Uncovering dynamic evolution in the plastid genome of seven Ligusticum species provides insights into species discrimination and phylogenetic implications

AbstractLigusticum L., one of the largest members in Apiaceae, encompasses medicinally important plants, the taxonomic statuses of which have been proved to be difficult to resolve. In the current study, the complete chloroplast genomes of seven crucial plants of the best-known herbs in Ligusticum were presented. The seven genomes ranged from 148,275 to 148,564 bp in length with a highly conserved gene content, gene order and genomic arrangement. A shared dramatic decrease in genome size resulted from a lineage-specific inverted repeat (IR) contraction, which could potentially be a promising diagnostic character for taxonomic investigation of Ligusticum, was discovered, without affecting the synonymous rate. Although a higher variability was uncovered in hotspot divergence regions that were unevenly distributed across the chloroplast genome, a concatenated strategy for rapid species identification was proposed because separate fragments inadequately provided variation for fine resolution. Phylogenetic inference using plastid genome-scale data produced a concordant topology receiving a robust support value, which revealed that L. chuanxiong had a closer relationship with L. jeholense than L. sinense, and L. sinense cv. Fuxiong had a closer relationship to L. sinense than L. chuanxiong, for the first time. Our results not only furnish concrete evidence for clarifying Ligusticum taxonomy but also provide a solid foundation for further pharmaphylogenetic investigation.

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Comparative Chloroplast Genomics of Litsea Lam. (Lauraceae) and Its Phylogenetic Implications

Forests ◽

10.3390/f12060744 ◽

2021 ◽

Vol 12 (6) ◽

pp. 744

Author(s):

Yunyan Zhang ◽

Yongjing Tian ◽

David Y. P. Tng ◽

Jingbo Zhou ◽

Yuntian Zhang ◽

...

Keyword(s):

Chloroplast Genome ◽

Phylogenetic Analyses ◽

Eastern China ◽

Chloroplast Microsatellites ◽

Endangered Tree ◽

Protein Coding ◽

Intergenic Spacers ◽

Chloroplast Genomes ◽

Phylogenetic Implications ◽

Chloroplast Genome Sequence

Litsea Lam. is an ecological and economic important genus of the “core Lauraceae” group in the Lauraceae. The few studies to date on the comparative chloroplast genomics and phylogenomics of Litsea have been conducted as part of other studies on the Lauraceae. Here, we sequenced the whole chloroplast genome sequence of Litsea auriculata, an endangered tree endemic to eastern China, and compared this with previously published chloroplast genome sequences of 11 other Litsea species. The chloroplast genomes of the 12 Litsea species ranged from 152,132 (L. szemaois) to 154,011 bp (L. garrettii) and exhibited a typical quadripartite structure with conserved genome arrangement and content, with length variations in the inverted repeat regions (IRs). No codon usage preferences were detected within the 30 codons used in the chloroplast genomes, indicating a conserved evolution model for the genus. Ten intergenic spacers (psbE–petL, trnH–psbA, petA–psbJ, ndhF–rpl32, ycf4–cemA, rpl32–trnL, ndhG–ndhI, psbC–trnS, trnE–trnT, and psbM–trnD) and five protein coding genes (ndhD, matK, ccsA, ycf1, and ndhF) were identified as divergence hotspot regions and DNA barcodes of Litsea species. In total, 876 chloroplast microsatellites were located within the 12 chloroplast genomes. Phylogenetic analyses conducted using the 51 additional complete chloroplast genomes of “core Lauraceae” species demonstrated that the 12 Litsea species grouped into four sub-clades within the Laurus-Neolitsea clade, and that Litsea is polyphyletic and closely related to the genera Lindera and Laurus. Our phylogeny strongly supported the monophyly of the following three clades (Laurus–Neolitsea, Cinnamomum–Ocotea, and Machilus–Persea) among the above investigated “core Lauraceae” species. Overall, our study highlighted the taxonomic utility of chloroplast genomes in Litsea, and the genetic markers identified here will facilitate future studies on the evolution, conservation, population genetics, and phylogeography of L. auriculata and other Litsea species.

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Efficient TALEN-mediated gene knockin at the bovine Y chromosome and generation of a sex-reversal bovine

Cellular and Molecular Life Sciences ◽

10.1007/s00018-021-03855-1 ◽

2021 ◽

Author(s):

Ming Wang ◽

ZhaoLin Sun ◽

Fangrong Ding ◽

Haiping Wang ◽

Ling Li ◽

...

Keyword(s):

Y Chromosome ◽

Nuclear Transfer ◽

Sex Reversal ◽

Practical Application ◽

Transcription Activator ◽

New Methods ◽

Fetal Fibroblasts ◽

Male Phenotype ◽

Solid Foundation ◽

First Time

AbstractFunctional elucidation of bovine Y-chromosome genes requires available genome editing technologies. Meanwhile, it has yet to be proven whether the bovine Sry gene is the main or single factor involved in the development of the male phenotype in bovine. Here, we efficiently knocked out four Y-linked genes (Sry, ZFY, DDX3Y, and EIF2S3Y) in bovine fetal fibroblasts (BFFs) with transcription activator-like effector nucleases (TALENs) individually. Furthermore, we used TALEN-mediated gene knockin at the Sry gene and generated a sex-reversal bovine by somatic cell nuclear transfer (SCNT). The resulting bovine had only one ovary and was sterile. We demonstrate, for the first time, that the Sry gene is an important sex-determining gene in bovine. Our method lays a solid foundation for detecting the biology of the bovine Y chromosome, as it may provide an alternative biological model system for the study of mammalian sex determination, and new methods for the practical application in agricultural, especially for sex predetermination.

