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Discovery of Simple Sequence Repeat Markers through Transcriptome Analysis of Baccaurea motleyana

Journal of Food Science and Engineering 2020年第2期10卷 33-46页

作者： Khairun Hisam Nasir Muhammad Fairuz mohd Yusof mohd shahril firdaus abdul razak Siti NorsaidahIbrahim Mira Farzana Mohamad Moktar Khadijah Awang mohd Shukri Mat Ali Centre for Molecular Marker Discovery and Validation(CMDV) Agri-Omic dan BioinformaticsBiotechnology and Nanotechnology Research CentreMalaysian Agricultural Research and Development Institute(MARDI)Serdang 43400SelangorMalaysia Industrial Crop Research Centre Malaysian Agricultural Research and Development Institute(MARDI)Serdang 43400SelangorMalaysia Horticulture Research Centre Malaysian Agricultural Research and Development Institute(MARDI)Serdang 43400SelangorMalaysia

Baccaurea motleyana(rambai)is underutilized fruits that are native to Malaysia,Indonesia and *** this study,a total of 54,779 unigenes identified from rambai transcriptome were used for simple sequence repeat(SSR)analysis by MIcroSAtellite(MISA).A total of 20,420 SSRs were found to be distributed within 37.27%of the total number of *** repeats represented the main type,accounting for 64.04%,followed by trinucleotide repeats(20.28%)and dinucleotide repeats(19.94%).Gene annotation to seven databases has a success ratio of 68.53%(National Center for Biotechnology Information(NCBI)protein sequences),53.68%(NCBI nucleotide sequences),27.43%(Kyoto Encyclopedia of Genes and Genome Ortholog),56.0%(SwissProt),52.44%(Protein family),53.99%(Gene Ontology)and 26.44%(Kluster of Orthologous Group).Further rambai SSRs were randomly selected and validated to ***(rambai),***(tampoi),***(jentik-jentik),***(pupor)and ***(setambun).

关键词： Baccaurea SSR transcriptome gene annotation and SSR validation

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Anthropogenic disturbance of aquatic biodiversity and water quality of an urban river in Penang, Malaysia

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Water Science and Engineering 2023年第3期16卷 234-242页

作者： Nur Azalina Suzianti Feisal Noor Haziqah Kamaludin Muhammad firdaus abdullah Sani Dayang Khairulnisa Awang Ahmad mohd Azwan Ahmad Nur Faiza abdul razak Tengku Nilam Baizura Tengku Ibrahim Department of Environmental Health Faculty of Health SciencesMAHSA UniversityBandar Saujana Putra42610 JenjaromMalaysia Center of Environmental Health&Safety Faculty of Health SciencesUniversiti Teknologi MARA42300 Puncak AlamMalaysia NaturePRO Services Port Dickson71000 Negeri SembilanMalaysia Department of Environmental Health Faculty of Health SciencesUniversiti Teknologi MARACawangan Pulau PinangKampus Bertam13200 Pulau PinangMalaysia

Malaysia's rapid economic and demographic development have placed negative pressure on its water supplies and the quality of the Juru River, which is close to the nation's capital and its major source of water. Healthy aquatic ecosystems are supported by physicochemical properties and biological diversity. This study evaluated the anthropogenic impacts on aquatic biodiversity, especially plankton, fish, and macrobenthos, as well as the water quality of the Juru River in the Penang area. Aquatic biodiversity and river water parameters were collected from ten sampling stations along the Juru River. Seven variables were used to assess the physicochemical environment: pH, temperature, total suspended solids (TSS), salinity, dissolved oxygen (DO), biochemical oxygen demand (BOD), and chemical oxygen demand. At each sampling station, the total number of plankton, fish, and macrobenthic taxa were counted and analyzed. The relationships between the physicochemical parameters and aquatic biodiversity were investigated with biotypological analysis, principal component analysis, hierarchical cluster analysis, and linear regression analysis. These analyses showed that the richness and diversity indices were generally influenced by salinity, temperature, TSS, BOD, and pH. The data obtained in this study supported the bioindicator concept. The findings, as they related to scientifically informed conservation, could serve as a model for Juru River management, as well as for river management throughout Malaysia and other tropical Asian countries.

关键词： Anthropogenic disturbance Aquatic biodiversity River water quality Urban river Hierarchical cluster analysis

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Development of Starfruit Simple Sequence Repeat (SSR) Using Next Generation Sequencing

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Journal of Food Science and Engineering 2019年第3期9卷 95-121页

作者： Khairun Hisam Nasir Muhammad Fairuz mohd Yusof mohd shahril firdaus Siti Zainab Jantan Mira Farzana Mohamad Moktar Siti Norsaidah Ibrahim Noor Baiti abdul Aziz Joanna Cho Lee Ying Centre for Molecular Marker Discovery and Validation (CMDV) Agri-Omic dan Bioinformatics Biotechnology and Nanotechnology Research Centre Malaysian Agricultural Research and Development Institute (MARDI) 43400 Serdang Selangor Malaysia Horticulture Research Centre Headquarters Malaysian Agricultural Research and Development Institute (MARDI) 43400 Serdang Selangor Malaysia

Starfruit (Averrhoa carambola L.) is an important fruit for Malaysian export and great attention has been made to improve starfruit fruit quality at Malaysian Agricultural Research and Development Institute (MARDI). The current study used next generation sequencing (NGS) technologies to develop starfruit simple sequence repeat (SSR) from 2 varieties namely B11 and B17 using Illumina HiSeq. The pre-processed reads were de novo assembled to generate approximately 75,000 and 74,000 scaffolds respectively. Total genome size for B11 and B17 were around 345 Mbp and 342 Mbp based on K-mer distribution analysis. In-silico microsatellite mining of each variety has identified more than 17,000 SSR in B11 and B17 respectively. Dinucleotides were the most abundant, accounting for more than 70% of all SSR and repeat motif GA (49%) was most common. A total of 239 SSR primer pairs were designed from contigs larger than 350 nucleotides and tested for amplification. The 30 polymorphic SSRs were used to DNA fingerprint of 12 starfruit hybrids. Polymorphism information content (PIC) ranged from 0.1411 to 0.6838, with an average of 0.3919. The Unweighted Pair-Group Method for Arithmetic Averages (UPGMA) dendrogram clustered 12 starfruit accessions into 2 groups.

关键词： Starfruit (Averrhoa carambola L.) next generation sequencing molecular marker simple sequence repeat

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