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A new species of Mud Snake (Serpentes, Homalopsidae, Gyiophis Murphy & Voris, 2014) from Myanmar with a first molecular phylogenetic assessment of the genus

Quah ESH, Grismer LL, Wood PLJ, Thura MK, Zin T, Kyaw H, et al.

Zootaxa, 2017 Mar 06;4238(4):571-582.
PMID: 28603251 DOI: 10.11646/zootaxa.4238.4.5

A newly discovered species of homalopsid snake from the genus Gyiophis Murphy & Voris is described from the lowlands of Mawlamyine District in Mon state, southeastern Myanmar. Gyiophis salweenensis sp. nov. is presumed to be closely related to G. maculosa Blanford and G. vorisi Murphy based on the similarities in pholidosis and patterning but can be separated from G. maculosa by the shape of its first three dorsal scale rows that are square, ventral scale pattern that lacks a central spot, and a faint stripe on dorsal scale rows 1-4. It can be further distinguished from G. vorisi by its lower number of ventral scales (129 vs. 142-152), lower number of subcaudals (30/29 vs. 41-58), narrow rostral scale, and having more rows of spots on the dorsum (four vs. three). A preliminary molecular analysis using 1050 base pairs of cytochrome b (cytb) recovered G. salweenensis sp. nov. as the sister species to the Chinese Mud Snake (Myrrophis chinensis). G. maculosa and G. vorisi were unavailable for the analysis. The discovery of G. salweenensis sp. nov. highlights the need for more surveys into the herpetological diversity of eastern Myanmar which remains very much underestimated.

Matched MeSH terms: Phylogeny
Revision of the horseface loaches (Cobitidae, Acantopsis), with descriptions of three new species from Southeast Asia

Boyd DA, Nithirojpakdee P, Deein G, Vidthayanon C, Grudpan C, Tangjitjaroen W, et al.

Zootaxa, 2017 Oct 31;4341(2):151-192.
PMID: 29245684 DOI: 10.11646/zootaxa.4341.2.1

Acantopsis (Cobitidae) is revised based on analysis of morphological and molecular data. Four of the six available names, A. dialuzona, A. spectabilis, A. octoactinotos, and A. thiemmedhi, are valid, and three new species, A. rungthipae, A. dinema, and A. ioa, are described. All species are described morphologically, distributions are mapped, and relationships are discussed for those for which molecular data (CO1, RAG1) are available. Labial barbels, color pattern, and meristic counts are the most diagnostic features. Although the long snout of Acantopsis is perhaps the most emblematic attribute of the genus, its relative length increases with growth, reducing its taxonomic value. Species can be difficult to identify on the basis of color pattern alone, as habitat and preservation methods appear to strongly influence the color pattern. Despite interspecific overlap of some highly variable traits, each species has a unique set of morphological characteristics that remain observable even when the color pattern is obscured, and some species are restricted to single drainages, greatly simplifying identification. The phylogenetic analyses revealed high molecular divergence between even the most morphologically similar species, with mean uncorrected CO1 p-distances between species ranging from 12.1-15.4%. Species of Acantopsis exhibit significant genetic structuring consistent with recognized freshwater ecoregions. Acanthopsis lachnostoma Rutter 1897, from Swatow, China, is not assignable to Acantopsis.

Matched MeSH terms: Phylogeny
Microcystin production by oscillatorialean cyanobacteria isolated from cryopreserved Antarctic mats

Usman AS, Merican F, Zaki S, Broady P, Convey P, Muangmai N

Harmful Algae, 2022 Dec;120:102336.
PMID: 36470600 DOI: 10.1016/j.hal.2022.102336

Twenty cyanobacterial strains of eight morphospecies isolated from deep-frozen (-15 °C) mat samples originally collected on Ross Island, in Victoria Land, and on the McMurdo Ice Shelf were screened for the presence of genes encoding for production of anatoxins, cylindrospermopsin, microcystin/nodularin and saxitoxin. One strain of each of Microcoleus autumnalis and Phormidesmis priestleyi and two strains of Wilmottia murrayi were found to produce microcystin. No toxin production was detected in the other 16 strains representing five species. The four toxin-producing strains were characterised using both morphological and molecular approaches. Phylogenetic analyses using partial 16S rRNA sequences were consistent with the morphological identification of all four strains. They were all found to contain a fragment of the mcyE gene, which is involved in microcystin biosynthesis. ELISA analysis of extracts from cultures of these strains confirmed the presence of low concentrations of microcystin: 0.35 μg/L in M. autumnalis, <0.15 μg/L in P. priestleyi, 1.60 μg/L in W. murrayi strain 1 and 0.9 μg/L in W. murrayi strain 2. This study includes the first report of microcystin synthesis by W. murrayi.

