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Multiplex sequencing of SARS-Cov-2 genome directly from clinical samples using the Ion Personal Genome Machine (PGM)

Tan KK, Tiong V, Tan JY, Wong JE, Teoh BT, Abd-Jamil J, et al.

Trop Biomed, 2021 Sep 01;38(3):283-288.
PMID: 34362871 DOI: 10.47665/tb.38.3.069

Various methods have been developed for rapid and high throughput full genome sequencing of SARS-CoV-2. Here, we described a protocol for targeted multiplex full genome sequencing of SARS-CoV-2 genomic RNA directly extracted from human nasopharyngeal swabs using the Ion Personal Genome Machine (PGM). This protocol involves concomitant amplification of 237 gene fragments encompassing the SARS-CoV-2 genome to increase the abundance and yield of viral specific sequencing reads. Five complete and one near-complete genome sequences of SARS-CoV-2 were generated with a single Ion PGM sequencing run. The sequence coverage analysis revealed two amplicons (positions 13 751-13 965 and 23 941-24 106), which consistently gave low sequencing read coverage in all isolates except 4Apr20-64- Hu. We analyzed the potential primer binding sites within these low covered regions and noted that the 4Apr20-64-Hu possess C at positions 13 730 and 23 929, whereas the other isolates possess T at these positions. The genome nucleotide variations observed suggest that the naturally occurring variations present in the actively circulating SARS-CoV-2 strains affected the performance of the target enrichment panel of the Ion AmpliSeq™ SARS CoV 2 Research Panel. The possible impact of other genome nucleotide variations warrants further investigation, and an improved version of the Ion AmpliSeq™ SARS CoV 2 Research Panel, hence, should be considered.

Matched MeSH terms: Genome, Viral*
A telomere-to-telomere chromosome-scale genome assembly of glass catfish (Kryptopterus vitreolus)

Bian C, Li D, Wang Y, He Z, Chen WT, Chong CM, et al.

Sci Data, 2025 Mar 23;12(1):483.
PMID: 40122884 DOI: 10.1038/s41597-025-04841-z

Glass catfish (Kryptopterus vitreolus) is commonly distributed in several Asian countries, such as Thailand, Malaysia, and Indonesia. It is renowned for its near-transparent appearance, which has drawn considerable attention for biomedical research and the tropical ornamental fish industry. Here, we successfully constructed the first telomere-to-telomere (T2T) chromosome-scale genome assembly for glass catfish, by integration of PacBio HiFi, Nanopore ONT ultra-long, and Hi-C sequencing technologies. The haplotypic assembly covers approximately 687.7 Mb in length, featuring a high contig N50 of 21.3 Mb. This assembly was then anchored into 32 chromosomes, presenting a complete set of 64 telomeres and 32 centromeres. It was predicted with 252.4 Mb of repetitive sequences and annotated with a total of 24,696 protein-coding genes. Subsequent BUSCO analysis revealed high genome completeness (up to 96.4%). This high-quality T2T genome assembly not only provides a valuable genetic resource for investigating the molecular mechanisms underlying transparency, but also supports in-depth studies on functional genomics, genetic diversity, and selective breeding for this economically important fish species.

Matched MeSH terms: Genome*
Fulltext Draft Genome Sequence of Erythrobacter vulgaris Strain O1, a Glycosyl Hydrolase-Producing Bacterium

Yaakop AS, Chan CS, Kahar UM, Ee R, Chan KG, Goh KM

Genome Announc, 2015;3(3).
PMID: 25977433 DOI: 10.1128/genomeA.00457-15

Erythrobacter vulgaris strain O1, a moderate halophile, was isolated from a beach in Johor, Malaysia. Here, we present the draft genome and suggest potential applications of this bacterium.

Matched MeSH terms: Genome, Bacterial
Draft genome sequence of a marine actinobacteria Sciscionella strain SE31

Teo WF, Wee WY, Choo SW, Tan GY

Mar Genomics, 2015 Apr;20:11-2.
PMID: 25554669 DOI: 10.1016/j.margen.2014.12.006

The bacterium strain SE31, a member of the genus Sciscionella, was isolated from intertidal sediments collected from Cape Rachado, Malaysia. The high quality draft genome sequence of Sciscionella strain SE31 with a genome size of approximately 7.4 Mbp is reported. Preliminary analysis revealed 46 putative gene clusters involved in the biosynthesis of secondary metabolites and 113 putative genes that are associated with bacterial virulence, disease and defense. Availability of the genome sequence of Sciscionella SE31 will contribute to a better understanding of the genus Sciscionella.

