Peer Review #2 of "Phylogenetic analysis of Fritillaria cirrhosa D. Don and its closely related species based on complete chloroplast genomes (v0.2)"

Fritillaria cirrhosa D. Don, whose bulb is used in a well-known traditional Chinese medicine to relieve cough and eliminate phlegm, is one of the most important medicinal plants of Fritillaria L. The species is widely distributed among the alpine regions in southwestern China and possesses complex morphological variations in different distributions. A series of newly related species were reported, based on obscure morphological differences. As a result, F. cirrhosa and its closely related species constitute a taxonomically complex group. However, it is difficult to accurately identify these species and reveal their phylogenetic relationships using traditional taxonomy. Molecular markers and gene fragments have been adopted but they are not able to afford sufficient phylogenetic resolution in the genus. Here, we report the complete chloroplast genome sequences of F. cirrhosa and its closely related species using next generation sequencing (NGS) technology. Eight plastid genomes ranged from 151,058 bp to 152,064 bp in length and consisted of 115 genes. Gene content, gene order, GC content, and IR/SC boundary structures were highly similar among these genomes. SSRs and five large repeat sequences were identified and the total number of them ranged from 73 to 79 and 63 to 75, respectively. Six highly divergent regions were successfully identified that could be used as potential genetic markers of Fritillaria. Phylogenetic analyses revealed that eight Fritillaria species were clustered into three clades with strong supports and F. cirrhosa was closely related to F. przewalskii and F. sinica. Overall, this study indicated that the complete chloroplast genome sequence was an efficient tool for identifying species in taxonomically complex groups and exploring their phylogenetic relationships.

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Species delimitation of colour polymorphic Cladophorus (Coleoptera: Lycidae) from New Guinea

Zootaxa ◽

10.11646/zootaxa.4320.3.6 ◽

2017 ◽

Vol 4320 (3) ◽

pp. 505 ◽

Cited By ~ 4

Author(s):

ROMANA KALOUSOVA ◽

LADISLAV BOCAK

Keyword(s):

Phylogenetic Analysis ◽

Mitochondrial Dna ◽

Related Species ◽

Species Delimitation ◽

Morphological Differentiation ◽

Morphological Characters ◽

Molecular Data ◽

Closely Related Species ◽

Dna Fragment ◽

Colour Patterns

Cladophorus Guérin-Méneville, 1830 are endemic Papuan net-winged beetles which take part in highly diverse Müllerian mimicry rings. Available specimens were sequenced for cox1–tRNA-Leu–cox2 mitochondrial DNA fragment and the species delimitations were based on the genetic distance, phylogenetic analysis, and morphology. Three earlier described species were identified in the recently collected material and further 10 species are described: C. pallescens sp. nov., C. bicolor sp. nov., C. craterensis sp. nov., C. motykai sp. nov., C. mindikensis sp. nov., C. kailakiensis sp. nov., C. manokwarensis sp. nov., C. haiaensis sp. nov., C. humeralis sp. nov., and C. boceki sp. nov. DNA-based identifications provided some ambiguous results and closely related species could not be robustly delimited using solely molecular data. Additionally, the species limits were based on clearly defined morphological characters and the morphological differentiation was found unlinked from the genetic divergence. Colour patterns cannot be used for identification because all species available in more specimens were polymorphic and followed various local co-mimics. The Papuan fauna of Cladophorus is very diverse and the closely related species regularly occur in limited regions. Differentiation within restricted ranges is therefore considered as the main speciation mode.

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Bryobilimbia, a new generic name for Lecidea hypnorum and closely related species

The Lichenologist ◽

10.1017/s0024282913000625 ◽

2014 ◽

Vol 46 (1) ◽

pp. 25-37 ◽

Cited By ~ 13

Author(s):

Alan M. FRYDAY ◽

Christian PRINTZEN ◽

Stefan EKMAN

Keyword(s):

Phylogenetic Analysis ◽

Related Species ◽

New Combinations ◽

Closely Related Species

AbstractThe new generic name Bryobilimbia is proposed for Lecidea hypnorum and the closely related taxa Lecidea ahlesii var. ahlesii, L. ahlesii var. nemoralis, L. diapensiae, L. sanguineoatra and Mycobilimbia australis. A phylogenetic analysis based on five genes shows that Lecidea berengeriana does not belong to this group but is more closely related to Romjularia. Both groups of species have been included in Mycobilimbia by some authors but are instead shown to be most closely related to a group of genera (including Clauzadea, Farnoldia, Lecidoma and Romjularia) that do not belong to Lecideaceae s. str. A neotype is selected for Lichen sanguineoater Wulfen and the new combinations Bryobilimbia ahlesii var. ahlesii, B. ahlesii var. nemoralis, B. australis, B. diapensiae, B. hypnorum and B. sanguineoatra are proposed. A lectotype is also selected for L. templetonii Taylor.