Matched MeSH terms: Phylogeny
Avian Haemosporidian (Plasmodium and Haemoproteus) Status in Two Bird Groups (Old-World Flycatchers and Thrushes) of India and Their Phylogenetic Relationships with Other Lineages of the World

Vipin, Singh A, Sharma V, Tripathi NK, Dixit R, Singh B, et al.

Acta Parasitol, 2022 Dec;67(4):1756-1766.
PMID: 36306015 DOI: 10.1007/s11686-022-00626-1

PURPOSE: Avian haemosporidian may affect the host from body damage to the extinction of a population. Knowledge of their status may help in future avifauna conservation plans. Hence, their status in two bird groups of India and their phylogenetic relationships with other known lineages of the world were examined.
METHODS: Cytochrome b gene sequences (479 bp) generated from India and available at MalAvi database were used to study the avian haemosporidian prevalence and phylogenetic analysis of lineages at local and world levels.
RESULTS: One common (COLL2) and only once in the study (CYOPOL01, CHD01, CYORUB01, EUMTHA01, GEOCIT01) haemosporidian lineages were discovered. 5.88% prevalence of haemosporidian infection was found in 102 samples belonging to 6 host species. Haemoproteus prevalence was 4.90% across five host species (Phylloscopus trochiloides, Cyornis poliogenys, C. hainanus dialilaemus, C. rubeculoides, Eumiyas thalassinus) and Plasmodium prevalence was 0.98% in Geokichla citrina. Spatial phylogeny at the global level showed that COLL2 lineage, found in C. poliogenys in India, was genetically identical to H. pallidus lineages (COLL2) in parts of Africa, Europe, North America, Malaysia, and the Philippines. The Plasmodium lineage (GEOCIT01) was related to PADOM16 in Egypt, but the sequences were only 93.89% alike.
CONCLUSIONS: Four new lineages of Haemoproteus and one of Plasmodium were reported. COLL2 similarity with other H. pallidus lineages may suggest their hosts as possible infection sources.

Matched MeSH terms: Phylogeny
Fulltext Wolbachia infection in field-collected Aedes aegypti in Yunnan Province, southwestern China

Zhang H, Gao J, Ma Z, Liu Y, Wang G, Liu Q, et al.

Front Cell Infect Microbiol, 2022;12:1082809.
PMID: 36530420 DOI: 10.3389/fcimb.2022.1082809

BACKGROUND: Wolbachia is gram-negative and common intracellular bacteria, which is maternally inherited endosymbionts and could expand their propagation in host populations by means of various manipulations. Recent reports reveal the natural infection of Wolbachia in Aedes Aegypti in Malaysia, India, Philippines, Thailand and the United States. At present, none of Wolbachia natural infection in Ae. aegypti has been reported in China.
METHODS: A total of 480 Ae. aegypti adult mosquitoes were collected from October and November 2018 based on the results of previous investigations and the distribution of Ae. aegypti in Yunnan. Each individual sample was processed and screened for the presence of Wolbachia by PCR with wsp primers. Phylogenetic trees for the wsp gene was constructed using the neighbour-joining method with 1,000 bootstrap replicates, and the p-distance distribution model of molecular evolution was applied.
RESULTS: 24 individual adult mosquito samples and 10 sample sites were positive for Wolbachia infection. The Wolbachia infection rate (IR) of each population ranged from 0 - 41.7%. The infection rate of group A alone was 0%-10%, the infection rate of group B alone was 0%-7.7%, and the infection rate of co-infection with A and B was 0-33.3%.
CONCLUSIONS: Wolbachia infection in wild Ae. aegypti in China is the first report based on PCR amplification of the Wolbachia wsp gene. The Wolbachia infection is 5%, and the wAlbA and wAlbB strains were found to be prevalent in the natural population of Ae. aegypti in Yunnan Province.

