Eyeing DNA barcoding for species identification of fish larvae DOI Creative Commons
Wan Wen Rochelle Chan, Jia Jin Marc Chang,

Charles Zhiming Tan

и другие.

Journal of Fish Biology, Год журнала: 2024, Номер unknown

Опубликована: Сен. 3, 2024

Abstract Identification of fish larvae based on morphology is typically limited to higher taxonomic ranks (e.g., family or order), as possess few morphological diagnostic characters for precise discrimination species. When many samples are presented at any one time, the use identify such specimens can be laborious and time‐consuming. Using a reverse workflow specimen sorting identification leveraging high‐throughput DNA sequencing, thousands barcoded sorted into molecular operational units (mOTUs) in single sequencing run with nanopore technology MinION). This process reduces time financial costs morphology‐based instead deploys experienced taxonomists species work where they needed most. In this study, total 3022 larval from plankton tows across four sites Singapore were collected workflow. Eye tissue individual was used extraction cytochrome c oxidase subunit I. We generated 2746 barcodes after quality filtering (90.9% barcoding success), identified 2067 (75.3% delimited 256 mOTUs (146 genera, 52 families). Our analyses specific challenges assignment, potential misidentification publicly available sequences reference barcodes. highlighted how conservative application comparison local sequence database help resolve conflicts. Overall, proposed approach enables expedites larvae, contributing enhancement barcode databases potentially better understanding connectivity.

Язык: Английский

Harnessing artificial intelligence to fill global shortfalls in biodiversity knowledge DOI Creative Commons
Laura J. Pollock, Justin Kitzes, Sara Beery

и другие.

Опубликована: Фев. 20, 2025

Язык: Английский

Процитировано

0
Large-Scale Rice Mutant Establishment and High-Throughput Mutant Manipulation Help Advance Rice Functional Genomics DOI Creative Commons

Eyob Kassaye Wolella,

Cheng Zhen, Mengyuan Li

и другие.

Plants, Год журнала: 2025, Номер 14(10), С. 1492 - 1492

Опубликована: Май 16, 2025

Rice (Oryza sativa L.) is a stable food for over half of the world population, contributing 50-80% daily calorie intake. The completion rice genome sequencing marks significant milestone in understanding functional genomics, yet systematic identification gene functions remains bottleneck improvement. Large-scale mutant libraries which genes are lost or gained (e.g., through chemical/physical treatments, T-DNA, transposons, RNAi, CRISPR/Cas9) have proven to be powerful tools linking genotypes phenotypes. So far, using different mutagenesis approaches, million lines been established and about 5-10% predicted identified due high demands labor low-throughput utilization. DNA-barcoding-based large-scale offers unprecedented precision scalability genomics. This review summarizes loss-of-function gain-of-function library development approaches emphasizes integration DNA barcoding pooled analysis. Unique barcodes can tagged transposons/retrotransposons, constructs, miRNA/siRNA, gRNA, cDNA, allowing pooling analysis assignment that cause phenotype alterations. In addition, high-throughput phenotyping OMICS technologies accelerate functions.

Язык: Английский

Процитировано

0
Eyeing DNA barcoding for species identification of fish larvae DOI Creative Commons
Wan Wen Rochelle Chan, Jia Jin Marc Chang,

Charles Zhiming Tan

и другие.

Journal of Fish Biology, Год журнала: 2024, Номер unknown

Опубликована: Сен. 3, 2024

Abstract Identification of fish larvae based on morphology is typically limited to higher taxonomic ranks (e.g., family or order), as possess few morphological diagnostic characters for precise discrimination species. When many samples are presented at any one time, the use identify such specimens can be laborious and time‐consuming. Using a reverse workflow specimen sorting identification leveraging high‐throughput DNA sequencing, thousands barcoded sorted into molecular operational units (mOTUs) in single sequencing run with nanopore technology MinION). This process reduces time financial costs morphology‐based instead deploys experienced taxonomists species work where they needed most. In this study, total 3022 larval from plankton tows across four sites Singapore were collected workflow. Eye tissue individual was used extraction cytochrome c oxidase subunit I. We generated 2746 barcodes after quality filtering (90.9% barcoding success), identified 2067 (75.3% delimited 256 mOTUs (146 genera, 52 families). Our analyses specific challenges assignment, potential misidentification publicly available sequences reference barcodes. highlighted how conservative application comparison local sequence database help resolve conflicts. Overall, proposed approach enables expedites larvae, contributing enhancement barcode databases potentially better understanding connectivity.

Язык: Английский

Процитировано

1