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Comparison among the chloroplast genomes of five species of Chamaerhodos (Rosaceae: Potentilleae): phylogenetic implications

Nordic Journal of Botany ◽

10.1111/njb.03121 ◽

2021 ◽

Vol 39 (6) ◽

Author(s):

Qin‐Qin Li ◽

Yan Yu ◽

Zhi‐Ping Zhang ◽

Jun Wen

Keyword(s):

Chloroplast Genomes ◽

Phylogenetic Implications

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European Mail Armour

10.5117/9789463721264 ◽

2021 ◽

Author(s):

Martijn A. Wijnhoven

Keyword(s):

Early Modern ◽

Middle Ages ◽

Iron Age ◽

Early Modern Period ◽

Vital Role ◽

Military Technology ◽

Roman Army ◽

Solid Foundation ◽

First Time

Mail armour (commonly mislabelled 'chainmail') was used for more than two millennia on the battlefield. After its invention in the Iron Age, mail rapidly spread all over Europe and beyond. The Roman army, keen on new military technology, soon adopted mail armour and used it successfully for centuries. Its history did not stop there and mail played a vital role in warfare during the Middle Ages up to the Early Modern Period. Given its long history, one would think mail is a well-documented material, but that is not the case. For the first time, this books lays a solid foundation for the understanding of mail armour and its context through time. It applies a long-term multi-dimensional approach to extract a wealth of as yet untapped information from archaeological, iconographic and written sources. This is complemented with technical insights on the mail maker’s chaîne opératoire.

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Filling missing links in albuneid crab distributions (superfamily Hippoidea) in the Bay of Bengal, eastern Indian Ocean

Crustaceana ◽

10.1163/15685403-00003846 ◽

2018 ◽

Vol 91 (12) ◽

pp. 1495-1504 ◽

Cited By ~ 2

Author(s):

Rajan Kumar ◽

Shikha Rahangdale ◽

Subal Kumar Roul

Keyword(s):

Indian Ocean ◽

Bay Of Bengal ◽

Morphological Characters ◽

Eastern Indian Ocean ◽

Species Discrimination ◽

Gulf Of Mannar ◽

Fishing Gear ◽

Morphometric Characters ◽

First Time

Abstract Albuneid crabs are specialized and active sand-burrowing organisms. Despite their substantial diversity, their ability to avoid fishing gear leads to “under collection” and a discontinuous record of distribution. The present study documents the first distributional record of Albunea occulta Boyko, 2002 from the Bay of Bengal, eastern Indian Ocean. Albunea thurstoni Henderson, 1893 is also recorded for the first time from the area, i.e., from the Gulf of Mannar, southwestern Bay of Bengal. This study further reports variation in morphological characters, especially in the carapace grooves (CG) from previous records and across specimens from different regions. Morphometric characters were found useful in species discrimination, which is explained as well.

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Whole Chloroplast Genomes reveals the uniqueness of Bolivian native cacao (Theobroma cacao) from the northern part of Bolivia

10.1101/2021.04.16.440153 ◽

2021 ◽

Author(s):

Marcia Gumiel ◽

Oscar M Rollano-Penaloza ◽

Carmelo Peralta-Rivero ◽

Leslie Tejeda ◽

Valeria D. Palma Encinas ◽

...

Keyword(s):

Phylogenetic Analysis ◽

Next Generation Sequencing ◽

Theobroma Cacao ◽

Phylogenetic Trees ◽

Plastid Genome ◽

Next Generation ◽

Center Of Origin ◽

Chloroplast Genomes ◽

Geographical Locations ◽

Generation Sequencing

We report the complete chloroplast sequences of two varieties of Theobroma cacao collected in the Bolivian Amazonia using Next-Generation Sequencing. Comparisons made between these two chloroplast genomes and the Belizean reference plastid genome identified 19 and 22 nucleotide variants. The phylogenetic analysis reported three main T. cacao clades belonging to the Forastero, Criollo and Trinitario groups. The Bolivian Native Cacao varieties were located inside the Trinitario group forming their unique branch. The Bolivian Native Cacao branch reveals a possible new subpopulation different from the well-characterized T. cacao subpopulations. The phylogenetic trees showed that the relationships among the T. cacao varieties were consistent with their geographical locations placing the Cacao Center of Origin in Western Amazon. The data presented here will contribute to the usage of ultrabarcoding to distinguish different T. cacao varieties and to identify native cacaos from introduced cacaos. Thus helping in the conservation of local native varieties of T. cacao.

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UPLC-MS/MS Identification and Quantification of Withanolides from Six Parts of the Medicinal Plant Datura Metel L.