Matched MeSH terms: Phylogeny
Molecular Identification and Genetic Variation of Rattus Species From Oil Palm Plantations of Malaysia Based on Mitochondrial Cytochrome Oxidase Subunit I (COI) Gene Sequences

Nasir MH, Bhassu S, Mispan MS, Bakar SA, Jing KJ, Omar H

Zoolog Sci, 2022 Dec;39(6):554-561.
PMID: 36495490 DOI: 10.2108/zs210093

Rats (Rattus species) are the most notorious vertebrate pests in Malaysian oil palm plantations. Although many studies have been conducted on Asian rats, little attention has been paid to their species composition and phylogenetic relationships in oil palm plantations in Peninsular Malaysia. We determined the mitochondrial cytochrome oxidase subunit I (COI) gene sequence (708 bp) for 216 individual rats collected from five oil palm plantations in Peninsular Malaysia. Phylogenetic analysis in conjunction with comparison with sequences from the nucleotide sequence database revealed five distinct lineages in the Malaysian oil plantations: Rattus tiomanicus, Rattus argentiventer, Rattus exulans, Rattus tanezumi, and a taxon corresponding to the Malayan house rat, which was most frequently observed (∼50%). The last taxon has traditionally been classified as a synonym of Rattus rattus (Rattus rattus diardii) or Rattus tanezumi, but our phylogenetic analysis placed it as an independent lineage, which is not particularly closely related to R. rattus or R. tanezumi, and which we refer to as Rattus diardii. The construction of the network showed that there is considerable genetic variation within the lineages of R. diardii and R tiomanicus, suggesting that these two species are native to the Malay Peninsula.

Matched MeSH terms: Phylogeny
Fulltext Characterization of the plastid genome of Cratoxylum species (Hypericaceae) and new insights into phylogenetic relationships

Sudmoon R, Kaewdaungdee S, Tanee T, Siripiyasing P, Ameamsri U, Syazwan SA, et al.

Sci Rep, 2022 Nov 05;12(1):18810.
PMID: 36335203 DOI: 10.1038/s41598-022-23639-2

To expand the genomic information of Hypericaceae, particularly on Cratoxylum, we characterized seven novel complete plastid genomes (plastomes) of five Cratoxylum and two of its allied taxa, including C. arborescens, C. formosum subsp. formosum, C. formosum subsp. pruniflorum, C. maingayi, C. sumatranum, Hypericum hookerianum, and Triadenum breviflorum. For Cratoxylum, the plastomes ranged from 156,962 to 157,792 bp in length. Genomic structure and gene contents were observed in the five plastomes, and were comprised of 128-129 genes, which includes 83-84 protein-coding (CDS), 37 tRNA, and eight rRNA genes. The plastomes of H. hookerianum and T. breviflorum were 138,260 bp and 167,693 bp, respectively. A total of 110 and 127 genes included 72 and 82 CDS, 34 and 37 tRNA, as well as four and eight rRNA genes. The reconstruction of the phylogenetic trees using maximum likelihood (ML) and Bayesian inference (BI) trees based on the concatenated CDS and internal transcribed spacer (ITS) sequences that were analyzed separately have revealed the same topology structure at genus level; Cratoxylum is monophyletic. However, C. formosum subsp. pruniflorum was not clustered together with its origin, raising doubt that it should be treated as a distinct species, C. pruniflorum based on molecular evidence that was supported by morphological descriptions.

Matched MeSH terms: Phylogeny
First molecular report of Babesia gibsoni infection in pet dogs in Hunan province, subtropical China

Tan SG, Xu PY

Trop Biomed, 2022 Dec 01;39(4):524-530.
PMID: 36602211 DOI: 10.47665/tb.39.4.007

Canine babesiosis caused by Babesia spp. is a noteworthy tick-borne zoonotic disease of domestic dogs and wild canids. In present study, a total of 556 blood samples were randomly collected from pet dogs in eight cities of Hunan province, subtropical China. Genomic DNA was extracted and Babesia DNA was detected by amplification of partial 18S rRNA gene sequences. A total of 56 (10.1%) blood samples were tested positive for Babesia species. Sequence analysis showed that 29 dogs (5.2%) were positive for B. gibsoni, and other 27 dogs for B. vogeli (4.9%). The age and health status were considered as important risk factors for B. gibsoni and B. vogeli infections in pet dogs in this study (P<0.05). Phylogenetic analysis showed that the examined positive samples were highly clustered in the same branch with B. gibsoni and B. vogeli, respectively. This is the first molecular report of B. gibsoni infection in pet dogs in Hunan province, subtropical China. Our finding has provided a guide for the control of dog babesiosis in China and elsewhere.