Matched MeSH terms: Genome, Bacterial*
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: Genome, Plastid*
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: Genome, Plastid/genetics
Fulltext Variants in the mitochondrial genome sequence of Oryctes rhinoceros (Coleoptera: Scarabaeidae) infected with Oryctes rhinoceros nudivirus in oil palm and coconut plantations

Anggraini E, Vadamalai G, Kong LL, Mat M, Lau WH

Sci Rep, 2023 Oct 06;13(1):16850.
PMID: 37803044 DOI: 10.1038/s41598-023-43691-w

The CRB (coconut rhinoceros beetle) haplotype was classified into CRB-S and CRB-G, based on the presence of single nucleotide polymorphisms (SNPs) in the mitochondrial cox1 gene. Mitochondrial genomes (mitogenomes) are the most widely used genetic resources for molecular evolution, phylogenetics, and population genetics in relation to insects. This study presents the mitogenome CRB-G and CRB-S which were collected in Johor, Malaysia. The mitogenome of CRB-G collected from oil palm plantations in 2020 and 2021, and wild coconut palms in 2021 was 15,315 bp, 15,475 bp, and 17,275 bp, respectively. The CRB-S was discovered in coconut and oil palms in 2021, and its mitogenome was 15,484 bp and 17,142 bp, respectively. All the mitogenomes have 37 genes with more than 99% nucleotide sequence homology, except the CRB-G haplotype collected from oil palm in 2021 with 89.24% nucleotide sequence homology. The mitogenome of Johor CRBs was variable in the natural population due to its elevated mutation rate. Substitutions and indels in cox1, cox2, nad2 and atp6 genes were able to distinguish the Johor CRBs into two haplotypes. The mitogenome data generated in the present study may provide baseline information to study the infection and relationship between the two haplotypes of Johor CRB and OrNV in the field. This study is the first report on the mitogenomes of mixed haplotypes of CRB in the field.

Matched MeSH terms: Genome, Mitochondrial*
Fulltext Characterization and Genomic Analysis of ssDNA Vibriophage vB_VpaM_PG19 within Microviridae, Representing a Novel Viral Genus

Guo R, Zheng K, Luo L, Liu Y, Shao H, Guo C, et al.

Microbiol Spectr, 2022 Aug 31;10(4):e0058522.
PMID: 35862991 DOI: 10.1128/spectrum.00585-22

Vibrio parahaemolyticus, a widespread marine bacterium, is responsible for a variety of diseases in marine organisms. Consumption of raw or undercooked seafood contaminated with V. parahaemolyticus is also known to cause acute gastroenteritis in humans. While numerous dsDNA vibriophages have been isolated so far, there have been few studies of vibriophages belonging to the ssDNA Microviridae family. In this study, a novel ssDNA phage, vB_VpaM_PG19 infecting V. parahaemolyticus, with a 5,572 bp ssDNA genome with a G+C content of 41.31% and encoded eight open reading frames, was isolated. Genome-wide phylogenetic analysis of the total phage isolates in the GenBank database revealed that vB_VpaM_PG19 was only related to the recently deposited vibriophage vB_VpP_WS1. The genome-wide average nucleotide homology of the two phages was 89.67%. The phylogenetic tree and network analysis showed that vB_VpaM_PG19 was different from other members of the Microviridae family and might represent a novel viral genus, together with vibriophage vB_VpP_WS1, named Vimicrovirus. One-step growth curves showed that vB_VpaM_PG19 has a short incubation period, suggesting its potential as an antimicrobial agent for pathogenic V. parahaemolyticus. IMPORTANCE Vibriophage vB_VpaM_PG19 was distant from other isolated microviruses in the phylogenetic tree and network analysis and represents a novel microviral genus, named Vimicrovirus. Our report describes the genomic and phylogenetic features of vB_VpaM_PG19 and provides a potential antimicrobial candidate for pathogenic V. parahaemolyticus.

