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Miga M, Jahari PNS, Parimannan S, Rajandas H, Latiff MAB, Jing Wei Y, Shamsir MS, Mohd Salleh F. Characterization of the nearly complete mitochondrial genome of ochraceous darkies, Euphaea ochracea Selys, 1859 (Odonata: Zygoptera: Euphaeidae) and phylogenetic analysis. Mitochondrial DNA B Resour 2023; 8:292-296. [PMID: 36845007 PMCID: PMC9946316 DOI: 10.1080/23802359.2023.2179355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2023] Open
Abstract
In the present study, the nearly complete mitochondrial genome of Euphaea ochracea was described and its phylogenetic position in the family Euphaeidae was analyzed. Here, we recovered 13 protein-coding genes, 22 transfer RNAs, 2 ribosomal RNAs and a partial control region, resulting in a mitogenome length of 15,545bp. All protein-coding genes were initiated by the typical ATN codon except nad3 and nad1, which utilizes the TTG codon. Four protein-coding genes (cox1, cox2, cox3 and nad5) are terminated by an incomplete stop codon T, while others end with either a TAA or TAG codon. The intergenic spacer region, S5, is absent in this mitogenome, supporting the lack of this region as a specific character in damselflies. Phylogenetic analysis showed that the newly sequenced E. ochracea is phylogenetically closer to E. ornata with a high support value.
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Affiliation(s)
- Marylin Miga
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, Johor, Malaysia
| | | | - Sivachandran Parimannan
- Centre of Excellence for Omics-Driven Computational Biodiscovery (COMBio), Faculty of Applied Sciences, AIMST University, Bedong, Kedah, Malaysia
| | - Heera Rajandas
- Centre of Excellence for Omics-Driven Computational Biodiscovery (COMBio), Faculty of Applied Sciences, AIMST University, Bedong, Kedah, Malaysia
| | - Muhammad Abu Bakar Latiff
- Environmental Management and Conservation Research Unit (ENCORE), Faculty of Applied Sciences and Technology (FAST), Universiti Tun Hussein Onn Malaysia, Pagoh Higher Education Hub, Muar, Johor, Malaysia
| | - Yap Jing Wei
- Centre of Research for Sustainable Uses of Natural Resources (SUNR), Faculty of Applied Sciences and Technology (FAST), Universiti Tun Hussein Onn Malaysia, Pagoh Higher Education Hub, Muar, Johor, Malaysia
| | - Mohd Shahir Shamsir
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, Johor, Malaysia
| | - Faezah Mohd Salleh
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, Johor, Malaysia,Centre of Excellence for Omics-Driven Computational Biodiscovery (COMBio), Faculty of Applied Sciences, AIMST University, Bedong, Kedah, Malaysia,Centre of Research for Sustainable Uses of Natural Resources (SUNR), Faculty of Applied Sciences and Technology (FAST), Universiti Tun Hussein Onn Malaysia, Pagoh Higher Education Hub, Muar, Johor, Malaysia,CONTACT Faezah Mohd Salleh Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, Johor, MalaysiaCentre of Excellence for Omics-Driven Computational Biodiscovery (COMBio), Faculty of Applied Sciences, AIMST University, Bedong, Kedah, Malaysia
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Miga M, Yap YZ, Jahari PNS, Parimannan S, Rajandas H, Abu Bakar-Latiff M, Jing Wei Y, Shamsir MS, Mohd Salleh F. Complete mitochondrial genome data and phylogenetic analysis of the Great Marquis, Bassarona dunya (Doubleday, 1848) (Lepidoptera: Nymphalidae: Limenitidinae) from Malaysia. Mitochondrial DNA B Resour 2023; 8:167-171. [PMID: 36733274 PMCID: PMC9888454 DOI: 10.1080/23802359.2023.2167476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
The Great Marquis or Bassarona dunya is a butterfly species commonly found in the tropical regions of Asia, America, and Africa. This butterfly is a member of the subfamily Limenitidinae and the classification within this subfamily has been unstable. Here, we report the first complete mitochondrial genome (mitogenome) of B. dunya sampled from Malaysia. The mitogenome is 15,242 bp long, comprising a set of 13 protein-coding genes (PCGs), 22 transfer RNAs (tRNAs), two ribosomal RNAs (rRNAs), and an A + T rich region. All PCGs were initiated by the typical ATN codon, except for COX1 which started with a CGA start codon. Nine PCGs were terminated with a TAA or TAG stop codon, while COX1, COX2, NAD4, and NAD5 ended with an incomplete T. The 12S and 16S rRNAs were 716 bp and 1269 bp in length, respectively. Phylogenetic analysis supported the placement of B. dunya within Limenitidinae with a high support value.