Matched MeSH terms: Phylogeny
Thousands of years of Malay and Chinese population history in Indonesia and its implication on Paternity Index in DNA paternity testing

Syukriani Y, Wulandari AS, Wanranto B, Hidayat Y

Sci Justice, 2023 Mar;63(2):229-237.
PMID: 36870702 DOI: 10.1016/j.scijus.2023.01.003

The existence of the Chinese population in the predominantly Malay population in Indonesia can be traced back thousands of years, and it has been suspected that it played an essential role in the history of the Malay population origin in Maritime South East Asia. With the fact that the Malay-Indonesian population is currently predominant compared to the Chinese population in Indonesia (Chinese-Indonesian), the selection of the origin of the STRs allele frequency panel population becomes an issue in DNA profiling, including in paternity testing. This study analyses the genetic relationship between the Chinese-Indonesian and Malay-Indonesian populations and how this affects the Paternity Index (PI) calculation in paternity test cases. The study of the relationship between populations was carried out using neighbour-joining (NJ) tree analysis and multidimensional scaling (MDS) on the allele frequency panel of 19 autosomal STRs loci of Malay-Indonesian (n = 210) and Chinese-Indonesian (n = 78) populations. Four population groups were used as references: Malay-Malaysian, Filipino, Chinese, and Caucasian. An MDS analysis was also performed based on the pairwise FST calculation. The combined Paternity Index (CPI) calculation was carried out on 132 paternity cases from the Malay-Indonesian population with inclusive results using a panel of allele frequencies from the six populations. The pairwise FST MDS indicates a closer relationship between the Chinese-Indonesian and Malay-Indonesian compared to the Chinese population, which is in line with the CPIs comparison test. The outcome suggests that the alternative use of allele frequency database between Malay-Indonesian and Chinese-Indonesian for CPI calculations is not very influential. These results can also be considered in studying the extent of genetic assimilation between the two populations. In addition, these results support the robustness claim of multivariate analysis to represent phenomena that phylogenetic analyses may not be able to demonstrate, especially for massive panel data.

Matched MeSH terms: Phylogeny
Redescription of Lernaeenicus longiventris Wilson, 1917 (Copepoda: Pennellidae) Parasitic on the Pacific Crevalle Jack Caranx caninus (Carangidae) Through Morphological and Molecular Analyses

Osuna-Cabanillas JM, Morales-Serna FN, Venmathi Maran BA, Cruz-Barraza JA

Acta Parasitol, 2023 Mar;68(1):84-90.
PMID: 36380161 DOI: 10.1007/s11686-022-00627-0

PURPOSE: The present study deals with a redescription of the copepod Lernaeenicus longiventris Wilson, 1917 (Copepoda: Siphonostomatoida: Pennellidae) found on the Pacific crevalle jack Caranx caninus Günther, using morphological and molecular analyses.
METHODS: Fish were collected off Mazatlán Port (23° 12' N, 106° 26' W), in the State of Sinaloa, Mexico (southeastern Gulf of California). The copepods were morphologically analyzed by light microscopy. Sequences of the COI mtDNA gene were generated for the first time for this species. These sequences were compared to COI sequences from six species of Lernaeenicus available in GenBank.
RESULTS: The specimens of the present study exhibited a cephalosome without apparent lateral processes, which were originally described for L. longiventris. No remarkable differences were observed with previous descriptions regarding appendages and body proportions. The phylogenetic tree based on COI sequences showed that L. longiventris was closer to L. radiatus although with low bootstrap values support in ML tree, both species formed a sister clade of L. sprattae.
CONCLUSIONS: Lernaeenicus longiventris is the unique species of the genus in the Mexican Pacific and the Gulf of California, and also the unique species of Lernaeenicus infecting C. caninus. Molecular data of L. longiventris from host and locality type are required to avoid misidentification of this species.

Matched MeSH terms: Phylogeny
Fulltext Disappearance of Imported Cases of Omicron Lineage BA.2.40 in West Kalimantan, Indonesia

Liana DF, Novianry V, Andriani A, Mahyarudin M, Astuti P

Iran J Med Sci, 2024 Mar;49(3):176-185.
PMID: 38584647 DOI: 10.30476/ijms.2023.97513.2935

BACKGROUND: The World Health Organization has declared Omicron as the fifth variant of concern with more than 50 mutations, particularly in the spike protein. Given increased viral infectivity due to mutations, worldwide genomic surveillance and detection of severe acute respiratory syndrome 2 (SARS-CoV-2) is essential. The present study aimed to track Omicron lineage BA.2.40 in West Kalimantan, Indonesia.
METHODS: In May-August 2022, nasopharyngeal swab samples (n=3,642) were collected from international travelers to West Kalimantan (active surveillance), and patients hospitalized due to SARS-CoV-2 infection (baseline surveillance). The samples were tested for Omicron lineages based on ORF1ab, N, and HV69-70del genes, followed by whole-genome sequencing. The sequences were then identified using two genomic databases, aligned against the reference genome (Wuhan/Hu-1/2019), and then compared with BA.2.40 lineage detected across the world. Phylogenetic analysis between the samples and other SARS-CoV-2 isolates was performed using molecular evolutionary genetics analysis software.
RESULTS: Based on the genomic databases, 10 isolates were identified as BA.2.40. All samples tested positive for the ORF1ab and N genes, but negative for the HV69-70del gene, which is a marker to detect the Omicron variant. Phylogenetic analysis showed the isolates were closely related to an isolate from Malaysia, an area dominated by BA.2.40.
CONCLUSION: Omicron lineage BA.2.40 has no HV69-70 deletion in the spike protein, a marker used to screen for the Omicron variant. BA.2.40 showed a high similarity to an isolate from Malaysia and was detected only during certain periods, indicating the effect of internationally imported cases.

