Poaceae Chloroplast Genome Sequencing: Great Leap Forward in Recent Ten Years

There is no author summary for this article yet. Authors can add summaries to their articles on ScienceOpen to make them more accessible to a non-specialist audience.

Abstract

The first complete chloroplast genome of rice ( Oryza sativa) was published in 1989, ushering in a new era of studies of chloroplast genomics in Poaceae. Progresses in Next-Generation Sequencing (NGS) and Third-Generation Sequencing (TGS) technologiesand in the development of genome assembly software, have significantly advanced chloroplast genomics research. Poaceae is one of the most targeted families in chloroplast genome research because of its agricultural, ecological, and economic importance. Over the last 30 years, 2,050 complete chloroplast genome sequences from 40 tribes and 282 genera have been generated, most (97%) of them in the recent ten years. The wealth of data provides the groundwork for studies on species evolution, phylogeny, genetic transformation, and other aspects of Poaceae chloroplast genomes. As a result, we have gained a deeper understanding of the properties of Poaceae chloroplast genomes. Here, we summarize the achievements of the studies of the Poaceae chloroplast genomes and envision the challenges for moving the area ahead.

Related collections

Most cited references 180

Record: found
Abstract: found
Article: not found

SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing.

Anton Bankevich, Sergey Nurk, Dmitry Antipov … (2012)

The lion's share of bacteria in various environments cannot be cloned in the laboratory and thus cannot be sequenced using existing technologies. A major goal of single-cell genomics is to complement gene-centric metagenomic data with whole-genome assemblies of uncultivated organisms. Assembly of single-cell data is challenging because of highly non-uniform read coverage as well as elevated levels of sequencing errors and chimeric reads. We describe SPAdes, a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler (specialized for single-cell data) and on popular assemblers Velvet and SoapDeNovo (for multicell data). SPAdes generates single-cell assemblies, providing information about genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. SPAdes is available online ( http://bioinf.spbau.ru/spades ). It is distributed as open source software.

0 comments Cited 7437 times – based on 0 reviews      Review now

Bookmark

Record: found
Abstract: found
Article: found

Is Open Access

NOVOPlasty: de novo assembly of organelle genomes from whole genome data

Nicolas Dierckxsens, Patrick Mardulyn, Guillaume Smits (2016)

Abstract The evolution in next-generation sequencing (NGS) technology has led to the development of many different assembly algorithms, but few of them focus on assembling the organelle genomes. These genomes are used in phylogenetic studies, food identification and are the most deposited eukaryotic genomes in GenBank. Producing organelle genome assembly from whole genome sequencing (WGS) data would be the most accurate and least laborious approach, but a tool specifically designed for this task is lacking. We developed a seed-and-extend algorithm that assembles organelle genomes from whole genome sequencing (WGS) data, starting from a related or distant single seed sequence. The algorithm has been tested on several new (Gonioctena intermedia and Avicennia marina) and public (Arabidopsis thaliana and Oryza sativa) whole genome Illumina data sets where it outperforms known assemblers in assembly accuracy and coverage. In our benchmark, NOVOPlasty assembled all tested circular genomes in less than 30 min with a maximum memory requirement of 16 GB and an accuracy over 99.99%. In conclusion, NOVOPlasty is the sole de novo assembler that provides a fast and straightforward extraction of the extranuclear genomes from WGS data in one circular high quality contig. The software is open source and can be downloaded at https://github.com/ndierckx/NOVOPlasty.

0 comments Cited 1378 times – based on 0 reviews      Review now

Bookmark

Record: found
Abstract: found
Article: found

Is Open Access

GetOrganelle: a fast and versatile toolkit for accurate de novo assembly of organelle genomes

Jian-Jun Jin, Wen-Bin Yu, Jun-Bo Yang … (2020)

GetOrganelle is a state-of-the-art toolkit to accurately assemble organelle genomes from whole genome sequencing data. It recruits organelle-associated reads using a modified “baiting and iterative mapping” approach, conducts de novo assembly, filters and disentangles the assembly graph, and produces all possible configurations of circular organelle genomes. For 50 published plant datasets, we are able to reassemble the circular plastomes from 47 datasets using GetOrganelle. GetOrganelle assemblies are more accurate than published and/or NOVOPlasty-reassembled plastomes as assessed by mapping. We also assemble complete mitochondrial genomes using GetOrganelle. GetOrganelle is freely released under a GPL-3 license (https://github.com/Kinggerm/GetOrganelle).

0 comments Cited 1369 times – based on 0 reviews      Review now

Bookmark

All references

Author and article information

Journal

Journal ID (nlm-ta): Curr Genomics

Journal ID (iso-abbrev): Curr Genomics

Journal ID (publisher-id): CG

Title: Current Genomics

Publisher: Bentham Science Publishers

ISSN (Print): 1389-2029

ISSN (Electronic): 1875-5488

Publication date (Electronic): 14 February 2023

Publication date (Print): 14 February 2023

Volume: 23

Issue: 6

Pages: 369-384

Affiliations

[1 ] deptDepartment of Rehabilitation Medicine, Sir Run Run Shaw Hospital , Zhejiang University School of Medicine , Hangzhou, , China;

[2 ] deptInstitute of Crop Science & Institute of Bioinformatics , Zhejiang University , Hangzhou, 310058 , China;

[3 ] CSIRO, Agriculture and Food , Canberra, , ACT 2601 , Australia

Author notes

[* ]Address correspondence to this author at the Department of Rehabilitation Medicine, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China; E-mail: zjdxsyfkfk@ 123456126.com

Article

Publisher ID: CG-23-369

DOI: 10.2174/1389202924666221201140603

PMC ID: 10173419

PubMed ID: 37920556

SO-VID: b809e70f-0947-4219-9710-c91cd1260f6f

License:

This is an open access article licensed under the terms of the Creative Commons Attribution-Non-Commercial 4.0 International Public License (CC BY-NC 4.0) ( https://creativecommons.org/licenses/by-nc/4.0/), which permits unrestricted, non-commercial use, distribution and reproduction in any medium, provided the work is properly cited.

History

Date received : 16 May 2022

Date revision received : 02 October 2022

Date accepted : 19 October 2022

Comments

Comment on this article

scite_

Smart Citations

Citing PublicationsSupportingMentioningContrasting

View Citations

See how this article has been cited at scite.ai

scite shows how a scientific paper has been cited by providing the context of the citation, a classification describing whether it supports, mentions, or contrasts the cited claim, and a label indicating in which section the citation was made.