Matched MeSH terms: Genome, Viral*
Fulltext Widespread ancient whole-genome duplications in Malpighiales coincide with Eocene global climatic upheaval

Cai L, Xi Z, Amorim AM, Sugumaran M, Rest JS, Liu L, et al.

New Phytol, 2019 Jan;221(1):565-576.
PMID: 30030969 DOI: 10.1111/nph.15357

Whole-genome duplications (WGDs) are widespread and prevalent in vascular plants and frequently coincide with major episodes of global and climatic upheaval, including the mass extinction at the Cretaceous-Tertiary boundary (c. 65 Ma) and during more recent periods of global aridification in the Miocene (c. 10-5 Ma). Here, we explore WGDs in the diverse flowering plant clade Malpighiales. Using transcriptomes and complete genomes from 42 species, we applied a multipronged phylogenomic pipeline to identify, locate, and determine the age of WGDs in Malpighiales using three means of inference: distributions of synonymous substitutions per synonymous site (Ks ) among paralogs, phylogenomic (gene tree) reconciliation, and a likelihood-based gene-count method. We conservatively identify 22 ancient WGDs, widely distributed across Malpighiales subclades. Importantly, these events are clustered around the Eocene-Paleocene transition (c. 54 Ma), during which time the planet was warmer and wetter than any period in the Cenozoic. These results establish that the Eocene Climatic Optimum likely represents a previously unrecognized period of prolific WGDs in plants, and lends further support to the hypothesis that polyploidization promotes adaptation and enhances plant survival during episodes of global change, especially for tropical organisms like Malpighiales, which have tight thermal tolerances.

Matched MeSH terms: Genome, Plant*
Genetic determinants of skin ageing: a systematic review and meta-analysis of genome-wide association studies and candidate genes

Wong C, Ng JY, Sio YY, Chew FT

J Physiol Anthropol, 2025 Feb 08;44(1):4.
PMID: 39923055 DOI: 10.1186/s40101-025-00384-9

BACKGROUND: Skin ageing is influenced by complex genetic factors. Various phenotypes such as wrinkling, pigmentation changes, and skin cancers have been linked to specific genetic loci. However, the underlying genetic mechanisms and pathways remain poorly understood. This systematic review and meta-analysis aims to summarise the genetic loci found to be associated with skin ageing phenotypes by published genome-wide association studies (GWAS) and candidate gene studies. We also evaluated the overall association of loci via meta-analysis and identified the association patterns to explore potential biological pathways contributing to skin ageing. The Web of Science, Embase, and PubMed databases were searched on January 2024 using specific exclusion criteria (e.g., study of non-human subjects, focus on skin diseases, or treatments) to identify relevant articles. There did not appear to be any significant publication bias observed across the all phenotypes.
MAIN BODY: A total of 48 studies were included, revealing 30 loci that were confirmed to be associated with skin ageing by multiple studies (e.g., AFG3L1P: odds ratio 1.133 95% confidence interval [1.044, 1.222]; BPIFA3: 1.859 [1.567, 2.151]; CLPTML1: 1.164 [1.0.99, 1.229]; CPNE7: 0.905 [0.852-0.958]; DEF8: 1.186 [1.042, 1.331]; IRF4: 1.260 [1.025, 1.495]; MYO16: 2.303 [1.697, 2.908]; PRDM16: 1.105 [1.084, 1.127]; RORA: 1.391 [1.206, 1.577]; SPG7: 0.922 [0.897, 0.947]; SPON1: 2.214 [1.204, 3.225]; SPTLC1: 1.464 [1.432, 1.495]; TYR: 1.175 [1.007, 1.343]). The lack of significance for many loci may be due to studies analysing different SNPs within the same locus, weakening the overall associations. Several loci were associated with specific phenotypic categories (e.g., skin colour related, skin cancer related, wrinkling and sagging related), suggesting shared biological pathways are involved in the pathogenesis of different skin ageing phenotypes. This pattern was also observed in several of the loci that do not have a significant overall association with skin ageing.
CONCLUSION: Despite significant heterogeneity among the included studies and the use of subjective visual methods for phenotype assessment, our review highlights the critical role of fundamental biological processes, such as development and cellular organisation, in skin ageing. Future research that targets the same SNP across multiple populations could strengthen the association of additional loci with skin ageing. Further investigation into these underlying biological processes would significantly advance our understanding of the pathogenesis of skin ageing phenotypes.