Matched MeSH terms: Phylogeny
RNA-seq transcriptome and pathway analysis of the medicinal mushroom Lignosus tigris (Polyporaceae) offer insights into its bioactive compounds with anticancer and antioxidant potential

Ng MJ, Mohamad Razif MF, Kong BH, Yap HY, Ng ST, Tan CS, et al.

J Ethnopharmacol, 2024 Jun 28;328:118073.
PMID: 38513780 DOI: 10.1016/j.jep.2024.118073

ETHNOPHARMACOLOGICAL RELEVANCE: Medicinal mushrooms belonging to the Lignosus spp., colloquially known as Tiger Milk mushrooms (TMMs), are used as traditional medicine by communities across various regions of China and Southeast Asia to enhance immunity and to treat various diseases. At present, three Lignosus species have been identified in Malaysia: L. rhinocerus, L. tigris, and L. cameronensis. Similarities in their macroscopic morphologies and the nearly indistinguishable appearance of their sclerotia often lead to interchangeability between them. Hence, substantiation of their traditional applications via identification of their individual bioactive properties is imperative in ensuring that they are safe for consumption. L. tigris was first identified in 2013. Thus far, studies on L. tigris cultivar sclerotia (Ligno TG-K) have shown that it possesses significant antioxidant activities and has greater antiproliferative action against selected cancer cells in vitro compared to its sister species, L. rhinocerus TM02®. Our previous genomics study also revealed significant genetic dissimilarities between them. Further omics investigations on Ligno TG-K hold immense potential in facilitating the identification of its bioactive compounds and their associated bioactivities.
AIM OF STUDY: The overall aim of this study was to investigate the gene expression profile of Ligno TG-K via de novo RNA-seq and pathway analysis. We also aimed to identify highly expressed genes encoding compounds that contribute to its cytotoxic and antioxidant properties, as well as perform a comparative transcriptomics analysis between Ligno TG-K and its sister species, L. rhinocerus TM02®.
MATERIALS AND METHODS: Total RNA from fresh 3-month-old cultivated L. tigris sclerotia (Ligno TG-K) was extracted and analyzed via de novo RNA sequencing. Expressed genes were analyzed using InterPro and NCBI-Nr databases for domain identification and homology search. Functional categorization based on gene functions and pathways was performed using Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and Clusters of Orthologous Genes (COG) databases. Selected genes were subsequently subjected to phylogenetic analysis.
RESULTS: Our transcriptomics analysis of Ligno TG-K revealed that 68.06% of its genes are expressed in the sclerotium; 80.38% of these were coding transcripts. Our analysis identified highly expressed transcripts encoding proteins with prospective medicinal properties. These included serine proteases (FPKM = 7356.68), deoxyribonucleases (FPKM = 3777.98), lectins (FPKM = 3690.87), and fungal immunomodulatory proteins (FPKM = 2337.84), all of which have known associations with anticancer activities. Transcripts linked to proteins with antioxidant activities, such as superoxide dismutase (FPKM = 1161.69) and catalase (FPKM = 1905.83), were also highly expressed. Results of our sequence alignments revealed that these genes and their orthologs can be found in other mushrooms. They exhibit significant sequence similarities, suggesting possible parallels in their anticancer and antioxidant bioactivities.
CONCLUSION: This study is the first to provide a reference transcriptome profile of genes expressed in the sclerotia of L. tigris. The current study also presents distinct COG profiles of highly expressed genes in Ligno TG-K and L. rhinocerus TM02®, highlighting that any distinctions uncovered may be attributed to their interspecies variations and inherent characteristics that are unique to each species. Our findings suggest that Ligno TG-K contains bioactive compounds with prospective medicinal properties that warrant further investigations.
CLASSIFICATION: Systems biology and omics.

