Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Complete Chloroplast Genome of Topotype Material of the Coast Live Oak Quercus agrifolia Nee var. agrifolia (Fagaceae) from California.

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.

SUBMITTER: Garcia AN

PROVIDER: S-EPMC9022551 | biostudies-literature | 2022 Apr

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Complete Chloroplast Genome of Topotype Material of the Coast Live Oak Quercus agrifolia Née var. agrifolia (Fagaceae) from California.

Garcia Adam N AN Ramos Jennifer Hernandez JH Mendoza Aileen G AG Muhrram Asmahan A Vidauri Jessica M JM Hughey Jeffery R JR

Microbiology resource announcements 20220307 4

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. ...[more]

PMID: 35254126

Similar Datasets

First Draft Assembly and Annotation of the Genome of a California Endemic Oak Quercus lobata Nee (Fagaceae).

Project description:Oak represents a valuable natural resource across Northern Hemisphere ecosystems, attracting a large research community studying its genetics, ecology, conservation, and management. Here we introduce a draft genome assembly of valley oak (Quercus lobata) using Illumina sequencing of adult leaf tissue of a tree found in an accessible, well-studied, natural southern California population. Our assembly includes a nuclear genome and a complete chloroplast genome, along with annotation of encoded genes. The assembly contains 94,394 scaffolds, totaling 1.17 Gb with 18,512 scaffolds of length 2 kb or longer, with a total length of 1.15 Gb, and a N50 scaffold size of 278,077 kb. The k-mer histograms indicate an diploid genome size of ∼720-730 Mb, which is smaller than the total length due to high heterozygosity, estimated at 1.25%. A comparison with a recently published European oak (Q. robur) nuclear sequence indicates 93% similarity. The Q. lobata chloroplast genome has 99% identity with another North American oak, Q. rubra Preliminary annotation yielded an estimate of 61,773 predicted protein-coding genes, of which 71% had similarity to known protein domains. We searched 956 Benchmarking Universal Single-Copy Orthologs, and found 863 complete orthologs, of which 450 were present in > 1 copy. We also examined an earlier version (v0.5) where duplicate haplotypes were removed to discover variants. These additional sources indicate that the predicted gene count in Version 1.0 is overestimated by 37-52%. Nonetheless, this first draft valley oak genome assembly represents a high-quality, well-annotated genome that provides a tool for forest restoration and management practices.

| S-EPMC5100847 | biostudies-literature

Foraging patterns of acorn woodpeckers (Melanerpes formicivorus) on valley oak (Quercus lobata Nee) in two California oak savanna-woodlands.

Project description:Landscape characteristics and social behavior can affect the foraging patterns of seed-dependent animals. We examine the movement of acorns from valley oak (Quercus lobata) trees to granaries maintained by acorn woodpeckers (Melanerpes formicivorus) in two California oak savanna-woodlands differing in the distribution of Q. lobata within each site. In 2004, we sampled Q. lobata acorns from 16 granaries at Sedgwick Reserve in Santa Barbara County and 18 granaries at Hastings Reserve in Monterey County. Sedgwick has lower site-wide density of Q. lobata than Hastings as well as different frequencies of other Quercus species common to both sites. We found acorn woodpeckers foraged from fewer Q. lobata seed source trees (K(g) = 4.1 ± 0.5) at Sedgwick than at Hastings (K(g) = 7.6 ± 0.6) and from fewer effective seed sources (N(em)* = 2.00 and 5.78, respectively). The differences between sites are due to a greater number of incidental seed sources used per granary at Hastings than at Sedgwick. We also found very low levels of seed source sharing between adjacent granaries, indicating that territoriality is strong at both sites and that each social group forages on its own subset of trees. We discovered an interesting spatial pattern in the location of granaries. At Sedgwick, acorn woodpeckers situated their granaries within areas of higher-than-average tree density, while at Hastings, they placed them within areas of lower-than-average tree density, with the outcome that granaries at the two sites were located in areas of similar valley oak density. Our results illustrate that landscape characteristics might influence the number of trees visited by acorn woodpeckers and the locations of territories, while woodpecker social behavior, such as territoriality, shapes which trees are visited and whether they are shared with other social groups.

| S-EPMC3074073 | biostudies-literature

Microsatellite primer development for post oak, Quercus stellata (Fagaceae).

Project description:The American Cross Timbers forest ecosystem runs from southeastern Kansas to Central Texas and is primarily composed of post oak (Quercus stellata). This old-growth forest currently occupies only about 2% of its ancestral range. To facilitate genetic research on this species, we developed microsatellite primers specific to post oak from reduced genomic libraries. • Two Q. stellata individuals, sampled from the northern and southern range of the post oak forest, were subject to genomic reduction and 454 pyrosequencing. Bioinformatic analysis identified putative microsatellites from which 12 polymorphic primer sets were screened on three populations. The number of alleles observed ranged from five to 20 across all populations, while observed and expected heterozygosity values ranged from 0.05 to 0.833 and 0.236 to 0.893, respectively, within individual populations. • We report the development of microsatellite markers, specific to post oak, to aid the study of genetic diversity and population structure of extant forest remnants.

| S-EPMC4189500 | biostudies-literature

The first complete chloroplast genome of Quercus coccinea (Scarlet Oak) and its phylogenetic position within Fagaceae.

