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We present the complete chloroplast genome sequence of an endophytic Ostreobium sp. isolated from a 19th-century coralline red algal specimen from St. Croix, U.S. Virgin Islands. The chloroplast genome is 84,848 bp in length, contains 114 genes, and has a high level of gene synteny to other Ostreobiaceae.

Here, we present the complete chloroplast genome sequence of Toxicodendron diversilobum , western poison oak, from Pacific Grove, California. The genome is 159,543 bp in length, contains 133 genes, and has a high level of gene synteny to other species of Toxicodendron .

Here, we present the complete chloroplast genomes of Quercus × morehus , Q. wislizeni , and Q. kelloggii from California. The genomes are 161,119 to 161,130 bp and encode 132 genes. Quercus × morehus and Q. wislizeni are identical in sequence but differ from Q. kelloggii by three indels and eight SNPs.

Here, we present the chloroplast genome sequence of Quercus agrifolia Née, the California live oak, an ecologically important oak species along the coast of California. The genome is 161,283 bp in length, encodes 132 genes, and has a high level of gene synteny to other Fagaceae.

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.

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 othe...

Palmaria decipiens (Reinsch) R.W.Ricker is a ecologically important red seaweed restricted to high latitudes of the southern hemisphere. Here, we contribute to the bioinformatics and evolut...

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.

Rupicola peruvianus Latham, known as the Andean Cock-of-the-Rock or locally as Tunqui, is distributed in the Andean cloud forests of South America from Venezuela to Bolivia. Here, we contribute to ...

Lessonia spicata (Suhr) Santelices is the most ecologically and economically important kelp from Pacific South America. Here, we contribute to the bioinformatics and evolutionary systematics of the species by performing high throughput sequencing on L. spicata from Valparaiso, Chile. The L. spicata complete mitogenome is 37,097 base pairs (bp) in length and contains 66 genes (GenBank accession MK965907), the complete plastid genome is 130,305 bp and has 173 genes (accession MK965908), and the data assembled 7,630 bp of the nuclear ribosomal cistron (accession MK965909). The organellar genomes are similar in structure and content to others published from the Laminariales.

Recent genetic studies of the Bangiales (Rhodophyta) led to the resurrection of the marine red algal genus Wildemania De Toni. To gain a better understanding of the phylogenetic history of this genus and its plastid genome structure, the holotype specimen of Wildemania schizophylla (Hollenberg) S. C. Lindstrom was analyzed using next generation sequencing technology. The plastid genome of W. schizophylla is 193,008 bp in length and contains 249 genes, including 47 ribosomal, 34 tRNA, 29 photosystem, 27 open reading frames, 25 hypothetical proteins, 10 phycobiliprotein, 8 ATP synthase, and 8 cytochrome b/f complex genes. The plastid genome shows similar organization and content to other Bangiaceae, except that it lacks the typical 16S and 23S ribosomal RNA repeat. Phylogenetic analysis of the W. schizophylla plastid genome against other Bangiaceae places W. schizophylla in a robustly supported position, intermediate between Porphyra C. Agardh and Pyropia J. Agardh. These data support the recent re...

An unidentified marine red algal species classified in Pyropia J. Agardh was discovered from Monterey, CA. Morphological, barcode, and complete mitochondrial genome analysis of the alga support its recognition as a new species, Pyropia nitida sp. nov. The species is a high-intertidal, winter annual that is lanceolate in shape, monostromatic, and dioecious. Based on CO1 sequences, P. nitida is closely allied with the P. nereocystis clade. The mitogenome of P. nitida is 35 313 bp in length and contains 53 genes, including two ribosomal RNAs, 24 transfer RNAs, four ribosomal proteins, two ymfs, four ORFs, and 17 genes involved in electron transport and oxidative phosphorylation. The results support the recognition of P. nitida as distinct from the morphologically similar P. lanceolata.

Genomic analysis of the kelp fly Fucellia costalis (Family Anthomyiidae) from Asilomar beach, Pacific Grove, California, resulted in the assembly of its complete mitogenome. The mitogenome is 16,17...

Genomic analysis of the marine alga Corallina chilensis from Tomales Bay, California, USA, resulted in the assembly of its complete mitogenome (GenBank accession number MK598844) and plastid genome...

An unknown species of marine sea lettuce was observed forming green tides consecutive years from 2014 to 2016 in Seaside, California. This Ulva sp. was similar in thallus size and shape to U. expansa. To confirm this identification, whole genome sequencing was performed on the bloom-forming species of Ulva and the holotype specimen of U. expansa. The complete green tide Ulva mitogenome is 64,143 bp in length, contains 65 genes, and displays high gene synteny with U. pertusa Kjellman. The mitogenome was incomplete for the holotype of U. expansa, but the analysis yielded the mitoexome, plastid, and nuclear genetic markers. These data verify that the native U. expansa is responsible for the blooms in central California.

Fucus spiralis L. is a broadly distributed monoecious intertidal seaweed. The specific status of F. spiralis however is debatable. Here, we contribute to the bioinformatics and systematics of F. spiralis by analysing the complete mitochondrial and plastid genomes of a specimen from California, U.S.A. The F. spiralis mitogenome is 36,396 base pairs (bp) in length and contains 67 genes, and the plastid genome is 125,066 bp in length and contains 171 genes. The F. spiralis genomes are 99.7% and 99.8% similar in nucleotide sequence to F. vesiculosus, and support the revised classification of F. spiralis to Fucus vesiculosus var. spiralis.