Matched MeSH terms: Phylogeny
Fulltext Echoes of ancient introgression punctuate stable genomic lineages in the evolution of figs

Gardner EM, Bruun-Lund S, Niissalo M, Chantarasuwan B, Clement WL, Geri C, et al.

Proc Natl Acad Sci U S A, 2023 Jul 11;120(28):e2222035120.
PMID: 37399402 DOI: 10.1073/pnas.2222035120

Studies investigating the evolution of flowering plants have long focused on isolating mechanisms such as pollinator specificity. Some recent studies have proposed a role for introgressive hybridization between species, recognizing that isolating processes such as pollinator specialization may not be complete barriers to hybridization. Occasional hybridization may therefore lead to distinct yet reproductively connected lineages. We investigate the balance between introgression and reproductive isolation in a diverse clade using a densely sampled phylogenomic study of fig trees (Ficus, Moraceae). Codiversification with specialized pollinating wasps (Agaonidae) is recognized as a major engine of fig diversity, leading to about 850 species. Nevertheless, some studies have focused on the importance of hybridization in Ficus, highlighting the consequences of pollinator sharing. Here, we employ dense taxon sampling (520 species) throughout Moraceae and 1,751 loci to investigate phylogenetic relationships and the prevalence of introgression among species throughout the history of Ficus. We present a well-resolved phylogenomic backbone for Ficus, providing a solid foundation for an updated classification. Our results paint a picture of phylogenetically stable evolution within lineages punctuated by occasional local introgression events likely mediated by local pollinator sharing, illustrated by clear cases of cytoplasmic introgression that have been nearly drowned out of the nuclear genome through subsequent lineage fidelity. The phylogenetic history of figs thus highlights that while hybridization is an important process in plant evolution, the mere ability of species to hybridize locally does not necessarily translate into ongoing introgression between distant lineages, particularly in the presence of obligate plant-pollinator relationships.

Matched MeSH terms: Phylogeny
Piece and parcel of gymnosperm organellar genomes

Cheng A, Sadali NM, Rejab NA, Uludag A

Planta, 2024 Jun 03;260(1):14.
PMID: 38829418 DOI: 10.1007/s00425-024-04449-4

Significant past, present, and potential future research into the organellar (plastid and mitochondrial) genomes of gymnosperms that can provide insight into the unknown origin and evolution of plants is highlighted. Gymnosperms are vascular seed plants that predominated the ancient world before their sister clade, angiosperms, took over during the Late Cretaceous. The divergence of gymnosperms and angiosperms took place around 300 Mya, with the latter evolving into the diverse group of flowering plants that dominate the plant kingdom today. Although gymnosperms have reportedly made some evolutionary innovations, the literature on their genome advances, particularly their organellar (plastid and mitochondrial) genomes, is relatively scattered and fragmented. While organellar genomes can shed light on plant origin and evolution, they are frequently overlooked, due in part to their limited contribution to gene expression and lack of evolutionary dynamics when compared to nuclear genomes. A better understanding of gymnosperm organellar genomes is critical because they reveal genetic changes that have contributed to their unique adaptations and ecological success, potentially aiding in plant survival, enhancement, and biodiversity conservation in the face of climate change. This review reveals significant information and gaps in the existing knowledge base of organellar genomes in gymnosperms, as well as the challenges and research needed to unravel their complexity.

Matched MeSH terms: Phylogeny
Fulltext Detection of novel coronaviruses from dusky fruit bat (Penthetor lucasi) in Sarawak, Malaysian Borneo

Habeebur-Rahman SP, Noni V, Khan FAA, Tan CS

Vet Med Sci, 2023 Nov;9(6):2634-2641.
PMID: 37658663 DOI: 10.1002/vms3.1251

BACKGROUND: Sarawak has one of the highest diversity of fruit bats species (family Pteropodidae) in Malaysia, with 19 species described. Most coronavirus (CoV) studies have mainly focused on insectivorous bats, resulting in a lack of information on CoVs present in frugivorous bats. In addition, bat CoV surveillance activities are lacking in Malaysia.
OBJECTIVES: Our study focuses on determining the presence of bat CoVs in dusky fruit bat (Penthetor lucasi).
METHODS: Guano samples belonging to P. lucasi were collected from Wind Cave Nature Reserve. The samples were screened for the presence of CoVs using validated hemi-nested consensus RNA-dependent RNA polymerase consensus primers.
RESULTS: The bat CoV positivity rate was 38.5% (n = 15/39), with the viruses belonging to two subgenera: Alphacoronavirus (α-CoV) and Betacoronavirus (β-CoV). Phylogenetic analysis revealed that CoVs from 14 samples of P. lucasi belong to the genus α-CoV and may represent previously described genetic lineages in insectivorous bats in Wind Cave. However, only one sample of P. lucasi was detected with β-CoV which is closely related to subgenus Nobecovirus, which is commonly seen in frugivorous bats.
CONCLUSIONS: This study provides the first available data on CoVs circulating in P. lucasi.

