Pan-cancer analysis of whole genomes

Cancer is driven by genetic change, and the advent of massively parallel sequencing has enabled systematic documentation of this variation at the whole-genome scale(1-3). Here we report the integrative analysis of 2,658 whole-cancer genomes and their matching normal tissues across 38 tumour types from the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA). We describe the generation of the PCAWG resource, facilitated by international data sharing using compute clouds. On average, cancer genomes contained 4-5 driver mutations when combining coding and non-coding genomic elements; however, in around 5% of cases no drivers were identified, suggesting that cancer driver discovery is not yet complete. Chromothripsis, in which many clustered structural variants arise in a single catastrophic event, is frequently an early event in tumour evolution; in acral melanoma, for example, these events precede most somatic point mutations and affect several cancer-associated genes simultaneously. Cancers with abnormal telomere maintenance often originate from tissues with low replicative activity and show several mechanisms of preventing telomere attrition to critical levels. Common and rare germline variants affect patterns of somatic mutation, including point mutations, structural variants and somatic retrotransposition. A collection of papers from the PCAWG Consortium describes non-coding mutations that drive cancer beyond those in the TERT promoter(4); identifies new signatures of mutational processes that cause base substitutions, small insertions and deletions and structural variation(5,6); analyses timings and patterns of tumour evolution(7); describes the diverse transcriptional consequences of somatic mutation on splicing, expression levels, fusion genes and promoter activity(8,9); and evaluates a range of more-specialized features of cancer genomes(8,10-18).Peer reviewe

Potential Bands of Sentinel-2A Satellite for Classification Problems in Precision Agriculture

Various indices are used for assessing vegetation and soil properties in satellite remote sensing applications. Some indices, such as normalized difference vegetation index (NDVI) and normalized difference water index (NDWI), are capable of simply differentiating crop vitality and water stress. Nowadays, remote sensing capabilities with high spectral, spatial and temporal resolution are available to analyse classification problems in precision agriculture. Many challenges in precision agriculture can be addressed by supervised classification, such as crop type classification, disease and stress (e.g., grass, water and nitrogen) monitoring. Instead of performing classification based on designated indices, this paper explores direct classification using different bands information as features. Land cover classification by using the recently launched Sentinel-2A image is adopted as a case study to validate our method. Four approaches of featured band selection are compared to classify five classes (crop, tree, soil, water and road) with the support vector machines (SVMs) algorithm, where the first approach utilizes traditional empirical indices as features and the latter three approaches adopt specific bands (red, near infrared and short wave infrared) related to indices, specific bands after ranking by mutual information (MI), and full bands of on board sensors as features, respectively. It is shown that a better classification performance can be achieved by directly using the selected bands after MI ranking compared with the one using empirical indices and specific bands related to indices, while the use of all 13 bands can marginally improve the classification accuracy than MI based one. Therefore, it is recommended that this approach can be applied for specific Sentinel-2A image classification problems in precision agriculture

Three new records of Lamiaceae from China and Uzbekistan

Zhao, Yue, Chi, Jian-Cai, Chen, Ya-Ping, Liang, Cun-Zhu, Turginov, Orzimat T., Pulatov, Sardor O., Rakhmatov, Abdurashid A., Aromov, Tolmas B., Xiang, Chun-Lei (2022): Three new records of Lamiaceae from China and Uzbekistan. Phytotaxa 531 (2): 111-111, DOI: 10.11646/phytotaxa.531.2.

Nepeta badachschanica Kudrjasch., Bot. Mater. Gerb. Inst. Bot. Zool. Akad. Nauk Uzbeksk. S. S. R.