Project description:Quercus coccinea is a native to North America, which grows well in acidic soil and resists cold to extreme low temperature -40 °C. The chloroplast (cp) genome of Q. coccinea, sequenced based on next-generation platform (NEOSAT), is 161,298 bp in size. The cp genome encodes 133 genes, including 88 protein-coding genes (PCGs), 8 rRNA genes, and 37 tRNA genes. Phylogenetic relationship analysis based on complete cp genome sequences exhibited that both of Q. coccinea and Q. rubra were phylogenetically closer to Q. aliena var. Acutiserrata.

| S-EPMC7707449 | biostudies-literature

PacBio Iso-Seq transcriptome for California Valley Oak, Quercus lobata (SW786)

Project description:Iso-Seq "full length" transcript sequences were used as one of many guides informing gene model annotation of the Valley Oak genome sequence.

2021-05-22 | GSE174827 | GEO

Analysing branching pattern in plantations of young red oak trees (Quercus rubra L., Fagaceae).

Project description:Branching patterns of the growth units of monocyclic or bicyclic annual shoots on the main axis of 5-year-old red oaks were studied in a plantation in south-western France. For each growth unit, the production of axillary structures associated with each node was described in the form of a sequence. For a given category of growth units, homogeneous zones (i.e. zones in which composition in terms of type of axillary production does not change substantially) were identified on such sequences using a dedicated statistical model called a hidden semi-Markov chain. For instance, on the first growth unit of bicyclic annual shoots, a zone with 1-year-delayed branches was found systematically below a zone with buds and one-cycle-delayed branches. Branching patterns shown by the growth unit of monocyclic annual shoots and on the second growth unit of bicyclic annual shoots were very similar. Branches with a 1-year delay in development tended to be polycyclic at the top of the growth unit and monocyclic lower down. The number of nodes shown by the branched zone of the growth unit of monocyclic annual shoots was stable, irrespective of the total number of nodes of the growth unit. In contrast, the second growth unit of bicyclic annual shoots exhibited a correlation between the number of nodes in the branching zone and the total number of nodes. The contribution made by this method to understanding plant functioning is discussed.

| S-EPMC4241068 | biostudies-literature

The complete chloroplast genome sequence of Quercus gilva（Fagaceae）.

Project description:Quercus gilva is classified as the national second-class protective tree species in China and is widely distributed in Middle East Asia. We determined the complete chloroplast genome sequence for Q. gilva using Illumina sequencing data. The complete chloroplast sequence is 160,763 bp, including large single-copy (LSC) region of 90,292 bp, small single-copy (SSC) region of 18,831 bp, and a pair of invert repeats (IR) regions of 25,820 bp. Plastid genome contains 128 genes, 80 protein-coding genes, 40 tRNA genes, and 8 rRNA genes. Phylogenetic analysis based on 26 chloroplast genomes indicates that Q. gilva is closely related to Q. sichourensis in Fagaceae.

| S-EPMC7687598 | biostudies-literature

The complete chloroplast genome sequence of Quercus myrsinifolia (Fagaceae).

Project description:Quercus myrsinifolia Blume is an evergreen oak tree species native to East Asia, and is also one of the dominant trees of subtropical evergreen broad-leaved forests. In this study, we sequenced and analysed the complete chloroplast (cp) genome of the species. The circular genome is 160,803 bp in size, consisting of two copies of inverted repeat (IR) regions of 25,840 bp, one large single-copy (LSC) region of 90,223 bp, and one small single-copy (SSC) region of 18,900 bp. It encodes a total of 114 unique genes, including 80 protein-coding genes, 30 tRNA genes, and four rRNA genes. Phylogenetic analysis based on 30 cp genome sequences indicated that Q. myrsinifolia was among the members of section Cyclobalanopsis, and was most closely related to Q. sichourensis.

| S-EPMC7706793 | biostudies-literature

The complete chloroplast genome sequence of Quercus phillyraeoides (Fagaceae).

Project description:Quercus phillyraeoides A. Gray is an evergreen oak species native to East Asia, and it plays a vital role in mountain ecosystems. In this study, we assembled the complete chloroplast genome of Q. phillyraeoides based on sequencing data. The genome was circular and 161,384 bp in length, consisting of a large single-copy region (90,617 bp), small single-copy region (19,035 bp), and two short inverted repeat regions (25,866 bp). We found that the cp genome encodes for 131 genes, including 85 protein-coding genes (PCGs), 8 rRNA genes, and 37 tRNA genes. The results of the phylogenetic analysis of the complete cp genome sequence illustrated that Q. phillyraeoides is a member of the section Quercus and it is most closely related to Q. tarokoensis.

| S-EPMC7748451 | biostudies-literature

The complete chloroplast genome of Quercus fabri (Fagaceae) from China.

Project description:The complete chloroplast (cp) genome sequence of Quercus fabri Hance has been characterized in this study. The length of cp genome was 161,227 bp, containing a large single-copy region (LSC) of 90,539 bp and a small single-copy region (SSC) of 19,048 bp, which were separated by a pair of 25,820 bp inverted repeat regions (IRs). The genome contained 134 genes, including 86 protein-coding genes, 40 tRNA genes, and 8 rRNA genes. The overall GC content is 36.82%. Further, phylogenetic analysis suggested that Q. fabri is clustered to section Quercus.

| S-EPMC7706987 | biostudies-literature