REFERENCS
Altschul, S. F., Gish, W., Miller, W., Myers, E. W., & Lipman, D. J.
(1990). Basic local alignment search tool. Journal of Molecular
Biology , 215 (3), 403–410.
Ashburner, M., Ball, C. A., Blake, J. A., Botstein, D., Butler, H.,
Cherry, J. M., … & Sherlock, J. (2000). Gene Ontology: tool for
the unification of biology. Nature Genetics , 25 (1), 25-29.
Aradhya, M. K., Potter, D., Gao, F., & Simon, C. J. (2007). Molecular
phylogeny of Juglans (Juglandaceae ): a biogeographic
perspective.Tree
Genetics & Genomes, 3 (4), 363-378.
Bairoch, A., & Apweiler, R. (2000). The SWISS-PROT protein sequence
database and its supplement TrEMBL in 2000. Nuclc Acids Research ,28 (1), 45-48.
Benson, G. (1999). Tandem repeats finder: a program to analyze DNA
sequences. Nucleic Acids Research , 27 (2), 573-580.
Bai, W. N., Wang, W. T., & Zhang, D. Y. (2014). Contrasts between the
phylogeographic patterns of chloroplast and nuclear DNA highlight a role
for pollen mediated gene flow in preventing population divergence in an
East Asian temperate tree. Molecular Phylogenetics and Evolution ,81 , 37-48.
Bai, W. N., Wang, W. T., & Zhang, D. Y. (2016). Phylogeographic breaks
within Asian butternuts indicate the existence of a phytogeographic
divide in East Asia. New Phytologist , 209 (4), 1757-1772.
Bai, W. N., Yan, P. C., Zhang, B. W., Woeste, K. E., Lin, K., & Zhang,
D. Y. (2018). Demographically idiosyncratic responses to climate change
and rapid Pleistocene diversification of the walnut genus Juglans(Juglandaceae) revealed by whole‐genome sequences. New
Phytologist , 217 (4), 1726-1736.
Bi, D., Zhao, Y., Jiang, R., Wang, Y., Tian, Y., Chen, X., … & She,
G. (2016). Phytochemistry, bioactivity and potential impact on health ofJuglans : the original plant of walnut. Natural Product
Communications , 11 (6), 870-879.
Bie, T. D., Cristianini, N., Demuth, J. P., & Hahn, M. W. (2006). CAFE:
a computational tool for the study of gene family evolution.Bioinformatics , 22 (10), 1269-1271.
Boeckmann, B., Bairoch, A., Apweiler, R., Blatter, M. C., Estreicher,
A., Gasteiger, E., …& Schneider, M. (2003). The SWISS-PROT
protein knowledgebase and its supplement TrEMBL in 2003. Nucleic
Acids Research , 31 (1), 365-370.
Camacho, C., Coulouris, G., Avagyan, V., Ma, N., Papadopoulos, J.,
Bealer, K., …& Madden, T. L. (2009). BLAST+: architecture and
applications. BMC Bioinformatics , 10(1), 421.
Chen, Y. X., Chen, Y. S., Shi, C. M., Huang, Z. B., Zhang, Y., Li, S.
K., …& Chen, Q. (2018). SOAPnuke: A mapreduce acceleration
supported software for integrated quality control and preprocessing of
High-Throughput sequencing data. GigaScience , 7 (1),
gix120.
Chen, Y., Ma, T., Zhang, L. S., Kang, M. H., Zhang, Z. Y., Zheng, Z. Y.,
… & Yang, Y. Z. (2020). Genomic analyses of a “living fossil”:
the endangered dove-tree. Molecular Ecology Resources, 10 , 1-14
Choi, J. Y., Lye, Z. N., Groen, S. C., Dai, X., Rughani, P., Zaaijer,
S., … & Purugganan, M. D. (2020). Nanopore sequencing-based genome
assembly and evolutionary genomics of circum-basmati rice. Genome
Biology , 21 (1), 21.
Durand, N. C., Shamim, M. S., Machol, I., Rao, S. S., Huntley, M. H.,
Lander, E. S., …& Aiden, E. L. (2016). Juicer provides a
one-click system for analyzing loop-resolution Hi-C experiments.Cell Systems , 3 (1), 95-98.
Dudchenko, O., Batra, S. S., Omer, A. D., Nyquist, S. K., Hoeger, M.,
Durand, N. C., …& Aiden, E. L. (2017). De novo assembly of theAedes aegypti genome using Hic yields chromosome-length
scaffolds. Science , 356 (6333), 92-95.
Dang, M., Liu, Z.L., Chen, X., Zhang, T., Zhou, H. J., Hu, Y. H.,
Woeste, K., & Zhao P. (2015). Identification, development, and
application of 12 polymorphic EST-SSR markers for an endemic Chinese
walnut (Juglans cathayensis L.) using next-generation sequencing
technology. Biochemical Systematics and Ecology, 60 ,
74-80.