Nepeta badachschanica Kudrjasch., Bot. Mater. Gerb. Inst. Bot. Zool. Akad. Nauk Uzbeksk. S.S.R. 9: 18. 1947. Type: — Tajikistan, Pamir occidentalis. Inter fl. Jazgulem et Vancz, in viciniis pag. Chej-Chak, 1620 m, 29 September 1932, Lanina 1240 (holotype: LE!). Perennial herbs, 30–50 cm tall. Numerous stems, stout, almost branched from the base, 3–4 mm diameter, white pubescent; internodes 3–6 cm long. Leaves opposite, lamina almost round, at the base slightly heart-shaped, 1.5–3.5 cm long, margine dentate-crenate, abaxially strongly wrinkled, with depressed veins on both sides, densely white pubescent; petioles densely white pubescent, 1.2–4 cm long. Verticillasters with lower peduncles longer than 1 cm, the upper ones are only 0.3–0.5 cm long; floral leaves similar to stem leaves, lamina 7–8 mm long; petioles 5–6 mm long; the uppermost floral leaves are narrow, entire, lanceolate-linear, 5–6× 1 mm, sessile, white pubescent; the bracts are shorter than half of the calyx, densely pubescent, curved upward; verticillasters 8–15 mm in diameter at fruiting, consisting of 6–8 flowers. The calyx is tubular, two-lipped, almost sessile or on a very short peduncle with 13 veins; the upper lip is three-toothed; the lanceolate teeth are 2 times shorter than the tube, the lower lip is bipartite, the teeth are narrower, 1.5 times shorter than the upper ones. Flowering calyx 7–8 mm, fruiting calyx 9–10 mm, densely pubescent. Corolla 12–13 mm long; tube protrudes slightly from the calyx, expanding towards the pharynx. The upper lip of the corolla is two–lobed, oval, pubescent outside, the lower lobe is tripartite, the lateral lobes are semicircular, triangular, the middle lobe is much wider, not dissected along the edge (Fig. 4). Phenology: —Flowering from July to September, fruiting from September to October. Distribution, habitat and ecology: — Uzbekistan and Tajikistan; new record for Uzbekistan, occurring in southern part Uzbekistan mountain, Babatag and Gissar ridge, mountain Tschulbair. This species grows in colored clays and fine-soil hillsides, 900–1600 m (Tschukervanik 1987) (Fig. 5). Etymology: —The specific epithet “ badachschanica ” derived from Badakhshan, Gorno-Badakhshan Autonomous region in Tajikistan, the type locality of this species. Common name (assigned here): — Badakhshon zufosi (Uzbekistan name). Taxonomic notes: —Morphologically, Nepeta badachschanica is obviously different from other Central Asia species by having numerous leafy axillary branches (vs. branches less) and general inflorescence paniculate (vs. less branched paniculate) (Pojarkova 1954). Conservation status in Uzbekistan: — Nepeta badachschanica Kudrjasch. is distributed in only two localities of southern Uzbekistan: the first population is in the mountain Babatag, the second population is in Gissar ridge, Tschulbair mountain. The distance between the populations is 50 km. In total, there are approximately more than 2,000 individuals in two populations. The populations are not declining; there are no current threats, and the species is very unlikely to become Extinct or Critically Endangered in a short time. Thus N. badachschanica should be classified as Least Concern (LC) based on the IUCN Red List Categories and Criteria (IUCN 2019). Additional specimens examined: UZBEKISTAN: Surkhandarya, mountain Babatag, near village Kuruksai, 38°18’15.26”N, 68°16’29.09” E, 12 Jun. 2019, O . T. Turginov s.n. (TASH!); Surkhandarya, South western Gissar, mountain Tschulbair, near village Sina, 38°23’19.13” N, 67°39’40.04” E, 24 May 2020, Pulatov et al. 604-619 (TASH!).Published as part of Zhao, Yue, Chi, Jian-Cai, Chen, Ya-Ping, Liang, Cun-Zhu, Turginov, Orzimat T., Pulatov, Sardor O., Rakhmatov, Abdurashid A., Aromov, Tolmas B. & Xiang, Chun-Lei, 2022, Three new records of Lamiaceae from China and Uzbekistan, pp. 111 in Phytotaxa 531 (2) on page 111, DOI: 10.11646/phytotaxa.531.2.3, http://zenodo.org/record/586918