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Evolutionary insights into Mariner-like elements in Apis species

10.1101/2020.04.15.035063 ◽

2020 ◽

Author(s):

Kakeru Yokoi ◽

Kiyoshi Kimura ◽

Hidemasa Bono

Keyword(s):

Phylogenetic Analysis ◽

Transposable Element ◽

Related Species ◽

Horizontal Transfer ◽

The Other ◽

Closely Related Species ◽

Sequences Analysis ◽

Almost All

AbstractBackgroundMariner and mariner-like elements (MLEs) are distributed in various species and their sequences are highly diverse. In previous reports, a few transposable element in the genomes of Apis species mainly consist of mariner and MLE. For further insight of Apis MLEs, detailed classifications of Apis MLE and sequences analysis of long MLEs, which may potentially encode the transposase, are needed.ResultsMuch more MLEs were detected in A. mellifera genome compared to other Apis species genomes. They were classified into 31 Drosophila MLE classes. In this classification, almost all of MLEs were classified into the three classes belonging to mellifera subfamilies, suggesting that Apis MLEs which exist thorough Apis species derived from single MLE belonging to mellifera subfamily. Phylogenetic analysis using MLEs in the three classes showed that there two types of clusters, of which one consist of multiple Apis species MLEs, and others of only A. mellifera MLEs. Long MLEs analysis showed that only one long MLE encoding complete transposase was found in all Apis genome except for A. mellifera genome, and the MLE and multiple MLEs similar to it were found in A. mellifera genome. The analysis also showed that other several long MLEs encoding complete transposase were found only in A. mellifera genome.ConclusionsAlmost all of Apis MLEs are mellifera subfamilies. Of these MLEs, one types of them settled in Apis species and burst in A. mellifera genome. The other one of MLEs invaded into A. mellifera genome by horizontal transfer and exploded in A. mellifera genome. This is the first example of the finer aspects of MLE evolution among closely related species.

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Phylogenetic analysis of genomic islands in closely-related species belonging to Sinorhizobium sp.

Abstract book of the 2nd International Scientific Conference "Plants and Microbes: the Future of Biotechnology" PLAMIC2020 ◽

10.28983/plamic2020.273 ◽

2020 ◽

Author(s):

M. E. Vladimirova ◽

V. S. Muntyan ◽

A. S. Saksaganskaya ◽

B. V. Simarov ◽

M. L. Roumiantseva

Keyword(s):

Phylogenetic Analysis ◽

Gene Transfer ◽

Horizontal Gene Transfer ◽

Related Species ◽

Genomic Islands ◽

Closely Related Species ◽

Homologous Sequences

Genomic islands of closely related S. meliloti and S. medicae species were evaluated and homologous sequences were identified; it has been suggested that horizontal gene transfer occurs at homologous tRNA sites.

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New records of two Lutjanus species (Teleostei: Perciformes: Lutjanidae) with re-description of six lutjanids from Saint Martin’s Island of the Bay of Bengal, Bangladesh

Bangladesh Journal of Zoology ◽

10.3329/bjz.v46i2.39056 ◽

2018 ◽

Vol 46 (2) ◽

pp. 239-253 ◽

Cited By ~ 1

Author(s):

Shilpi Saha ◽

Sanjay Chakraborty ◽

Subrina Sehrin ◽

Abdullah Al Masud ◽

Kazi Ahsan Habib ◽

...

Keyword(s):

Phylogenetic Analysis ◽

Bay Of Bengal ◽

Related Species ◽

Genetic Divergence ◽

New Records ◽

Morphological Differentiation ◽

Morphological Characters ◽

Mitochondrial Cytochrome ◽

Closely Related Species ◽

Mitochondrial Cytochrome Oxidase

Investigations on Snapper fish of the genus Lutjanus were conducted from October 2015 to April 2016 in the coral ecosystem of St. Martin’s Island, Bangladesh. Twenty one individuals of 8 species of Lutjanus were collected from local fishermen. Both morphological characters and DNA barcoding approach by mitochondrial cytochrome oxidase I subunit (COI) were used to confirm the identification of all species. Present study recorded the first national occurrence of two reef associated Lutjanus species (L. xanthopinnis and L. indicus). In addition six species (L. rivulatus, L. lutjanus, L. vitta, L. lemniscatus, L. fulviflamma and L. johnii) were re-described. Distinct morphological differentiation were found between more closely related species L. xanthopinnis, L. vitta and L. lutjanus. Three different appearances of L. johnii, two different appearances of L. rivulatus and L. lemniscatus were confirmed as same species. Phylogenetic analysis showed monophylotic clade for conspecific individuals and paraphyletic clade for congeneric individuals. Average genetic divergence for intraspecific level was 1.5% and 12.5% for interspecific level. Current study increased the number of Lutjanus species in Bangladesh from 15 to 17 and extended the distribution range of those new recorded species in northeastern part of the Bay of Bengal. Bangladesh J. Zool. 46(2): 239-253, 2018

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