Populations and Evolution
New submissions
Showing new listings for Monday, 19 October 2026
Total of 7 entries | Cross submissions
Cross submissions (showing 7 of 7 entries)
- [1] CCCURJ:2610.00013 (cross-list from q-bio.GN) [pdf]
-
Research note Complete chloroplast genome of the federally endangered Menzies' wallflower Erysimum menziesii (Brassicaceae, Anthophyta) from California, USAComments: 4 pages. Republished from Microbiology Resource Announcements 15(3):e0129825 (2026) under CC BY 4.0; not submitted to CCCURJSubjects: Genomics (q-bio.GN); Populations and Evolution (q-bio.PE)
We present the complete chloroplast genome of the federally endangered plant species Erysimum menziesii from Pacific Grove, California, USA. The chloroplast genome is circular, AT skewed (63.4%), and 154,668 bp in length. The genome is quadripartite in structure and contains 85 protein-coding, 37 transfer RNA, and 8 ribosomal RNA genes.
- [2] CCCURJ:2610.00012 (cross-list from q-bio.GN) [pdf]
-
Research note Complete mitochondrial genome of the introduced Indian walking stick Carausius morosus (Lonchodidae, Insecta) from CaliforniaComments: 4 pages. Republished from Microbiology Resource Announcements 13(7):e0032124 (2024) under CC BY 4.0; not submitted to CCCURJSubjects: Genomics (q-bio.GN); Populations and Evolution (q-bio.PE)
We present the complete mitochondrial genome of Carausius morosus from Salinas, CA. The mitochondrial genome of C. morosus is circular, AT rich (78.1%), and 16,671 bp in length. It consists of 13 protein-coding, 22 transfer RNA, and 2 ribosomal RNA genes and is identical in gene content to Carausius sp.
- [3] CCCURJ:2610.00009 (cross-list from q-bio.GN) [pdf]
-
Research note The complete chloroplast genome of the threatened Napa False Indigo Amorpha californica var. napensis Jeps. 1925 (Fabaceae) from Northern California, USAComments: 3 pages. Republished from Mitochondrial DNA Part B 7(1):283–285 (2022) under CC BY 4.0; not submitted to CCCURJSubjects: Genomics (q-bio.GN); Populations and Evolution (q-bio.PE)
Amorpha californica var. napensis Jeps. 1925, the Napa false indigo, is a threatened shrub endemic to northern California. Here the complete chloroplast genome of topotype material of var. napensis was assembled and characterized to contribute to the bioinformatics, systematics, and conservation of this variety. The chloroplast genome (GenBank accession OK274088) is 158,294 base pairs (bp) in length, encodes 130 genes including 85 protein-coding, 37 tRNA, 8 rRNA, and shows a high-level of gene synteny to other Papilionoideae. Phylogenetic analysis fully resolved var. napensis in a clade with A. fruticosa L. and A. roemeriana Scheele, sister to the Dalbergieae. The newly sequenced chloroplast genome shows that the genetic differences between var. napensis and Amorpha californica Nutt. var. californica are greater than the variation observed between var. napensis and many other Amorpha spp. sequences deposited in GenBank. These data suggest that var. napensis should be elevated to full species rank.
- [4] CCCURJ:2610.00008 (cross-list from q-bio.GN) [pdf]
-
Research article Metagenomic Insights into the Composition and Function of Microbes Associated with the Rootzone of Datura inoxiaComments: 16 pages. Republished from Biotech 11(1):1 (2022) under CC BY 4.0; not submitted to CCCURJSubjects: Genomics (q-bio.GN); Populations and Evolution (q-bio.PE)
The purpose of this paper is to elucidate the roles that microbes may be playing in the rootzone of the medicinal plant Daturainoxia. We hypothesized that the microbes associated with the Datura rootzone would be significantly different than the similar surrounding fields in composition and function. We also hypothesized that rhizospheric and endophytic microbes would be associated with similar metabolic functions to the plant rootzone they inhabited. The methods employed were microbial barcoding, tests of essential oils against antibiotic resistant bacteria and other soil bacterial isolates, 16S Next Generation Sequencing (NGS) metabarcoding, and Whole Genome Shotgun (WGS) taxonomic and functional analyses. A few of the main bacterial genera of interest that were differentially abundant in the Datura root microbiome were Flavobacterium (p = 0.007), Chitinophaga (p = 0.0007), Pedobacter (p = 6 × 10-5), Bradyhizobium (p = 1 × 10-8), and Paenibacillus (p = 1.46 × 10-6). There was significant evidence that the microbes associated with the Datura rootzone had elevated function related to bacterial chalcone synthase (p = 1.49 × 10-3) and permease genes (p < 0.003). There was some evidence that microbial functions in the Datura rootzone provided precursors to important plant bioactive molecules or were beneficial to plant growth. This is important because these compounds are phyto-protective antioxidants and are precursors to many aromatic bioactive compounds that are relevant to human health. In the context of known interactions, and current results, plants and microbes influence the flavonoid biosynthetic pathways of one other, in terms of the regulation of the phenylpropanoid pathway. This is the first study to focus on the microbial ecology of the Datura rootzone. There are possible biopharmaceutical and agricultural applications of the natural interplay that was discovered during this study of the Datura inoxia rhizosphere.
