The complete chloroplast genome of an economic and ecological plant, paper mulberry (Broussonetia kazinoki × Broussonetia papyifera)

Xu, Zhenggang; Yang, Guiyan; Meng, Dong; Wu, Liang; Zhang, Wan; Zhao, Yunlin

doi:10.1080/23802359.2017.1419088

Cited by 12 publications

(10 citation statements)

References 10 publications

(15 reference statements)

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“…Two genes ( ycf3 and clpP ) contained two introns. These two genes were similar to those in the Orpheus flower Haberlea rhodopensis and Broussonetia papyrifera (Ivanova et al, 2017; Xu et al, 2018). Unlike most angiosperm chloroplast genomes (Jin et al, 2014; Kong & Yang, 2015; Wang et al, 2016), among the 11 genes, four ( atpF , rpoC1 , ycf3 , clpP ) of which were located in the LSC region, two ( ndhA and trnI-GAU ) in the SSC region, other four ( rpl2 ×2, ndhB ×2) in the IR region, and one gene ( ycf1 ) was a trans-spliced gene with its start codon located in the SSC region, stop codon in the IRb region, and possibly missing 3′ end.…”

Section: Results and Analysissupporting

confidence: 58%

Determination of the evolutionary pressure onCamellia oleiferaon Hainan Island using the complete chloroplast genome sequence

Zhang

Zhao

Yang

et al. 2019

PeerJ

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Camellia oleifera is one of the four largest woody edible oil plants in the world with high ecological and medicinal values. Due to frequent interspecific hybridization, it was difficult to study its genetics and evolutionary history. This study used C. oleifera that was collected on Hainan Island to conduct our research. The unique island environment makes the quality of tea oil higher than that of other species grown in the mainland. Moreover, a long-term geographic isolation might affect gene structure. In order to better understand the molecular biology of this species, protect excellent germplasm resources, and promote the population genetics and phylogenetic studies of Camellia plants, high-throughput sequencing technology was used to obtain the chloroplast genome sequence of Hainan C. oleifera. The results showed that the whole chloroplast genome of C. oleifera in Hainan was 156,995 bp in length, with a typical quadripartite structure of a large single copy (LSC) region of 86,648 bp, a small single copy (SSC) region of 18,297 bp, and a pair of inverted repeats (IRs) of 26,025 bp. The whole genome encoded a total of 141 genes (115 different genes), including 88 protein-coding genes, 45 tRNA genes, and eight rRNA genes. Among these genes, nine genes contained one intron, two genes contained two introns, and four overlapping genes were also detected. The total GC content of Hainan C. oleifera’s chloroplast genome was 37.29%. The chloroplast genome structure characteristics of Hainan C. oleifera were compared with mainland C. oleifera and those of the other eight closely related Theaceae species; it was found that the contractions and expansions of the IR/LSC and IR/SSC regions affected the length of chloroplast genome. The chloroplast genome sequences of these Theaceae species were highly similar. A comparative analysis indicated that the Theaceae species were conserved in structure and evolution. A total of 51 simple sequence repeat (SSR) loci were detected in the chloroplast genome of Hainan C. oleifera, and all Camellia plants did not have pentanucleotide repeats, which could be used as a good marker in phylogenetic studies. We also detected seven long repeats, the base composition of all repeats was biased toward A/T, which was consistent with the codon bias. It was found that Hainan C. oleifera had a similar evolutionary relationship with C. crapnelliana, through the use of codons and phylogenetic analysis. This study can provide an effective genomic resource for the evolutionary history of Theaceae family.

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Section: Results and Analysissupporting

confidence: 58%

Determination of the evolutionary pressure onCamellia oleiferaon Hainan Island using the complete chloroplast genome sequence

Zhang

Zhao

Yang

et al. 2019

PeerJ

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“…And its maternal B. kazinoki has experienced controversy [15,54], therefore, it is necessary to compare ZJGS and its hybrid parent systematically. Unlike the previous study [36], the cp genome of ZJGS was analyzed in detail. Through comparison, it is found that the total length and total GC content of ZJGS cp genome sequence (160,903 bp and 35.74%, respectively) are closest to its maternal B. kazinoki (160,841 bp and 35.73%, respectively), while its paternal B. papyrifera is 160,239 bp and 35.83%, respectively.…”

