAV therapy. In this study, we describe a relatively easy and safe cell-based screening system for anti-IAV replication inhibitors using a non-replicative strain of IAV. A nickel (II) complex of polyhydroxybenzaldehyde N4-thiosemicarbazone (NiPT5) was recently found to exhibit anti-inflammatory activity in vivo and in vitro. NiPT5 impedes the signaling cascades that lead to the activation of NF-κB in response to different stimuli, such as LPS and TNFα. Using our cell-based screening system, we report that pretreating cells with NiPT5 protects cells from influenza A virus (IAV) and vesicular stomatitis virus (VSV) infection. Furthermore, NiPT5 inhibits replication of IAV by inhibiting transcription and translation of vRNAs of IAV. Additionally, NiPT5 reduces IAV-induced type I interferon response and cytokines production. Moreover, NiPT5 prevents activation of NF-κB, and IRF3 in response to IAV infection. These results demonstrate that NiPT5 is a potent antiviral agent that inhibits the early phase of IAV replication.
Fulltext Shearwave Elastography Increases Diagnostic Accuracy in Characterization of Breast Lesions

Ng WL, Rahmat K, Fadzli F, Rozalli FI, Mohd-Shah MN, Chandran PA, et al.

Medicine (Baltimore), 2016 Mar;95(12):e3146.
PMID: 27015196 DOI: 10.1097/MD.0000000000003146

The purpose of this study was to investigate the diagnostic efficacy of shearwave elastography (SWE) in differentiating between benign and malignant breast lesions.One hundred and fifty-nine lesions were assessed using B-mode ultrasound (US) and SWE parameters were recorded (Emax, Emean, Emin, Eratio, SD). SWE measurements were then correlated with histopathological diagnosis.The final sample contained 85 benign and 74 malignant lesions. The maximum stiffness (Emax) with a cutoff point of ≥ 56.0 kPa (based on ROC curves) provided sensitivity of 100.0%, specificity of 97.6%, positive predictive value (PPV) of 97.4%, and negative predictive value (NPV) of 100% in detecting malignant lesions. A cutoff of ≥80 kPa managed to downgrade 95.5% of the Breast Imaging-Reporting and Data System (BI-RADS) 4a lesions to BI-RADS 3, negating the need for biopsy. Using a combination of BI-RADS and SWE, the authors managed to improve the PPV from 2.3% to 50% in BI-RADS 4a lesions.SWE of the breast provides highly specific and sensitive quantitative values that are beneficial in the characterization of breast lesions. Our results showed that Emax is the most accurate value for differentiating benign from malignant lesions.
Fulltext Inducible RasGEF1B circular RNA is a positive regulator of ICAM-1 in the TLR4/LPS pathway

Ng WL, Marinov GK, Liau ES, Lam YL, Lim YY, Ea CK

RNA Biol, 2016 09;13(9):861-71.
PMID: 27362560 DOI: 10.1080/15476286.2016.1207036

Circular RNAs (circRNAs) constitute a large class of RNA species formed by the back-splicing of co-linear exons, often within protein-coding transcripts. Despite much progress in the field, it remains elusive whether the majority of circRNAs are merely aberrant splicing by-products with unknown functions, or their production is spatially and temporally regulated to carry out specific biological functions. To date, the majority of circRNAs have been cataloged in resting cells. Here, we identify an LPS-inducible circRNA: mcircRasGEF1B, which is predominantly localized in cytoplasm, shows cell-type specific expression, and has a human homolog with similar properties, hcircRasGEF1B. We show that knockdown of the expression of mcircRasGEF1B reduces LPS-induced ICAM-1 expression. Additionally, we demonstrate that mcircRasGEF1B regulates the stability of mature ICAM-1 mRNAs. These findings expand the inventory of functionally characterized circRNAs with a novel RNA species that may play a critical role in fine-tuning immune responses and protecting cells against microbial infection.
Fulltext Frontal mucocele masked as upper lid abcess- a case report