The complete genome sequence from a nonhemolytic strain of Streptococcus agalactiae from the oral cavity of a canine was assembled. The genome is 2,165,968 bp, contains 2,055 genes, and is classified as group B streptococcus (GBS) serotype V, strain 1. A comparison to other S. agalactiae sequences shows high gene synteny with human and bovine strains.

Ancient DNA methodologies can be applied in the investigation of the genetics of extinct populations. A search for beta thalassemia mutations was performed on 49 Minoan individuals from the Bronze Age who were living in the island of Crete approximately 4000 Years Before Present (YBP). Standard precautionary measures were employed in the laboratory to ensure authenticity of the DNA extracted from the ancient bones, resulting in the successful analysis of DNA of 24 Minoans. DNA sequencing focused on the Intervening Sequence 1 (IVS-1) of the beta globin gene and its splicing junctions. 63% of the thalassemia mutations observed among modern Cretans reside in beta IVS-1. None of the Minoan individuals carried one of the IVS-1 mutations known to cause beta thalassemia; however, only one was expected to be observed if the average frequency of beta thalassemia heterozygotes in the Minoan population was the same with that of modern day Cretans (7.6%). One individual contained a C to G substitution in position 91 of the IVS-1, located 40 bp 5′ to the intron 1/exon 2 junction. Functional studies indicated that the mutation did not affect mRNA splicing or stability, and most likely represented an innocent single nucleotide polymorphism.

Analysis of Phrynosoma blainvillii Gray from Marina, Monterey County, California, using 150 bp paired-end Illumina sequences (Illumina, San Diego, CA) resulted in the assembly of its complete mitogenome. The mitogenome is 16,946 bp in length and contains a putative origin of light strand replication (OL), control region, 22 tRNA, 2 rRNA, and 13 protein-coding genes. Its content and organization are similar to other Squamata. Phylogenetic analysis of P. blainvillii resolves it in a clade with P. sherbrookei Nieto-Montes de Oca, Arenas-Moreno, Beltran-Sanchez & Leache, sister in position to Uma notata Baird. Mitochondrial marker analysis of P. blainvillii from Marina shows that it belongs to a coastal Santa Lucia Mountain Range haplogroup that is distinct from other populations of P. blainvillii in California.

Analysis of the marine black prickleback Xiphister atropurpureus Kittlitz using 76 bp paired-end Illumina sequences resulted in the assembly of its complete mitogenome. The mitogenome is 16,518 bp in length and contains an origin of light strand replication (OL), control region, 22 tRNA, 2 rRNA, and 13 protein-coding genes. Content and organization of the X. atropurpureus mitogenome is consistent with other teleost. Phylogenetic analysis of X. atropurpureus resolves it in a clade with another member of the Stichaeidae, Chirolophis japonicus Herzenstein.

Analysis of the marine red algal species Dasya binghamiae A.J.K. Millar using paired-end 36 bp Illumina sequences resulted in the assembly of its complete mitochondrial and plastid genomes. The mitogenome is 26,052 bp in length and contains 46 genes, and the plastome is 177,213 bp with 228 genes. The plastid genome shows high gene synteny with previously published Florideophyceae; however, the mitogenome contains several multigene rearrangements. These organellar data confirm the placement of D. binghamiae in Dasya C. Agardh.

The article of record as published may be found at http://dx.doi.org/10.1038/srep05113 Plant species, including algae and fungi, are based on type specimens to which the name of a taxon is permanently attached. Applying a scientific name to any specimen therefore requires demonstrating correspondence between the type and that specimen. Traditionally, identifications are based on morpho-anatomical characters, but recently systematists are using DNA sequence data. These studies are flawed if the DNA is isolated from misidentified modern specimens. We propose a genome-based solution. Using 4x4 mm² of material from type specimens, we assembled 14 plastid and 15 mitochondrial genomes attributed to the red algae Pyropia perforata, Py. fucicola, and Py. kanakaensis. The chloroplast genomes were fairly conserved, but the mitochondrial genomes differed significantly among populations in content and length. Complete genomes are attainable from 19th and early 20th century type specimens; this validates the effort and cost of their curation as well as supports the practice of the type method. P.W.G. and Dr. Kelly Locke, Title V grant director at Hartnell College Grant number- PO31C110168

DNA was extracted from a red algal herbarium specimen collected in 1920 and subjected to next generation sequencing. Here we report the assembly of the mitogenome of a marine mussel, Mytilus trossulus, deciphered from this plant museum specimen. The mitogenome is 16,744 bp in length, contains 38 genes, and is more similar to other M. trossulus reported from the Baltic Sea. The data show that in addition to plant DNA, herbarium specimens also contain genetic information from invertebrates that may be valuable for genomic, population and phylogenetic studies of animals.

Analysis of the marine red algal species Mastocarpus papillatus (C. Agardh) Kützing using paired-end 36 bp Illumina sequences resulted in the assembly of its complete mitochondrial and plastid genomes. The mitogenome is 25,906 bp in length and contains 50 genes, and the plastid genome is 184,382 bp with 234 genes. The mitochondrial and plastid genomes show high gene synteny with published Florideophyceae.

Ion Proton data was used to assemble the complete mitochondrial genome from the holotype specimen of Wildemania schizophylla (29,156 bp). The mitogenome contains 50 genes, including 2 ribosomal RNA, 23 transfer RNA, 4 ribosomal proteins, 2 ymfs, 3 open reading frames (ORFs), and 19 genes involved in cellular respiration. Although gene synteny is conserved, the mitogenome of W. schizophylla is significantly smaller due to the lack of large intronic ORFs present in the cytochrome oxidase locus of other Bangiales. The results support the recognition of Wildemania as distinct from Porphyra, and demonstrate that small amounts of type material are suitable for genomic studies.