DNA overview

cpDNA (plastid genomes, or plastomes)

The plastid genome of Malvaceae, like those of the majority of plants has a circular map divided into large and small single copy (LSC, SSC) regions separated by inverted repeat (IR) regions. It is generally considered that the normal state for the genome is a circular DNA molecule, but doubt has been cast on the ubiquity of this form; linear DNA molecules are frequently seen under microscopic investigation, and there are conflicting explanations - either that they are the result of breakage during preparation of samples, or that this is a common configuration in the natural state [1]. It has been convincingly shown that a sample of angiosperms, including several species of Malvaceae, display heteroplasty, with individuals containing a mixture of chloroplasts with one of two different structural haplotypes, differing in the orientation of the SSC region [2], and this may be reasonably extrapolated to Malvaceae (and angiosperms) in general.

A total of at least 591 plastid sequences for Malvaceae are available at GenBank, DataDryad [3,4] or the Pilbara Sequence Project [5]. At least another 32 have been described in the literature.

At least 447 plastid genome sequences are deposited in GenBank for Malvaceae.

The Pilbara Sequence Project adds another 76, and expands taxonomic coverage to include the bytternioid tribes Hermanieae and Lasiopetaleae. It includes several grewioids, but does not much expand the taxonomic coverage of that subfamily. An additional 70 sequences are available on DataDryad [3, 4] (some of these are available on GenBank, but the correspondence between sequences on two sites is unclear).

There are number of papers which report additional sequences, where I haven't been able to locate the sequences. A paywalled paper reports 3 sequences for Abelmoschus esculentus cultivars [a]. A Chinese language paper [6] reports the de novo sequencing of 29 taxa. It also references short read archives for 8 species. Another paper on Gossypium hirsutum reports 17 de novo sequences, and 7 extracted from GenBank's Short Reads Archive [7]; while all sequences are stated to have been submitted to GenBank, and GenBank reference codes are given, the latter are not available in GenBank.

The published sequences do not provide uniform coverage of the family, and until recently provided incomplete coverage on a broad scale. Two years ago, approaching half the sequences were Gossypium, reflecting the importance of cotton as a fibre crop. Even now it represents about 20% of all sequences, have been overtaken in number by Hibiscus, where a lot of Hibiscus syriacus cultivars have been sequenced. Early sequences had a bias to crop species such as Abelmoschus esculentus (okra), Corchorus capsularis (jute), Corchorus olitorius (jute), Durio zibethinus (durian), Hibiscus cannabinus (kenaf) and Theobroma cacao (cacao) and ornamentals such as Hibiscus mutabilis (Confederate rose), Hibiscus rosa-sinensis (tropical hibiscus) and Hibiscus syriacus (hardy shrub hibiscus), with clusters in Tilia and the sterculioid genera Firmiana and Heritiera, with the absence of Cola nitida (kola) being striking.

