WEEK 5 READING GUIDE AND VOCABULARY
Rensing et al 2008 (first Moss genome): PARTS OF THIS PAPER ARE NEEDED TO
COMPLEMENT THE BANK READING (see syllabus): Abstract, Intro, Fig. 1, Ks plot,
and conclusions.
This article has lots of quantitative facts about the different sequence types, no need to
focus on the numbers, focus on the overall quality of the sequences found (what types
of gene families? Are there duplications? Are TEs and repetitive elements abundant? T
Chamydomonas reinhardtii is used as a unicellular green alga representative (Fig. 4).
S3 figure (Ks plot) is useful and posted.
See moss life cycle here http://moss.nibb.ac.jp/
 Bryophyte (see Pires tree week 4 vocab), haploid phase, diploid phase, gametes,
 whole-genome shotgun sequencing, scaffold, expressed sequence tag (EST),
alternative splicing,
 LTR-Rs (long terminal repeat retrotransposons), solo LTR (repeat without
transposon).
 Ks distribution plot (as a method to estimate past whole genome duplications),
tandemly arrayed genes, Pfam domain names (http://pfam.xfam.org/),
 tandemly arrayed genes
 two component signaling
 dessication tolerance, lignin, cutin, phototoxic stress tolerance.
Banks 2011: (Selaginella genome, a lycopod)
This article presents the first genome of a lycopod, a representative of the earliest
lineage of vascular plants. The authors emphasize numbers of gene families present
in relation to other genomes sequenced at the time: an alga, a moss, for which you
need to read sections (see above), and several angiosperms. They are trying to test
which transitions required the most new gene families, comparing the transition
from water to land, from non-vascular to vascular and finally to seed plants and
angiosperms.
The article is short (2 figures), and goes together with 2 figures and parts of the text
of the moss genome paper (see above and syllabus).
Kim et al 2014 (hot pepper genome):
Every genome needs to have a story in order to be publishable; this one is about the
evolution of “hotness” via capsaicin metabolism. It also ties nicely into our
domestication sessions, as they compare the domesticated and wild species. The
paper includes a story of neofunctionalization, another recurrent topic in evo-devo.
Do not get lost in the sequencing acquisition/assembly details (but worth
appreciating how involved this can be), keep your eye in the broader topics
emerging from the analysis of the data.