Matched MeSH terms: Genome-Wide Association Study*
A chromosome phased diploid genome assembly of African hunting dog (Lycaon pictus)

Kliver S, Kovacic I, Mak S, Sinding MS, Stagegaard J, Petersen B, et al.

J Hered, 2025 Jan 03;116(1):78-87.
PMID: 39316562 DOI: 10.1093/jhered/esae052

The African hunting dog (Lycaon pictus, 2n = 78) once ranged over most sub-Saharan ecosystems except its deserts and rainforests. However, as a result of (still ongoing) population declines, today they remain only as small fragmented populations. Furthermore, the future of the species remains unclear, due to both anthropogenic pressure and interactions with domestic dogs, thus their preservation is a conservation priority. On the tree of life, the hunting dog is basal to Canis and Cuon and forms a crown group with them, making it a useful species for comparative genomic studies. Here, we present a diploid chromosome-level assembly of an African hunting dog. Assembled according to Vertebrate Genomes Project guidelines from a combination of PacBio HiFi reads and HiC data, it is phased at the level of individual chromosomes. The maternal (pseudo)haplotype (mat) of our assembly has a length of 2.38 Gbp, and 99.36% of the sequence is encompassed by 39 chromosomal scaffolds. The rest is included in only 36 unplaced short scaffolds. At the contig level, the mat consists of only 166 contigs with an N50 of 39 Mbp. BUSCO (Benchmarking Universal Single-Copy Orthologue) analysis showed 95.4% completeness based on Carnivora conservative genes (carnivora_odb10). When compared with other available genomes from subtribe Canina, the quality of the assembly is excellent, typically between the first and third depending on the parameter used, and a significant improvement on previously published genomes for the species. We hope this assembly will play an important role in future conservation efforts and comparative studies of canid genomes.

Matched MeSH terms: Genome*; Genomics/methods
A genome-based phylogeny for Mollusca is concordant with fossils and morphology

Chen Z, Baeza JA, Chen C, Gonzalez MT, González VL, Greve C, et al.

Science, 2025 Feb 28;387(6737):1001-1007.
PMID: 40014700 DOI: 10.1126/science.ads0215

Extreme morphological disparity within Mollusca has long confounded efforts to reconstruct a stable backbone phylogeny for the phylum. Familiar molluscan groups-gastropods, bivalves, and cephalopods-each represent a diverse radiation with myriad morphological, ecological, and behavioral adaptations. The phylum further encompasses many more unfamiliar experiments in animal body-plan evolution. In this work, we reconstructed the phylogeny for living Mollusca on the basis of metazoan BUSCO (Benchmarking Universal Single-Copy Orthologs) genes extracted from 77 (13 new) genomes, including multiple members of all eight classes with two high-quality genome assemblies for monoplacophorans. Our analyses confirm a phylogeny proposed from morphology and show widespread genomic variation. The flexibility of the molluscan genome likely explains both historic challenges with their genomes and their evolutionary success.

Matched MeSH terms: Genome*
Complete mitochondrial genomes of the tooth of a poached Bornean banteng (Bos javanicus lowi; Cetartiodactyla, Bovidae)

Ishige T, Gakuhari T, Hanzawa K, Kono T, Sunjoto I, Sukor JR, et al.

Mitochondrial DNA A DNA Mapp Seq Anal, 2016 Jul;27(4):2453-4.
PMID: 26075477 DOI: 10.3109/19401736.2015.1033694

Here we report the complete mitochondrial genome of the Bornean banteng Bos javanicus lowi (Cetartiodactyla, Bovidae), which was determined using next-generation sequencing. The mitochondrial genome is 16,344 bp in length containing 13 protein-coding genes, 21 tRNAs and 2 rRNAs. It shows the typical pattern of bovine mitochondrial arrangement. Phylogenetic tree analysis of complete mtDNA sequences showed that Bornean banteng is more closely related to gaur than to other banteng subspecies. Divergence dating indicated that Bornean banteng and gaur diverged from their common ancestor approximately 5.03 million years ago. These results suggest that Bornean banteng might be a distinct species in need of conservation.

