Construction and characterization of a de novo draft genome of garden cress (Lepidium sativum L.)

Patat, Aysenur Soyturk; Sen, Fatima; Erdoğdu, Behiç Selman; Uncu, Ali Tevfik; Uncu, Ayşe Özgür

doi:10.1007/s10142-022-00866-4

Cited by 4 publications

(1 citation statement)

References 42 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…This is expected to improve dramatically with the use of a more accurate nanopore flow cell that will become available in the near future (Luo et al 2022 ). PacBio’s HiFi sequencing is also available as a highly accurate long read sequence (Wenger et al 2019 ; Patat et al 2022 ), but is still relatively expensive. We also used LoopSeq as a synthetic long-read method using Illumina, but this method uses UMI tags in the kit, so it is not possible to use custom UMI tags.…”

Section: Discussionmentioning

confidence: 99%

Pilot study of a comprehensive resource estimation method from environmental DNA using universal D-loop amplification primers

Yoshitake

Yanagisawa

Sugimoto

et al. 2023

Funct Integr Genomics

View full text Add to dashboard Cite

Many studies have investigated the ability of environmental DNA (eDNA) to identify the species. However, when individual species are to be identified, accurate estimation of their abundance using traditional eDNA analyses is still difficult. We previously developed a novel analytical method called HaCeD-Seq (haplotype count from eDNA by sequencing), which focuses on the mitochondrial D-loop sequence for eels and tuna. In this study, universal D-loop primers were designed to enable the comprehensive detection of multiple fish species by a single sequence. To sequence the full-length D-loop with high accuracy, we performed nanopore sequencing with unique molecular identifiers (UMI). In addition, to determine the D-loop reference sequence, whole genome sequencing was performed with thin coverage, and complete mitochondrial genomes were determined. We developed a UMI-based Nanopore D-loop sequencing analysis pipeline and released it as open-source software. We detected 5 out of 15 species (33%) and 10 haplotypes out of 35 individuals (29%) among the detected species. This study demonstrates the possibility of comprehensively obtaining information related to population size from eDNA. In the future, this method can be used to improve the accuracy of fish resource estimation, which is currently highly dependent on fishing catches.

show abstract

Section: Discussionmentioning

confidence: 99%