Molecules ◽

10.3390/molecules25061260 ◽

2020 ◽

Vol 25 (6) ◽

pp. 1260

Author(s):

Shi Hui Yang ◽

Yan Liu ◽

Qi Wang ◽

Yan Ping Sun ◽

Wei Guan ◽

...

Keyword(s):

Total Content ◽

Qualitative And Quantitative Analysis ◽

Plant Parts ◽

Datura Metel ◽

Value Range ◽

Solid Foundation ◽

G Value ◽

Production Areas ◽

First Time

Withanolides from six parts (flower, leaf, stem, root, seed, and peel) of Datura metel L. (D metel L.) obtained from ten production areas in China were identified and quantified by UPLC-MS/MS. A total of 85 withanolides were characterized for the first time using the UPLC-Q-TOF-MS/MS system. Additionally, a simultaneous, rapid and accurate measurement method was developed for the determination of 22 bioactive withanolides from ten production areas with the UPLC-Q-TRAP-MS/MS system. The results show the total withanolide content is highest in the leaves (155640.0 ng/g) and lowest in the roots (14839.8 ng/g). Compared with other production areas, the total content of plants from Dujiangyan was the highest at 82013.9 ng/g (value range of ten areas: 82013.9–42278.5 ng/g). The results also show significant differences in the distribution of withanolides in the different plant parts, as well as across different production areas. This is a breakthrough report providing a simultaneous qualitative and quantitative analysis of 22 withanolides in D. metel L. It could be the basis for the more rational use of various parts of D. metel L., and the expansion of medicinal resources. This work also lays a solid foundation for research on the quality control of D. metel L.

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The mosaic of ancestral karyotype blocks in the Sinapis alba L. genome

Genome ◽

10.1139/g10-097 ◽

2011 ◽

Vol 54 (1) ◽

pp. 33-41 ◽

Cited By ~ 11

Author(s):

Matthew N. Nelson ◽

Isobel A.P. Parkin ◽

Derek J. Lydiate

Keyword(s):

Genetic Research ◽

Brassica Species ◽

Sinapis Alba ◽

Ancestral Karyotype ◽

Crop Species ◽

B Genome ◽

A Genome ◽

The Rich ◽

Conserved Gene ◽

First Time

The organisation of the Sinapis alba genome, comprising 12 linkage groups (n = 12), was compared with the Brassicaceae ancestral karyotype (AK) genomic blocks previously described in other crucifer species. Most of the S. alba genome falls into conserved triplicated genomic blocks that closely match the AK-defined genomic blocks found in other crucifer species including the A, B, and C genomes of closely related Brassica species. In one instance, an S. alba linkage group (S05) was completely collinear with one AK chromosome (AK1), the first time this has been observed in a member of the Brassiceae tribe. However, as observed for other members of the Brassiceae tribe, ancestral genomic blocks were fragmented in the S. alba genome, supporting previously reported comparative chromosome painting describing rearrangements of the AK karyotype prior to the divergence of the Brassiceae from other crucifers. The presented data also refute previous phylogenetic reports that suggest S. alba was more closely related to Brassica nigra (B genome) than to B. rapa (A genome) and B. oleracea (C genome). A comparison of the S. alba and Arabidopsis thaliana genomes revealed many regions of conserved gene order, which will facilitate access to the rich genomic resources available in the model species A. thaliana for genetic research in the less well-resourced crop species S. alba.

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Characterization and Comparative Analysis of Two Rheum Complete Chloroplast Genomes

BioMed Research International ◽

10.1155/2020/6490164 ◽

2020 ◽

Vol 2020 ◽

pp. 1-11

Author(s):

Kaihui Zhao ◽

Lianqiang Li ◽

Yazhou Lu ◽

Junbo Yang ◽

Zhirong Zhang ◽

...

Keyword(s):

Economic Value ◽

Evolutionary Analysis ◽

Phylogenetic Studies ◽

Chloroplast Genomes ◽

Circular Structure ◽

Mutational Hotspots ◽

Single Clade ◽

History Of ◽

History Of Use ◽

Genome Scale

Rheum species present a significant economic value. Traditional Chinese medicine rhubarb is an important medicinal material in China. It has a long history of use, with a record of use as early as two thousand years ago. Here, we determined the complete chloroplast genome sequences of Rheum nobile and Rheum acuminatum and comprehensively compared them to two other available Rheum cp genomes at the genome scale. The results revealed cp genomes ranging in size from 159,051 to 161,707 bp with a similar typical quadripartite and circular structure. The genome organization, gene numbers, gene order, and GC contents of these four Rheum cp genomes were similar to those of many angiosperm cp genomes. Repeats and microsatellites were detected in the R. nobile and R. acuminatum cp genomes. The Mauve alignment revealed that there were no rearrangements in the cp genomes of the four Rheum species. Thirteen mutational hotspots for genome divergence were identified, which could be utilized as potential markers for phylogenetic studies and the identification of Rheum species. The phylogenetic relationships of the four species showed that the members of Rheum cluster into a single clade, indicating their close relationships. Our study provides valuable information for the taxonomic, phylogenetic, and evolutionary analysis of Rheum.

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