We sought to learn more about the identity of Betula kenaica W.H.Evans, the Kenai birch, which has remained somewhat enigmatic since its description in 1899.
Tissue samples were collected from two birch specimens on August 12, 2019. Cuttings were taken from a B. kenaica individual ("BK01" in this dataset, https://arctos.database.museum/guid/KNWR:Herb:11553) from Kasilof Beach, Kasilof, Alaska, one of the two type localities of B. kenaica. Cuttings were also taken from a Betula pendula subsp. mandshurica (Regel) Ashburner & McAll. individual ("BP01" in this dataset, https://arctos.database.museum/guid/KNWR:Herb:11556) from Soldotna, Alaska.
The cuttings were shipped to SNPsaurus (Eugene, Oregon, USA, https://www.snpsaurus.com/) for whole genome sequencing.
This dataset includes specimen collection data, the sample sample submission form, and the three files delivered by SNPsaurus.
Notes
Notes from SNPsaurus:
2019-09-10:
We were having some issues with the DNA isolated from the fresh material (sticky, hard to work with). We have the libraries on a SMRT cell in line to be sequenced...maybe in a week. But we are doing it as a test to make sure it all looks good. If it does look good we will be able to go for full sequencing soon after.
2019-09-20:
We ran out the two libraries made and they ended up getting 35X read depth data back, so I ran BK01 through the assembler as a test. It definitely all looks good. It assembled to 330 Mb with a N50 contig length of 80kb...not bad for not full sequencing. I did a quick blastn of the contigs and they hit Betula and Quercus and other trees so that all looks good as well. I think Allison had to run everything she had but we will be motivated to do another round of extractions and finish these off.
2019-11-25:
I have been fiddling with BP01...we doubled the read count but the assembly just isn't improving. BK01 got longer contigs after it got extra reads, so I ran the gene annotation and have a download link for you. I will start the gene annotation for BP01 and get that for you soon while we think about how we can get the assembly working better. [...] the DNA from that sample remained sticky and hard to work with so that likely affected the library prep/DNA fragment length.