Ng, WL, Umi Kalthum MN, Jemaima CH, Norshamsiah MD

Journal of Surgical Academia, 2016;6(1):43-45.
MyJurnal

Frontal mucocele is not commonly masked as upper lid abscess.A 72-year-old Chinese man with underlying hyperthyroidism complained of left upper eyelid swelling of 6 months duration. The swelling had persisted and worsen when intravenous antibiotic was changed oral type. Visual acuity on presentation was hand motion and reverse relative afferent pupillary defect was present. Because the swelling was large and resulted in mechanical ptosis and ophthalmoplegia, a CT imaging was performed, which showed huge left frontal mucocele eroding the supereromedial orbital rim. The left globe was displaced inferolaterally but there was no extension into brain parenchyma. Fundus examination showed pale optic disc with dull macula. Old laser marks were seen at peripheral fundus. Referral to ortholaryngologist was made and endoscopic sinus surgery and evacuation of mucopyocoele was done. Culture and sensitivity of the fluid showed no organism. He recovered well postoperatively with additional two weeks of antibiotics. We highlight the necessity of surgical drainage of mucocele, following a course of antibiotic.
Fulltext DNA Barcoding of the Endangered Aquilaria (Thymelaeaceae) and Its Application in Species Authentication of Agarwood Products Traded in the Market

Lee SY, Ng WL, Mahat MN, Nazre M, Mohamed R

PLoS One, 2016;11(4):e0154631.
PMID: 27128309 DOI: 10.1371/journal.pone.0154631

The identification of Aquilaria species from their resinous non-wood product, the agarwood, is challenging as conventional techniques alone are unable to ascertain the species origin. Aquilaria is a highly protected species due to the excessive exploitation of its precious agarwood. Here, we applied the DNA barcoding technique to generate barcode sequences for Aquilaria species and later applied the barcodes to identify the source species of agarwood found in the market. We developed a reference DNA barcode library using eight candidate barcode loci (matK, rbcL, rpoB, rpoC1, psbA-trnH, trnL-trnF, ITS, and ITS2) amplified from 24 leaf accessions of seven Aquilaria species obtained from living trees. Our results indicated that all single barcodes can be easily amplified and sequenced with the selected primers. The combination of trnL-trnF+ITS and trnL-trnF+ITS2 yielded the greatest species resolution using the least number of loci combination, while matK+trnL-trnF+ITS showed potential in detecting the geographical origins of Aquilaria species. We propose trnL-trnF+ITS2 as the best candidate barcode for Aquilaria as ITS2 has a shorter sequence length compared to ITS, which eases PCR amplification especially when using degraded DNA samples such as those extracted from processed agarwood products. A blind test conducted on eight agarwood samples in different forms using the proposed barcode combination proved successful in their identification up to the species level. Such potential of DNA barcoding in identifying the source species of agarwood will contribute to the international timber trade control, by providing an effective method for species identification and product authentication.
Fulltext Transcriptomic analysis of the role of RasGEF1B circular RNA in the TLR4/LPS pathway

Ng WL, Marinov GK, Chin YM, Lim YY, Ea CK

Sci Rep, 2017 09 25;7(1):12227.
PMID: 28947785 DOI: 10.1038/s41598-017-12550-w

Circular RNAs (circRNAs) have recently emerged as a large class of novel non-coding RNA species. However, the detailed functional significance of the vast majority of them remains to be elucidated. Most functional characterization studies targeting circRNAs have been limited to resting cells, leaving their role in dynamic cellular responses to stimuli largely unexplored. In this study, we focus on the LPS-induced cytoplasmic circRNA, mcircRasGEF1B, and combine targeted mcircRasGEF1B depletion with high-throughput transcriptomic analysis to gain insight into its function during the cellular response to LPS stimulation. We show that knockdown of mcircRasGEF1B results in altered expression of a wide array of genes. Pathway analysis revealed an overall enrichment of genes involved in cell cycle progression, mitotic division, active metabolism, and of particular interest, NF-κB, LPS signaling pathways, and macrophage activation. These findings expand the set of functionally characterized circRNAs and support the regulatory role of mcircRasGEF1B in immune response during macrophage activation and protection against microbial infections.
Shear wave elastography for characterization of breast lesions: Shearlet transform and local binary pattern histogram techniques

Acharya UR, Ng WL, Rahmat K, Sudarshan VK, Koh JEW, Tan JH, et al.

