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

Jin, Jianjun; Yu, Wen Bin; Yang, Jun; Song, Yu; dePamphilis, Claude W.; Yi, Ting Shuang; D, Li

doi:10.1186/s13059-020-02154-5

Cited by 1,714 publications

(976 citation statements)

References 71 publications

(88 reference statements)

Supporting

Mentioning

975

Contrasting

Order By: Relevance

“…clean reads from the 50 newly sequenced species, with the mean base coverage ranging from 110× ( Congea tomentosa Roxb.) to 3104× ( Lamium amplexicaule L.) estimated by the GetOrganelle pipeline [ 68 ]. Since we failed to assemble the complete plastome of Callicarpa americana L., the average base coverage for this species is unavailable (noted as “NA” in Table 1 ).…”

Section: Resultsmentioning

confidence: 99%

“…Quality control of raw sequence reads was carried out using FastQC toolkit [ 210 ] ( http://www.bioinformatics.babraham.ac.uk/projects/fastqc ) with the parameter set as Q ≥ 25 to acquire high-quality clean reads. The de novo assembling of the plastome was implemented in the GetOrganelle pipeline [ 68 ], in which plastome reads were extracted from total genomic reads and then SPAdes v.3.10 [ 211 ] was used for assembly. For those plastomes we can acquire complete sequences, genome annotation was performed using Geneious v.11.0.3 [ 212 ], and the start and stop codons were manually adjusted by comparison with the plastome of Salvia miltiorrhiza Bunge [ 213 ] (HF586694).…”

Section: Methodsmentioning

confidence: 99%

See 1 more Smart Citation

An updated tribal classification of Lamiaceae based on plastome phylogenomics

et al. 2021

View full text Add to dashboard Cite

Background A robust molecular phylogeny is fundamental for developing a stable classification and providing a solid framework to understand patterns of diversification, historical biogeography, and character evolution. As the sixth largest angiosperm family, Lamiaceae, or the mint family, consitutes a major source of aromatic oil, wood, ornamentals, and culinary and medicinal herbs, making it an exceptionally important group ecologically, ethnobotanically, and floristically. The lack of a reliable phylogenetic framework for this family has thus far hindered broad-scale biogeographic studies and our comprehension of diversification. Although significant progress has been made towards clarifying Lamiaceae relationships during the past three decades, the resolution of a phylogenetic backbone at the tribal level has remained one of the greatest challenges due to limited availability of genetic data. Results We performed phylogenetic analyses of Lamiaceae to infer relationships at the tribal level using 79 protein-coding plastid genes from 175 accessions representing 170 taxa, 79 genera, and all 12 subfamilies. Both maximum likelihood and Bayesian analyses yielded a more robust phylogenetic hypothesis relative to previous studies and supported the monophyly of all 12 subfamilies, and a classification for 22 tribes, three of which are newly recognized in this study. As a consequence, we propose an updated phylogenetically informed tribal classification for Lamiaceae that is supplemented with a detailed summary of taxonomic history, generic and species diversity, morphology, synapomorphies, and distribution for each subfamily and tribe. Conclusions Increased taxon sampling conjoined with phylogenetic analyses based on plastome sequences has provided robust support at both deep and shallow nodes and offers new insights into the phylogenetic relationships among tribes and subfamilies of Lamiaceae. This robust phylogenetic backbone of Lamiaceae will serve as a framework for future studies on mint classification, biogeography, character evolution, and diversification. Graphical abstract

show abstract

Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

An updated tribal classification of Lamiaceae based on plastome phylogenomics

et al. 2021

View full text Add to dashboard Cite

show abstract

“…Genome assembly was performed using GetOrganelle v1.6.2d with default parameters (Jin et al, 2020). The GetOrganelle first filtered plastid-like reads, conducted the de novo assembly, purified the assembly, and finally generated the complete plastid genomes (Camacho et al, 2009;Bankevich et al, 2012;Langmead and Salzberg, 2012).…”

