Title: Complete Chloroplast Genome of an Endophytic Ostreobium sp. (Ostreobiaceae) from the U.S. Virgin Islands
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. more »« less
Ahmed, Layla T; Alesmail, Hiba; Beltran_Rodriguez, Stephanie; Christian, Rachel; Coronado, Jonathan; Elledge, Alice A; Estrada, America; Fierro, Alena; Garcia_Mora, Angel; Gonzalez, Kayla; et al
(, Microbiology Resource Announcements)
Dennehy, John J
(Ed.)
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.
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.
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.
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.
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_10465597,
place = {Country unknown/Code not available},
title = {Complete Chloroplast Genome of an Endophytic Ostreobium sp. (Ostreobiaceae) from the U.S. Virgin Islands},
url = {https://par.nsf.gov/biblio/10465597},
DOI = {10.1128/mra.00272-23},
abstractNote = {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.},
journal = {Microbiology Resource Announcements},
volume = {12},
number = {5},
author = {Alesmail, Mustafa and Becerra, Yulissa and Betancourt, Kimberly J. and Bracy, Shelly M. and Castro, Anevay T. and Cea, Cynthia and Chavez, Justin and Del Angel, Janet and Diaz, Edgar and Diaz-Guzman, Yael and Dominguez, Jonathan and Estrada, Jocelynnicole G. and Frei, Lashabelle G. and Gabrielson, Paul W. and Gallardo, Andrea and Garcia, Miriam R. and Gonzalez, Eva and Gonzalez Rocha, Anthony and Guzman-Bermudez, Diego and Hebert, Cassidy R. and Hernandez, Marlene and Hughey, Jeffery R. and Lee, Zachary and Leyva Romero, Alexandra and Martinez, Eric and Martinez, Nathaniel and Medina, Kazimiera H. and Morales, Miguel and Moreno, Alexis M. and Nava, Isabella and Nono, Alyssa N. and Ochoa, Samuel A. and Perez, Amy and Perez, Natasha and Perez Pulido, Edwin and Poduska, Sophie and Ramirez, Kimberly N. and Reyes, Denise and Richardson, Kelsey and Rodriguez, Juanaisa and Rodriguez, Alondra M. and Serrano-Lopez, Clarisa and Velasquez, Andrea G. and Villanueva, Gezelle},
editor = {Dennehy, John J.}
}
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