Matched MeSH terms: Phylogeny
Molecular cloning and in silico analysis of chalcone isomerase from Polygonum minus

Shah FLA, Baharum SN, Goh HH, Leow TC, Ramzi AB, Oslan SN, et al.

Mol Biol Rep, 2023 Jun;50(6):5283-5294.
PMID: 37148413 DOI: 10.1007/s11033-023-08417-1

BACKGROUND: Chalcone isomerase (CHI; EC 5.5.1.6) is one of the key enzymes in the flavonoid biosynthetic pathway that is responsible for the intramolecular cyclization of chalcones into specific 2S-flavanones.
METHODS AND RESULTS: In this study, the open reading frame (ORF) of CHI was successfully isolated from the cDNA of Polygonum minus at 711-bp long, encoding for 236 amino acid residues, with a predicted molecular weight of 25.4 kDa. Multiple sequence alignment and phylogenetic analysis revealed that the conserved residues (Thr50, Tyr108, Asn115, and Ser192) in the cleft of CHI enzyme group active site are present in PmCHI protein sequence and classified as type I. PmCHI comprises more hydrophobic residues without a signal peptide and transmembrane helices. The three-dimensional (3D) structure of PmCHI predicted through homology modeling was validated by Ramachandran plot and Verify3D, with values within the acceptable range of a good model. PmCHI was cloned into pET-28b(+) plasmid, expressed in Escherichia coli BL21(DE3) at 16 °C and partially purified.
CONCLUSION: These findings contribute to a deeper understanding of the PmCHI protein and its potential for further characterization of its functional properties in the flavonoid biosynthetic pathway.

Matched MeSH terms: Phylogeny
New species and new records of Xyleborini from the Oriental region, Japan and Papua New Guinea (Coleoptera: Curculionidae: Scolytinae)

Smith SM, Beaver RA, Pham TH, Cognato AI

Zootaxa, 2022 Nov 15;5209(1):1-33.
PMID: 37045407 DOI: 10.11646/zootaxa.5209.1.1

Eighteen xyleborine ambrosia beetles are described and illustrated: Anisandrus proscissus Smith, Beaver, Pham & Cognato sp. nov. (Vietnam), Anisandrus simplex Smith, Beaver & Cognato sp. nov. (Nepal), Arixyleborus belalongi Smith, Beaver & Cognato sp. nov. (Brunei Darussalam), Beaverium brevicaudatus Smith, Beaver & Cognato sp. nov. (Indonesia), Cnestus luculentus Smith, Beaver & Cognato sp. nov. (India), Cyclorhipidion achlys Smith, Beaver, Pham & Cognato sp. nov. (Vietnam), Cyclorhipidion conidentatus Smith, Beaver & Cognato sp. nov. (Indonesia), Cyclorhipidion gladigerum Smith, Beaver & Cognato sp. nov. (Thailand), Cyclorhipidion lapilliferum Smith, Beaver, Pham & Cognato sp. nov. (Vietnam), Cyclorhipidion nepalense Smith, Beaver & Cognato sp. nov. (Nepal), Cyclorhipidion taedulum Smith, Beaver, Pham & Cognato sp. nov. (Vietnam), Cyclorhipidion titorum Smith, Beaver, Pham & Cognato sp. nov. (Vietnam), Euwallacea alastos Smith, Beaver & Cognato sp. nov. (Japan), Leptoxyleborus regina Smith, Beaver & Cognato sp. nov. (Papua New Guinea), Tricosa hipparion Smith, Beaver & Cognato sp. nov. (Malaysia), Xyleborinus acanthopteron Smith, Beaver & Cognato sp. nov. (Thailand), Xyleborinus dumosus Smith, Beaver, Pham & Cognato sp. nov. (Vietnam), Xyleborinus nobuchii Smith, Beaver & Cognato sp. nov. (Japan). New distribution records are reported for 67 Asian species. Cyclorhipidion nemesis Smith & Cognato, described from U. S. A., is reported from Asia (China), its hypothesized native continent, for the first time. Its identity is confirmed with COI and CAD DNA within a phylogenetic analysis including other Cyclorhipidion species.