Section: Genome Assembly and Genome Annotationmentioning

confidence: 99%

Initial Complete Chloroplast Genomes of Alchemilla (Rosaceae): Comparative Analysis and Phylogenetic Relationships

et al. 2020

View full text Add to dashboard Cite

The genus Alchemilla L., known for its medicinal and ornamental value, is widely distributed in the Holarctic regions with a few species found in Asia and Africa. Delimitation of species within Alchemilla is difficult due to hybridization, autonomous apomixes, and polyploidy, necessitating efficient molecular-based characterization. Herein, we report the initial complete chloroplast (cp) genomes of Alchemilla. The cp genomes of two African (Afromilla) species Alchemilla pedata and Alchemilla argyrophylla were sequenced, and phylogenetic and comparative analyses were conducted in the family Rosaceae. The cp genomes mapped a typical circular quadripartite structure of lengths 152,438 and 152,427 base pairs (bp) in A. pedata and A. argyrophylla, respectively. Alchemilla cp genomes were composed of a pair of inverted repeat regions (IRa/IRb) of length 25,923 and 25,915 bp, separating the small single copy (SSC) region of 17,980 and 17,981 bp and a large single copy (LSC) region of 82,612 and 82,616 bp in A. pedata and A. argyrophylla, respectively. The cp genomes encoded 114 unique genes including 88 protein-coding genes, 37 transfer RNA (tRNA) genes, and 4 ribosomal RNA (rRNA) genes. Additionally, 88 and 95 simple sequence repeats (SSRs) and 37 and 40 tandem repeats were identified in A. pedata and A. argyrophylla, respectively. Significantly, the loss of group II intron in atpF gene in Alchemilla species was detected. Phylogenetic analysis based on 26 whole cp genome sequences and 78 protein-coding gene sequences of 27 Rosaceae species revealed a monophyletic clustering of Alchemilla nested within subfamily Rosoideae. Based on a protein-coding region, negative selective pressure (Ka/Ks < 1) was detected with an average Ka/Ks value of 0.1322 in A. argyrophylla and 0.1418 in A. pedata. The availability of complete cp genome in the genus Alchemilla will contribute to species delineation and further phylogenetic and evolutionary studies in the family Rosaceae.

show abstract

“…The 150 bp pair-end reads were generated by Illumina Hi-Seq 2500 using 500 bp insert size library. Around 7.25 Gb clean data with 20,455,554 reads were de novo assembled using GetOrganelle toolkit (Jin et al 2020 ). The plastome was annotated using GeSeq (Tillich et al.…”

mentioning

confidence: 99%

Complete plastome sequence of Aspidopterys obcordata (Malpighiaceae), a traditional Dai medicinal plant from Xishuangbanna, Yunnan, China

Gong

Jiang

Zhang

et al. 2020

Mitochondrial DNA Part B

Self Cite

View full text Add to dashboard Cite

We reported the first complete plastid genome of Aspidopterys (Malpighiaceae) in this study. The complete plastome of Aspidopterys obcordata is 160,453 bp in length with a base composition of A (31.4%), G (18.5%), C (18.2%), and T (32.0%). Structurally, the genome contains two short inverted repeats (26,905 bp for each), which are separated by a large single copy region (88,491 bp) and a small single copy region (18,152 bp). The plastome contained 113 unique genes, including 79 protein-coding genes, 30 transfer RNAs, and 4 ribosomal RNAs. Phylogenetic analyses showed that A. obcordata was sister to Bunchosia argentea in the monophyletic Malpighiaceae. This study provided a high-quality plastome sequence for future studies in Aspidopterys, as well as Malpighiaceae.

show abstract

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

Cited by 1,714 publications

References 71 publications

An updated tribal classification of Lamiaceae based on plastome phylogenomics

An updated tribal classification of Lamiaceae based on plastome phylogenomics

Initial Complete Chloroplast Genomes of Alchemilla (Rosaceae): Comparative Analysis and Phylogenetic Relationships

Complete plastome sequence of Aspidopterys obcordata (Malpighiaceae), a traditional Dai medicinal plant from Xishuangbanna, Yunnan, China

Contact Info

Product

Resources

About