Characterization of the chloroplast genome of Erythrophleum fordii (Fabaceae)

Huang, Songyi; Wu, Wei; Chen, Zheng; Zhu, Qiaoming; Ng, Wei Lun; Zhou, Qiujie

doi:10.1007/s12686-018-0990-7

Cited by 4 publications

(4 citation statements)

References 6 publications

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“…(Dugas et al, 2015; GenBank accession KT428297), and Erythrophleum fordii Oliv. (Huang et al, 2018; GenBank accession MG644609), assembled chloroplast sequences for all accessions, and extracted the coding sequences gene by gene using a custom Python script with BLAST searches, confirming that sequence data for the chloroplast genome can be efficiently extracted and analyzed from off-target reads in hybrid capture experiments as shown by Weitemier et al (2014). The clpP gene was discarded because it shows accelerated evolution (Williams et al, 2015;Dugas et al, 2015) and yields a tree that strongly conflicts with those inferred using the other chloroplast genes.…”

Section: Assembly Of Sequence Data and Aligned Matricesmentioning

confidence: 91%

Hybrid capture of 964 nuclear genes resolves evolutionary relationships in the mimosoid legumes and reveals the polytomous origins of a large pantropical radiation

Koenen

Kidner

Souza

et al. 2020

American J of Botany

217

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The field of molecular plant phylogenetics has had tremendous impacts on botanical studies and taxonomic classification, macroevolution and biogeography, ever since the pioneering studies of Chase et al. (1993) based on DNA sequence data. While those early studies used just a single locus, the plastid gene rbcL, modern studies often employ hundreds to several thousands of genes to infer phylogenetic relationships (e.g.,

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Section: Assembly Of Sequence Data and Aligned Matricesmentioning

confidence: 91%

Hybrid capture of 964 nuclear genes resolves evolutionary relationships in the mimosoid legumes and reveals the polytomous origins of a large pantropical radiation

Koenen

Kidner

Souza

et al. 2020

American J of Botany

217

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“…Erythrophleum fordii Oliv. is the only species of this genus distributed in China [ 10 ]. Except for China, E. fordii is also found in Vietnam.…”

Section: Objectivementioning

confidence: 99%

“…Some triterpenoids in E. fordii are species specific [ 1 ]. Due to its high economic value, it has been overexploited in history in both China and Vietnam, making it endangered in the wild [ 3 , 10 , 11 ]. For endangered species, contiguous, accurate and annotated genome assemblies greatly enhance their conservation [ 15 ].…”

Section: Objectivementioning

confidence: 99%

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Genome assembly of Erythrophleum Fordii, a special “ironwood” tree in China

Wen,

Lian,

Peng

et al. 2023

BMC Genom Data

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ObjectivesErythrophleumis a genus in the Fabaceae family. The genus contains only about 10 species, and it is best known for its hardwood and medical properties worldwide.Erythrophleum fordiiOliv. is the only species of this genus distributed in China. It has superior wood and can be used in folk medicine, which leads to its overexploitation in the wild. For its effective conservation and elucidation of the distinctive genetic traits of wood formation and medical components, we present its first genome assembly.Data descriptionThis work generated ~ 160.8 Gb raw Nanopore whole genome sequencing (WGS) long reads, ~ 126.0 Gb raw MGI WGS short reads and ~ 29.0 Gb raw RNA-seq reads usingE. fordiileaf tissues. Thede novoassembly contained 864,825,911 bp in theE. fordiigenome, with 59 contigs and a contig N50 of 30,830,834 bp. Benchmarking Universal Single-Copy Orthologs (BUSCO) revealed 98.7% completeness of the assembly. The assembly contained 471,006,885 bp (54.4%) repetitive sequences and 28,761 genes that coded for 33,803 proteins. The protein sequences were functionally annotated against multiple databases, facilitating comparative genomic analysis.

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