Dang, M., Zhang, T., Hu, Y. H., Zhou, H. J., Woeste, K., & Zhao P.
(2016). De novo assembly and characterization of bud, leaf and
flowers transcriptome from Juglans regia L. for the
identification and characterization of new EST-SSRs. Forests ,7 (10), 247.
Dang, M., Yue, M., Zhang, M., Zhao, G. F., & Zhao, P. (2019). Gene
introgression among closely related species in sympatric populations: a
case study of three walnut (Juglans ) species. Forests ,10 (11), 965.
Dong, X. G., Wang, Z., Tian, L. M., Zhang, Y., Qi, D., Huo, H. L.,
…& Cao, Y. F. (2019). De novo assembly of a wild pear
(Pyrus betuleafolia ) genome. Plant Biotechnology Journal ,18 (2), 581-595.
DeMaere, M. Z., & Darling, A. E. (2019). bin3C: Exploiting Hi-C
sequencing data to accurately resolve metagenome-assembled genomes.Genome Biology , 20 (1), 46.
Edgar, R.C., & Myers, E.W. (2005). PILER: identification and
classification of genomic repeats. Bioinformatics , 21 ,
152.
Feng, X. J., Zhou, H.J., Zulfiqar, S., Luo, X., Hu, Y. H., Feng, L.,
…& Zhao, P. (2018). The phytogeographic history of common walnut
in China. Frontiers in Plant Science , 9, 1399.
Fischer, S., Brunk, B. P., Chen F., Gao X., Harb O., Iodice, J. B.,
…& Stoeckert, C. J. (2011). Using OrthoMCL to assign proteins to
OrthoMCL-DB groups or to cluster proteomes into new ortholog groups.
Current Protocols in Bioinformatics, 6(6), 12-19.
Griffiths-Jones, S., Moxon, S., Marshall, M., Khanna, A., Eddy, S. R.,
& Bateman, A. (2005). Rfam: annotating non-coding RNAs in complete
genomes. Nucleic Acids Research , 33 (1), 121-124.
Gross, S. S., Do, C. B., Sirota, M., & Batzoglou, S. (2007). CONTRAST:
a discriminative, phylogeny-free approach to multiple informantde
novogene prediction. Genome Biology , 8 (12), R267.
Haas, B. J., Salzberg, S. L., Zhu, W., Pertea, M., Allen, J. E., Orvis,
J., …& Wortman, J. R. (2008). Automated eukaryotic gene
structure annotation using EVidenceModeler and the Program to Assemble
Spliced Alignments. Genome Biology , 9 (1), R7.
Han, H., Woeste, K., Hu Y., Dang, M., Zhang, T., Gao, X. X., …&
Zhao, P. (2016). Genetic diversity and population structure of common
walnut (Juglans regia ) in China based on EST-SSRs and the nuclear
gene phenylalanine ammonia lyase (PAL ). Tree Genetics &
Genomes , 12 (6), 111–122.
Holt, C., & Yandell, M. (2011). MAKER2: an annotation pipeline and
genome-database management tool for second-generation genome projects.BMC Bioinformatics , 12 (1), 491.
Hu, Y. H., Woeste, K., & Zhao, P. (2017). Completion of the chloroplast
genomes of five Chinese Juglans and their contribution to
chloroplast phylogeny. Frontiers in Plant Science , 7, 1955.
Raval,
S.,
Gowda,
S. B.,
Singh,
D. D., &
Chandra,
N. R. (2005). A database analysis of jacalin-like lectins:
sequence-structure-function relationships. Glycobiology ,14 (12), 1247-1263.
Johnson, A. D., Handsaker, R. E., Pulit, S. L., & Nizzari, M. (2008).
SNAP: a web-based tool for identification and annotation of proxy SNPs
using HapMap. Bioinformatics , 24 (24), 2938-2939.
Jurka, J. (2000). Repbase Update: A database and an electronic journal
of repetitive elements. Trends in Genetics , 16 (9),
418-420.
Kanehisa, M., & Goto, S. (2000). KEGG: kyoto encyclopedia of genes and
genomes. Nucleic Acids Research , 28 (1), 27-30.
Kaori, I., & Murphy, D. (2013). Application of ggplot2 to
pharmacometric graphics. CPT: Pharmacometrics and Systems
Pharmacology , 2(10), e79.
Koonin, E. V., Fedorova, N. D., Jackson, J. D., Jacobs, A. R., Krylov,
D. M., Makarova, K. S., …& Natale, D. A. (2004). A comprehensive
evolutionary classification of proteins encoded in complete eukaryotic
genomes. Genome Biology , 5 (2), R7.