- [5] CCCURJ:2610.00007 (cross-list from q-bio.GN) [pdf]
-
Research note The complete mitochondrial genome of the strawberry aphid Chaetosiphon fragaefolii Cockerell, 1901 (Hemiptera: Aphididae) from California, USAComments: 3 pages. Republished from Mitochondrial DNA Part B 6(8):2373–2375 (2021) under CC BY 4.0; not submitted to CCCURJSubjects: Genomics (q-bio.GN); Populations and Evolution (q-bio.PE)
The aphid Chaetosiphon fragaefolii Cockerell, 1901 is an agricultural pest and known vector of strawberry viruses. To better understand its biology and systematics, we performed a genomic analysis on C. fragaefolii collected from Quinalt strawberry plants from Pacific Grove, Monterey county, California, USA using Oxford Nanopore and Illumina sequencing. The resulting data were used to assemble the aphids complete mitogenome. The mitogenome of C. fragaefolii is 16,108 bp in length and contains 2 rRNA, 13 protein-coding, and 22 tRNA genes (GenBank accession number LC590896). The mitogenome is similar in content and organization to other Aphididae. Phylogenetic analysis of the C. fragaefolii mitogenome resolved it in a fully supported clade in the tribe Macrosiphini. Analysis of the cox1 barcode sequence of C. fragaefolii from California found exact and nearly identical sequences to C. fragaefolii and Chaetosiphon thomasi Hille Ris Lambers, 1953, suggesting the two species are conspecific.
- [6] CCCURJ:2610.00006 (cross-list from q-bio.GN) [pdf]
-
Research note The complete mitochondrial and plastid genomes of the invasive marine red alga Caulacanthus okamurae (Caulacanthaceae, Rhodophyta) from Moss Landing, California, USAComments: 3 pages. Republished from Mitochondrial DNA Part B 5(3):2067–2069 (2020) under CC BY 4.0; not submitted to CCCURJSubjects: Genomics (q-bio.GN); Populations and Evolution (q-bio.PE)
Caulacanthus okamurae is an invasive red alga that forms extensive mats in sheltered marine habitats around the world. To determine its genomic structure and genetic relationship to native and other non-native populations of C. okamurae, high-throughput sequencing analysis was performed on an introduced specimen from Bennett Slough, Moss Landing, California, USA. Assembly of 23,146,595 filtered 150 bp paired-end Illumina sequencing reads yielded its complete mitogenome (GenBank accession MT193839) and plastid genome (GenBank accession MT193838). The mitogenome is 25,995 bp in length and contains 50 genes. The plastid genome is 173,516 bp and contains 234 genes. Comparison of the organellar chromosomes to other Gigartinales revealed a high-level of gene synteny. BLAST analysis of marker sequences (rbcL, cox1, cox2) of C. okamurae from Moss Landing identified four identical DNA sequences: one from a specimen from a native population of C. okamurae from South Korea and three from specimens representing invasive populations from France, Spain, and the USA. These genetic results confirm the presence of C. okamurae in central California, USA, and represent the first complete mitogenome and plastid genome from the Caulacanthaceae.
- [7] CCCURJ:2610.00005 (cross-list from q-bio.GN) [pdf]
-
Research note The complete mitogenome of the invasive Japanese mud snail Batillaria attramentaria (Gastropoda: Batillariidae) from Elkhorn Slough, California, USAComments: 2 pages. Republished from Mitochondrial DNA Part B 4(2):4031–4032 (2019) under CC BY 4.0; not submitted to CCCURJSubjects: Genomics (q-bio.GN); Populations and Evolution (q-bio.PE)
Genomic analysis of the invasive marine snail Batillaria attramentaria from Elkhorn Slough, Moss Landing, California, USA using 150 bp paired-end Illumina sequences resulted in the assembly of its complete mitogenome. The mitogenome is 16,095 bp in length and contains 2 rRNA, 13 protein-coding, and 22 tRNA genes (GenBank Accession MN557850). Gene content and organization of B. attramentaria are identical to the Turritellidae and Pachychilidae. The phylogenetic analysis of B. attramentaria resolves it in a fully supported clade with these same two families in the superfamily Cerithioidea. Nucleotide BLAST searches of the Elkhorn Slough cox1 gene of B. attramentaria yielded identical sequences from invasive populations from California and British Columbia, and native populations from northeastern and central Japan. These data show that mitogenome sequencing is a useful tool for studying the classification and phylogenetic history Cerithioidea.