Identification of nuclear low-copy genes and their phylogenetic utility in rosids

By far, the interordinal relationships in rosids remain poorly resolved. Previous studies based on chloroplast, mitochondrial, and nuclear DNA has produced conflicting phylogenetic resolutions that has become a widely concerned problem in recent phylogenetic studies. Here, a total of 96 single-copy nuclear gene loci were identified from the KOG (eukaryotic orthologous groups) database, most of which were first used for phylogenetic analysis of angiosperms. The orthologous sequence datasets from completely sequenced genomes of rosids were assembled for the resolution of the position of the COM (Celastrales–Oxalidales–Malpighiales) clade in rosids. Our analysis revealed strong and consistent support for CM topology (the COM clade as sister to the malvids). Our results will contribute to further exploring the underlying cause of conflict between chloroplast, mitochondrial, and nuclear data. In addition, our study identified a few novel nuclear molecular markers with potential to investigate the deep phylogenetic relationship of plants or other eukaryotic taxonomical groups.

Download Full-text

Geographic Structure of Mitochondrial and Nuclear Gene Polymorphisms in Australian Green Turtle Populations and Male-Biased Gene Flow

Genetics ◽

10.1093/genetics/147.4.1843 ◽

1997 ◽

Vol 147 (4) ◽

pp. 1843-1854 ◽

Cited By ~ 8

Author(s):

Nancy N FitzSimmons ◽

Craig Moritz ◽

Colin J Limpus ◽

Lisa Pope ◽

Robert Prince

Keyword(s):

Gene Flow ◽

Genetic Structure ◽

Green Turtle ◽

Nuclear Dna ◽

Nuclear Gene ◽

Chelonia Mydas ◽

Single Copy ◽

Microsatellite Data ◽

Ecological Data ◽

Infinite Allele Model

Abstract The genetic structure of green turtle (Chelonia mydas) rookeries located around the Australian coast was assessed by (1) comparing the structure found within and among geographic regions, (2) comparing microsatellite loci vs. restriction fragment length polymorphism analyses of anonymous single copy nuclear DNA (ascnDNA) loci, and (3) comparing the structure found at nuclear DNA markers to that of previously analyzed mitochondrial (mtDNA) control region sequences. Significant genetic structure was observed over all regions at both sets of nuclear markers, though the microsatellite data provided greater resolution in identifying significant genetic differences in pairwise tests between regions. Inferences about population structure and migration rates from the microsatellite data varied depending on whether statistics were based on the stepwise mutation or infinite allele model, with the latter being more congruent with geography. Estimated rates of gene flow were generally higher than expected for nuclear DNA (nDNA) in comparison to mtDNA, and this difference was most pronounced in comparisons between the northern and southern Great Barrier Reef (GBR). The genetic data combined with results from physical tagging studies indicate that the lack of nuclear gene divergence through the GBR is likely due to the migration of sGBR turtles through the courtship area of the nGBR population, rather than male-biased dispersal. This example highlights the value of combining comparative studies of molecular variation with ecological data to infer population processes.

Download Full-text

Single copy nuclear gene analysis of polyploidy in wild potatoes (Solanum section Petota)

BMC Evolutionary Biology ◽

10.1186/1471-2148-12-70 ◽

2012 ◽

Vol 12 (1) ◽

pp. 70 ◽

Cited By ~ 19

Author(s):

Danying Cai ◽

Flor Rodríguez ◽

Yuanwen Teng ◽

Cécile Ané ◽

Meredith Bonierbale ◽

...

Keyword(s):

Nuclear Gene ◽

Single Copy ◽

Gene Analysis ◽

Single Copy Nuclear Gene ◽

Solanum Section Petota ◽

Section Petota ◽

Wild Potatoes

Download Full-text

Generating single-copy nuclear gene data for a recent adaptive radiation

Molecular Phylogenetics and Evolution ◽

10.1016/j.ympev.2005.10.010 ◽

2006 ◽

Vol 39 (1) ◽

pp. 124-134 ◽

Cited By ~ 49

Author(s):

Justen B. Whittall ◽

Andrew Medina-Marino ◽

Elizabeth A. Zimmer ◽

Scott A. Hodges

Keyword(s):

Adaptive Radiation ◽

Nuclear Gene ◽

Single Copy ◽

Single Copy Nuclear Gene ◽

Gene Data

Download Full-text

General-use polymerase chain reaction primers for amplification and direct sequencing of enolase, a single-copy nuclear gene, from different animal phyla