Matched MeSH terms: Genome, Mitochondrial*; Genome Size
Fulltext The Genome and mRNA Transcriptome of the Cosmopolitan Calanoid Copepod Acartia tonsa Dana Improve the Understanding of Copepod Genome Size Evolution

Jørgensen TS, Petersen B, Petersen HCB, Browne PD, Prost S, Stillman JH, et al.

Genome Biol Evol, 2019 May 01;11(5):1440-1450.
PMID: 30918947 DOI: 10.1093/gbe/evz067

Members of the crustacean subclass Copepoda are likely the most abundant metazoans worldwide. Pelagic marine species are critical in converting planktonic microalgae to animal biomass, supporting oceanic food webs. Despite their abundance and ecological importance, only six copepod genomes are publicly available, owing to a number of factors including large genome size, repetitiveness, GC-content, and small animal size. Here, we report the seventh representative copepod genome and the first genome and the first transcriptome from the calanoid copepod species Acartia tonsa Dana, which is among the most numerous mesozooplankton in boreal coastal and estuarine waters. The ecology, physiology, and behavior of A. tonsa have been studied extensively. The genetic resources contributed in this work will allow researchers to link experimental results to molecular mechanisms. From PCR-free whole genome sequence and mRNA Illumina data, we assemble the largest copepod genome to date. We estimate that A. tonsa has a total genome size of 2.5 Gb including repetitive elements we could not resolve. The nonrepetitive fraction of the genome assembly is estimated to be 566 Mb. Our DNA sequencing-based analyses suggest there is a 14-fold difference in genome size between the six members of Copepoda with available genomic information. This finding complements nucleus staining genome size estimations, where 100-fold difference has been reported within 70 species. We briefly analyze the repeat structure in the existing copepod whole genome sequence data sets. The information presented here confirms the evolution of genome size in Copepoda and expands the scope for evolutionary inferences in Copepoda by providing several levels of genetic information from a key planktonic crustacean species.

Matched MeSH terms: Genome; Genome Size*
Fulltext The complex genome and adaptive evolution of polyploid Chinese pepper (Zanthoxylum armatum and Zanthoxylum bungeanum)

Hu L, Xu Z, Fan R, Wang G, Wang F, Qin X, et al.

Plant Biotechnol J, 2023 Jan;21(1):78-96.
PMID: 36117410 DOI: 10.1111/pbi.13926

Zanthoxylum armatum and Zanthoxylum bungeanum, known as 'Chinese pepper', are distinguished by their extraordinary complex genomes, phenotypic innovation of adaptive evolution and species-special metabolites. Here, we report reference-grade genomes of Z. armatum and Z. bungeanum. Using high coverage sequence data and comprehensive assembly strategies, we derived 66 pseudochromosomes comprising 33 homologous phased groups of two subgenomes, including autotetraploid Z. armatum. The genomic rearrangements and two whole-genome duplications created large (~4.5 Gb) complex genomes with a high ratio of repetitive sequences (>82%) and high chromosome number (2n = 4x = 132). Further analysis of the high-quality genomes shed lights on the genomic basis of involutional reproduction, allomones biosynthesis and adaptive evolution in Chinese pepper, revealing a high consistent relationship between genomic evolution, environmental factors and phenotypic innovation. Our study provides genomic resources and new insights for investigating diversification and phenotypic innovation in Chinese pepper, with broader implications for the protection of plants under severe environmental changes.

Matched MeSH terms: Genome, Plant
Mining the genome of Bacillus velezensis FS26 for probiotic markers and secondary metabolites with antimicrobial properties against aquaculture pathogens

Sam-On MFS, Mustafa S, Mohd Hashim A, Yusof MT, Zulkifly S, Malek AZA, et al.

