ArticleBMC bioinformatics2019
Stepwise large genome assembly approach: a case of Siberian larch (Larix sibirica Ledeb).
Article in BMC bioinformatics, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
29 citing papers in PubMed, 54 citations in OpenAlex.
- Variation of and associations with the depth and evenness of sequencing coverage in archived plastid genomes.Scientific reports · 2025Article
- Variation of and associations with the depth and evenness of sequencing coverage in archived plastid genomes.Research square · 2025Article
- Biological Processes Underlying Genetic Adaptation of Larches to Cold and Dry Winter Conditions in Eastern Siberia.Ecology and evolution · 2025Article
- The age-related expression patterns ofForestry research · 2025Article
- Bioinformatics in Russia: history and present-day landscape.Briefings in bioinformatics · 2024Review
- A genome sequence for the threatened whitebark pine.G3 (Bethesda, Md.) · 2024Article
- The Development of Plant Genome Sequencing Technology and Its Conservation and Application in Endangered Gymnosperms.Plants (Basel, Switzerland) · 2023Review
- Genetic Adaptation of Siberian Larch (International journal of molecular sciences · 2023Article
- Larches of Kuzhanovo Have a Unique Mutation in theInternational journal of molecular sciences · 2023Article
- Comprehensive collection of genes and comparative analysis of full-length transcriptome sequences from Japanese larch (Larix kaempferi) and Kuril larch (Larix gmelinii var. japonica).BMC plant biology · 2022Article
- Environmental factors have a major effect in shaping the gene expression of Siberian larch in the Altai Mountains of China.The plant genome · 2022Article
- Evolution of complex genome architecture in gymnosperms.GigaScience · 2022Article
- Annotation of Siberian Larch (Plants (Basel, Switzerland) · 2022Article
- Actual prospects of using some types of larch growing in Kazakhstan in medicine.Journal of medicine and life · 2022Article
- A revised view on the evolution of glutamine synthetase isoenzymes in plants.The Plant journal : for cell and molecular biology · 2022Article
- Comparative Genomics of Seasonal Senescence in Forest Trees.International journal of molecular sciences · 2022Article
- Genome-Wide Prediction of Transcription Start Sites in Conifers.International journal of molecular sciences · 2022Article
- From Genome Sequencing to CRISPR-Based Genome Editing for Climate-Resilient Forest Trees.International journal of molecular sciences · 2022Review
- Assembled and annotated 26.5 Gbp coast redwood genome: a resource for estimating evolutionary adaptive potential and investigating hexaploid origin.G3 (Bethesda, Md.) · 2022Article
- Comparative Genomics Analysis of Repetitive Elements in Ten Gymnosperm Species: "Dark Repeatome" and Its Abundance in Conifer andLife (Basel, Switzerland) · 2021Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
8 authors at 4 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundDe novo assembling of large genomes, such as in conifers (~ 12-30 Gbp), which also consist of ~ 80% of repetitive DNA, is a very complex and computationally intense endeavor. One of the main problems in assembling such genomes lays in computing limitations of nucleotide sequence assembly programs (DNA assemblers). As a rule, modern assemblers are usually designed to assemble genomes with a length not exceeding the length of the human genome (3.24 Gbp). Most assemblers cannot handle the amount of input sequence data required to provide sufficient coverage needed for a high-quality assembly.
resultsAn original stepwise method of de novo assembly by parts (sets), which allows to bypass the limitations of modern assemblers associated with a huge amount of data being processed, is presented in this paper. The results of numerical assembling experiments conducted using the model plant Arabidopsis thaliana, Prunus persica (peach) and four most popular assemblers, ABySS, SOAPdenovo, SPAdes, and CLC Assembly Cell, showed the validity and effectiveness of the proposed stepwise assembling method.
conclusionUsing the new stepwise de novo assembling method presented in the paper, the genome of Siberian larch, Larix sibirica Ledeb. (12.34 Gbp) was completely assembled de novo by the CLC Assembly Cell assembler. It is the first genome assembly for larch species in addition to only five other conifer genomes sequenced and assembled for Picea abies, Picea glauca, Pinus taeda, Pinus lambertiana, and Pseudotsuga menziesii var. menziesii.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.