Molecular Ecology Resources ◽

10.1111/j.1755-0998.2008.02210.x ◽

2009 ◽

Vol 9 (1) ◽

pp. 144-147 ◽

Cited By ~ 3

Author(s):

RYAN P. KELLY ◽

STEPHEN R. PALUMBI

Keyword(s):

Polymerase Chain Reaction ◽

Direct Sequencing ◽

Nuclear Gene ◽

Single Copy ◽

Chain Reaction ◽

Single Copy Nuclear Gene ◽

Animal Phyla ◽

Polymerase Chain ◽

Polymerase Chain Reaction Primers

Download Full-text

Evaluation of the geographical pattern of genetic diversity of Glycine soja and Glycine max based on four single copy nuclear gene loci: For conservation of soybean germplasm

Biochemical Systematics and Ecology ◽

10.1016/j.bse.2015.09.006 ◽

2015 ◽

Vol 62 ◽

pp. 229-235 ◽

Cited By ~ 6

Author(s):

Yunsheng Wang ◽

Muhammad Qasim Shahid ◽

Fozia Ghouri ◽

Faheem Shehzad Baloch ◽

Ying Wang ◽

...

Keyword(s):

Genetic Diversity ◽

Glycine Max ◽

Glycine Soja ◽

Nuclear Gene ◽

Single Copy ◽

Geographical Pattern ◽

Soybean Germplasm ◽

Single Copy Nuclear Gene

Download Full-text

Development of 16 single‐copy nuclear gene markers for Oreocharis auricula , a perennial herb in China

Applications in Plant Sciences ◽

10.1002/aps3.11304 ◽

2019 ◽

Vol 7 (11) ◽

Author(s):

Zhixia Sun ◽

Chao Feng ◽

Lihua Yang ◽

Hanghui Kong

Keyword(s):

Nuclear Gene ◽

Single Copy ◽

Perennial Herb ◽

Gene Markers ◽

Single Copy Nuclear Gene

Download Full-text

Complete Chloroplast Genomes of Chlorophytum comosum and Chlorophytum gallabatense: Genome Structures, Comparative and Phylogenetic Analysis

Plants ◽

10.3390/plants9030296 ◽

2020 ◽

Vol 9 (3) ◽

pp. 296 ◽

Cited By ~ 3

Author(s):

Jacinta N. Munyao ◽

Xiang Dong ◽

Jia-Xin Yang ◽

Elijah M. Mbandi ◽

Vincent O. Wanga ◽

...

Keyword(s):

Phylogenetic Analysis ◽

Single Copy ◽

Rrna Genes ◽

Trna Genes ◽

Important Species ◽

Genomic Resources ◽

Phylogenetic Studies ◽

Chloroplast Genomes ◽

Cp Genome ◽

High Level

The genus Chlorophytum includes many economically important species well-known for medicinal, ornamental, and horticultural values. However, to date, few molecular genomic resources have been reported for this genus. Therefore, there is limited knowledge of phylogenetic studies, and the available chloroplast (cp) genome of Chlorophytum (C. rhizopendulum) does not provide enough information on this genus. In this study, we present genomic resources for C. comosum and C. gallabatense, which had lengths of 154,248 and 154,154 base pairs (bp), respectively. They had a pair of inverted repeats (IRa and IRb) of 26,114 and 26,254 bp each in size, separating the large single-copy (LSC) region of 84,004 and 83,686 bp from the small single-copy (SSC) region of 18,016 and 17,960 bp in C. comosum and C. gallabatense, respectively. There were 112 distinct genes in each cp genome, which were comprised of 78 protein-coding genes, 30 tRNA genes, and four rRNA genes. The comparative analysis with five other selected species displayed a generally high level of sequence resemblance in structural organization, gene content, and arrangement. Additionally, the phylogenetic analysis confirmed the previous phylogeny and produced a phylogenetic tree with similar topology. It showed that the Chlorophytum species (C. comosum, C. gallabatense and C. rhizopendulum) were clustered together in the same clade with a closer relationship than other plants to the Anthericum ramosum. This research, therefore, presents valuable records for further molecular evolutionary and phylogenetic studies which help to fill the gap in genomic resources and resolve the taxonomic complexes of the genus.

Download Full-text