Koren, S., Walenz, B. P., Berlin, K., Miller, J. R., Bergman, N. H., &
Phillippy, A. M. (2017). Canu: scalable and accurate long-read assembly
via adaptive k-mer weighting and repeat separation. Genome
Research , 27 (5), 722-736.
Langmead, B., & Salzberg, S. L. (2012). Fast gapped-read alignment with
Bowtie 2. Nature Methods , 9 (4), 357.
Li, H. (2013). Aligning sequence reads, clone sequences and assembly
contigs with BWA-MEM. Genomics , 1303 , 3997.
Li,
J., Sun, J. X., Yu, H. Y., Chen, Z. Y., Zhao, X. Y., & Ruan, H. L.
(2013). Diarylheptanoids from the root bark of Juglans
cathayensis. Chinese Chemical Letters , 24 (6), 521-523.
Li,
Y. X.,
Ruan,
H. L., Zhou, X. F.,
Zhang,
Y. H.,
Pi,
H. F., &
Wu,
J. Z. (2008). Cytotoxic Diarylheptanoids from Pericarps of Juglans
cathayensis Dode. Chemical Research in Chinese Universities ,24 (4), 427-429.
Lowe, T. M., & Eddy, S. R. (1997). tRNAscan-SE: a program for improved
detection of transfer RNA genes in genomic sequence. Nucleic
Aacids Research , 25 (5), 955-964.
Maja T. G, & Chen N. S. (2009). Using RepeatMasker to identify
repetitive elements in genomic sequences. Current Protocols in
Bioinformatics , 4(4), 10.
Manning, W. E. (1978). The classification within the Juglandaceae.Annals of the Missouri Botanical Garden , 65 (4), 1058-1087.
Martínez-García, P. J., Crepeau, M. W., Puiu, D., Gonzalez-Ibeas, D.,
Whalen, J., Stevens, K. A., … & Neale, D. B. (2016). The walnut
(Juglans regia ) genome sequence reveals diversity in genes coding
for the biosynthesis of non-structural polyphenols. The Plant
Journal , 87, 507–532.
Nawrocki, E. P., & Eddy, S. R. (2013). Infernal 1.1: 100-fold faster
RNA homology searches. Bioinformatics, 29 (22), 2933-2935.
Panaro,
N.
J.,Yuen,
P. K.,
Sakazume,
T.,
Fortina,
P.,
Kricka,
L. J., &
Wilding,
P. (2000). Evaluation of DNA fragment sizing and quantification by the
Agilent 2100 Bioanalyzer. Clinical Chemistry , 46 (11),
1851-1853.
Servant, N.,
Varoquaux,
N.,
Lajoie,
B.R.,
Viara,
E., Chen, C.J., Vert, J.P., …& Barillot, E. (2015). HiC-Pro: an
optimized and flexible pipeline for Hi-C data processing. Genome
Biology , 16 (1), 259.
Simão, F. A., Waterhouse, R.M., Ioannidis, P., Kriventseva, E. V., &
Zdobnov, E.M. (2015). BUSCO: assessing genome assembly and annotation
completeness with single-copy orthologs. Bioinformatics ,31 (19), 3210-3212.
Shu, Z., Zhang, X., Yu, D., Xue, S., & Wang, H. (2016). Natural
hybridization between Persian walnut and Chinese walnut revealed by
simple sequence repeat markers. Journal of the American Society
for Horticultural Science , 141 (2), 146-150.
Slater, G. S. C., & Birney, E. (2005). Automated generation of
heuristics for biological sequence comparison. BMC
Bioinformatics , 6(1), 31-40.
Stanke, M., Keller, O., Gunduz, I., Hayes, A., Waack, S., &
Morgenstern, B. (2006). AUGUSTUS: ab initio prediction of alternative
transcripts. Nucleic Acids Research , 34 , W435-W439.
Stevens, K. A., Woeste, K., Chakraborty, S., Crepeau, M. W., Leslie, C.
A., Martínez-García, P. J., … & Kluepfel, D. (2018). Genomic
variation among and within six Juglans species. G3-Genes
Genomes Genetics , 8 (7), 2153-2165.
Sun,
J. X.,
Zhao,
X. Y.,
Fu,
X. F.,
Yu,
H. Y.,
Li,
X.,
Li,
S. M., …&
Ruan,
H. L. (2012). ChemInform abstract:three new naphthalenyl glycosides from
the root Bark of Juglans cathayensis . Chemical &
pharmaceutical bulletin , 60 (6), 785-789.
Suryamohan, K., Krishnankutty, S. P., Guillory, J., Jevit, M., Schröder,
M. S., Wu, M., …& Seshagiri, S. (2020). The Indian cobra
reference genome and transcriptome enables comprehensive identification
of venom toxins. Nature Genetics , 52 , 1-12.
