Title: Complete chloroplast genome of the marine red alga Rhodochorton tenue (Rhodochortonaceae, Rhodophyta) from San Juan Island, Washington
We present the complete chloroplast genome sequence of Rhodochorton tenue from San Juan Island, Washington. The chloroplast genome of R. tenue is 192,037 bp in length, contains 244 genes, and is similar in content to Acrochaetium secundatum. Rhodochorton tenue is genetically distinct from Rhodochorton purpureum from the North Atlantic Ocean. more »« less
Alesmail, Mustafa; Becerra, Yulissa; Betancourt, Kimberly J.; Bracy, Shelly M.; Castro, Anevay T.; Cea, Cynthia; Chavez, Justin; Del Angel, Janet; Diaz, Edgar; Diaz-Guzman, Yael; et al
(, Microbiology Resource Announcements)
Dennehy, John J.
(Ed.)
ABSTRACT 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.
Garcia, Adam N.; Ramos, Jennifer Hernandez; Mendoza, Aileen G.; Muhrram, Asmahan; Vidauri, Jessica M.; Hughey, Jeffery R.
(, Microbiology Resource Announcements)
Stajich, Jason E.
(Ed.)
ABSTRACT 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.
Abdulrahman, Sosan; Aguirre, Adilene; Arriaga, Eliana; Avina, Ashley C; Badajos, Angeles; Badillo, Yureni A; Bañuelos, Alexis M; Pulido, Javier; Bucio_Valdovinos, Bet-sua; Champaco, Taliyah; et al
(, Microbiology Resource Announcements)
Pritchard, Leighton
(Ed.)
ABSTRACT We present the complete chloroplast genome of the eelgrassZostera pacificafrom Monterey, California. The genome is circular and 144,675 bp in length. It consists of 82 protein-coding, 31 transfer RNA, and 8 ribosomal RNA genes and is 99.44%–99.42% similar in nucleotide pairwise identity to the closely related speciesZostera marina.
Abstract Co-adaptation of cytoplasmic and nuclear genomes are critical to physiological function for many species. Despite this understanding, hybridization can disrupt co-adaptation leading to a mismatch between maternally-inherited cytoplasmic genomes and biparentally inherited nuclear genomes. Few studies have examined the consequences of cytonuclear interactions to physiological function across environments. Here, we quantify the degree of co-introgression between chloroplast and nuclear-chloroplast (N-cp) genes across repeated hybrid zones and its consequences to physiological function across environments. We use whole-genome resequencing and common garden experiments with clonally replicated genotypes sampled across the natural hybrid zone betweenPopulus trichocarpaandP. balsamifera. We use geographic clines to test for co-introgression of the chloroplast genome with N-cp and non-interacting nuclear genes. Co-introgression of chloroplast and N-cp genes was limited although contact zone-specific patterns suggest that local environments may influence co-introgression. Combining ancestry estimates with phenotypic data across common gardens revealed that mismatches between chloroplast and nuclear ancestry can influence physiological performance, but the strength and direction of these effects vary depending on the environment. Overall, this study highlights the importance of cytonuclear interactions to adaptation, and the role of environment in modifying the effect of those interactions.
Harkess, Alex; McLoughlin, Fionn; Bilkey, Natasha; Elliott, Kiona; Emenecker, Ryan; Mattoon, Erin; Miller, Kari; Czymmek, Kirk; Vierstra, Richard D; Meyers, Blake C; et al
(, Journal of Experimental Botany)
Melzer, Rainer
(Ed.)
Abstract Duckweeds are a monophyletic group of rapidly reproducing aquatic monocots in the Lemnaceae family. Given their clonal, exponentially fast reproduction, a key question is whether genome structure is conserved across the species in the absence of meiotic recombination. Here, we studied the genome and proteome of Spirodela polyrhiza, or greater duckweed, which has the largest body plan yet the smallest genome size in the family (1C=150 Mb). Using Oxford Nanopore sequencing combined with Hi-C scaffolding, we generated a highly contiguous, chromosome-scale assembly of S. polyrhiza line Sp7498 (Sp7498_HiC). Both the Sp7498_HiC and Sp9509 genome assemblies reveal large chromosomal misorientations relative to a recent PacBio assembly of Sp7498, highlighting the need for orthogonal long-range scaffolding techniques such as Hi-C and BioNano optical mapping. Shotgun proteomics of Sp7498 verified the expression of ~2250 proteins and revealed a high abundance of proteins involved in photosynthesis and carbohydrate metabolism among other functions. In addition, a strong increase in chloroplast proteins was observed that correlated to chloroplast density. This Sp7498_HiC genome was generated cheaply and quickly with a single Oxford Nanopore MinION flow cell and one Hi-C library in a classroom setting. Combining these data with a mass spectrometry-generated proteome illustrates the utility of duckweed as a model for genomics- and proteomics-based education.
@article{osti_10544986,
place = {Country unknown/Code not available},
title = {Complete chloroplast genome of the marine red alga Rhodochorton tenue (Rhodochortonaceae, Rhodophyta) from San Juan Island, Washington},
url = {https://par.nsf.gov/biblio/10544986},
DOI = {10.1128/mra.01068-23},
abstractNote = {We present the complete chloroplast genome sequence of Rhodochorton tenue from San Juan Island, Washington. The chloroplast genome of R. tenue is 192,037 bp in length, contains 244 genes, and is similar in content to Acrochaetium secundatum. Rhodochorton tenue is genetically distinct from Rhodochorton purpureum from the North Atlantic Ocean.},
journal = {Microbiology Resource Announcements},
volume = {13},
number = {2},
publisher = {American Society of Microbiology},
author = {Ahmed, Layla T and Alesmail, Hiba and Beltran_Rodriguez, Stephanie and Christian, Rachel and Coronado, Jonathan and Elledge, Alice A and Estrada, America and Fierro, Alena and Garcia_Mora, Angel and Gonzalez, Kayla and Gonzalez-Leon, Samantha and Guijarro, Arely M and Islas-Quintana, Jennifer and Juarez-Guido, David and Hughey, Jeffery R and Lara, Edward J and Lara, Jamileth and Leonard, Carson T and Lockard, Kaylee A and Lopez, Enzou and Martin, Stephanie and Martinez, Miriam and Mederos, Brianna and Medina_Pizano, Alejandro and Medley, Casey J and Mohsin, Sarah and Mumford, Thomas F and Muñoz, Raphael Araujo and Nachtigall, Renee and Noriega, Jannette and Ochoa_Cendejas, Pedro and Ordaz, Jessika and Parra, Alberto J and Pizano, Julian and Reimold, Michelle and Rivera, Kristalyn and Rocha, Ayleen and Rodriguez, Karolina C and Tena-Garcia, Ivan and Vargas, Matthew M and Velasquez, Jose},
editor = {Dennehy, John J}
}
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