Comput Biol Med, 2017 12 01;91:13-20.
PMID: 29031099 DOI: 10.1016/j.compbiomed.2017.10.001

Shear wave elastography (SWE) examination using ultrasound elastography (USE) is a popular imaging procedure for obtaining elasticity information of breast lesions. Elasticity parameters obtained through SWE can be used as biomarkers that can distinguish malignant breast lesions from benign ones. Furthermore, the elasticity parameters extracted from SWE can speed up the diagnosis and possibly reduce human errors. In this paper, Shearlet transform and local binary pattern histograms (LBPH) are proposed as an original algorithm to differentiate malignant and benign breast lesions. First, Shearlet transform is applied on the SWE images to acquire low frequency, horizontal and vertical cone coefficients. Next, LBPH features are extracted from the Shearlet transform coefficients and subjected to dimensionality reduction using locality sensitivity discriminating analysis (LSDA). The reduced LSDA components are ranked and then fed to several classifiers for the automated classification of breast lesions. A probabilistic neural network classifier trained only with seven top ranked features performed best, and achieved 98.08% accuracy, 98.63% sensitivity, and 97.59% specificity in distinguishing malignant from benign breast lesions. The high sensitivity and specificity of our system indicates that it can be employed as a primary screening tool for faster diagnosis of breast malignancies, thereby possibly reducing the mortality rate due to breast cancer.
Fulltext The real-world use of different anti-tumor necrosis factor agents in a Northern European population of patients with Behçet's disease

Adeeb F, Ng WL, Khan MU, Devlin J, Stack AG, Fraser AD

Eur J Rheumatol, 2017 Dec;4(4):254-259.
PMID: 29308279 DOI: 10.5152/eurjrheum.2017.17046

Objective: The aim of this study was to evaluate prescription practices, treatment responses, and serious adverse events of anti-tumor necrosis factor (anti-TNF) therapies in Behçet's disease (BD).
Material and Methods: Patients with BD satisfying the International Study Group for Behçet's Disease or the International Criteria for Behçet's Disease criteria were recruited from a regional rheumatology program. The choice of anti-TNF, treatment response, and adverse events were specified. Response to treatment was evaluated by the detection of new, worsening, or improving clinical features, and management was benchmarked against current The European League against Rheumatism recommendations published in 2008.
Results: Out of the total of 22 patients, 18 (81.9%) received anti-TNF therapies, resulting in 14 (77.8%) complete and 4 (22.2%) partial remissions. Eleven (61.1%) patients switched to a second anti-TNF, seven patients (38.9%) required three different anti-TNFs, and one required a fourth anti-TNF to achieve remission. Two patients required retrials before their disease was controlled. Anti-TNF therapy included infliximab (IFX): n=15, 83.3%; adalimumab (ADA): n=9, 50%; golimumab: n=6, 33.3%; etanercept: n=5, 27.8%; and certolizumab pegol: n=2, 11.1%. Secondary failure was observed with IFX (4/15; 26.7%) and ADA (2/9; 22.2%), and these (100%) were manifested after at least 2 years of treatment. Five patients with potentially life-threatening laryngeal involvement received anti-TNFs successfully halting disease progression. Five allergic reactions were encountered, and five serious infections were documented involving three patients aged ≥ 50 years, all with the use of IFX.
Conclusion: Anti-TNF therapy induced a clinical response in 100% patients and achieved complete remission in 78% patients. It provides an effective alternative option for first-line therapy in severe BD where many conventional immunosuppressive therapies fail. Patients with BD who do not respond to one or more anti-TNFs because of intolerance, ineffectiveness, or secondary failure might benefit from switching to another drug from this group or even a retrial of a previously administered anti-TNF because unsatisfactory results with one biologic is not predictive of response to another anti-TNF. For those with potentially life-threatening destructive laryngeal manifestation, anti-TNF as a first choice may be considered.
Fulltext Identification of 5-Methoxy-2-(Diformylmethylidene)-3,3-Dimethylindole as an Anti-Influenza A Virus Agent

Tan MC, Wong WY, Ng WL, Yeo KS, Mohidin TB, Lim YY, et al.