It might be possible to extract further plastid genome sequences from GenBank's Short Reads Archive. While most data for malvaceous taxa therein is for taxa for which plastid genomes have been published, there is data for the bombacoids Adansonia (7 species), Ceiba (2 species), Chiranthodendron pentadactylon, Eriotheca macrophylla, Fremontodendron californicum, Gyranthera amphibiolepis, Huberodendron swietenioides, Pseudobombax ellipticum, Scleronema micranthum and Spirotheca rosea; the brownlowioids Brownlowia (3 species), Berrya javanica, Carpodiptera (2 species), Christiana africana, Diplodiscus paniculatus, Indagator fordii, and Pentace (2 species); the byttnerioids Abroma angustum, Androcalva fragifolia, Ayenia (3 species), Byttneria aculeata, Dicarpidium monoicum, Glossostemon bruguieri, Guazuma ulmifolia, Guichenotia (2 species), Hannafordia (2 species), Hermannia (2 species), Herrania (2 species), Kleinhovia hospita, Lasiopetalum (2 species), Leptonychia (2 species), Lysiosepalum (2 species), Megatritheca grossedenticulata, Melochia (2 species), Scaphopetalum thonneri, Seringia (2 species), Theobroma (5 species) and Thomasia (2 species); the dombeyoids Burretiodendron esquirolii, Cheirolaena linearis, Dombeya (2 species), Eriolaena candollei, Helmiopsis sp., Helmiopsiella madagascariensis, Melhania (2 species), Pentapetes phoenicea, Pterospermum (2 species), Ruizia cordata and Trochetiopsis ×benjaminii; the grewioids Ancistrocarpus densispinosus, Apeiba (2 species), Clappertonia ficifolia, Colona aequilateralis, Desplatsia (2 species), Duboscia viridiflora, Eleutherostylis renistipulata, Entelea arborescens, Erinocarpus nimmonii, Glyphaea (2 species), Goethalsia meiantha, Grewia (4 species), Heliocarpus (2 species), Hydrogaster trinervis, Luehea (2 species), Lueheopsis rosea, Microcos antidesmifolia, Mollia (2 species), Pseudocorchorus rostratus, Sparmannia (2 species), Trichospermum mexicanum, Triumfetta pilosa and Vasivaea alchorneoides; the helicteroids Coelostegia sp., Helicteres (2 species), Kostermansia malayana, Mansonia altissima, Neesia sp., Reevesia (2 species), Triplochiton scleroxylon and Ungeria floribunda, and the malvoids Allosidastrum pyramidatum, Alyogyne (2 species), Anoda (2 species), Asterotrichion discolor, Azanza thespesioides, Batesimalva killipii, Callirhoe (2 species), Camptostemon schultzii, Cephalohibiscus peekelii, Cristaria (19 species), Decaschistia byrnesii, Fuertesimalva jacens, Gaya (2 species), Gossypioides kirkii, Herissantia crispa, Hibiscadelphus wilderianus, Hibiscus (7 species), Howittia trilocularis, Humbertiella (2 species), Kearnemalvastrum lacteum, Kitaibela vitifolia, Kokia drynarioides, Kydia sp., Lagunaria patersonia, Lawrencia berthae, Leconophora (2 species), Malva (3 species), Matisia (2 species), Megistostegium (3 species), Napaea dioica, Nayariophyton zizyphifolium, Papuodendron lepidotum, Pavonia (4 species), Pentaplaris davidsmithii, Phragmotheca (2 species), Phymosia umbellata, Quararibea (2 species), Radyera farragei, Robinsonella mirandae, Sida (2 species), Talipariti (4 species), Thespesia garckeana, Urena australiensis and Wercklea horrida; and the sterculioids Acropogon schumanniana, Brachychiton bidwillii, Firmiana papuana, Franciscodendron laurifolium, Heritiera utilis, Hildegardia barteri, Neoregnellia cubensis, Pterygota brasiliensis, Scaphium macropodum and Sterculia (3 species). In addition the Short Reads Archive contains further entries duplicating taxa for which plastomes are published. Eight of the Short Read Archives were used in the Chinese language paper mentioned above [6], but most of those correspond to already published plastomes.

While plastomes cannot always be extracted from a Short Reads Archive [8], if all potentially available sequences were used that would be more or less enough for a backbone phylogeny of Malvaceae; the most noticeable omission is Mortoniodendron (basal in Tilioideae).

Coverage remains uneven with 3 sequences from Byttnerieae, 22 from Theobromateae (most Theobroma cacoa), 1 from Hermannieae, 5 from Lasiopetaleae, 9 from Grewieae, 23 from Apeibeae (mostly Corchorus and Triumfetta), 20 from Helictereae (18 of which are Reevesia), 5 from Durioneae (all Durio), 54 from Tilioideae (mostly Tilia), 43 from Sterculioideae, 5 from Brownlowioideae, 15 from Dombeyoideae, 12 from Bombacoideae, 162 from Hibisceae, 127 from Gossypieae and 68 from Malveae.

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