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Affiliation(s)
- Marylin Miga
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, Johor Bahru, Malaysia
| | - Yong Zi Yap
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, Johor Bahru, Malaysia
| | | | - Sivachandran Parimannan
- Faculty of Applied Sciences, Centre of Excellence for Omics-Driven Computational Biodiscovery (COMBio), AIMST University, Bedong, Malaysia
| | - Heera Rajandas
- Faculty of Applied Sciences, Centre of Excellence for Omics-Driven Computational Biodiscovery (COMBio), AIMST University, Bedong, Malaysia
| | - Muhammad Abu Bakar-Latiff
- Faculty of Applied Sciences and Technology (FAST), Environmental Management and Conservation Research Unit (ENCORE), Universiti Tun Hussein Onn Malaysia, Pagoh Higher Education Hub, Muar, Malaysia
| | - Yap Jing Wei
- Faculty of Applied Sciences and Technology (FAST), Centre of Research for Sustainable Uses of Natural Resources (SUNR), Universiti Tun Hussein Onn Malaysia, Pagoh Higher Education Hub, Muar, Malaysia
| | - Mohd Shahir Shamsir
- Faculty of Applied Sciences and Technology (FAST), Centre of Research for Sustainable Uses of Natural Resources (SUNR), Universiti Tun Hussein Onn Malaysia, Pagoh Higher Education Hub, Muar, Malaysia
| | - Faezah Mohd Salleh
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, Johor Bahru, Malaysia,Faculty of Applied Sciences, Centre of Excellence for Omics-Driven Computational Biodiscovery (COMBio), AIMST University, Bedong, Malaysia,Faculty of Applied Sciences and Technology (FAST), Environmental Management and Conservation Research Unit (ENCORE), Universiti Tun Hussein Onn Malaysia, Pagoh Higher Education Hub, Muar, Malaysia,Faculty of Applied Sciences and Technology (FAST), Centre of Research for Sustainable Uses of Natural Resources (SUNR), Universiti Tun Hussein Onn Malaysia, Pagoh Higher Education Hub, Muar, Malaysia,CONTACT Faezah Mohd Salleh Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, Johor, Malaysia
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Unfolding the mitochondrial genome structure of green semilooper (Chrysodeixis acuta Walker): An emerging pest of onion (Allium cepa L.). PLoS One 2022; 17:e0273635. [PMID: 36040876 PMCID: PMC9426943 DOI: 10.1371/journal.pone.0273635] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Accepted: 08/12/2022] [Indexed: 11/19/2022] Open
Abstract
Onion is the most important crop challenged by a diverse group of insect pests in the agricultural ecosystem. The green semilooper (Chrysodeixis acuta Walker), a widespread tomato and soybean pest, has lately been described as an emergent onion crop pest in India. C. acuta whole mitochondrial genome was sequenced in this work. The circular genome of C. acuta measured 15,743 base pairs (bp) in length. Thirteen protein-coding genes (PCGs), 22 tRNA genes, two rRNA genes, and one control region were found in the 37 sequence elements. With an average 395 bp gene length, the maximum and minimum gene length observed was 1749 bp and 63 bp of nad5 and trnR, respectively. Nine of the thirteen PCGs have (ATN) as a stop codon, while the other four have a single (T) as a stop codon. Except for trnS1, all of the tRNAs were capable of producing a conventional clover leaf structure. Conserved ATAGA motif sequences and poly-T stretch were identified at the start of the control region. Six overlapping areas and 18 intergenic spacer regions were found, with sizes ranged from 1 to 20 bp and 1 to 111 bp correspondingly. Phylogenetically, C. acuta belongs to the Plusiinae subfamily of the Noctuidae superfamily, and is closely linked to Trichoplusia ni species from the same subfamily. In the present study, the emerging onion pest C. acuta has its complete mitochondrial genome sequenced for the first time.