PLoS One, 2017;12(1):e0170352.
PMID: 28114392 DOI: 10.1371/journal.pone.0170352

Influenza virus is estimated to cause 3-5 million severe complications and about 250-500 thousand deaths per year. Different kinds of anti-influenza virus drugs have been developed. However, the emergence of drug resistant strains has presented a big challenge for efficient antiviral therapy. Indole derivatives have been shown to exhibit both antiviral and anti-inflammatory activities. In this study, we adopted a cell-based system to screen for potential anti-IAV agents. Four indole derivatives (named 525A, 526A, 527A and 528A) were subjected to the antiviral screening, of which 526A was selected for further investigation. We reported that pre-treating cells with 526A protects cells from IAV infection. Furthermore, 526A inhibits IAV replication by inhibiting the expression of IAV genes. Interestingly, 526A suppresses the activation of IRF3 and STAT1 in host cells and thus represses the production of type I interferon response and cytokines in IAV-infected cells. Importantly, 526A also partially blocks the activation of RIG-I pathway. Taken together, these results suggest that 526A may be a potential anti-influenza A virus agent.
Fulltext Bilateral pulmonary sequestrations mimicking advanced lung malignancy

Poh ME, Ng WL, Liam CK, Ramli NM, Hashim S

J Thorac Dis, 2018 Sep;10(9):E710-E713.
PMID: 30416823 DOI: 10.21037/jtd.2018.09.12
Fulltext The complete chloroplast genome of Aquilaria malaccensis Lam. (Thymelaeaceae), an important and threatened agarwood-producing tree species

Lee SY, Ng WL, Mohamed R, Terhem R

Mitochondrial DNA B Resour, 2018 Oct 29;3(2):1120-1121.
PMID: 33474439 DOI: 10.1080/23802359.2018.1519382

Known for its valuable agarwood, Aquilaria malaccensis Lam. is an evergreen tropical forest tree species endemic to the Indo-malesian region. Indiscriminate damaging and harvesting of the trees in the wild have resulted in it being listed in the CITES Appendix II for controlled trade and in the IUCN Red List as 'Vulnerable (VU)'. In this study, the complete chloroplast genome of A. malaccensis was assembled using data from high-throughput Illumina sequencing. The chloroplast genome was 174,832 bp in size, which included two inverted repeat regions of 42,091 bp each, separated by a large single copy region of 87,302 bp and a small single copy region of 3,348 bp. A total of 139 genes were predicted, including 39 tRNA, 8 rRNA, and 92 protein-coding genes. Phylogenetic analysis placed A. malaccensis within the family Thymelaeaceae. The chloroplast genome sequence of A. malaccensis offers a useful resource for future studies on the taxonomy and conservation of the threatened Aquilaria trees.
Functional role of circular RNAs in cancer development and progression

Ng WL, Mohd Mohidin TB, Shukla K

RNA Biol, 2018;15(8):995-1005.
PMID: 29954251 DOI: 10.1080/15476286.2018.1486659

Circular RNAs (circRNAs) are a large class of endogenously expressed non-coding RNAs formed by covalently closed loops through back-splicing. High throughput sequencing technologies have identified thousands of circRNAs with high sequence conservation and cell type specific expression in eukaryotes. CircRNAs play multiple important roles in cellular physiology functioning as miRNA sponges, transcriptional regulators, RBP binding molecules, templates for protein translation, and immune regulators. In a clinical context, circRNAs expression is correlated with patient's clinicopathological features in cancers including breast, liver, gastric, colorectal, and lung cancer. Additionally, distinct properties of circRNAs, such as high stability, exonuclease resistance, and existence in body fluids, show promising role for circRNAs as molecular biomarkers for tumor diagnosis, non-invasive monitoring, prognosis, and therapeutic intervention. Therefore, it is critical to further understand the molecular mechanism underlying circRNAs interaction in tumors and the recent progress of this RNA species in cancer development. In this review, we provide a detailed description of biological functions, molecular role of circRNAs in different cancers, and its potential role as biomarkers in a clinical context.
Fulltext Genetic variation and DNA fingerprinting of durian types in Malaysia using simple sequence repeat (SSR) markers

