date, the only Charophyte draft genome available through NCBI is that of
Klebsormidium nitens (formerly K. flaccidum) (Hori et al. 2014).
• Liverworts – A draft genome for a single liverwort species (Marchantia
polymorpha) is in NCBI Genome.
• Hornworts – No draft sequences are available.
• Lycophytes (club mosses, firmosses, quillworts, scale trees, and spikemosses) –
The lycophytes are represented by two draft genomes, both representing the genus
Selaginella. The S. moellendorffii genome is in fairly good shape (Banks et al.
2011), while the S. kraussiana genome is still quite fragmented (Ge et al. 2016).
• Monilophytes (ferns and horsetails) – While fern genomes are being explored,
there are no fern draft genomes in NCBI (Wolf et al. 2015). Horsetails have
enormous genomes (12.6–29.7 Gb; Bennett and Leitch 2012b), and thus it is
unlikely that a reference-quality horsetail genome will be available anytime soon.
• Mosses – The first draft of the Physcomitrella patens genome was published
10 years ago (Rensing et al. 2008). Since then, the genome has been greatly
improved; it now consists of <2,000 scaffolds (Lang et al. 2018). It is the sole
moss draft genome in NCBI.
• Gymnosperms (conifers, gnetophytes, cycads, and ginkgo) – While gnetophytes,
cycads, and ginkgo have relictual distributions, some coniferous gymnosperms
(most notably, pines, spruces, firs, Douglas firs, larches, cedars, and junipers)
dominate many of the world’s temperate and boreal forest ecosystems (Farjon
2008). Moreover, in a number of regions, the value of conifers as sources of
lumber and pulp/paper is enormous (Farjon 2010).
All gymnosperms have large genomes (mean 1C DNA content ¼ 17.7 Gb) with
the conifers having genomes between 8.9 and 35.3 Gb (Murray et al. 2012). Initially,
socioeconomic value was the driving force in determining which gymnosperm
genomes were subjects of genome sequencing efforts; in other words, the first
gymnosperm species were all large genome conifers in the family Pinaceae. To
date, draft genome sequences have been generated for Picea abies (Nystedt et al.
2013), Pinus taeda (Neale et al. 2014; Zimin et al. 2017), and Picea glauca (Birol
et al. 2013; Warren et al. 2015a) which possess 1C DNA contents of 19.6, 21.6, and
15.8 Gb, respectively (Murray et al. 2012). None of these genomes approach reference genome quality, although they have provided considerable insight into conifer
evolution. A genome sequencing project on Douglas fir (Pseudotsuga menziesii) is
now underway as well (1C ¼ 18.6 Gb; Murray et al. 2012). More recently, draft
genomes have been published for Ginkgo biloba (1C ¼ 10.61 Gb; Guan et al. 2016)
and the gnetophyte Gnetum montanum (1C ¼ 4.2 Gb; Wan et al. 2018).
Although Table 3 is chock full of angiosperms and contains a few chlorophyte
algae, there is definitely a skew toward certain clades. Three of the four chlorophytes
are in the same family; two are in the same genus. Of the >400 angiosperm families
(Haston et al. 2009), members of 23 families are represented in Table 3. The families
with the highest levels of representation are the grasses (Poaceae), the legumes
(Leguminosae or Fabaceae), the crucifers (Brassicaceae), the mallows (Malvaceae),
the roses (Rosaceae), and the nightshades (Solanaceae) with 17, 12, 9, 4, 4, and
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Klebsormidium nitens (formerly K. flaccidum) (Hori et al. 2014).
• Liverworts – A draft genome for a single liverwort species (Marchantia
polymorpha) is in NCBI Genome.
• Hornworts – No draft sequences are available.
• Lycophytes (club mosses, firmosses, quillworts, scale trees, and spikemosses) –
The lycophytes are represented by two draft genomes, both representing the genus
Selaginella. The S. moellendorffii genome is in fairly good shape (Banks et al.
2011), while the S. kraussiana genome is still quite fragmented (Ge et al. 2016).
• Monilophytes (ferns and horsetails) – While fern genomes are being explored,
there are no fern draft genomes in NCBI (Wolf et al. 2015). Horsetails have
enormous genomes (12.6–29.7 Gb; Bennett and Leitch 2012b), and thus it is
unlikely that a reference-quality horsetail genome will be available anytime soon.
• Mosses – The first draft of the Physcomitrella patens genome was published
10 years ago (Rensing et al. 2008). Since then, the genome has been greatly
improved; it now consists of <2,000 scaffolds (Lang et al. 2018). It is the sole
moss draft genome in NCBI.
• Gymnosperms (conifers, gnetophytes, cycads, and ginkgo) – While gnetophytes,
cycads, and ginkgo have relictual distributions, some coniferous gymnosperms
(most notably, pines, spruces, firs, Douglas firs, larches, cedars, and junipers)
dominate many of the world’s temperate and boreal forest ecosystems (Farjon
2008). Moreover, in a number of regions, the value of conifers as sources of
lumber and pulp/paper is enormous (Farjon 2010).
All gymnosperms have large genomes (mean 1C DNA content ¼ 17.7 Gb) with
the conifers having genomes between 8.9 and 35.3 Gb (Murray et al. 2012). Initially,
socioeconomic value was the driving force in determining which gymnosperm
genomes were subjects of genome sequencing efforts; in other words, the first
gymnosperm species were all large genome conifers in the family Pinaceae. To
date, draft genome sequences have been generated for Picea abies (Nystedt et al.
2013), Pinus taeda (Neale et al. 2014; Zimin et al. 2017), and Picea glauca (Birol
et al. 2013; Warren et al. 2015a) which possess 1C DNA contents of 19.6, 21.6, and
15.8 Gb, respectively (Murray et al. 2012). None of these genomes approach reference genome quality, although they have provided considerable insight into conifer
evolution. A genome sequencing project on Douglas fir (Pseudotsuga menziesii) is
now underway as well (1C ¼ 18.6 Gb; Murray et al. 2012). More recently, draft
genomes have been published for Ginkgo biloba (1C ¼ 10.61 Gb; Guan et al. 2016)
and the gnetophyte Gnetum montanum (1C ¼ 4.2 Gb; Wan et al. 2018).
Although Table 3 is chock full of angiosperms and contains a few chlorophyte
algae, there is definitely a skew toward certain clades. Three of the four chlorophytes
are in the same family; two are in the same genus. Of the >400 angiosperm families
(Haston et al. 2009), members of 23 families are represented in Table 3. The families
with the highest levels of representation are the grasses (Poaceae), the legumes
(Leguminosae or Fabaceae), the crucifers (Brassicaceae), the mallows (Malvaceae),
the roses (Rosaceae), and the nightshades (Solanaceae) with 17, 12, 9, 4, 4, and
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167