Phlomoides zenaidae Adylov, Kamelin & Makhmedov

Phlomoides zenaidae (Popov)Adylov, Kamelin & Makhmedov, in Opred.Rast.Sred. Azii 9: 101. 1987. ≡ Eremostachys zenaidae Popov, in Nouv. Mem. Soc. Nat. Mosc. xix. 71. 1941. Type: — Kazakhstan, Eastern Tianshan mountain, Tscharyn river, arid hillsides, 20 June 1937, M. G . Popov. s.n. (holotype: LE!; isotype: LE!). Perennial herbs, 40–60 cm tall. Roots linear-tuberous. Stems erect, subquadrangular, purple, 1–3 branched, glabrous. Basal leaves with petioles 4–6 cm long, white, margin white pilose; lamina oblong, margin coarsely crenate, thick papery, 10 × 3–4 cm, adaxially green, glabrous, abaxially light green, with sparse, simple and stellate pilose hairs; stem leaves opposite, similar to basal leaves; petioles short, 0.5–1 cm long. Verticillasters 6–10 flowered, distant; floral leaves sessile, rhombus-oblong, subglabrous, margin remotely dentate, shorter than verticillasters, gradually reduced upward; bracts ovate-lanceolate, 6–8 mm long, glabrous, margin sparsely ciliate. Calyx tubular-campanulate, ca. 18 mm long, glabrous outside, teeth subequal, 1.5–2 mm long, apical emarginate, with spines 1–1.5 mm long, tufted hairy inside. Corolla purple, ca. 3.5 cm long, 2-lipped; upper lip ca. 15 mm long, galeate, densely stellate tomentose outside, margin entire, glabrous inside, margin ciliate; lower lip 3-lobed, ca. 20 mm long, flabellate, middle lobe largest, oblong, lateral lobes ovate; tube slender, ca. 18 mm long, annulate pilose inside near base. Stamens 4, included, glabrous, posterior filaments with upwardly curved appendages at base. Style included, apex unequally 2-lobbed. Mericarps elliptic, glabrous (Fig. 1). Phenology: —Flowering from May to July, fruiting from July to September. Distribution, habitat and ecology: — China and Kazakhstan; new record for China, occurring in Nilka County, Xinjiang province. It grows on arid gravel hillsides, 1100–1200 m, together with other species, such as Ixiolirion songaricum Ping Yan (1996: 605), Scutellaria przewalskii Juzepczuk (1951: 400), Ziziphora tenuior Linnaeus (1753: 21), etc. (Fig. 2). Etymology: —The specific epithet refers to a Russian botanist Zinaida Petrovna Bochantseva. Common name (assigned here): —Xin jiang sha sui (Ǜḋỳffi; Chinese name). Taxonomic notes: —Morphologically, Phlomoides zenaidae is obviously different from other Chinese species by posterior lip being glabrous inside with an entire margin (vs. posterior lip bearded inside with a denticulate margin). Conservation status in China: — Phlomoides zenaidae is restricted to one locality in Nilka County, Xinjiang province. In total, approximately 1,000 individuals were found in a semiarid desert grassland. This species maybe easily threatened by habitat lose. Thus P. zenaidae should be classified as Vulnerable (VU: D1) based on the IUCN Red List Categories and Criteria (IUCN 2019). Additional specimens examined: KAZAKHSTAN: Almaty province, Zhungar Alata, Charin river, 1100 m, 21 May 2019, Ziyoviddin Yusupov & Maxhmudjanov Dilmurod ZD 1134 (KUN!); Zailiyskiy Alatau, eastern end of the Turaigyr ridge, near the Charyn river, rocky slopes, 15 May 1953, V. P . Goloskov s.n. (MW!). CHINA: Xinjiang province, Nilka County, Keling Village, 1200 m, 26 Sep. 2020, J. C . Chi 1265 (KUN!).Published as part of Zhao, Yue, Chi, Jian-Cai, Chen, Ya-Ping, Liang, Cun-Zhu, Turginov, Orzimat T., Pulatov, Sardor O., Rakhmatov, Abdurashid A., Aromov, Tolmas B. & Xiang, Chun-Lei, 2022, Three new records of Lamiaceae from China and Uzbekistan, pp. 111 in Phytotaxa 531 (2) on page 111, DOI: 10.11646/phytotaxa.531.2.3, http://zenodo.org/record/586918