Siew GY, Ng WL, Tan SW, Alitheen NB, Tan SG, Yeap SK

PeerJ, 2018;6:e4266.
PMID: 29511604 DOI: 10.7717/peerj.4266

Durian (Durio zibethinus) is one of the most popular tropical fruits in Asia. To date, 126 durian types have been registered with the Department of Agriculture in Malaysia based on phenotypic characteristics. Classification based on morphology is convenient, easy, and fast but it suffers from phenotypic plasticity as a direct result of environmental factors and age. To overcome the limitation of morphological classification, there is a need to carry out genetic characterization of the various durian types. Such data is important for the evaluation and management of durian genetic resources in producing countries. In this study, simple sequence repeat (SSR) markers were used to study the genetic variation in 27 durian types from the germplasm collection of Universiti Putra Malaysia. Based on DNA sequences deposited in Genbank, seven pairs of primers were successfully designed to amplify SSR regions in the durian DNA samples. High levels of variation among the 27 durian types were observed (expected heterozygosity,H
E
= 0.35). The DNA fingerprinting power of SSR markers revealed by the combined probability of identity (PI) of all loci was 2.3×10-3. Unique DNA fingerprints were generated for 21 out of 27 durian types using five polymorphic SSR markers (the other two SSR markers were monomorphic). We further tested the utility of these markers by evaluating the clonal status of shared durian types from different germplasm collection sites, and found that some were not clones. The findings in this preliminary study not only shows the feasibility of using SSR markers for DNA fingerprinting of durian types, but also challenges the current classification of durian types, e.g., on whether the different types should be called "clones", "varieties", or "cultivars". Such matters have a direct impact on the regulation and management of durian genetic resources in the region.
Fulltext Comparative transcriptomics sheds light on differential adaptation and species diversification between two Melastoma species and their F1 hybrid

Ng WL, Wu W, Zou P, Zhou R

AoB Plants, 2019 Apr;11(2):plz019.
PMID: 31037213 DOI: 10.1093/aobpla/plz019

Variation in gene expression has been shown to promote adaptive divergence, and can lead to speciation. The plant genus Melastoma, thought to have diversified through adaptive radiation, provides an excellent model for the study of gene expressional changes during adaptive differentiation and following interspecific hybridization. In this study, we performed RNA-seq on M. candidum, M. sanguineum and their F1 hybrid, to investigate the role of gene expression in species diversification within the genus. Reference transcriptomes were assembled using combined data from both parental species, resulting in 50 519 and 48 120 transcripts for the leaf and flower petal, after removing redundancy. Differential expression analysis uncovered 3793 and 2116 differentially expressed (DE) transcripts, most of which are between M. candidum and M. sanguineum. Differential expression was observed for genes related to light responses, as well as genes that regulate the development of leaf trichomes, a trait that among others is thought to protect plants against sunlight, suggesting the differential adaptation of the species to sunlight intensity. The analysis of positively selected genes between the two species also revealed possible differential adaptation to other abiotic stresses such as drought and temperature. In the hybrid, almost all possible modes of expression were observed at the DE transcripts, although at most transcripts, the expression levels were similar to that of either parent instead of being intermediate. A small number of transgressively expressed transcripts that matched genes known to promote plant growth and adaptation to stresses in new environments were also found, possibly explaining the vigour observed in the hybrid. The findings in this study provided insights into the role of gene expression in the diversification of Melastoma, which we believe is an important example for more cross-taxa comparisons in the future.
Fulltext Discovery of novel genic-SSR markers from transcriptome dataset of an important non-human primate, Macaca fascicularis