Trouern-Trend, A., Falk, T., Zaman, S., Caballero, M., Neale, D. B.,
Langley, C. H., … & Wegrzyn, J. L. (2020). Comparative genomics of
six Juglans species reveals disease‐associated gene family
contractions. The Plant Journal , doi: 10.1111/tpj.14630
Walker, B. J., Abeel, T., Shea, T., Priest, M., Abouelliel, A.,
Sakthikumar, S., … & Earl, A. M. (2014). Pilon: an integrated tool
for comprehensive microbial variant detection and genome assembly
improvement. PloS One , 9 (11).
Wang, D., Zhang, Y., Zhang, Z., Zhu, J., & Yu, J. (2010).
KaKs_Calculator 2.0: a toolkit incorporating gamma-series methods and
sliding window strategies. Genomics, Proteomics &
Bioinformatics , 8 (1), 77-80.
Wang, Y. P., Tang, H. B., Debarry, J. D., Tan, X., Li, J. P., Wang, X.
Y., …& Paterson, A. H. (2012). MCScanX: a toolkit for detection
and evolutionary analysis of gene synteny and collinearity.Nucleic Acids Research , 40 (7), e49.
Wu, T. D., & Watanabe, C. K. (2005). GMAP: a genomic mapping and
alignment program for mRNA and EST sequences. Bioinformatics ,21 (9), 1859.
Xu, Y., Zhang, M. Y., Gao, L., & Liu, J. F. (2007) Development of new
lines from walnut interspaces hybrids. Shandong Agriculture
Science , 3 , 25–27.
Yang, Z. H. (2007). PAML 4: phylogenetic analysis by maximum likelihood.Molecular Biology and Evolution , 24 (8), 1586-1591.
Yu, H. Y., Li, X., Meng, F. Y., Pi, H. F., Zhang, P., & Ruan, H. L.
(2011). Naphthoquinones from the root barks of Juglans
cathayensis Dode. Journal of Asian Natural Products Research ,13 (7), 581-587.
Zdobnov, E., & Apweiler, R. (2001). InterProScan–an integration
platform for the signature-recognition methods in InterPro.Bioinformatics , 17 (9), 847-848.
Zhao, P., Zhou, H.J., Potter, D., Hu, Y.H., Feng, X.J., Dang, M.,
…& Woeste, K. (2018) Population genetics, phylogenomics and
hybrid speciation of Juglans in China determined from whole
chloroplast genomes, transcriptomes, and genotyping-by-sequencing (GBS).Molecular Phylogenetics and Evolution , 126 , 250-265.
Zhao, P., Zhao, G. F., Zhang, S. X., Zhou, H. J., Hu, Y. H., & Woeste,
K. (2014). RAPD derived markers for separating Manchurian walnut
(Juglans mandshurica ) and Japanese walnut (J.
ailantifolia ) from close congeners. Journal of Systematics and
Evolution , 52 (1), 101–111.
Zhao, X., & Hao, W. (2007). LTR_FINDER: an efficient tool for the
prediction of full-length LTR retrotransposons. Nucleic Acids
Research , 35, W265-W268.
Zhang, B. W., Xu, L. L., Li, N., Yan, P. C., Jiang, X. H., Woeste, K.
E., … & Bai, W. N. (2019). Phylogenomics reveals an ancient hybrid
origin of the Persian walnut. Molecular Biology and Evolution ,36 (11), 2451-2461.
Zhang, W., Jiao, Z., Shang, T., & Yang, Y. (2015). Demography and
spectrum analysis of Juglans cathayensis populations at different
altitudes in the west Tianshan valley in Xinjiang, China. The
Journal of Applied Ecology , 26 (4), 1091–1098.
Zhang, Z., Chen, Y., Zhang, J., Ma, X., Li, Y., Li, M., … & Ma,
T. (2020a). Improved genome assembly provides new insights into genome
evolution in a desert poplar (Populus euphratica ).Molecular Ecology Resources , 1-14,
https://doi.org/10.1111/1755-0998.13142
Zhang, J., Zhang, W., Ji, F., Qiu, J., Song, X., Bu, D., … & Chang,
Y. (2020b). A high-quality walnut genome assembly reveals extensive gene
expression divergences after whole-genome duplication. Plant
Biotechnology Journal , 1-3. https://doi.org/10.1111/pbi.13350
Zhang, T., Ren, X. Y., Zhang, Z., Ming, Y., Yang, Z., Hu, J. B.,
…& Sun, Z. Q. (2020c). Long-read sequencing and de novo assembly
of the Luffa cylindrica (L.) Roem. genome. Molecular
Ecology Resources , 20 (2), 511-519.
Zhou, Z., Han, M., Hou, M., Deng, X., Tian, R., Min, S., …&
Zhang, J. (2017). Comparative study of the leaf transcriptomes and
ionoms of Juglans regia and its wild relative species Juglans
cathayensis . Acta Physiologiae Plantarum , 39 (10), 224.