Microb Pathog, 2023 Aug;181:106161.
PMID: 37207784 DOI: 10.1016/j.micpath.2023.106161

Bacillus velezensis FS26 is a bacterium from the genus Bacillus that has been proven as a potential probiotic in aquaculture with a good antagonistic effect on Aeromonas spp. and Vibrio spp. Whole-genome sequencing (WGS) allows a comprehensive and in-depth analysis at the molecular level, and it is becoming an increasingly significant technique in aquaculture research. Although numerous probiotic genomes have been sequenced and investigated recently, there are minimal data on in silico analysis of B. velezensis as a probiotic bacterium isolated from aquaculture sources. Thus, this study aims to analyse the general genome characteristics and probiotic markers from the B. velezensis FS26 genome with secondary metabolites predicted against aquaculture pathogens. The B. velezensis FS26 genome (GenBank Accession: JAOPEO000000000) assembly proved to be of high quality, with eight contigs containing 3,926,371 bp and an average G + C content of 46.5%. According to antiSMASH analysis, five clusters of secondary metabolites from the B. velezensis FS26 genome showed 100% similarity. These clusters include Cluster 2 (bacilysin), Cluster 6 (bacillibactin), Cluster 7 (fengycin), Cluster 8 (bacillaene), and Cluster 9 (macrolactin H), which signify promising antibacterial, antifungal, and anticyanobacterial agents against pathogens in aquaculture. The probiotic markers of B. velezensis FS26 genome for adhesion capability in the hosts' intestine, as well as the acid and bile salt-tolerant genes, were also detected through the Prokaryotic Genome Annotation System (Prokka) annotation pipeline. These results are in agreement with our previous in vitro data, suggesting that the in silico investigation facilitates establishing B. velezensis FS26 as a beneficial probiotic for use in aquaculture.

Matched MeSH terms: Genome, Bacterial
Long read sequencing of Toona sinensis (A. Juss) Roem: A chromosome-level reference genome for the family Meliaceae

Ji YT, Xiu Z, Chen CH, Wang Y, Yang JX, Sui JJ, et al.

Mol Ecol Resour, 2021 May;21(4):1243-1255.
PMID: 33421343 DOI: 10.1111/1755-0998.13318

Chinese mahogany (Toona sinensis) is a woody plant that is widely cultivated in China and Malaysia. Toona sinensis is important economically, including as a nutritious food source, as material for traditional Chinese medicine and as a high-quality hardwood. However, the absence of a reference genome has hindered in-depth molecular and evolutionary studies of this plant. In this study, we report a high-quality T. sinensis genome assembly, with scaffolds anchored to 28 chromosomes and a total assembled length of 596 Mb (contig N50 = 1.5 Mb and scaffold N50 = 21.5 Mb). A total of 34,345 genes were predicted in the genome after homology-based and de novo annotation analyses. Evolutionary analysis showed that the genomes of T. sinensis and Populus trichocarpa diverged ~99.1-103.1 million years ago, and the T. sinensis genome underwent a recent genome-wide duplication event at ~7.8 million years and one more ancient whole genome duplication event at ~71.5 million years. These results provide a high-quality chromosome-level reference genome for T. sinensis and confirm its evolutionary position at the genomic level. Such information will offer genomic resources to study the molecular mechanism of terpenoid biosynthesis and the formation of flavour compounds, which will further facilitate its molecular breeding. As the first chromosome-level genome assembled in the family Meliaceae, it will provide unique insights into the evolution of members of the Meliaceae.

Matched MeSH terms: Genome, Plant*
Fulltext Genome-wide association analysis of adaptation to oxygen stress in Nile tilapia (Oreochromis niloticus)

Yu X, Megens HJ, Mengistu SB, Bastiaansen JWM, Mulder HA, Benzie JAH, et al.