Chang W, Ee-Uli J, Ng WL, Rovie-Ryan JJ, Tan SG, Yong CSY

Sci Rep, 2019 06 11;9(1):8504.
PMID: 31186469 DOI: 10.1038/s41598-019-44870-4

Macaca fascicularis, also known as the cynomolgus macaque, is an important non-human primate animal model used in biomedical research. It is an Old-World primate widely distributed in Southeast Asia and is one of the most abundant macaque species in Malaysia. However, the genetic structure of wild cynomolgus macaque populations in Malaysia has not been thoroughly elucidated. In this study, we developed genic-simple sequence repeat (genic-SSR) markers from an in-house transcriptome dataset generated from the Malaysian cynomolgus macaque via RNA sequencing, and applied these markers on 26 cynomolgus macaque individuals. A collection of 14,751 genic-SSRs were identified, where 13,709 were perfect SSRs. Dinucleotide repeats were the most common repeat motifs with a frequency of 65.05%, followed by trinucleotide repeats (20.55%). Subsequently, we designed 300 pairs of primers based on perfect di- and trinucleotide SSRs, in which 105 SSRs were associated with functional genes. A subset of 30 SSR markers were randomly selected and validated, yielding 19 polymorphic markers with an average polymorphism information content value of 0.431. The development of genic-SSR markers in this study is indeed timely to provide useful markers for functional and population genetic studies of the cynomolgus macaque and other related non-human primate species.
Fulltext The complete chloroplast genome sequence of Chengal (Neobalanocarpus heimii, Dipterocarpaceae), a durable tropical hardwood

Lee SY, Ng WL, Hishamuddin MS, Mohamed R

Mitochondrial DNA B Resour, 2019;4(1):19-20.
PMID: 33365402 DOI: 10.1080/23802359.2018.1535848

Known for its durable timber quality, Neobalanocarpus heimii (King) Ashton is a highly sought after tree species endemic to the Malay Peninsula. Due to its scarcity and high value, the tree is classified under the IUCN Red List categories of Vulnerable. In this study, we assembled the complete chloroplast (cp) genome of N. heimii using data from high-throughput Illumina sequencing. The Chengal cp genome is 151,191 bp in size and includes two inverted repeat regions of 23,721 bp each, which is separated by a large single copy region of 83,801 bp and a small single copy region of 19,948 bp. A total of 130 genes were predicted, including 37 tRNA, 8 rRNA, and 85 protein-coding genes. Phylogenetic analysis placed N. heimii within the order Malvales.
Fulltext Analyses of Plastome Sequences Improve Phylogenetic Resolution and Provide New Insight Into the Evolutionary History of Asian Sonerileae/Dissochaeteae

Zhou Q, Lin CW, Ng WL, Dai J, Denda T, Zhou R, et al.

Front Plant Sci, 2019;10:1477.
PMID: 31824528 DOI: 10.3389/fpls.2019.01477

Sonerileae/Dissochaeteae (Melastomataceae) comprises ca. 50 genera, two thirds of which occur in Southeast Asia. Phylogenetic relationships within this clade remain largely unclear, which hampers our understanding of its origin, evolution, and biogeography. Here, we explored the use of chloroplast genomes in phylogenetic reconstruction of Sonerileae/Dissochaeteae, by sampling 138 species and 23 genera in this clade. A total of 151 complete plastid genomes were assembled for this study. Plastid genomic data provided better support for the backbone of the Sonerileae/Dissochaeteae phylogeny, and also for relationships among most closely related species, but failed to resolve the short internodes likely resulted from rapid radiation. Trees inferred from plastid genome and nrITS sequences were largely congruent regarding the major lineages of Sonerileae/Dissochaeteae. The present analyses recovered 15 major lineages well recognized in both nrITS and plastid phylogeny. Molecular dating and biogeographical analyses indicated a South American origin for Sonerileae/Dissochaeteae during late Eocene (stem age: 34.78 Mya). Two dispersal events from South America to the Old World were detected in late Eocene (33.96 Mya) and Mid Oligocene (28.33 Mya) respectively. The core Asian clade began to diversify around early Miocene in Indo-Burma and dispersed subsequently to Malesia and Sino-Japanese regions, possibly promoted by global temperature changes and East Asian monsoon activity. Our analyses supported previous hypothesis that Medinilla reached Madagascar by transoceanic dispersal in Miocene. In addition, generic limits of some genera concerned were discussed.

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