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Hussin N, Azmir IA, Esa Y, Ahmad A, Salleh FM, Jahari PNS, Munian K, Gan HM. Characterization of the first mitogenomes of the smallest fish in the world, Paedocypris progenetica, from peat swamp of Peninsular Malaysia, Selangor, and Perak. Genomics Inform 2022; 20:e12. [PMID: 35399011 PMCID: PMC9001995 DOI: 10.5808/gi.21081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 03/17/2022] [Indexed: 11/20/2022] Open
Abstract
The two complete mitochondrial genomes (mitogenomes) of Paedocypris progenetica, the smallest fish in the world which belonged to the Cyprinidae family, were sequenced and assembled. The circular DNA molecules of mitogenomes P1-P. progenetica and S3-P. progenetica were 16,827 and 16,616 bp in length, respectively, and encoded 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes, and one control region. The gene arrangements of P. progenetica were identical to those of other Paedocypris species. BLAST and phylogenetic analyses revealed variations in the mitogenome sequences of two Paedocypris species from Perak and Selangor. The circular DNA molecule of P. progenetica yield a standard vertebrate gene arrangement and an overall nucleotide composition of A 33.0%, T 27.2%, C 23.5%, and G 15.5%. The overall AT content of this species was consistent with that of other species in other genera. The negative GC-skew and positive AT-skew of the control region in P. progenetica indicated rich genetic variability and AT nucleotide bias, respectively. The results of this study provide genomic variation information and enhance the understanding of the mitogenome of P. progenetica. They could later deliver highly valuable new insight into data for phylogenetic analysis and population genetics.
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Affiliation(s)
- NorJasmin Hussin
- Faculty of Applied Sciences, Universiti Teknologi MARA (UiTM), 40450 Shah Alam, Malaysia.,School of Biology, Faculty of Applied Sciences, Universiti Teknologi MARA (UiTM) Negeri Sembilan, Kampus Kuala Pilah, Pekan Parit Tinggi, 72000 Kuala Pilah, Malaysia
| | - Izzati Adilah Azmir
- School of Biology, Faculty of Applied Sciences, Universiti Teknologi MARA (UiTM) Negeri Sembilan, Kampus Kuala Pilah, Pekan Parit Tinggi, 72000 Kuala Pilah, Malaysia
| | - Yuzine Esa
- Department of Aquaculture, Faculty of Agriculture, Universiti Putra Malaysia, 43400 Serdang, Malaysia
| | - Amirrudin Ahmad
- School of Marine and Environmental Sciences, Universiti Malaysia Terengganu, 21030 Kuala Nerus, Malaysia.,Institute of Tropical Biodiversity and Sustainable Development, Universiti Malaysia Terengganu, 21030 Kuala Nerus, Malaysia
| | - Faezah Mohd Salleh
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, Johor, Johor Bahru 81310, Malaysia
| | - Puteri Nur Syahzanani Jahari
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, Johor, Johor Bahru 81310, Malaysia
| | - Kaviarasu Munian
- Forest Biodiversity Division, Forest Research Institute Malaysia, Kepong 52109, Malaysia
| | - Han Ming Gan
- GeneSEQ Sdn Bhd, Bukit Beruntung, 48300 Rawang, Malaysia
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