Matched MeSH terms: Phylogeny
Taxonomy of the genus Andrikothelyna Pace, 2000 (Coleoptera: Staphylinidae: Aleocharinae), with description of three new species from Taiwan and Japan

Nozaki T

Zootaxa, 2023 Apr 12;5264(1):64-76.
PMID: 37044963 DOI: 10.11646/zootaxa.5264.1.4

The rove beetle genus Andrikothelyna Pace, 2000 is reviewed. Speiraphallusa Pace, 2013 is synonymized with Andrikothelyna due to the morphological similarities. A revised diagnosis and redescription of the genus are presented, and three new species are described. As a result of this study, this genus consists of the following two known species and three new species: Andrikothelyna papuana Pace, 2000, from Papua New Guinea; Andrikothelyna orientis (Pace, 2013) comb. nov. from Malaysia; Andrikothelyna rubiginosa sp. nov. from Taiwan (Nantou); Andrikothelyna limbata sp. nov. from Japan (Honshu, Kyushu and Ryukyu); and Andrikothelyna naomichii sp. nov. from Japan (Ryukyu). This study reports the newly recorded presence of the genus Andrikothelyna in Taiwan and Japan. In addition, the key to the species is given and the taxonomic position of the genus is discussed. Observation of the living individuals reveals part of the biology of the new species.

Matched MeSH terms: Phylogeny
Characterization of white rot fungi from wood decayed for lignin degradation

Nurul-Aliyaa YA, Awang NA, Mohd MH

Lett Appl Microbiol, 2023 Oct 04;76(10).
PMID: 37777838 DOI: 10.1093/lambio/ovad118

The present study was conducted to isolate and identify white rot fungi (WRF) from wood decayed and to determine their ability to produce lignin-modifying enzymes (LMEs), specifically laccase (Lac), lignin peroxidase (LiP), and manganese peroxidase (MnP), on solid and liquid media supplemented with synthetic dyes namely 2,2'-Azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) (ABTS), azure B, and phenol red. A total of 23 isolates of WRF were isolated from decayed wood and identified as eight different species namely Phanerochaete australis, Perenniporia tephropora, Lentinus squarrosulus, Ganoderma australe, Trametes polyzona, Lentinus sajor-caju, Gymnopilus dilepis, and Fomitopsis palustris based on morphological characteristics, DNA sequences of the internal transcribed spacer (ITS) region, and phylogenetic inference. The fungal isolates can be divided into four groups based on the type of LMEs produced, namely A (Lac-LiP-MnP) with 16 isolates, B (Lac-MnP) (three isolates), C (Lac) (three isolates), and D (MnP) (one isolate). This study highlights P. australis (BJ38) as the best producer of Lac and LiP, while L. squarrosulus (IPS72) is the best producer of MnP. The present study is the first reported P. australis as an efficient lignin degrader by demonstrating the highest activity of two important LMEs.

Matched MeSH terms: Phylogeny
Fulltext Molecular characterization and comparative genomic analysis of Acinetobacter baumannii isolated from the community and the hospital: an epidemiological study in Segamat, Malaysia

Muzahid NH, Hussain MH, Huët MAL, Dwiyanto J, Su TT, Reidpath D, et al.

Microb Genom, 2023 Apr;9(4).
PMID: 37018035 DOI: 10.1099/mgen.0.000977

Acinetobacter baumannii is a common cause of multidrug-resistant (MDR) nosocomial infections around the world. However, little is known about the persistence and dynamics of A. baumannii in a healthy community. This study investigated the role of the community as a prospective reservoir for A. baumannii and explored possible links between hospital and community isolates. A total of 12 independent A. baumannii strains were isolated from human faecal samples from the community in Segamat, Malaysia, in 2018 and 2019. Another 15 were obtained in 2020 from patients at the co-located tertiary public hospital. The antimicrobial resistance profile and biofilm formation ability were analysed, and the relatedness of community and hospital isolates was determined using whole-genome sequencing (WGS). Antibiotic profile analysis revealed that 12 out of 15 hospital isolates were MDR, but none of the community isolates were MDR. However, phylogenetic analysis based on single-nucleotide polymorphisms (SNPs) and a pangenome analysis of core genes showed clustering between four community and two hospital strains. Such clustering of strains from two different settings based on their genomes suggests that these strains could persist in both. WGS revealed 41 potential resistance genes on average in the hospital strains, but fewer (n=32) were detected in the community strains. In contrast, 68 virulence genes were commonly seen in strains from both sources. This study highlights the possible transmission threat to public health posed by virulent A. baumannii present in the gut of asymptomatic individuals in the community.

Matched MeSH terms: Phylogeny

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