BMC Genomics, 2021 Jun 09;22(1):426.
PMID: 34107887 DOI: 10.1186/s12864-021-07486-5

BACKGROUND: Tilapia is one of the most abundant species in aquaculture. Hypoxia is known to depress growth rate, but the genetic mechanism by which this occurs is unknown. In this study, two groups consisting of 3140 fish that were raised in either aerated (normoxia) or non-aerated pond (nocturnal hypoxia). During grow out, fish were sampled five times to determine individual body weight (BW) gains. We applied a genome-wide association study to identify SNPs and genes associated with the hypoxic and normoxic environments in the 16th generation of a Genetically Improved Farmed Tilapia population.
RESULTS: In the hypoxic environment, 36 SNPs associated with at least one of the five body weight measurements (BW1 till BW5), of which six, located between 19.48 Mb and 21.04 Mb on Linkage group (LG) 8, were significant for body weight in the early growth stage (BW1 to BW2). Further significant associations were found for BW in the later growth stage (BW3 to BW5), located on LG1 and LG8. Analysis of genes within the candidate genomic region suggested that MAPK and VEGF signalling were significantly involved in the later growth stage under the hypoxic environment. Well-known hypoxia-regulated genes such as igf1rb, rora, efna3 and aurk were also associated with growth in the later stage in the hypoxic environment. Conversely, 13 linkage groups containing 29 unique significant and suggestive SNPs were found across the whole growth period under the normoxic environment. A meta-analysis showed that 33 SNPs were significantly associated with BW across the two environments, indicating a shared effect independent of hypoxic or normoxic environment. Functional pathways were involved in nervous system development and organ growth in the early stage, and oocyte maturation in the later stage.
CONCLUSIONS: There are clear genotype-growth associations in both normoxic and hypoxic environments, although genome architecture involved changed over the growing period, indicating a transition in metabolism along the way. The involvement of pathways important in hypoxia especially at the later growth stage indicates a genotype-by-environment interaction, in which MAPK and VEGF signalling are important components.

Matched MeSH terms: Genome-Wide Association Study*
Fulltext The Crown Pearl: a draft genome assembly of the European freshwater pearl mussel Margaritifera margaritifera (Linnaeus, 1758)

Gomes-Dos-Santos A, Lopes-Lima M, Machado AM, Marcos Ramos A, Usié A, Bolotov IN, et al.

DNA Res, 2021 May 02;28(2).
PMID: 33755103 DOI: 10.1093/dnares/dsab002

Since historical times, the inherent human fascination with pearls turned the freshwater pearl mussel Margaritifera margaritifera (Linnaeus, 1758) into a highly valuable cultural and economic resource. Although pearl harvesting in M. margaritifera is nowadays residual, other human threats have aggravated the species conservation status, especially in Europe. This mussel presents a myriad of rare biological features, e.g. high longevity coupled with low senescence and Doubly Uniparental Inheritance of mitochondrial DNA, for which the underlying molecular mechanisms are poorly known. Here, the first draft genome assembly of M. margaritifera was produced using a combination of Illumina Paired-end and Mate-pair approaches. The genome assembly was 2.4 Gb long, possessing 105,185 scaffolds and a scaffold N50 length of 288,726 bp. The ab initio gene prediction allowed the identification of 35,119 protein-coding genes. This genome represents an essential resource for studying this species' unique biological and evolutionary features and ultimately will help to develop new tools to promote its conservation.

Matched MeSH terms: Genome*; Genomics
Fulltext Adapting the ACMG/AMP variant classification framework: A perspective from the ClinGen Hemoglobinopathy Variant Curation Expert Panel

Kountouris P, Stephanou C, Lederer CW, Traeger-Synodinos J, Bento C, Harteveld CL, et al.

Hum Mutat, 2022 Aug;43(8):1089-1096.
PMID: 34510646 DOI: 10.1002/humu.24280

Accurate and consistent interpretation of sequence variants is integral to the delivery of safe and reliable diagnostic genetic services. To standardize the interpretation process, in 2015, the American College of Medical Genetics and Genomics (ACMG) and the Association for Molecular Pathology (AMP) published a joint guideline based on a set of shared standards for the classification of variants in Mendelian diseases. The generality of these standards and their subjective interpretation between laboratories has prompted efforts to reduce discordance of variant classifications, with a focus on the expert specification of the ACMG/AMP guidelines for individual genes or diseases. Herein, we describe our experience as a ClinGen Variant Curation Expert Panel to adapt the ACMG/AMP criteria for the classification of variants in three globin genes (HBB, HBA2, and HBA1) related to recessively inherited hemoglobinopathies, including five evidence categories, as use cases demonstrating the process of specification and the underlying rationale.

Matched MeSH terms: Genome, Human*

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