Section: Discussionmentioning

confidence: 99%

“…Our research group rst reported the complete cp genome of ZJGS and the sequence was submitted to Genebank with the accession number of MF496038. The more experiment details can be got from the announcement [36]. At the same time, 12 Moraceae plants, including six Broussonetia species and six Morus species were selected to compare cp genomes structure with ZJGS.…”

Section: Comparative Analyses Of Cp Genomes Structurementioning

confidence: 99%

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The Chloroplast Genome Comparative Characteristic of Artificial Breeding Tree, a Case About Broussonetia Kazinoki × Broussonetia Papyifera

Wan

Yang

Zhao

et al. 2020

Preprint

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Background: Broussonetia kazinoki × Broussonetia papyifera (ZJGS) is a hybrid species, which has a very complicated hybrid origin. Its excellent characteristics make it both ecological benefits and economically valuable.Results: This study aimes to further understand ZJGS and Moraceae taxa through the ZJGS chloroplast (cp) genome structure and the comparative with 12 closely related Moraceae species, especially the cross parent B. kazinoki and B. papyrifera. The analyses show that ZJGS cp genome is 160,903 bp in length. Among the 13 Moraceae species, the cp genome length of seven Broussonetia species (ranges from 160,239 bp to 162,594 bp) is larger than that of six Morus species (ranges from 158,459 bp to 159,265 bp). However, the average GC content of Broussonetia species is lower than that of Morus species, which is 35.72% and 36.26%, respectively. Compared with Moraceae species, the ZJGS cp genome has a high degree of sequence similarity with B. kazinoki and B. monoica. In the comparison of repeated sequences, ZJGS and its maternal species B. kazinoki shows similar simple sequence repeats (SSRs) frequency. Among the 77 shared protein-coding genes (PCGs) in Moraceae species, the obvious positive selection of Ka/Ks ratios acted on petD and rpl16 genes of B. kazinoki and B. papyrifera, respectively, and the Ka/Ks ratio > 3. Phylogenetic analysis based on shared PCGs from 28 species shows that ZJGS is closely related to maternal B. kazinoki.Conclusions: These findings provide data support for the origin of ZJGS hybridization, and provide genomic resources for future ZJGS resource development and molecular breeding.

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“…In China, B. × kazinoki is highly valued not only for its fiber, but also as nonconventional forage, food additives, and traditional medicine, and its transcriptome (Xianjin et al, 2014) and chloroplast (cp) genome (Xu et al, 2018) has been studied.…”

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confidence: 99%

Test of the hybrid origin of Broussonetia × kazinoki (Moraceae) in Korea using molecular markers

Won

2019

Korean J. Pl. Taxon

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Broussonetia × kazinoki Siebold has long been utilized as a major component in the manufacturing of Korean traditional paper, hanji, and has been suggested as a hybrid species of B. papyrifera and B. monoica. By applying three molecular markers, chloroplast (cp) ndhF-rpl32 IGS, a nuclear ribosomal internal transcribed spacer, and the TOPO6 gene, the hybrid origin of B. × kazinoki is tested. As a result, B. × kazinoki in Korea is demonstrated to be a hybrid of B. monoica × B. papyrifera, most likely formed naturally in Korea. The cp haplotypes detected provided information about the origins and genetic diversity of the maternal lineage B. monoica and paternal lineage B. papyrifera. The two nuclear markers were supplemented to each other, leading to the discovery of introgression in Broussonetia.

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The complete chloroplast genome of an economic and ecological plant, paper mulberry (Broussonetia kazinoki × Broussonetia papyifera)

Abstract: (2018) The complete chloroplast genome of an economic and ecological plant, paper mulberry (Broussonetiakazinoki × Broussonetiapapyifera), Mitochondrial DNA Part B, 3:1, 28-29,

Cited by 12 publications

References 10 publications

Determination of the evolutionary pressure onCamellia oleiferaon Hainan Island using the complete chloroplast genome sequence

Determination of the evolutionary pressure onCamellia oleiferaon Hainan Island using the complete chloroplast genome sequence

The Chloroplast Genome Comparative Characteristic of Artificial Breeding Tree, a Case About Broussonetia Kazinoki × Broussonetia Papyifera

Test of the hybrid origin of <i>Broussonetia</i> × <i>kazinoki</i> (Moraceae) in Korea using molecular markers

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